[ B12 ] [ atoms ] C27 C 0.38000 0 ; from GLN residue O28 O -0.38000 0 ; from GLN residue N29 NT -0.83000 0 ; from GLN residue HAE H 0.41500 0 ; from GLN residue HAD H 0.41500 0 ; from GLN residue C32 C 0.38000 1 ; from GLN residue O34 O -0.38000 1 ; from GLN residue N33 NT -0.83000 1 ; from GLN residue HAG H 0.41500 1 ; from GLN residue HAF H 0.41500 1 ; from GLN residue C38 C 0.38000 2 ; from GLN residue O39 O -0.38000 2 ; from GLN residue N40 NT -0.83000 2 ; from GLN residue HAI H 0.41500 2 ; from GLN residue HAH H 0.41500 2 ; from GLN residue C43 C 0.38000 3 ; from GLN residue O44 O -0.38000 3 ; from GLN residue N45 NT -0.83000 3 ; from GLN residue HAK H 0.41500 3 ; from GLN residue HAJ H 0.41500 3 ; from GLN residue C50 C 0.38000 4 ; from GLN residue O51 O -0.38000 4 ; from GLN residue N52 NT -0.83000 4 ; from GLN residue HAM H 0.41500 4 ; from GLN residue HAL H 0.41500 4 ; from GLN residue C61 C 0.38000 5 ; from GLN residue O63 O -0.38000 5 ; from GLN residue N62 NT -0.83000 5 ; from GLN residue HAO H 0.41500 5 ; from GLN residue HAN H 0.41500 5 ; from GLN residue C20 CH3 0.00000 6 ; methyl group C25 CH3 0.00000 7 ; methyl group C36 CH3 0.00000 8 ; methyl group C46 CH3 0.00000 9 ; methyl group C47 CH3 0.00000 10 ; methyl group C54 CH3 0.00000 11 ; methyl group C26 CH2 0.00000 12 ; non-polar CHn fragments C30 CH2 0.00000 13 ; non-polar CHn fragments C31 CH2 0.00000 13 ; non-polar CHn fragments C37 CH2 0.00000 14 ; non-polar CHn fragments C41 CH2 0.00000 15 ; non-polar CHn fragments C42 CH2 0.00000 15 ; non-polar CHn fragments C48 CH2 0.00000 16 ; non-polar CHn fragments C49 CH2 0.00000 16 ; non-polar CHn fragments C56 CH2 0.00000 17 ; non-polar CHn fragments C55 CH2 0.00000 17 ; non-polar CHn fragments C60 CH2 0.00000 18 ; non-polar CHn fragments C2R CH1 0.15000 19 ; C2*-O2*-H2* from ADE O7R OA -0.54800 19 ; C2*-O2*-H2* from ADE HAA H 0.39800 19 ; C2*-O2*-H2* from ADE C1R CH1 0.20000 20 ; C1*-O4*-C4* from ADE O6R OA -0.36000 20 ; C1*-O4*-C4* from ADE C4R CH1 0.16000 20 ; C1*-O4*-C4* from ADE C3R CH1 0.00000 21 ; C3* from ADE C5R CH2 0.15000 22 ; C2*-O2*-H2* from ADE O8R OA -0.54800 22 ; C2*-O2*-H2* from ADE HAB H 0.39800 22 ; C2*-O2*-H2* from ADE P P 2.20000 23 ; PO3+O3* fragment from ADE O2 OA -0.80000 23 ; PO3+O3* fragment from ADE O4 OM -1.00000 23 ; PO3+O3* fragment from ADE O5 OM -1.00000 23 ; PO3+O3* fragment from ADE O3 OA -0.80000 23 ; PO3+O3* fragment from ADE C2P CH1 0.35000 24 ; non-polar CHn fragment C3P CH3 0.00000 24 ; non-polar CHn fragment C1P CH2 0.00000 24 ; non-polar CHn fragment N59 N -0.28000 25 ; tempered GLN fragment charges HAC H 0.28000 25 ; tempered GLN fragment charges C57 C 0.38000 25 ; tempered GLN fragment charges O58 O -0.38000 25 ; tempered GLN fragment charges C5B C 0.00000 26 ; dimethylbenzimidazole C-CH3 group (non-polar) C5M CH3 0.00000 26 ; dimethylbenzimidazole C-CH3 group (non-polar) C6B C 0.00000 27 ; dimethylbenzimidazole C-CH3 group (non-polar) C6M CH3 0.00000 27 ; dimethylbenzimidazole C-CH3 group (non-polar) C4B C -0.14000 28 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H4B H 0.14000 28 ; dimethylbenzimidazole aromatic C-H from TRP, PHE C7B C -0.14000 29 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H7B H 0.14000 29 ; dimethylbenzimidazole aromatic C-H from TRP, PHE N3B NR -0.55000 30 ; dimethylbenzimidazole polar aromatic NC fragment C9B C 0.20000 30 ; dimethylbenzimidazole polar aromatic NC fragment N1B NR -0.30000 31 ; dimethylbenzimidazole polar aromatic NC fragment C8B C 0.20000 31 ; dimethylbenzimidazole polar aromatic NC fragment C2B C 0.23000 32 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H2B H 0.23000 32 ; dimethylbenzimidazole aromatic C-H from TRP, PHE C5 C -0.05000 33 ; C-CH3 group (non-polar) C35 CH3 0.00000 33 ; C-CH3 group (non-polar) C15 C -0.05000 34 ; C-CH3 group (non-polar) C53 CH3 0.00000 34 ; C-CH3 group (non-polar) FE FE 0.62000 35 ; HEMC Fe-N group N21 NR -0.44000 35 ; HEMC Fe-N group N22 NR -0.50000 35 ; HEMC Fe-N group N23 NR -0.50000 35 ; HEMC Fe-N group N24 NR -0.44000 35 ; HEMC Fe-N group C1 CH0 0.22000 36 ; non-polar HEMC-derived corrin atoms C2 CH0 0.00000 36 ; non-polar HEMC-derived corrin atoms C3 CH1 0.00000 36 ; non-polar HEMC-derived corrin atoms C4 C 0.38000 36 ; non-polar HEMC-derived corrin atoms C6 C 0.29000 37 ; non-polar HEMC-derived corrin atoms C7 CH0 0.00000 37 ; non-polar HEMC-derived corrin atoms C8 CH1 0.00000 37 ; non-polar HEMC-derived corrin atoms C9 C 0.35000 37 ; non-polar HEMC-derived corrin atoms C16 C 0.38000 38 ; non-polar HEMC-derived corrin atoms C17 CH0 0.00000 38 ; non-polar HEMC-derived corrin atoms C18 CH1 0.00000 38 ; non-polar HEMC-derived corrin atoms C19 CH1 0.24000 38 ; non-polar HEMC-derived corrin atoms C11 C 0.35000 39 ; non-polar HEMC-derived corrin atoms C12 CH0 0.00000 39 ; non-polar HEMC-derived corrin atoms C13 CH1 0.00000 39 ; non-polar HEMC-derived corrin atoms C14 C 0.29000 39 ; non-polar HEMC-derived corrin atoms C10 C -0.24000 40 ; aromatic C-H from TRP, PHE H10 H 0.14000 40 ; aromatic C-H from TRP, PHE ; ; Since CO is not defined as an atom in GROMOSxx, CO is converted to FE and the HEME ; values are employed. This is a workaround due for proper implementation. ; [ bonds ] ; ai aj gromos type C26 C27 gb_27 ; from GLN fragment 0 C27 O28 gb_5 ; from GLN C27 N29 gb_9 ; from GLN N29 HAE gb_2 ; from GLN N29 HAD gb_2 ; from GLN C31 C32 gb_27 ; from GLN fragment 1 C32 O34 gb_5 ; from GLN C32 N33 gb_9 ; from GLN N33 HAG gb_2 ; from GLN N33 HAF gb_2 ; from GLN C37 C38 gb_27 ; from GLN fragment 2 C38 O39 gb_5 ; from GLN C38 N40 gb_9 ; from GLN N40 HAI gb_2 ; from GLN N40 HAH gb_2 ; from GLN C42 C43 gb_27 ; from GLN fragment 3 C43 O44 gb_5 ; from GLN C43 N45 gb_9 ; from GLN N45 HAK gb_2 ; from GLN N45 HAJ gb_2 ; from GLN C49 C50 gb_27 ; from GLN fragment 4 C50 O51 gb_5 ; from GLN C50 N52 gb_9 ; from GLN N52 HAM gb_2 ; from GLN N52 HAL gb_2 ; from GLN C60 C61 gb_27 ; from GLN fragment 5 C61 O63 gb_5 ; from GLN C61 N62 gb_9 ; from GLN N62 HAO gb_2 ; from GLN N62 HAN gb_2 ; from GLN FE N21 gb_35 ; FE-N bond from HEMC FE N22 gb_35 ; FE-N bond from HEMC FE N23 gb_35 ; FE-N bond from HEMC FE N24 gb_35 ; FE-N bond from HEMC FE N3B gb_37 ; FE-N3B bond from HEMC not in corrin ring P O2 gb_28 ; from ADE phosphate P O4 gb_24 ; from ADE phosphate P O5 gb_24 ; from ADE phosphate P O3 gb_28 ; from ADE phosphate N21 C1 gb_21 ; corrin ring N-CHn bonds N21 C4 gb_14 ; corrin ring N-C bonds N22 C6 gb_14 ; corrin ring N-C bonds N22 C9 gb_14 ; corrin ring N-C bonds N23 C11 gb_14 ; corrin ring N-C bonds N23 C14 gb_14 ; corrin ring N-C bonds N24 C16 gb_14 ; corrin ring N-C bonds N24 C19 gb_21 ; corrin ring N-CHn bonds C30 C31 gb_27 ; CH2-CH2 bonds C41 C42 gb_27 ; CH2-CH2 bonds C48 C49 gb_27 ; CH2-CH2 bonds C55 C56 gb_27 ; CH2-CH2 bonds C56 C57 gb_27 ; CH2-CH2 bonds N1B C1R gb_22 ; sugar bonds from ADE C1R C2R gb_26 ; sugar bonds from ADE C2R O7R gb_20 ; sugar bonds from ADE O7R HAA gb_1 ; sugar bonds from ADE C2R C3R gb_26 ; sugar bonds from ADE C3R C4R gb_26 ; sugar bonds from ADE C3R O2 gb_20 ; sugar bonds from ADE C4R C5R gb_26 ; sugar bonds from ADE C5R O8R gb_20 ; sugar bonds from ADE O8R HAB gb_1 ; sugar bonds from ADE C4R O6R gb_20 ; sugar bonds from ADE O6R C1R gb_20 ; sugar bonds from ADE C1P N59 gb_9 ; amide corrin - phosphate linkage C1P C2P gb_27 ; amide corrin - phosphate linkage C2P C3P gb_27 ; amide corrin - phosphate linkage C2P O3 gb_20 ; amide corrin - phosphate linkage N59 HAC gb_2 ; amide corrin - phosphate linkage N59 C57 gb_9 ; amide corrin - phosphate linkage C57 O58 gb_5 ; amide corrin - phosphate linkage N1B C2B gb_10 ; dimethylbenzimidazole ring C2B N3B gb_10 ; dimethylbenzimidazole ring C2B H2B gb_3 ; dimethylbenzimidazole ring N3B C9B gb_10 ; dimethylbenzimidazole ring C9B C4B gb_16 ; dimethylbenzimidazole ring C4B C5B gb_16 ; dimethylbenzimidazole ring C4B H4B gb_3 ; dimethylbenzimidazole ring C5B C6B gb_16 ; dimethylbenzimidazole ring C5B C5M gb_27 ; dimethylbenzimidazole ring C6B C7B gb_16 ; dimethylbenzimidazole ring C6B C6M gb_27 ; dimethylbenzimidazole ring C7B C8B gb_16 ; dimethylbenzimidazole ring C7B H7B gb_3 ; dimethylbenzimidazole ring C8B N1B gb_10 ; dimethylbenzimidazole ring C8B C9B gb_16 ; dimethylbenzimidazole ring C1 C20 gb_27 ; corrin ring carbon framework C1 C2 gb_27 ; corrin ring carbon framework C2 C3 gb_27 ; corrin ring carbon framework C2 C25 gb_27 ; corrin ring carbon framework C2 C26 gb_27 ; corrin ring carbon framework C3 C4 gb_27 ; corrin ring carbon framework C3 C30 gb_27 ; corrin ring carbon framework C4 C5 gb_17 ; corrin ring carbon framework C5 C6 gb_17 ; corrin ring carbon framework C5 C35 gb_27 ; corrin ring carbon framework C6 C7 gb_27 ; corrin ring carbon framework C7 C8 gb_27 ; corrin ring carbon framework C7 C37 gb_27 ; corrin ring carbon framework C7 C36 gb_27 ; corrin ring carbon framework C8 C9 gb_27 ; corrin ring carbon framework C8 C41 gb_27 ; corrin ring carbon framework C9 C10 gb_17 ; corrin ring carbon framework C10 C11 gb_17 ; corrin ring carbon framework C11 C12 gb_27 ; corrin ring carbon framework C12 C46 gb_27 ; corrin ring carbon framework C12 C47 gb_27 ; corrin ring carbon framework C12 C13 gb_27 ; corrin ring carbon framework C13 C14 gb_27 ; corrin ring carbon framework C13 C48 gb_27 ; corrin ring carbon framework C14 C15 gb_17 ; corrin ring carbon framework C15 C16 gb_17 ; corrin ring carbon framework C15 C53 gb_27 ; corrin ring carbon framework C16 C17 gb_27 ; corrin ring carbon framework C17 C18 gb_27 ; corrin ring carbon framework C17 C54 gb_27 ; corrin ring carbon framework C17 C55 gb_27 ; corrin ring carbon framework C18 C19 gb_27 ; corrin ring carbon framework C18 C60 gb_27 ; corrin ring carbon framework C19 C1 gb_27 ; corrin ring carbon framework C10 H10 gb_3 ; corrin ring C10-H10 bond [ exclusions ] ; ai aj FE C2 FE C3 FE C5 FE C7 FE C8 FE C10 FE C12 FE C13 FE C15 FE C17 FE C18 FE C20 N21 C25 N21 C26 N21 C30 N21 C35 N21 C6 N21 C9 N21 C11 N21 C14 N21 C16 N21 C19 N21 C10 N22 C1 N22 C4 N22 C36 N22 C37 N22 C11 N22 C14 N22 C16 N22 C19 N22 C15 N23 C16 N23 C19 N23 C1 N23 C4 N23 C6 N23 C9 N23 C46 N23 C47 N23 C48 N23 C5 N24 C4 N24 C5 N24 C6 N24 C9 N24 C10 N24 C11 N24 C14 N24 C55 N24 C54 N24 C60 C1R C7B C1R C9B C1R N3B N1B C6B N1B C4B C8B C5B C8B C5M C8B C6M C7B C4B C7B N3B C7B C2B C2B C9B C5B C2B C5M C6M C1 C30 ; HEMC-based C framework exclusions C1 C5 ; HEMC-based C framework exclusions C2 C5 ; HEMC-based C framework exclusions C3 C35 ; HEMC-based C framework exclusions C3 C6 ; HEMC-based C framework exclusions C4 C26 ; HEMC-based C framework exclusions C4 C7 ; HEMC-based C framework exclusions C30 C26 ; HEMC-based C framework exclusions C30 C5 ; HEMC-based C framework exclusions C5 C8 ; HEMC-based C framework exclusions C5 C9 ; HEMC-based C framework exclusions C5 C36 ; HEMC-based C framework exclusions C5 C37 ; HEMC-based C framework exclusions C35 C7 ; HEMC-based C framework exclusions C6 C41 ; HEMC-based C framework exclusions C6 C10 ; HEMC-based C framework exclusions C7 C10 ; HEMC-based C framework exclusions C8 H10 ; HEMC-based C framework exclusions C8 C11 ; HEMC-based C framework exclusions C9 C36 ; HEMC-based C framework exclusions C9 C37 ; HEMC-based C framework exclusions C9 C12 ; HEMC-based C framework exclusions C36 C41 ; HEMC-based C framework exclusions C37 C10 ; HEMC-based C framework exclusions C10 C13 ; HEMC-based C framework exclusions C10 C14 ; HEMC-based C framework exclusions C10 C46 ; HEMC-based C framework exclusions C10 C47 ; HEMC-based C framework exclusions H10 C12 ; HEMC-based C framework exclusions C11 C48 ; HEMC-based C framework exclusions C11 C15 ; HEMC-based C framework exclusions C12 C15 ; HEMC-based C framework exclusions C13 C53 ; HEMC-based C framework exclusions C13 C16 ; HEMC-based C framework exclusions C14 C46 ; HEMC-based C framework exclusions C14 C47 ; HEMC-based C framework exclusions C14 C17 ; HEMC-based C framework exclusions C46 C48 ; HEMC-based C framework exclusions C47 C48 ; HEMC-based C framework exclusions C48 C15 ; HEMC-based C framework exclusions C15 C18 ; HEMC-based C framework exclusions C15 C19 ; HEMC-based C framework exclusions C15 C54 ; HEMC-based C framework exclusions C15 C55 ; HEMC-based C framework exclusions C53 C17 ; HEMC-based C framework exclusions C16 C60 ; HEMC-based C framework exclusions C19 C54 ; HEMC-based C framework exclusions C19 C55 ; HEMC-based C framework exclusions C54 C60 ; HEMC-based C framework exclusions C55 C60 ; HEMC-based C framework exclusions [ angles ] ; ai aj ak gromos type C2 C26 C27 ga_15 ; from GLN, fragment 1 C26 C27 O28 ga_30 ; from GLN C26 C27 N29 ga_19 ; from GLN O28 C27 N29 ga_33 ; from GLN C27 N29 HAE ga_23 ; from GLN C27 N29 HAD ga_23 ; from GLN HAE N29 HAD ga_24 ; from GLN C30 C31 C32 ga_15 ; from GLN, fragment 2 C31 C32 O34 ga_30 ; from GLN C31 C32 N33 ga_19 ; from GLN O34 C32 N33 ga_33 ; from GLN C32 N33 HAG ga_23 ; from GLN C32 N33 HAF ga_23 ; from GLN HAG N33 HAF ga_24 ; from GLN C7 C37 C38 ga_15 ; from GLN, fragment 3 C37 C38 O39 ga_30 ; from GLN C37 C38 N40 ga_19 ; from GLN O39 C38 N40 ga_33 ; from GLN C38 N40 HAI ga_23 ; from GLN C38 N40 HAH ga_23 ; from GLN HAI N40 HAH ga_24 ; from GLN C41 C42 C43 ga_15 ; from GLN, fragment 4 C42 C43 O44 ga_30 ; from GLN C42 C43 N45 ga_19 ; from GLN O44 C43 N45 ga_33 ; from GLN C43 N45 HAK ga_23 ; from GLN C43 N45 HAJ ga_23 ; from GLN HAK N45 HAJ ga_24 ; from GLN C48 C49 C50 ga_15 ; from GLN, fragment 5 C49 C50 O51 ga_30 ; from GLN C49 C50 N52 ga_19 ; from GLN O51 C50 N52 ga_33 ; from GLN C50 N52 HAM ga_23 ; from GLN C50 N52 HAL ga_23 ; from GLN HAM N52 HAL ga_24 ; from GLN C18 C60 C61 ga_15 ; from GLN, fragment 6 C60 C61 O63 ga_30 ; from GLN C60 C61 N62 ga_19 ; from GLN O63 C61 N62 ga_33 ; from GLN C61 N62 HAO ga_23 ; from GLN C61 N62 HAN ga_23 ; from GLN HAO N62 HAN ga_24 ; from GLN N21 FE N22 ga_2 ; corrin ring Fe-N angle N21 FE N24 ga_2 ; corrin ring Fe-N angle N22 FE N23 ga_2 ; corrin ring Fe-N angle N23 FE N24 ga_2 ; corrin ring Fe-N angle N21 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N22 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N23 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N24 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole FE N21 C1 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N21 C4 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N22 C6 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N22 C9 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N23 C11 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N23 C14 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N24 C16 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N24 C19 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N3B C9B ga_34 ; Fe-dimethylbenzimidazole-N,C angle FE N3B C2B ga_34 ; Fe-dimethylbenzimidazole-N,C angle C8B N1B C2B ga_7 ; angle containing C8B, see minimization issues discussion N1B C8B C9B ga_7 ; angle containing C8B, see minimization issues discussion C8B C9B N3B ga_7 ; angle containing C8B, see minimization issues discussion C7B C8B N1B ga_39 ; angle containing C8B, see minimization issues discussion C8B N1B C1R ga_37 ; angle containing C8B, see minimization issues discussion C4B C9B C8B ga_27 ; angle containing C8B, see minimization issues discussion C6B C7B C8B ga_27 ; angle containing C8B, see minimization issues discussion C7B C8B C9B ga_27 ; angle containing C8B, see minimization issues discussion N21 C1 C2 ga_13 ; corrin ring-specific but HEMC-derived angles N21 C1 C20 ga_13 ; corrin ring-specific but HEMC-derived angles N21 C4 C3 ga_33 ; corrin ring-specific but HEMC-derived angles C4 N21 C1 ga_6 ; corrin ring-specific but HEMC-derived angles C5 C4 N21 ga_33 ; corrin ring-specific but HEMC-derived angles C19 C1 N21 ga_13 ; corrin ring-specific but HEMC-derived angles N22 C6 C5 ga_33 ; corrin ring-specific but HEMC-derived angles N22 C6 C7 ga_33 ; corrin ring-specific but HEMC-derived angles N22 C9 C8 ga_33 ; corrin ring-specific but HEMC-derived angles C9 N22 C6 ga_6 ; corrin ring-specific but HEMC-derived angles C10 C9 N22 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C11 C10 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C11 C12 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C14 C13 ga_33 ; corrin ring-specific but HEMC-derived angles C14 N23 C11 ga_6 ; corrin ring-specific but HEMC-derived angles C15 C14 N23 ga_33 ; corrin ring-specific but HEMC-derived angles N24 C16 C15 ga_33 ; corrin ring-specific but HEMC-derived angles N24 C19 C1 ga_13 ; corrin ring-specific but HEMC-derived angles C19 N24 C16 ga_6 ; corrin ring-specific but HEMC-derived angles C17 C16 N24 ga_33 ; corrin ring-specific but HEMC-derived angles C18 C19 N24 ga_13 ; corrin ring-specific but HEMC-derived angles C3R O2 P ga_26 ; phosphate angle from ADE O2 P O3 ga_5 ; phosphate angle from ADE O2 P O4 ga_14 ; phosphate angle from ADE O2 P O5 ga_14 ; phosphate angle from ADE O3 P O4 ga_14 ; phosphate angle from ADE O3 P O5 ga_14 ; phosphate angle from ADE O4 P O5 ga_29 ; phosphate angle from ADE P O3 C2P ga_26 ; phosphate angle from ADE O2 C3R C2R ga_9 ; phosphate oxygen to CHn carbons from ADE O2 C3R C4R ga_9 ; phosphate oxygen to CHn carbons from ADE O3 C2P C1P ga_9 ; phosphate oxygen to CHn carbons from ADE O3 C2P C3P ga_9 ; phosphate oxygen to CHn carbons from ADE C1 C2 C26 ga_13 ; CHn-CHn-CHn angles C1 C2 C25 ga_13 ; CHn-CHn-CHn angles C1 C2 C3 ga_13 ; CHn-CHn-CHn angles C1 C19 C18 ga_13 ; CHn-CHn-CHn angles C2 C1 C19 ga_13 ; CHn-CHn-CHn angles C2 C1 C20 ga_13 ; CHn-CHn-CHn angles C2 C3 C30 ga_13 ; CHn-CHn-CHn angles C3 C2 C25 ga_13 ; CHn-CHn-CHn angles C3 C2 C26 ga_13 ; CHn-CHn-CHn angles C3 C30 C31 ga_13 ; CHn-CHn-CHn angles C7 C8 C41 ga_13 ; CHn-CHn-CHn angles C8 C41 C42 ga_13 ; CHn-CHn-CHn angles C12 C13 C48 ga_13 ; CHn-CHn-CHn angles C13 C12 C46 ga_13 ; CHn-CHn-CHn angles C13 C12 C47 ga_13 ; CHn-CHn-CHn angles C13 C48 C49 ga_13 ; CHn-CHn-CHn angles C17 C18 C19 ga_13 ; CHn-CHn-CHn angles C17 C18 C60 ga_13 ; CHn-CHn-CHn angles C17 C55 C56 ga_13 ; CHn-CHn-CHn angles C18 C17 C54 ga_13 ; CHn-CHn-CHn angles C18 C17 C55 ga_13 ; CHn-CHn-CHn angles C19 C1 C20 ga_13 ; CHn-CHn-CHn angles C19 C18 C60 ga_13 ; CHn-CHn-CHn angles C25 C2 C26 ga_13 ; CHn-CHn-CHn angles C46 C12 C47 ga_13 ; CHn-CHn-CHn angles C54 C17 C55 ga_13 ; CHn-CHn-CHn angles C36 C7 C37 ga_13 ; CHn-CHn-CHn angles C2 C3 C4 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C4 C3 C30 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C8 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C36 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C37 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C7 C8 C9 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C8 C7 C36 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C8 C7 C37 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C9 C8 C41 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C13 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C46 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C47 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C12 C13 C14 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C14 C13 C48 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C18 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C54 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C55 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C4 C5 C6 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C9 C10 C11 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C14 C15 C16 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C3 C4 C5 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C4 C5 C35 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C5 C6 C7 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C6 C5 C35 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C8 C9 C10 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C10 C11 C12 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C13 C14 C15 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C14 C15 C53 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C15 C16 C17 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C16 C15 C53 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C5M C5B C4B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C5M C5B C6B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C6M C6B C5B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C6M C6B C7B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C4B C5B C6B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle C5B C4B C9B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle C5B C6B C7B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle N1B C1R C2R ga_9 ; from ADE Nsp2-containing dimethylbenzimidazole angle N1B C1R O6R ga_9 ; from ADE Nsp2-containing dimethylbenzimidazole angle N1B C2B N3B ga_7 ; from ADE Nsp2-containing dimethylbenzimidazole angle C2B N1B C1R ga_37 ; from ADE Nsp2-containing dimethylbenzimidazole angle N3B C9B C4B ga_39 ; from ADE Nsp2-containing dimethylbenzimidazole angle C9B N3B C2B ga_7 ; from ADE Nsp2-containing dimethylbenzimidazole angle C1R C2R C3R ga_8 ; from ADE sugar angle C1R C2R O7R ga_9 ; from ADE sugar angle C1R O6R C4R ga_10 ; from ADE sugar angle C2R C1R O6R ga_9 ; from ADE sugar angle C2R C3R C4R ga_8 ; from ADE sugar angle C2R O7R HAA ga_12 ; from ADE sugar angle C3R C2R O7R ga_9 ; from ADE sugar angle C3R C4R C5R ga_8 ; from ADE sugar angle C3R C4R O6R ga_9 ; from ADE sugar angle C4R C5R O8R ga_9 ; from ADE sugar angle C5R O8R HAB ga_12 ; from ADE sugar angle C5R C4R O6R ga_9 ; from ADE sugar angle C1P C2P C3P ga_13 ; amide linkage angle C57 C56 C55 ga_13 ; amide linkage angle C57 N59 HAC ga_23 ; from GLN angle N59 C57 O58 ga_33 ; from GLN angle C56 C57 N59 ga_19 ; from GLN angle O58 C57 C56 ga_30 ; from GLN angle C1P N59 C57 ga_31 ; from force field angle definitions C1P N59 HAC ga_18 ; from force field angle definitions C2P C1P N59 ga_15 ; from force field angle definitions C5B C4B H4B ga_25 ; from PHE C-C-H angle C9B C4B H4B ga_25 ; from PHE C-C-H angle C6B C7B H7B ga_25 ; from PHE C-C-H angle C8B C7B H7B ga_25 ; from PHE C-C-H angle N1B C2B H2B ga_36 ; from ADE N-C-H angle N3B C2B H2B ga_36 ; from ADE N-C-H angle C9 C10 H10 ga_25 ; corrin ring C-C10-H angle C11 C10 H10 ga_20 ; corrin ring C-C10-H angle [ impropers ] ; ai aj ak al gromos type C1R C8B C2B N1B gi_1 ; dimethylbenzimidazole improper for planarity N1B C8B C9B N3B gi_1 ; dimethylbenzimidazole improper for planarity C8B N1B C7B C9B gi_1 ; dimethylbenzimidazole improper for planarity C8B N1B C2B N3B gi_1 ; dimethylbenzimidazole improper for planarity C8B C7B C6B C5B gi_1 ; dimethylbenzimidazole improper for planarity C8B C9B N3B C2B gi_1 ; dimethylbenzimidazole improper for planarity C7B C8B C9B C4B gi_1 ; dimethylbenzimidazole improper for planarity C7B C6B C5B C4B gi_1 ; dimethylbenzimidazole improper for planarity C6B C5B C4B C9B gi_1 ; dimethylbenzimidazole improper for planarity C5B C4B C9B C8B gi_1 ; dimethylbenzimidazole improper for planarity C9B C8B C7B C6B gi_1 ; dimethylbenzimidazole improper for planarity C9B C4B N3B C8B gi_1 ; dimethylbenzimidazole improper for planarity C9B N3B C2B N1B gi_1 ; dimethylbenzimidazole improper for planarity C2B N1B C8B C9B gi_1 ; dimethylbenzimidazole improper for planarity C5M C4B C6B C5B gi_1 ; dimethylbenzimidazole methyl groups C6M C7B C5B C6B gi_1 ; dimethylbenzimidazole methyl groups C2B N1B N3B H2B gi_1 ; dimethylbenzimidazole H atom-containing planarity C4B C9B C5B H4B gi_1 ; dimethylbenzimidazole H atom-containing planarity C7B C8B C6B H7B gi_1 ; dimethylbenzimidazole H atom-containing planarity N3B FE C2B C9B gi_1 ; Fe-dimethylbenzimidazole planarity N21 C4 C5 C6 gi_1 ; HEMC-based conjugated corrin ring improper planarity N22 C6 C5 C4 gi_1 ; HEMC-based conjugated corrin ring improper planarity N22 C9 C10 C11 gi_1 ; HEMC-based conjugated corrin ring improper planarity N23 C11 C10 C9 gi_1 ; HEMC-based conjugated corrin ring improper planarity N23 C14 C15 C16 gi_1 ; HEMC-based conjugated corrin ring improper planarity N24 C16 C15 C14 gi_1 ; HEMC-based conjugated corrin ring improper planarity C5 C4 C6 C35 gi_1 ; corrin ring on-Csp2 methyl group improper planarity C15 C16 C14 C53 gi_1 ; corrin ring on-Csp2 methyl group improper planarity C27 O28 N29 C26 gi_1 ; from GLN improper torsion definition N29 HAE HAD C27 gi_1 ; from GLN improper torsion definition C32 O34 N33 C31 gi_1 ; from GLN improper torsion definition N33 HAG HAF C32 gi_1 ; from GLN improper torsion definition C38 O39 N40 C37 gi_1 ; from GLN improper torsion definition N40 HAI HAH C38 gi_1 ; from GLN improper torsion definition C43 O44 N45 C42 gi_1 ; from GLN improper torsion definition N45 HAK HAJ C43 gi_1 ; from GLN improper torsion definition C50 O51 N52 C49 gi_1 ; from GLN improper torsion definition N52 HAM HAL C50 gi_1 ; from GLN improper torsion definition C61 O63 N62 C60 gi_1 ; from GLN improper torsion definition N62 HAO HAN C61 gi_1 ; from GLN improper torsion definition C57 C56 O58 N59 gi_1 ; amide linkage C57 planarity N59 C57 C1P HAC gi_1 ; amide linkage N59 planarity C4 N21 C3 C5 gi_1 ; corrin ring C sp2 planarity C5 C4 C6 C35 gi_1 ; corrin ring C sp2 planarity C6 N22 C5 C7 gi_1 ; corrin ring C sp2 planarity C9 N22 C10 C8 gi_1 ; corrin ring C sp2 planarity C11 N23 C10 C12 gi_1 ; corrin ring C sp2 planarity C14 N23 C15 C13 gi_1 ; corrin ring C sp2 planarity C15 C14 C16 C53 gi_1 ; corrin ring C sp2 planarity C16 N24 C15 C17 gi_1 ; corrin ring C sp2 planarity C10 C9 C11 H10 gi_1 ; corrin ring C10 planarity C18 C17 C19 C60 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C19 N24 C18 C1 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C3 C2 C30 C4 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C8 C9 C7 C41 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C13 C14 C12 C48 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C2P C1P O3 C3P gi_2 ; corrin ring C atom sp3 tetrahedral geometry C1R N1B C2R O6R gi_2 ; sugar C atom tetrahedral geometry C2R O7R C3R C1R gi_2 ; sugar C atom tetrahedral geometry C3R C5R O6R C4R gi_2 ; sugar C atom tetrahedral geometry C3R C2R O2 C4R gi_2 ; sugar C atom tetrahedral geometry FE C1 C4 N21 gi_3 ; HEMC improper definition FE C6 C9 N22 gi_3 ; HEMC improper definition FE C11 C14 N23 gi_3 ; HEMC improper definition FE C16 C19 N24 gi_3 ; HEMC improper definition [ dihedrals ] ; ai aj ak al gromos type C3R O2 P O3 gd_20 ; from ADE phosphate definition C3R O2 P O3 gd_27 ; from ADE phosphate definition C2P O3 P O2 gd_20 ; from ADE phosphate definition C2P O3 P O2 gd_27 ; from ADE phosphate definition P O3 C2P C1P gd_7 ; from ADE phosphate definition C2R C3R O2 P gd_29 ; from ADE phosphate definition O8R C5R C4R O6R gd_8 ; from ADE sugar dihedrals O8R C5R C4R O6R gd_25 ; from ADE sugar dihedrals O8R C5R C4R C3R gd_17 ; from ADE sugar dihedrals O8R C5R C4R C3R gd_34 ; from ADE sugar dihedrals C3R C4R O6R C1R gd_29 ; from ADE sugar dihedrals C5R C4R C3R C2R gd_34 ; from ADE sugar dihedrals C5R C4R C3R O2 gd_17 ; from ADE sugar dihedrals O6R C4R C3R C2R gd_17 ; from ADE sugar dihedrals O6R C4R C3R O2 gd_18 ; from ADE sugar dihedrals C4R O6R C1R C2R gd_29 ; from ADE sugar dihedrals O6R C1R C2R O7R gd_18 ; from ADE sugar dihedrals O6R C1R C2R C3R gd_17 ; from ADE sugar dihedrals O6R C1R C2R C3R gd_34 ; from ADE sugar dihedrals C1R C2R C3R C4R gd_34 ; from ADE sugar dihedrals C1R C2R C3R O2 gd_17 ; from ADE sugar dihedrals O7R C2R C3R C4R gd_17 ; from ADE sugar dihedrals O7R C2R C3R O2 gd_18 ; from ADE sugar dihedrals C1R C2R O7R HAA gd_23 ; from ADE sugar dihedrals N1B C1R C2R O7R gd_17 ; from ADE sugar dihedrals O6R C1R N1B C8B gd_16 ; from ADE sugar dihedrals C4R C5R O8R HAB gd_2 ; additional ADE-based sugar dihedral N1B C1R C2R C3R gd_17 ; additional ADE-based sugar dihedral N1B C1R O6R C4R gd_17 ; additional ADE-based sugar dihedral C2 C26 C27 N29 gd_40 ; from GLN dihedral C26 C27 N29 HAD gd_14 ; from GLN dihedral C30 C31 C32 N33 gd_40 ; from GLN dihedral C31 C32 N33 HAF gd_14 ; from GLN dihedral C7 C37 C38 N40 gd_40 ; from GLN dihedral C37 C38 N40 HAH gd_14 ; from GLN dihedral C41 C42 C43 N45 gd_40 ; from GLN dihedral C42 C43 N45 HAJ gd_14 ; from GLN dihedral C48 C49 C50 N52 gd_40 ; from GLN dihedral C49 C50 N52 HAL gd_14 ; from GLN dihedral C18 C60 C61 N62 gd_40 ; from GLN dihedral C60 C61 N62 HAN gd_14 ; from GLN dihedral C5M C5B C6B C6M gd_33 ; dimethylbenzimidazole methyl dihedral fix C4B C5B C6B C6M gd_10 ; dimethylbenzimidazole methyl dihedral fix C8B C7B C6B C6M gd_10 ; dimethylbenzimidazole methyl dihedral fix C7B C6B C5B C5M gd_10 ; dimethylbenzimidazole methyl dihedral fix C9B C4B C5B C5M gd_10 ; dimethylbenzimidazole methyl dihedral fix C35 C5 C4 N21 gd_10 ; corrin ring methyl planarity C35 C5 C6 N22 gd_10 ; corrin ring methyl planarity C53 C15 C14 N23 gd_10 ; corrin ring methyl planarity C53 C1 C16 N24 gd_10 ; corrin ring methyl planarity N24 C19 C1 N21 gd_34 ; corrin ring but HEMC-derived N,C torsions N24 C19 C1 N21 gd_34 ; corrin ring but HEMC-derived N,C torsions N21 C4 C5 C6 gd_15 ; corrin ring but HEMC-derived N,C torsions C4 C5 C6 N22 gd_15 ; corrin ring but HEMC-derived N,C torsions N22 C9 C10 C11 gd_15 ; corrin ring but HEMC-derived N,C torsions C9 C10 C11 N23 gd_15 ; corrin ring but HEMC-derived N,C torsions N23 C14 C15 C16 gd_15 ; corrin ring but HEMC-derived N,C torsions C14 C15 C16 N24 gd_15 ; corrin ring but HEMC-derived N,C torsions C1 C2 C26 C27 gd_40 ; corrin ring HEMC derived CHn torsions C25 C2 C26 C27 gd_34 ; corrin ring HEMC derived CHn torsions C2 C26 C27 O28 gd_34 ; corrin ring HEMC derived CHn torsions C2 C3 C30 C31 gd_9 ; corrin ring HEMC derived CHn torsions C3 C30 C31 C32 gd_40 ; corrin ring HEMC derived CHn torsions C30 C31 C32 O34 gd_40 ; corrin ring HEMC derived CHn torsions C6 C7 C37 C38 gd_40 ; corrin ring HEMC derived CHn torsions C36 C7 C37 C38 gd_40 ; corrin ring HEMC derived CHn torsions C7 C37 C38 O39 gd_40 ; corrin ring HEMC derived CHn torsions C7 C8 C41 C42 gd_9 ; corrin ring HEMC derived CHn torsions C8 C41 C42 C43 gd_34 ; corrin ring HEMC derived CHn torsions C41 C42 C43 O44 gd_40 ; corrin ring HEMC derived CHn torsions C12 C13 C48 C49 gd_9 ; corrin ring HEMC derived CHn torsions C13 C48 C49 C50 gd_34 ; corrin ring HEMC derived CHn torsions C48 C49 C50 O51 gd_40 ; corrin ring HEMC derived CHn torsions C16 C17 C55 C56 gd_40 ; corrin ring HEMC derived CHn torsions C54 C17 C56 C57 gd_40 ; corrin ring HEMC derived CHn torsions C17 C55 C56 C57 gd_34 ; corrin ring HEMC derived CHn torsions C55 C56 C57 O58 gd_40 ; corrin ring HEMC derived CHn torsions C17 C18 C60 C61 gd_9 ; corrin ring HEMC derived CHn torsions C18 C60 C61 O63 gd_34 ; corrin ring HEMC derived CHn torsions C18 C17 C55 C56 gd_9 ; corrin ring HEMC derived CHn torsions N59 C1P C2P O3 gd_34 ; amide linkage torsion terms N59 C1P C2P C3P gd_34 ; amide linkage torsion terms C2P C1P N59 C57 gd_34 ; amide linkage torsion terms C56 C57 N59 C1P gd_14 ; amide linkage torsion terms C55 C56 C57 N59 gd_40 ; amide linkage torsion terms C17 C55 C56 C57 gd_40 ; amide linkage torsion terms C5 C4 N21 C1 gd_14 ; corrin ring sp3-containing torsions C10 C9 N22 C6 gd_14 ; corrin ring sp3-containing torsions C5 C6 N22 C9 gd_14 ; corrin ring sp3-containing torsions C15 C14 N23 C11 gd_14 ; corrin ring sp3-containing torsions C10 C11 N23 C14 gd_14 ; corrin ring sp3-containing torsions C15 C16 N24 C19 gd_14 ; corrin ring sp3-containing torsions C4 N21 C1 C2 gd_40 ; corrin ring sp3-containing torsions C18 C19 N24 C16 gd_40 ; corrin ring sp3-containing torsions N22 C6 C5 C4 gd_33 ; corrin ring sp3-containing torsions N23 C11 C10 C9 gd_33 ; corrin ring sp3-containing torsions C19 C18 C17 C55 gd_34 ; corrin ring sp3-containing torsions C55 C17 C16 C15 gd_40 ; corrin ring sp3-containing torsions C17 C18 C19 C1 gd_34 ; corrin ring sp3-containing torsions C18 C19 C1 C2 gd_34 ; corrin ring sp3-containing torsions C17 C16 C15 C14 gd_10 ; corrin ring sp3-containing torsions C16 C15 C14 C13 gd_10 ; corrin ring sp3-containing torsions C15 C14 C13 C12 gd_40 ; corrin ring sp3-containing torsions C6 C7 C8 C9 gd_34 ; corrin ring sp3-containing torsions C8 C7 C6 C5 gd_34 ; corrin ring sp3-containing torsions C30 C3 C2 C1 gd_34 ; corrin ring sp3-containing torsions C11 C12 C13 C14 gd_34 ; corrin ring sp3-containing torsions C13 C12 C11 C10 gd_34 ; corrin ring sp3-containing torsions C10 C9 C8 C7 gd_10 ; corrin ring sp3-containing torsions C5 C4 C3 C30 gd_34 ; corrin ring sp3-containing torsions C3 C2 C1 C19 gd_34 ; corrin ring sp3-containing torsions C9B N3B FE N21 gd_38 ; THIS IS NEW!!! N3B FE N21 C1 gd_38 ; THIS IS NEW!!! N3B FE N22 C6 gd_38 ; THIS IS NEW!!! N3B FE N23 C11 gd_38 ; THIS IS NEW!!! N3B FE N24 C16 gd_38 ; THIS IS NEW!!! [ LYB ] [ atoms ] C27 C 0.38000 0 ; from GLN residue O28 O -0.38000 0 ; from GLN residue N29 NT -0.83000 0 ; from GLN residue HAE H 0.41500 0 ; from GLN residue HAD H 0.41500 0 ; from GLN residue C32 C 0.38000 1 ; from GLN residue O34 O -0.38000 1 ; from GLN residue N33 NT -0.83000 1 ; from GLN residue HAG H 0.41500 1 ; from GLN residue HAF H 0.41500 1 ; from GLN residue C38 C 0.38000 2 ; from GLN residue O39 O -0.38000 2 ; from GLN residue N40 NT -0.83000 2 ; from GLN residue HAI H 0.41500 2 ; from GLN residue HAH H 0.41500 2 ; from GLN residue C43 C 0.38000 3 ; from GLN residue O44 O -0.38000 3 ; from GLN residue N45 NT -0.83000 3 ; from GLN residue HAK H 0.41500 3 ; from GLN residue HAJ H 0.41500 3 ; from GLN residue C50 C 0.38000 4 ; from GLN residue O51 O -0.38000 4 ; from GLN residue N52 NT -0.83000 4 ; from GLN residue HAM H 0.41500 4 ; from GLN residue HAL H 0.41500 4 ; from GLN residue C61 C 0.38000 5 ; from GLN residue O63 O -0.38000 5 ; from GLN residue N62 NT -0.83000 5 ; from GLN residue HAO H 0.41500 5 ; from GLN residue HAN H 0.41500 5 ; from GLN residue C20 CH3 0.00000 6 ; methyl group C25 CH3 0.00000 7 ; methyl group C36 CH3 0.00000 8 ; methyl group C46 CH3 0.00000 9 ; methyl group C47 CH3 0.00000 10 ; methyl group C54 CH3 0.00000 11 ; methyl group C26 CH2 0.00000 12 ; non-polar CHn fragments C30 CH2 0.00000 13 ; non-polar CHn fragments C31 CH2 0.00000 13 ; non-polar CHn fragments C37 CH2 0.00000 14 ; non-polar CHn fragments C41 CH2 0.00000 15 ; non-polar CHn fragments C42 CH2 0.00000 15 ; non-polar CHn fragments C48 CH2 0.00000 16 ; non-polar CHn fragments C49 CH2 0.00000 16 ; non-polar CHn fragments C56 CH2 0.00000 17 ; non-polar CHn fragments C55 CH2 0.00000 17 ; non-polar CHn fragments C60 CH2 0.00000 18 ; non-polar CHn fragments C2R CH1 0.15000 19 ; C2*-O2*-H2* from ADE O7R OA -0.54800 19 ; C2*-O2*-H2* from ADE HAA H 0.39800 19 ; C2*-O2*-H2* from ADE C1R CH1 0.20000 20 ; C1*-O4*-C4* from ADE O6R OA -0.36000 20 ; C1*-O4*-C4* from ADE C4R CH1 0.16000 20 ; C1*-O4*-C4* from ADE C3R CH1 0.00000 21 ; C3* from ADE C5R CH2 0.15000 22 ; C2*-O2*-H2* from ADE O8R OA -0.54800 22 ; C2*-O2*-H2* from ADE ; O8R OA -0.54800 22 ; C2*-O2*-H2* from ADE ; original from B12 ; ; HAB from B12 is gone in LYB, where the lysine fragment is added via CLB ; HAB H 0.39800 22 ; C2*-O2*-H2* from ADE ; HAB from B12 is gone in LYB, where the lysine fragment is added via CLB ; P P 2.20000 23 ; PO3+O3* fragment from ADE ; ; the O2P is a special mod to the PDB file. The O2 (fine in B12) is a "special" label ; that pdb2gmx has some kind of structure prep issue with. This, like the CO to FE, is a ; by-hand hack of the PDB file (for now) ; O2P OA -0.80000 23 ; PO3+O3* fragment from ADE O4 OM -1.00000 23 ; PO3+O3* fragment from ADE O5 OM -1.00000 23 ; PO3+O3* fragment from ADE O3 OA -0.80000 23 ; PO3+O3* fragment from ADE C2P CH1 0.35000 24 ; non-polar CHn fragment C3P CH3 0.00000 24 ; non-polar CHn fragment C1P CH2 0.00000 24 ; non-polar CHn fragment N59 N -0.28000 25 ; tempered GLN fragment charges HAC H 0.28000 25 ; tempered GLN fragment charges C57 C 0.38000 25 ; tempered GLN fragment charges O58 O -0.38000 25 ; tempered GLN fragment charges C5B C 0.00000 26 ; dimethylbenzimidazole C-CH3 group (non-polar) C5M CH3 0.00000 26 ; dimethylbenzimidazole C-CH3 group (non-polar) C6B C 0.00000 27 ; dimethylbenzimidazole C-CH3 group (non-polar) C6M CH3 0.00000 27 ; dimethylbenzimidazole C-CH3 group (non-polar) C4B C -0.14000 28 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H4B H 0.14000 28 ; dimethylbenzimidazole aromatic C-H from TRP, PHE C7B C -0.14000 29 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H7B H 0.14000 29 ; dimethylbenzimidazole aromatic C-H from TRP, PHE N3B NR -0.55000 30 ; dimethylbenzimidazole polar aromatic NC fragment C9B C 0.20000 30 ; dimethylbenzimidazole polar aromatic NC fragment N1B NR -0.30000 31 ; dimethylbenzimidazole polar aromatic NC fragment C8B C 0.20000 31 ; dimethylbenzimidazole polar aromatic NC fragment C2B C 0.23000 32 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H2B H 0.23000 32 ; dimethylbenzimidazole aromatic C-H from TRP, PHE C5 C -0.05000 33 ; C-CH3 group (non-polar) C35 CH3 0.00000 33 ; C-CH3 group (non-polar) C15 C -0.05000 34 ; C-CH3 group (non-polar) C53 CH3 0.00000 34 ; C-CH3 group (non-polar) FE FE 0.62000 35 ; HEMC Fe-N group N21 NR -0.44000 35 ; HEMC Fe-N group N22 NR -0.50000 35 ; HEMC Fe-N group N23 NR -0.50000 35 ; HEMC Fe-N group N24 NR -0.44000 35 ; HEMC Fe-N group C1 CH0 0.22000 36 ; non-polar HEMC-derived corrin atoms C2 CH0 0.00000 36 ; non-polar HEMC-derived corrin atoms C3 CH1 0.00000 36 ; non-polar HEMC-derived corrin atoms C4 C 0.38000 36 ; non-polar HEMC-derived corrin atoms C6 C 0.29000 37 ; non-polar HEMC-derived corrin atoms C7 CH0 0.00000 37 ; non-polar HEMC-derived corrin atoms C8 CH1 0.00000 37 ; non-polar HEMC-derived corrin atoms C9 C 0.35000 37 ; non-polar HEMC-derived corrin atoms C16 C 0.38000 38 ; non-polar HEMC-derived corrin atoms C17 CH0 0.00000 38 ; non-polar HEMC-derived corrin atoms C18 CH1 0.00000 38 ; non-polar HEMC-derived corrin atoms C19 CH1 0.24000 38 ; non-polar HEMC-derived corrin atoms C11 C 0.35000 39 ; non-polar HEMC-derived corrin atoms C12 CH0 0.00000 39 ; non-polar HEMC-derived corrin atoms C13 CH1 0.00000 39 ; non-polar HEMC-derived corrin atoms C14 C 0.29000 39 ; non-polar HEMC-derived corrin atoms C10 C -0.24000 40 ; aromatic C-H from TRP, PHE H10 H 0.14000 40 ; aromatic C-H from TRP, PHE ; ; Since CO is not defined as an atom in GROMOSxx, CO is converted to FE and the HEME ; values are employed. This is a workaround due for proper implementation. ; N N -0.31000 41 ; standard LYS (lysine) atom information H H 0.31000 41 ; standard LYS (lysine) atom information CA CH1 0.00000 42 ; standard LYS (lysine) atom information CB CH2 0.00000 42 ; standard LYS (lysine) atom information CG CH2 0.00000 43 ; standard LYS (lysine) atom information CD CH2 0.00000 43 ; standard LYS (lysine) atom information CE CH2 0.00000 44 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information NZ NT -0.34000 44 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information HZ1 H 0.34000 44 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information ; CE CH2 -0.24000 44 ; standard LYS (lysine) atom information ; NZ NT -0.64000 44 ; standard LYS (lysine) atom information ; HZ1 H 0.44000 44 ; standard LYS (lysine) atom information ; ; this H atom is gone, replaced by the linkage CLB atom. ; HZ2 H 0.44000 44 ; standard LYS (lysine) atom information ; this H atom is gone, replaced by the linkage CLB atom. ; C C 0.20000 45 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information O O -0.20000 45 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information ; C C 0.45000 45 ; standard LYS (lysine) atom information ; O O -0.45000 45 ; standard LYS (lysine) atom information ; ; linkage atoms (added new) ; CLB C 0.00000 46 ; this is the linkage carbon atom between LYS and B12 OLB O 0.00000 46 ; this is the additional =O at the linkage position ; [ bonds ] ; ai aj gromos type C26 C27 gb_27 ; from GLN fragment 0 C27 O28 gb_5 ; from GLN C27 N29 gb_9 ; from GLN N29 HAE gb_2 ; from GLN N29 HAD gb_2 ; from GLN C31 C32 gb_27 ; from GLN fragment 1 C32 O34 gb_5 ; from GLN C32 N33 gb_9 ; from GLN N33 HAG gb_2 ; from GLN N33 HAF gb_2 ; from GLN C37 C38 gb_27 ; from GLN fragment 2 C38 O39 gb_5 ; from GLN C38 N40 gb_9 ; from GLN N40 HAI gb_2 ; from GLN N40 HAH gb_2 ; from GLN C42 C43 gb_27 ; from GLN fragment 3 C43 O44 gb_5 ; from GLN C43 N45 gb_9 ; from GLN N45 HAK gb_2 ; from GLN N45 HAJ gb_2 ; from GLN C49 C50 gb_27 ; from GLN fragment 4 C50 O51 gb_5 ; from GLN C50 N52 gb_9 ; from GLN N52 HAM gb_2 ; from GLN N52 HAL gb_2 ; from GLN C60 C61 gb_27 ; from GLN fragment 5 C61 O63 gb_5 ; from GLN C61 N62 gb_9 ; from GLN N62 HAO gb_2 ; from GLN N62 HAN gb_2 ; from GLN FE N21 gb_35 ; FE-N bond from HEMC FE N22 gb_35 ; FE-N bond from HEMC FE N23 gb_35 ; FE-N bond from HEMC FE N24 gb_35 ; FE-N bond from HEMC FE N3B gb_37 ; FE-N3B bond from HEMC not in corrin ring P O2P gb_28 ; from ADE phosphate P O4 gb_24 ; from ADE phosphate P O5 gb_24 ; from ADE phosphate P O3 gb_28 ; from ADE phosphate N21 C1 gb_21 ; corrin ring N-CHn bonds N21 C4 gb_14 ; corrin ring N-C bonds N22 C6 gb_14 ; corrin ring N-C bonds N22 C9 gb_14 ; corrin ring N-C bonds N23 C11 gb_14 ; corrin ring N-C bonds N23 C14 gb_14 ; corrin ring N-C bonds N24 C16 gb_14 ; corrin ring N-C bonds N24 C19 gb_21 ; corrin ring N-CHn bonds C30 C31 gb_27 ; CH2-CH2 bonds C41 C42 gb_27 ; CH2-CH2 bonds C48 C49 gb_27 ; CH2-CH2 bonds C55 C56 gb_27 ; CH2-CH2 bonds C56 C57 gb_27 ; CH2-CH2 bonds N1B C1R gb_22 ; sugar bonds from ADE C1R C2R gb_26 ; sugar bonds from ADE C2R O7R gb_20 ; sugar bonds from ADE O7R HAA gb_1 ; sugar bonds from ADE C2R C3R gb_26 ; sugar bonds from ADE C3R C4R gb_26 ; sugar bonds from ADE C3R O2P gb_20 ; sugar bonds from ADE C4R C5R gb_26 ; sugar bonds from ADE C5R O8R gb_20 ; sugar bonds from ADE ; ; HAB is deleted from B12 for LYB O8R HAB gb_1 ; sugar bonds from ADE ; C4R O6R gb_20 ; sugar bonds from ADE O6R C1R gb_20 ; sugar bonds from ADE C1P N59 gb_9 ; amide corrin - phosphate linkage C1P C2P gb_27 ; amide corrin - phosphate linkage C2P C3P gb_27 ; amide corrin - phosphate linkage C2P O3 gb_20 ; amide corrin - phosphate linkage N59 HAC gb_2 ; amide corrin - phosphate linkage N59 C57 gb_9 ; amide corrin - phosphate linkage C57 O58 gb_5 ; amide corrin - phosphate linkage N1B C2B gb_10 ; dimethylbenzimidazole ring C2B N3B gb_10 ; dimethylbenzimidazole ring C2B H2B gb_3 ; dimethylbenzimidazole ring N3B C9B gb_10 ; dimethylbenzimidazole ring C9B C4B gb_16 ; dimethylbenzimidazole ring C4B C5B gb_16 ; dimethylbenzimidazole ring C4B H4B gb_3 ; dimethylbenzimidazole ring C5B C6B gb_16 ; dimethylbenzimidazole ring C5B C5M gb_27 ; dimethylbenzimidazole ring C6B C7B gb_16 ; dimethylbenzimidazole ring C6B C6M gb_27 ; dimethylbenzimidazole ring C7B C8B gb_16 ; dimethylbenzimidazole ring C7B H7B gb_3 ; dimethylbenzimidazole ring C8B N1B gb_10 ; dimethylbenzimidazole ring C8B C9B gb_16 ; dimethylbenzimidazole ring C1 C20 gb_27 ; corrin ring carbon framework C1 C2 gb_27 ; corrin ring carbon framework C2 C3 gb_27 ; corrin ring carbon framework C2 C25 gb_27 ; corrin ring carbon framework C2 C26 gb_27 ; corrin ring carbon framework C3 C4 gb_27 ; corrin ring carbon framework C3 C30 gb_27 ; corrin ring carbon framework C4 C5 gb_17 ; corrin ring carbon framework C5 C6 gb_17 ; corrin ring carbon framework C5 C35 gb_27 ; corrin ring carbon framework C6 C7 gb_27 ; corrin ring carbon framework C7 C8 gb_27 ; corrin ring carbon framework C7 C37 gb_27 ; corrin ring carbon framework C7 C36 gb_27 ; corrin ring carbon framework C8 C9 gb_27 ; corrin ring carbon framework C8 C41 gb_27 ; corrin ring carbon framework C9 C10 gb_17 ; corrin ring carbon framework C10 C11 gb_17 ; corrin ring carbon framework C11 C12 gb_27 ; corrin ring carbon framework C12 C46 gb_27 ; corrin ring carbon framework C12 C47 gb_27 ; corrin ring carbon framework C12 C13 gb_27 ; corrin ring carbon framework C13 C14 gb_27 ; corrin ring carbon framework C13 C48 gb_27 ; corrin ring carbon framework C14 C15 gb_17 ; corrin ring carbon framework C15 C16 gb_17 ; corrin ring carbon framework C15 C53 gb_27 ; corrin ring carbon framework C16 C17 gb_27 ; corrin ring carbon framework C17 C18 gb_27 ; corrin ring carbon framework C17 C54 gb_27 ; corrin ring carbon framework C17 C55 gb_27 ; corrin ring carbon framework C18 C19 gb_27 ; corrin ring carbon framework C18 C60 gb_27 ; corrin ring carbon framework C19 C1 gb_27 ; corrin ring carbon framework C10 H10 gb_3 ; corrin ring C10-H10 bond ; ; linker bond from B12 to CLB ; O8R CLB gb_5 ; LYS B12 linker (CLB replaces H) ; ; Lysine bond topology ; N H gb_2 ; standard LYS (lysine) N CA gb_21 ; standard LYS (lysine) CA CB gb_27 ; standard LYS (lysine) CA C gb_27 ; standard LYS (lysine) CB CG gb_27 ; standard LYS (lysine) CG CD gb_27 ; standard LYS (lysine) CD CE gb_27 ; standard LYS (lysine) CE NZ gb_21 ; standard LYS (lysine) NZ HZ1 gb_2 ; standard LYS (lysine) ; ; this replaces the HZ2 with CLB for the B12-LYS connection ; NZ CLB gb_9 ; standard LYS (lysine) C O gb_5 ; standard LYS (lysine) C +N gb_10 ; standard LYS (lysine) ; ; below is the C=O bond on the B12-LYS linkage (OLB is only connected to CLB) ; CLB OLB gb_27 ; CLB-OLB linkage bond (previously nowhere in the structure) [ exclusions ] ; ai aj FE C2 FE C3 FE C5 FE C7 FE C8 FE C10 FE C12 FE C13 FE C15 FE C17 FE C18 FE C20 N21 C25 N21 C26 N21 C30 N21 C35 N21 C6 N21 C9 N21 C11 N21 C14 N21 C16 N21 C19 N21 C10 N22 C1 N22 C4 N22 C36 N22 C37 N22 C11 N22 C14 N22 C16 N22 C19 N22 C15 N23 C16 N23 C19 N23 C1 N23 C4 N23 C6 N23 C9 N23 C46 N23 C47 N23 C48 N23 C5 N24 C4 N24 C5 N24 C6 N24 C9 N24 C10 N24 C11 N24 C14 N24 C55 N24 C54 N24 C60 C1R C7B C1R C9B C1R N3B N1B C6B N1B C4B C8B C5B C8B C5M C8B C6M C7B C4B C7B N3B C7B C2B C2B C9B C5B C2B C5M C6M C1 C30 ; HEMC-based C framework exclusions C1 C5 ; HEMC-based C framework exclusions C2 C5 ; HEMC-based C framework exclusions C3 C35 ; HEMC-based C framework exclusions C3 C6 ; HEMC-based C framework exclusions C4 C26 ; HEMC-based C framework exclusions C4 C7 ; HEMC-based C framework exclusions C30 C26 ; HEMC-based C framework exclusions C30 C5 ; HEMC-based C framework exclusions C5 C8 ; HEMC-based C framework exclusions C5 C9 ; HEMC-based C framework exclusions C5 C36 ; HEMC-based C framework exclusions C5 C37 ; HEMC-based C framework exclusions C35 C7 ; HEMC-based C framework exclusions C6 C41 ; HEMC-based C framework exclusions C6 C10 ; HEMC-based C framework exclusions C7 C10 ; HEMC-based C framework exclusions C8 H10 ; HEMC-based C framework exclusions C8 C11 ; HEMC-based C framework exclusions C9 C36 ; HEMC-based C framework exclusions C9 C37 ; HEMC-based C framework exclusions C9 C12 ; HEMC-based C framework exclusions C36 C41 ; HEMC-based C framework exclusions C37 C10 ; HEMC-based C framework exclusions C10 C13 ; HEMC-based C framework exclusions C10 C14 ; HEMC-based C framework exclusions C10 C46 ; HEMC-based C framework exclusions C10 C47 ; HEMC-based C framework exclusions H10 C12 ; HEMC-based C framework exclusions C11 C48 ; HEMC-based C framework exclusions C11 C15 ; HEMC-based C framework exclusions C12 C15 ; HEMC-based C framework exclusions C13 C53 ; HEMC-based C framework exclusions C13 C16 ; HEMC-based C framework exclusions C14 C46 ; HEMC-based C framework exclusions C14 C47 ; HEMC-based C framework exclusions C14 C17 ; HEMC-based C framework exclusions C46 C48 ; HEMC-based C framework exclusions C47 C48 ; HEMC-based C framework exclusions C48 C15 ; HEMC-based C framework exclusions C15 C18 ; HEMC-based C framework exclusions C15 C19 ; HEMC-based C framework exclusions C15 C54 ; HEMC-based C framework exclusions C15 C55 ; HEMC-based C framework exclusions C53 C17 ; HEMC-based C framework exclusions C16 C60 ; HEMC-based C framework exclusions C19 C54 ; HEMC-based C framework exclusions C19 C55 ; HEMC-based C framework exclusions C54 C60 ; HEMC-based C framework exclusions C55 C60 ; HEMC-based C framework exclusions [ angles ] ; ai aj ak gromos type C2 C26 C27 ga_15 ; from GLN, fragment 1 C26 C27 O28 ga_30 ; from GLN C26 C27 N29 ga_19 ; from GLN O28 C27 N29 ga_33 ; from GLN C27 N29 HAE ga_23 ; from GLN C27 N29 HAD ga_23 ; from GLN HAE N29 HAD ga_24 ; from GLN C30 C31 C32 ga_15 ; from GLN, fragment 2 C31 C32 O34 ga_30 ; from GLN C31 C32 N33 ga_19 ; from GLN O34 C32 N33 ga_33 ; from GLN C32 N33 HAG ga_23 ; from GLN C32 N33 HAF ga_23 ; from GLN HAG N33 HAF ga_24 ; from GLN C7 C37 C38 ga_15 ; from GLN, fragment 3 C37 C38 O39 ga_30 ; from GLN C37 C38 N40 ga_19 ; from GLN O39 C38 N40 ga_33 ; from GLN C38 N40 HAI ga_23 ; from GLN C38 N40 HAH ga_23 ; from GLN HAI N40 HAH ga_24 ; from GLN C41 C42 C43 ga_15 ; from GLN, fragment 4 C42 C43 O44 ga_30 ; from GLN C42 C43 N45 ga_19 ; from GLN O44 C43 N45 ga_33 ; from GLN C43 N45 HAK ga_23 ; from GLN C43 N45 HAJ ga_23 ; from GLN HAK N45 HAJ ga_24 ; from GLN C48 C49 C50 ga_15 ; from GLN, fragment 5 C49 C50 O51 ga_30 ; from GLN C49 C50 N52 ga_19 ; from GLN O51 C50 N52 ga_33 ; from GLN C50 N52 HAM ga_23 ; from GLN C50 N52 HAL ga_23 ; from GLN HAM N52 HAL ga_24 ; from GLN C18 C60 C61 ga_15 ; from GLN, fragment 6 C60 C61 O63 ga_30 ; from GLN C60 C61 N62 ga_19 ; from GLN O63 C61 N62 ga_33 ; from GLN C61 N62 HAO ga_23 ; from GLN C61 N62 HAN ga_23 ; from GLN HAO N62 HAN ga_24 ; from GLN N21 FE N22 ga_2 ; corrin ring Fe-N angle N21 FE N24 ga_2 ; corrin ring Fe-N angle N22 FE N23 ga_2 ; corrin ring Fe-N angle N23 FE N24 ga_2 ; corrin ring Fe-N angle N21 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N22 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N23 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N24 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole FE N21 C1 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N21 C4 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N22 C6 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N22 C9 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N23 C11 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N23 C14 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N24 C16 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N24 C19 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N3B C9B ga_34 ; Fe-dimethylbenzimidazole-N,C angle FE N3B C2B ga_34 ; Fe-dimethylbenzimidazole-N,C angle C8B N1B C2B ga_7 ; angle containing C8B, see minimization issues discussion N1B C8B C9B ga_7 ; angle containing C8B, see minimization issues discussion C8B C9B N3B ga_7 ; angle containing C8B, see minimization issues discussion C7B C8B N1B ga_39 ; angle containing C8B, see minimization issues discussion C8B N1B C1R ga_37 ; angle containing C8B, see minimization issues discussion C4B C9B C8B ga_27 ; angle containing C8B, see minimization issues discussion C6B C7B C8B ga_27 ; angle containing C8B, see minimization issues discussion C7B C8B C9B ga_27 ; angle containing C8B, see minimization issues discussion N21 C1 C2 ga_13 ; corrin ring-specific but HEMC-derived angles N21 C1 C20 ga_13 ; corrin ring-specific but HEMC-derived angles N21 C4 C3 ga_33 ; corrin ring-specific but HEMC-derived angles C4 N21 C1 ga_6 ; corrin ring-specific but HEMC-derived angles C5 C4 N21 ga_33 ; corrin ring-specific but HEMC-derived angles C19 C1 N21 ga_13 ; corrin ring-specific but HEMC-derived angles N22 C6 C5 ga_33 ; corrin ring-specific but HEMC-derived angles N22 C6 C7 ga_33 ; corrin ring-specific but HEMC-derived angles N22 C9 C8 ga_33 ; corrin ring-specific but HEMC-derived angles C9 N22 C6 ga_6 ; corrin ring-specific but HEMC-derived angles C10 C9 N22 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C11 C10 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C11 C12 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C14 C13 ga_33 ; corrin ring-specific but HEMC-derived angles C14 N23 C11 ga_6 ; corrin ring-specific but HEMC-derived angles C15 C14 N23 ga_33 ; corrin ring-specific but HEMC-derived angles N24 C16 C15 ga_33 ; corrin ring-specific but HEMC-derived angles N24 C19 C1 ga_13 ; corrin ring-specific but HEMC-derived angles C19 N24 C16 ga_6 ; corrin ring-specific but HEMC-derived angles C17 C16 N24 ga_33 ; corrin ring-specific but HEMC-derived angles C18 C19 N24 ga_13 ; corrin ring-specific but HEMC-derived angles C3R O2P P ga_26 ; phosphate angle from ADE O2P P O3 ga_5 ; phosphate angle from ADE O2P P O4 ga_14 ; phosphate angle from ADE O2P P O5 ga_14 ; phosphate angle from ADE O3 P O4 ga_14 ; phosphate angle from ADE O3 P O5 ga_14 ; phosphate angle from ADE O4 P O5 ga_29 ; phosphate angle from ADE P O3 C2P ga_26 ; phosphate angle from ADE O2P C3R C2R ga_9 ; phosphate oxygen to CHn carbons from ADE O2P C3R C4R ga_9 ; phosphate oxygen to CHn carbons from ADE O3 C2P C1P ga_9 ; phosphate oxygen to CHn carbons from ADE O3 C2P C3P ga_9 ; phosphate oxygen to CHn carbons from ADE C1 C2 C26 ga_13 ; CHn-CHn-CHn angles C1 C2 C25 ga_13 ; CHn-CHn-CHn angles C1 C2 C3 ga_13 ; CHn-CHn-CHn angles C1 C19 C18 ga_13 ; CHn-CHn-CHn angles C2 C1 C19 ga_13 ; CHn-CHn-CHn angles C2 C1 C20 ga_13 ; CHn-CHn-CHn angles C2 C3 C30 ga_13 ; CHn-CHn-CHn angles C3 C2 C25 ga_13 ; CHn-CHn-CHn angles C3 C2 C26 ga_13 ; CHn-CHn-CHn angles C3 C30 C31 ga_13 ; CHn-CHn-CHn angles C7 C8 C41 ga_13 ; CHn-CHn-CHn angles C8 C41 C42 ga_13 ; CHn-CHn-CHn angles C12 C13 C48 ga_13 ; CHn-CHn-CHn angles C13 C12 C46 ga_13 ; CHn-CHn-CHn angles C13 C12 C47 ga_13 ; CHn-CHn-CHn angles C13 C48 C49 ga_13 ; CHn-CHn-CHn angles C17 C18 C19 ga_13 ; CHn-CHn-CHn angles C17 C18 C60 ga_13 ; CHn-CHn-CHn angles C17 C55 C56 ga_13 ; CHn-CHn-CHn angles C18 C17 C54 ga_13 ; CHn-CHn-CHn angles C18 C17 C55 ga_13 ; CHn-CHn-CHn angles C19 C1 C20 ga_13 ; CHn-CHn-CHn angles C19 C18 C60 ga_13 ; CHn-CHn-CHn angles C25 C2 C26 ga_13 ; CHn-CHn-CHn angles C46 C12 C47 ga_13 ; CHn-CHn-CHn angles C54 C17 C55 ga_13 ; CHn-CHn-CHn angles C36 C7 C37 ga_13 ; CHn-CHn-CHn angles C2 C3 C4 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C4 C3 C30 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C8 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C36 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C37 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C7 C8 C9 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C8 C7 C36 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C8 C7 C37 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C9 C8 C41 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C13 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C46 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C47 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C12 C13 C14 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C14 C13 C48 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C18 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C54 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C55 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C4 C5 C6 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C9 C10 C11 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C14 C15 C16 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C3 C4 C5 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C4 C5 C35 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C5 C6 C7 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C6 C5 C35 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C8 C9 C10 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C10 C11 C12 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C13 C14 C15 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C14 C15 C53 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C15 C16 C17 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C16 C15 C53 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C5M C5B C4B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C5M C5B C6B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C6M C6B C5B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C6M C6B C7B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C4B C5B C6B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle C5B C4B C9B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle C5B C6B C7B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle N1B C1R C2R ga_9 ; from ADE Nsp2-containing dimethylbenzimidazole angle N1B C1R O6R ga_9 ; from ADE Nsp2-containing dimethylbenzimidazole angle N1B C2B N3B ga_7 ; from ADE Nsp2-containing dimethylbenzimidazole angle C2B N1B C1R ga_37 ; from ADE Nsp2-containing dimethylbenzimidazole angle N3B C9B C4B ga_39 ; from ADE Nsp2-containing dimethylbenzimidazole angle C9B N3B C2B ga_7 ; from ADE Nsp2-containing dimethylbenzimidazole angle C1R C2R C3R ga_8 ; from ADE sugar angle C1R C2R O7R ga_9 ; from ADE sugar angle C1R O6R C4R ga_10 ; from ADE sugar angle C2R C1R O6R ga_9 ; from ADE sugar angle C2R C3R C4R ga_8 ; from ADE sugar angle C2R O7R HAA ga_12 ; from ADE sugar angle C3R C2R O7R ga_9 ; from ADE sugar angle C3R C4R C5R ga_8 ; from ADE sugar angle C3R C4R O6R ga_9 ; from ADE sugar angle C4R C5R O8R ga_9 ; from ADE sugar angle ; ; HAB angle is gone from B12 for LYB C5R O8R HAB ga_12 ; from ADE sugar angle ; C5R C4R O6R ga_9 ; from ADE sugar angle C1P C2P C3P ga_13 ; amide linkage angle C57 C56 C55 ga_13 ; amide linkage angle C57 N59 HAC ga_23 ; from GLN angle N59 C57 O58 ga_33 ; from GLN angle C56 C57 N59 ga_19 ; from GLN angle O58 C57 C56 ga_30 ; from GLN angle C1P N59 C57 ga_31 ; from force field angle definitions C1P N59 HAC ga_18 ; from force field angle definitions C2P C1P N59 ga_15 ; from force field angle definitions C5B C4B H4B ga_25 ; from PHE C-C-H angle C9B C4B H4B ga_25 ; from PHE C-C-H angle C6B C7B H7B ga_25 ; from PHE C-C-H angle C8B C7B H7B ga_25 ; from PHE C-C-H angle N1B C2B H2B ga_36 ; from ADE N-C-H angle N3B C2B H2B ga_36 ; from ADE N-C-H angle C9 C10 H10 ga_25 ; corrin ring C-C10-H angle C11 C10 H10 ga_20 ; corrin ring C-C10-H angle C5R O8R CLB ga_12 ; for LYS-B12 bridge (just replaces O8R H atom with CLB) ; ; standard Lysine angle topology ; -C N H ga_32 ; Standard LYS (lysine) -C N CA ga_31 ; Standard LYS (lysine) H N CA ga_18 ; Standard LYS (lysine) N CA CB ga_13 ; Standard LYS (lysine) N CA C ga_13 ; Standard LYS (lysine) CB CA C ga_13 ; Standard LYS (lysine) CA CB CG ga_15 ; Standard LYS (lysine) CB CG CD ga_15 ; Standard LYS (lysine) CG CD CE ga_15 ; Standard LYS (lysine) CD CE NZ ga_15 ; Standard LYS (lysine) CE NZ HZ1 ga_11 ; Standard LYS (lysine) CE NZ CLB ga_6 ; Modification from LYS (CLB from NZ H atom) HZ1 NZ CLB ga_23 ; Modification from LYS (CLB from NZ H atom) CA C O ga_30 ; Standard LYS (lysine) CA C +N ga_19 ; Standard LYS (lysine) O C +N ga_33 ; Standard LYS (lysine) ; ; additional CLB-OLB angle linkages ; OLB CLB O8R ga_33 ; new OLB-CLB linkage angles OLB CLB NZ ga_33 ; new OLB-CLB linkage angles O8R CLB NZ ga_33 ; new OLB-CLB linkage angles [ impropers ] ; ai aj ak al gromos type C1R C8B C2B N1B gi_1 ; dimethylbenzimidazole improper for planarity N1B C8B C9B N3B gi_1 ; dimethylbenzimidazole improper for planarity C8B N1B C7B C9B gi_1 ; dimethylbenzimidazole improper for planarity C8B N1B C2B N3B gi_1 ; dimethylbenzimidazole improper for planarity C8B C7B C6B C5B gi_1 ; dimethylbenzimidazole improper for planarity C8B C9B N3B C2B gi_1 ; dimethylbenzimidazole improper for planarity C7B C8B C9B C4B gi_1 ; dimethylbenzimidazole improper for planarity C7B C6B C5B C4B gi_1 ; dimethylbenzimidazole improper for planarity C6B C5B C4B C9B gi_1 ; dimethylbenzimidazole improper for planarity C5B C4B C9B C8B gi_1 ; dimethylbenzimidazole improper for planarity C9B C8B C7B C6B gi_1 ; dimethylbenzimidazole improper for planarity C9B C4B N3B C8B gi_1 ; dimethylbenzimidazole improper for planarity C9B N3B C2B N1B gi_1 ; dimethylbenzimidazole improper for planarity C2B N1B C8B C9B gi_1 ; dimethylbenzimidazole improper for planarity C5M C4B C6B C5B gi_1 ; dimethylbenzimidazole methyl groups C6M C7B C5B C6B gi_1 ; dimethylbenzimidazole methyl groups C2B N1B N3B H2B gi_1 ; dimethylbenzimidazole H atom-containing planarity C4B C9B C5B H4B gi_1 ; dimethylbenzimidazole H atom-containing planarity C7B C8B C6B H7B gi_1 ; dimethylbenzimidazole H atom-containing planarity N3B FE C2B C9B gi_1 ; Fe-dimethylbenzimidazole planarity N21 C4 C5 C6 gi_1 ; HEMC-based conjugated corrin ring improper planarity N22 C6 C5 C4 gi_1 ; HEMC-based conjugated corrin ring improper planarity N22 C9 C10 C11 gi_1 ; HEMC-based conjugated corrin ring improper planarity N23 C11 C10 C9 gi_1 ; HEMC-based conjugated corrin ring improper planarity N23 C14 C15 C16 gi_1 ; HEMC-based conjugated corrin ring improper planarity N24 C16 C15 C14 gi_1 ; HEMC-based conjugated corrin ring improper planarity C5 C4 C6 C35 gi_1 ; corrin ring on-Csp2 methyl group improper planarity C15 C16 C14 C53 gi_1 ; corrin ring on-Csp2 methyl group improper planarity C27 O28 N29 C26 gi_1 ; from GLN improper torsion definition N29 HAE HAD C27 gi_1 ; from GLN improper torsion definition C32 O34 N33 C31 gi_1 ; from GLN improper torsion definition N33 HAG HAF C32 gi_1 ; from GLN improper torsion definition C38 O39 N40 C37 gi_1 ; from GLN improper torsion definition N40 HAI HAH C38 gi_1 ; from GLN improper torsion definition C43 O44 N45 C42 gi_1 ; from GLN improper torsion definition N45 HAK HAJ C43 gi_1 ; from GLN improper torsion definition C50 O51 N52 C49 gi_1 ; from GLN improper torsion definition N52 HAM HAL C50 gi_1 ; from GLN improper torsion definition C61 O63 N62 C60 gi_1 ; from GLN improper torsion definition N62 HAO HAN C61 gi_1 ; from GLN improper torsion definition C57 C56 O58 N59 gi_1 ; amide linkage C57 planarity N59 C57 C1P HAC gi_1 ; amide linkage N59 planarity C4 N21 C3 C5 gi_1 ; corrin ring C sp2 planarity C5 C4 C6 C35 gi_1 ; corrin ring C sp2 planarity C6 N22 C5 C7 gi_1 ; corrin ring C sp2 planarity C9 N22 C10 C8 gi_1 ; corrin ring C sp2 planarity C11 N23 C10 C12 gi_1 ; corrin ring C sp2 planarity C14 N23 C15 C13 gi_1 ; corrin ring C sp2 planarity C15 C14 C16 C53 gi_1 ; corrin ring C sp2 planarity C16 N24 C15 C17 gi_1 ; corrin ring C sp2 planarity C10 C9 C11 H10 gi_1 ; corrin ring C10 planarity C18 C17 C19 C60 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C19 N24 C18 C1 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C3 C2 C30 C4 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C8 C9 C7 C41 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C13 C14 C12 C48 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C2P C1P O3 C3P gi_2 ; corrin ring C atom sp3 tetrahedral geometry C1R N1B C2R O6R gi_2 ; sugar C atom tetrahedral geometry C2R O7R C3R C1R gi_2 ; sugar C atom tetrahedral geometry C3R C5R O6R C4R gi_2 ; sugar C atom tetrahedral geometry C3R C2R O2P C4R gi_2 ; sugar C atom tetrahedral geometry FE C1 C4 N21 gi_3 ; HEMC improper definition FE C6 C9 N22 gi_3 ; HEMC improper definition FE C11 C14 N23 gi_3 ; HEMC improper definition FE C16 C19 N24 gi_3 ; HEMC improper definition ; ; standard Lysine improper torsions ; N -C CA H gi_1 ; Standard LYS (lysine) CA N C CB gi_2 ; Standard LYS (lysine) C CA +N O gi_1 ; Standard LYS (lysine) CLB O8R OLB NZ gi_1 ; Linkage improper torsion to maintain planarity at CLB [ dihedrals ] ; ai aj ak al gromos type C3R O2P P O3 gd_20 ; from ADE phosphate definition C3R O2P P O3 gd_27 ; from ADE phosphate definition C2P O3 P O2P gd_20 ; from ADE phosphate definition C2P O3 P O2P gd_27 ; from ADE phosphate definition P O3 C2P C1P gd_7 ; from ADE phosphate definition C2R C3R O2P P gd_29 ; from ADE phosphate definition O8R C5R C4R O6R gd_8 ; from ADE sugar dihedrals O8R C5R C4R O6R gd_25 ; from ADE sugar dihedrals O8R C5R C4R C3R gd_17 ; from ADE sugar dihedrals O8R C5R C4R C3R gd_34 ; from ADE sugar dihedrals C3R C4R O6R C1R gd_29 ; from ADE sugar dihedrals C5R C4R C3R C2R gd_34 ; from ADE sugar dihedrals C5R C4R C3R O2P gd_17 ; from ADE sugar dihedrals O6R C4R C3R C2R gd_17 ; from ADE sugar dihedrals O6R C4R C3R O2P gd_18 ; from ADE sugar dihedrals C4R O6R C1R C2R gd_29 ; from ADE sugar dihedrals O6R C1R C2R O7R gd_18 ; from ADE sugar dihedrals O6R C1R C2R C3R gd_17 ; from ADE sugar dihedrals O6R C1R C2R C3R gd_34 ; from ADE sugar dihedrals C1R C2R C3R C4R gd_34 ; from ADE sugar dihedrals C1R C2R C3R O2P gd_17 ; from ADE sugar dihedrals O7R C2R C3R C4R gd_17 ; from ADE sugar dihedrals O7R C2R C3R O2P gd_18 ; from ADE sugar dihedrals C1R C2R O7R HAA gd_23 ; from ADE sugar dihedrals N1B C1R C2R O7R gd_17 ; from ADE sugar dihedrals O6R C1R N1B C8B gd_16 ; from ADE sugar dihedrals ; ; HAB-based torsion gone for LYB C4R C5R O8R HAB gd_2 ; additional ADE-based sugar dihedral ; N1B C1R C2R C3R gd_17 ; additional ADE-based sugar dihedral N1B C1R O6R C4R gd_17 ; additional ADE-based sugar dihedral C2 C26 C27 N29 gd_40 ; from GLN dihedral C26 C27 N29 HAD gd_14 ; from GLN dihedral C30 C31 C32 N33 gd_40 ; from GLN dihedral C31 C32 N33 HAF gd_14 ; from GLN dihedral C7 C37 C38 N40 gd_40 ; from GLN dihedral C37 C38 N40 HAH gd_14 ; from GLN dihedral C41 C42 C43 N45 gd_40 ; from GLN dihedral C42 C43 N45 HAJ gd_14 ; from GLN dihedral C48 C49 C50 N52 gd_40 ; from GLN dihedral C49 C50 N52 HAL gd_14 ; from GLN dihedral C18 C60 C61 N62 gd_40 ; from GLN dihedral C60 C61 N62 HAN gd_14 ; from GLN dihedral C5M C5B C6B C6M gd_33 ; dimethylbenzimidazole methyl dihedral fix C4B C5B C6B C6M gd_10 ; dimethylbenzimidazole methyl dihedral fix C8B C7B C6B C6M gd_10 ; dimethylbenzimidazole methyl dihedral fix C7B C6B C5B C5M gd_10 ; dimethylbenzimidazole methyl dihedral fix C9B C4B C5B C5M gd_10 ; dimethylbenzimidazole methyl dihedral fix C35 C5 C4 N21 gd_10 ; corrin ring methyl planarity C35 C5 C6 N22 gd_10 ; corrin ring methyl planarity C53 C15 C14 N23 gd_10 ; corrin ring methyl planarity C53 C1 C16 N24 gd_10 ; corrin ring methyl planarity N24 C19 C1 N21 gd_34 ; corrin ring but HEMC-derived N,C torsions N24 C19 C1 N21 gd_34 ; corrin ring but HEMC-derived N,C torsions N21 C4 C5 C6 gd_15 ; corrin ring but HEMC-derived N,C torsions C4 C5 C6 N22 gd_15 ; corrin ring but HEMC-derived N,C torsions N22 C9 C10 C11 gd_15 ; corrin ring but HEMC-derived N,C torsions C9 C10 C11 N23 gd_15 ; corrin ring but HEMC-derived N,C torsions N23 C14 C15 C16 gd_15 ; corrin ring but HEMC-derived N,C torsions C14 C15 C16 N24 gd_15 ; corrin ring but HEMC-derived N,C torsions C1 C2 C26 C27 gd_40 ; corrin ring HEMC derived CHn torsions C25 C2 C26 C27 gd_34 ; corrin ring HEMC derived CHn torsions C2 C26 C27 O28 gd_34 ; corrin ring HEMC derived CHn torsions C2 C3 C30 C31 gd_9 ; corrin ring HEMC derived CHn torsions C3 C30 C31 C32 gd_40 ; corrin ring HEMC derived CHn torsions C30 C31 C32 O34 gd_40 ; corrin ring HEMC derived CHn torsions C6 C7 C37 C38 gd_40 ; corrin ring HEMC derived CHn torsions C36 C7 C37 C38 gd_40 ; corrin ring HEMC derived CHn torsions C7 C37 C38 O39 gd_40 ; corrin ring HEMC derived CHn torsions C7 C8 C41 C42 gd_9 ; corrin ring HEMC derived CHn torsions C8 C41 C42 C43 gd_34 ; corrin ring HEMC derived CHn torsions C41 C42 C43 O44 gd_40 ; corrin ring HEMC derived CHn torsions C12 C13 C48 C49 gd_9 ; corrin ring HEMC derived CHn torsions C13 C48 C49 C50 gd_34 ; corrin ring HEMC derived CHn torsions C48 C49 C50 O51 gd_40 ; corrin ring HEMC derived CHn torsions C16 C17 C55 C56 gd_40 ; corrin ring HEMC derived CHn torsions C54 C17 C56 C57 gd_40 ; corrin ring HEMC derived CHn torsions C17 C55 C56 C57 gd_34 ; corrin ring HEMC derived CHn torsions C55 C56 C57 O58 gd_40 ; corrin ring HEMC derived CHn torsions C17 C18 C60 C61 gd_9 ; corrin ring HEMC derived CHn torsions C18 C60 C61 O63 gd_34 ; corrin ring HEMC derived CHn torsions C18 C17 C55 C56 gd_9 ; corrin ring HEMC derived CHn torsions N59 C1P C2P O3 gd_34 ; amide linkage torsion terms N59 C1P C2P C3P gd_34 ; amide linkage torsion terms C2P C1P N59 C57 gd_34 ; amide linkage torsion terms C56 C57 N59 C1P gd_14 ; amide linkage torsion terms C55 C56 C57 N59 gd_40 ; amide linkage torsion terms C17 C55 C56 C57 gd_40 ; amide linkage torsion terms C5 C4 N21 C1 gd_14 ; corrin ring sp3-containing torsions C10 C9 N22 C6 gd_14 ; corrin ring sp3-containing torsions C5 C6 N22 C9 gd_14 ; corrin ring sp3-containing torsions C15 C14 N23 C11 gd_14 ; corrin ring sp3-containing torsions C10 C11 N23 C14 gd_14 ; corrin ring sp3-containing torsions C15 C16 N24 C19 gd_14 ; corrin ring sp3-containing torsions C4 N21 C1 C2 gd_40 ; corrin ring sp3-containing torsions C18 C19 N24 C16 gd_40 ; corrin ring sp3-containing torsions N22 C6 C5 C4 gd_33 ; corrin ring sp3-containing torsions N23 C11 C10 C9 gd_33 ; corrin ring sp3-containing torsions C19 C18 C17 C55 gd_34 ; corrin ring sp3-containing torsions C55 C17 C16 C15 gd_40 ; corrin ring sp3-containing torsions C17 C18 C19 C1 gd_34 ; corrin ring sp3-containing torsions C18 C19 C1 C2 gd_34 ; corrin ring sp3-containing torsions C17 C16 C15 C14 gd_10 ; corrin ring sp3-containing torsions C16 C15 C14 C13 gd_10 ; corrin ring sp3-containing torsions C15 C14 C13 C12 gd_40 ; corrin ring sp3-containing torsions C6 C7 C8 C9 gd_34 ; corrin ring sp3-containing torsions C8 C7 C6 C5 gd_34 ; corrin ring sp3-containing torsions C30 C3 C2 C1 gd_34 ; corrin ring sp3-containing torsions C11 C12 C13 C14 gd_34 ; corrin ring sp3-containing torsions C13 C12 C11 C10 gd_34 ; corrin ring sp3-containing torsions C10 C9 C8 C7 gd_10 ; corrin ring sp3-containing torsions C5 C4 C3 C30 gd_34 ; corrin ring sp3-containing torsions C3 C2 C1 C19 gd_34 ; corrin ring sp3-containing torsions ; ; standard Lysine torsion topology ; -CA -C N CA gd_14 ; Standard LYS (lysine) -C N CA C gd_39 ; Standard LYS (lysine) N CA CB CG gd_34 ; Standard LYS (lysine) N CA C +N gd_40 ; Standard LYS (lysine) CA CB CG CD gd_34 ; Standard LYS (lysine) CB CG CD CE gd_34 ; Standard LYS (lysine) CG CD CE NZ gd_34 ; Standard LYS (lysine) CD CE NZ HZ1 gd_29 ; Standard LYS (lysine) C4R C5R O8R CLB gd_23 ; LYS-B12 linkage dihedral terms C5R O8R CLB OLB gd_12 ; LYS-B12 linkage dihedral terms O8R CLB NZ CE gd_14 ; LYS-B12 linkage dihedral terms OLB CLB NZ CE gd_14 ; LYS-B12 linkage dihedral terms C9B N3B FE N21 gd_38 ; THIS IS NEW!!! N3B FE N21 C1 gd_38 ; THIS IS NEW!!! N3B FE N22 C6 gd_38 ; THIS IS NEW!!! N3B FE N23 C11 gd_38 ; THIS IS NEW!!! N3B FE N24 C16 gd_38 ; THIS IS NEW!!! ; ; Use of LYB, which employs the pdb2gmx method for sewing the peptide chain together, ; requires the addition of this very new, bulky amino acid to aminoacids.dat. [ BCN ] ; ; cyanocobalamin based on the HEMC CO parameters ; [ atoms ] C27 C 0.38000 0 ; from GLN residue O28 O -0.38000 0 ; from GLN residue N29 NT -0.83000 0 ; from GLN residue HAE H 0.41500 0 ; from GLN residue HAD H 0.41500 0 ; from GLN residue C32 C 0.38000 1 ; from GLN residue O34 O -0.38000 1 ; from GLN residue N33 NT -0.83000 1 ; from GLN residue HAG H 0.41500 1 ; from GLN residue HAF H 0.41500 1 ; from GLN residue C38 C 0.38000 2 ; from GLN residue O39 O -0.38000 2 ; from GLN residue N40 NT -0.83000 2 ; from GLN residue HAI H 0.41500 2 ; from GLN residue HAH H 0.41500 2 ; from GLN residue C43 C 0.38000 3 ; from GLN residue O44 O -0.38000 3 ; from GLN residue N45 NT -0.83000 3 ; from GLN residue HAK H 0.41500 3 ; from GLN residue HAJ H 0.41500 3 ; from GLN residue C50 C 0.38000 4 ; from GLN residue O51 O -0.38000 4 ; from GLN residue N52 NT -0.83000 4 ; from GLN residue HAM H 0.41500 4 ; from GLN residue HAL H 0.41500 4 ; from GLN residue C61 C 0.38000 5 ; from GLN residue O63 O -0.38000 5 ; from GLN residue N62 NT -0.83000 5 ; from GLN residue HAO H 0.41500 5 ; from GLN residue HAN H 0.41500 5 ; from GLN residue C20 CH3 0.00000 6 ; methyl group C25 CH3 0.00000 7 ; methyl group C36 CH3 0.00000 8 ; methyl group C46 CH3 0.00000 9 ; methyl group C47 CH3 0.00000 10 ; methyl group C54 CH3 0.00000 11 ; methyl group C26 CH2 0.00000 12 ; non-polar CHn fragments C30 CH2 0.00000 13 ; non-polar CHn fragments C31 CH2 0.00000 13 ; non-polar CHn fragments C37 CH2 0.00000 14 ; non-polar CHn fragments C41 CH2 0.00000 15 ; non-polar CHn fragments C42 CH2 0.00000 15 ; non-polar CHn fragments C48 CH2 0.00000 16 ; non-polar CHn fragments C49 CH2 0.00000 16 ; non-polar CHn fragments C56 CH2 0.00000 17 ; non-polar CHn fragments C55 CH2 0.00000 17 ; non-polar CHn fragments C60 CH2 0.00000 18 ; non-polar CHn fragments C2R CH1 0.15000 19 ; C2*-O2*-H2* from ADE O7R OA -0.54800 19 ; C2*-O2*-H2* from ADE HAA H 0.39800 19 ; C2*-O2*-H2* from ADE C1R CH1 0.20000 20 ; C1*-O4*-C4* from ADE O6R OA -0.36000 20 ; C1*-O4*-C4* from ADE C4R CH1 0.16000 20 ; C1*-O4*-C4* from ADE C3R CH1 0.00000 21 ; C3* from ADE C5R CH2 0.15000 22 ; C2*-O2*-H2* from ADE O8R OA -0.54800 22 ; C2*-O2*-H2* from ADE HAB H 0.39800 22 ; C2*-O2*-H2* from ADE P P 2.20000 23 ; PO3+O3* fragment from ADE O2 OA -0.80000 23 ; PO3+O3* fragment from ADE O4 OM -1.00000 23 ; PO3+O3* fragment from ADE O5 OM -1.00000 23 ; PO3+O3* fragment from ADE O3 OA -0.80000 23 ; PO3+O3* fragment from ADE C2P CH1 0.35000 24 ; non-polar CHn fragment C3P CH3 0.00000 24 ; non-polar CHn fragment C1P CH2 0.00000 24 ; non-polar CHn fragment N59 N -0.28000 25 ; tempered GLN fragment charges HAC H 0.28000 25 ; tempered GLN fragment charges C57 C 0.38000 25 ; tempered GLN fragment charges O58 O -0.38000 25 ; tempered GLN fragment charges C5B C 0.00000 26 ; dimethylbenzimidazole C-CH3 group (non-polar) C5M CH3 0.00000 26 ; dimethylbenzimidazole C-CH3 group (non-polar) C6B C 0.00000 27 ; dimethylbenzimidazole C-CH3 group (non-polar) C6M CH3 0.00000 27 ; dimethylbenzimidazole C-CH3 group (non-polar) C4B C -0.14000 28 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H4B H 0.14000 28 ; dimethylbenzimidazole aromatic C-H from TRP, PHE C7B C -0.14000 29 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H7B H 0.14000 29 ; dimethylbenzimidazole aromatic C-H from TRP, PHE N3B NR -0.55000 30 ; dimethylbenzimidazole polar aromatic NC fragment C9B C 0.20000 30 ; dimethylbenzimidazole polar aromatic NC fragment N1B NR -0.30000 31 ; dimethylbenzimidazole polar aromatic NC fragment C8B C 0.20000 31 ; dimethylbenzimidazole polar aromatic NC fragment C2B C 0.23000 32 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H2B H 0.23000 32 ; dimethylbenzimidazole aromatic C-H from TRP, PHE C5 C -0.05000 33 ; C-CH3 group (non-polar) C35 CH3 0.00000 33 ; C-CH3 group (non-polar) C15 C -0.05000 34 ; C-CH3 group (non-polar) C53 CH3 0.00000 34 ; C-CH3 group (non-polar) FE FE 1.00000 35 ; HEMC Fe-N group N21 NR -0.44000 35 ; HEMC Fe-N group N22 NR -0.50000 35 ; HEMC Fe-N group N23 NR -0.50000 35 ; HEMC Fe-N group N24 NR -0.44000 35 ; HEMC Fe-N group C1 CH0 0.22000 36 ; non-polar HEMC-derived corrin atoms C2 CH0 0.00000 36 ; non-polar HEMC-derived corrin atoms C3 CH1 0.00000 36 ; non-polar HEMC-derived corrin atoms C4 C 0.38000 36 ; non-polar HEMC-derived corrin atoms C6 C 0.29000 37 ; non-polar HEMC-derived corrin atoms C7 CH0 0.00000 37 ; non-polar HEMC-derived corrin atoms C8 CH1 0.00000 37 ; non-polar HEMC-derived corrin atoms C9 C 0.35000 37 ; non-polar HEMC-derived corrin atoms C16 C 0.38000 38 ; non-polar HEMC-derived corrin atoms C17 CH0 0.00000 38 ; non-polar HEMC-derived corrin atoms C18 CH1 0.00000 38 ; non-polar HEMC-derived corrin atoms C19 CH1 0.24000 38 ; non-polar HEMC-derived corrin atoms C11 C 0.35000 39 ; non-polar HEMC-derived corrin atoms C12 CH0 0.00000 39 ; non-polar HEMC-derived corrin atoms C13 CH1 0.00000 39 ; non-polar HEMC-derived corrin atoms C14 C 0.29000 39 ; non-polar HEMC-derived corrin atoms C10 C -0.24000 40 ; aromatic C-H from TRP, PHE H10 H 0.14000 40 ; aromatic C-H from TRP, PHE ; ; cyano group addition to the original B12 topology ; C1N C 0.04000 41 ; CN group on Fe N1C N -0.42000 41 ; CN group on Fe ; ; Since CO is not defined as an atom in GROMOSxx, CO is converted to FE and the HEME ; values are employed. This is a workaround due for proper implementation. ; [ bonds ] ; ai aj gromos type C26 C27 gb_27 ; from GLN fragment 0 C27 O28 gb_5 ; from GLN C27 N29 gb_9 ; from GLN N29 HAE gb_2 ; from GLN N29 HAD gb_2 ; from GLN C31 C32 gb_27 ; from GLN fragment 1 C32 O34 gb_5 ; from GLN C32 N33 gb_9 ; from GLN N33 HAG gb_2 ; from GLN N33 HAF gb_2 ; from GLN C37 C38 gb_27 ; from GLN fragment 2 C38 O39 gb_5 ; from GLN C38 N40 gb_9 ; from GLN N40 HAI gb_2 ; from GLN N40 HAH gb_2 ; from GLN C42 C43 gb_27 ; from GLN fragment 3 C43 O44 gb_5 ; from GLN C43 N45 gb_9 ; from GLN N45 HAK gb_2 ; from GLN N45 HAJ gb_2 ; from GLN C49 C50 gb_27 ; from GLN fragment 4 C50 O51 gb_5 ; from GLN C50 N52 gb_9 ; from GLN N52 HAM gb_2 ; from GLN N52 HAL gb_2 ; from GLN C60 C61 gb_27 ; from GLN fragment 5 C61 O63 gb_5 ; from GLN C61 N62 gb_9 ; from GLN N62 HAO gb_2 ; from GLN N62 HAN gb_2 ; from GLN FE N21 gb_35 ; FE-N bond from HEMC FE N22 gb_35 ; FE-N bond from HEMC FE N23 gb_35 ; FE-N bond from HEMC FE N24 gb_35 ; FE-N bond from HEMC FE N3B gb_37 ; FE-N3B bond from HEMC not in corrin ring P O2 gb_28 ; from ADE phosphate P O4 gb_24 ; from ADE phosphate P O5 gb_24 ; from ADE phosphate P O3 gb_28 ; from ADE phosphate N21 C1 gb_21 ; corrin ring N-CHn bonds N21 C4 gb_14 ; corrin ring N-C bonds N22 C6 gb_14 ; corrin ring N-C bonds N22 C9 gb_14 ; corrin ring N-C bonds N23 C11 gb_14 ; corrin ring N-C bonds N23 C14 gb_14 ; corrin ring N-C bonds N24 C16 gb_14 ; corrin ring N-C bonds N24 C19 gb_21 ; corrin ring N-CHn bonds C30 C31 gb_27 ; CH2-CH2 bonds C41 C42 gb_27 ; CH2-CH2 bonds C48 C49 gb_27 ; CH2-CH2 bonds C55 C56 gb_27 ; CH2-CH2 bonds C56 C57 gb_27 ; CH2-CH2 bonds N1B C1R gb_22 ; sugar bonds from ADE C1R C2R gb_26 ; sugar bonds from ADE C2R O7R gb_20 ; sugar bonds from ADE O7R HAA gb_1 ; sugar bonds from ADE C2R C3R gb_26 ; sugar bonds from ADE C3R C4R gb_26 ; sugar bonds from ADE C3R O2 gb_20 ; sugar bonds from ADE C4R C5R gb_26 ; sugar bonds from ADE C5R O8R gb_20 ; sugar bonds from ADE O8R HAB gb_1 ; sugar bonds from ADE C4R O6R gb_20 ; sugar bonds from ADE O6R C1R gb_20 ; sugar bonds from ADE C1P N59 gb_9 ; amide corrin - phosphate linkage C1P C2P gb_27 ; amide corrin - phosphate linkage C2P C3P gb_27 ; amide corrin - phosphate linkage C2P O3 gb_20 ; amide corrin - phosphate linkage N59 HAC gb_2 ; amide corrin - phosphate linkage N59 C57 gb_9 ; amide corrin - phosphate linkage C57 O58 gb_5 ; amide corrin - phosphate linkage N1B C2B gb_10 ; dimethylbenzimidazole ring C2B N3B gb_10 ; dimethylbenzimidazole ring C2B H2B gb_3 ; dimethylbenzimidazole ring N3B C9B gb_10 ; dimethylbenzimidazole ring C9B C4B gb_16 ; dimethylbenzimidazole ring C4B C5B gb_16 ; dimethylbenzimidazole ring C4B H4B gb_3 ; dimethylbenzimidazole ring C5B C6B gb_16 ; dimethylbenzimidazole ring C5B C5M gb_27 ; dimethylbenzimidazole ring C6B C7B gb_16 ; dimethylbenzimidazole ring C6B C6M gb_27 ; dimethylbenzimidazole ring C7B C8B gb_16 ; dimethylbenzimidazole ring C7B H7B gb_3 ; dimethylbenzimidazole ring C8B N1B gb_10 ; dimethylbenzimidazole ring C8B C9B gb_16 ; dimethylbenzimidazole ring C1 C20 gb_27 ; corrin ring carbon framework C1 C2 gb_27 ; corrin ring carbon framework C2 C3 gb_27 ; corrin ring carbon framework C2 C25 gb_27 ; corrin ring carbon framework C2 C26 gb_27 ; corrin ring carbon framework C3 C4 gb_27 ; corrin ring carbon framework C3 C30 gb_27 ; corrin ring carbon framework C4 C5 gb_17 ; corrin ring carbon framework C5 C6 gb_17 ; corrin ring carbon framework C5 C35 gb_27 ; corrin ring carbon framework C6 C7 gb_27 ; corrin ring carbon framework C7 C8 gb_27 ; corrin ring carbon framework C7 C37 gb_27 ; corrin ring carbon framework C7 C36 gb_27 ; corrin ring carbon framework C8 C9 gb_27 ; corrin ring carbon framework C8 C41 gb_27 ; corrin ring carbon framework C9 C10 gb_17 ; corrin ring carbon framework C10 C11 gb_17 ; corrin ring carbon framework C11 C12 gb_27 ; corrin ring carbon framework C12 C46 gb_27 ; corrin ring carbon framework C12 C47 gb_27 ; corrin ring carbon framework C12 C13 gb_27 ; corrin ring carbon framework C13 C14 gb_27 ; corrin ring carbon framework C13 C48 gb_27 ; corrin ring carbon framework C14 C15 gb_17 ; corrin ring carbon framework C15 C16 gb_17 ; corrin ring carbon framework C15 C53 gb_27 ; corrin ring carbon framework C16 C17 gb_27 ; corrin ring carbon framework C17 C18 gb_27 ; corrin ring carbon framework C17 C54 gb_27 ; corrin ring carbon framework C17 C55 gb_27 ; corrin ring carbon framework C18 C19 gb_27 ; corrin ring carbon framework C18 C60 gb_27 ; corrin ring carbon framework C19 C1 gb_27 ; corrin ring carbon framework C10 H10 gb_3 ; corrin ring C10-H10 bond ; ; cyano group addition to the original B12 topology ; FE C1N gb_30 ; cyano group on the Fe C1N N1C gb_4 ; cyano group on the Fe [ exclusions ] ; ai aj FE N1C ; new add FE C1 ; new add FE C2 FE C3 FE C5 FE C7 FE C8 FE C10 FE C12 FE C13 FE C15 FE C17 FE C18 FE C20 N21 C25 N21 C26 N21 C30 N21 C35 N21 C6 N21 C9 N21 C11 N21 C14 N21 C16 N21 C19 N21 C10 N22 C1 N22 C4 N22 C36 N22 C37 N22 C11 N22 C14 N22 C16 N22 C19 N22 C15 N23 C16 N23 C19 N23 C1 N23 C4 N23 C6 N23 C9 N23 C46 N23 C47 N23 C48 N23 C5 N24 C4 N24 C5 N24 C6 N24 C9 N24 C10 N24 C11 N24 C14 N24 C55 N24 C54 N24 C60 C1R C7B C1R C9B C1R N3B N1B C6B N1B C4B C8B C5B C8B C5M C8B C6M C7B C4B C7B N3B C7B C2B C2B C9B C5B C2B C5M C6M C1 C30 ; HEMC-based C framework exclusions C1 C5 ; HEMC-based C framework exclusions C2 C5 ; HEMC-based C framework exclusions C3 C35 ; HEMC-based C framework exclusions C3 C6 ; HEMC-based C framework exclusions C4 C26 ; HEMC-based C framework exclusions C4 C7 ; HEMC-based C framework exclusions C30 C26 ; HEMC-based C framework exclusions C30 C5 ; HEMC-based C framework exclusions C5 C8 ; HEMC-based C framework exclusions C5 C9 ; HEMC-based C framework exclusions C5 C36 ; HEMC-based C framework exclusions C5 C37 ; HEMC-based C framework exclusions C35 C7 ; HEMC-based C framework exclusions C6 C41 ; HEMC-based C framework exclusions C6 C10 ; HEMC-based C framework exclusions C7 C10 ; HEMC-based C framework exclusions C8 H10 ; HEMC-based C framework exclusions C8 C11 ; HEMC-based C framework exclusions C9 C36 ; HEMC-based C framework exclusions C9 C37 ; HEMC-based C framework exclusions C9 C12 ; HEMC-based C framework exclusions C36 C41 ; HEMC-based C framework exclusions C37 C10 ; HEMC-based C framework exclusions C10 C13 ; HEMC-based C framework exclusions C10 C14 ; HEMC-based C framework exclusions C10 C46 ; HEMC-based C framework exclusions C10 C47 ; HEMC-based C framework exclusions H10 C12 ; HEMC-based C framework exclusions C11 C48 ; HEMC-based C framework exclusions C11 C15 ; HEMC-based C framework exclusions C12 C15 ; HEMC-based C framework exclusions C13 C53 ; HEMC-based C framework exclusions C13 C16 ; HEMC-based C framework exclusions C14 C46 ; HEMC-based C framework exclusions C14 C47 ; HEMC-based C framework exclusions C14 C17 ; HEMC-based C framework exclusions C46 C48 ; HEMC-based C framework exclusions C47 C48 ; HEMC-based C framework exclusions C48 C15 ; HEMC-based C framework exclusions C15 C18 ; HEMC-based C framework exclusions C15 C19 ; HEMC-based C framework exclusions C15 C54 ; HEMC-based C framework exclusions C15 C55 ; HEMC-based C framework exclusions C53 C17 ; HEMC-based C framework exclusions C16 C60 ; HEMC-based C framework exclusions C19 C54 ; HEMC-based C framework exclusions C19 C55 ; HEMC-based C framework exclusions C54 C60 ; HEMC-based C framework exclusions C55 C60 ; HEMC-based C framework exclusions ; ; cyano group addition to the original B12 topology ; N21 N1C ; cyano exclusions from HEMC CO group N22 N1C ; cyano exclusions from HEMC CO group N23 N1C ; cyano exclusions from HEMC CO group N24 N1C ; cyano exclusions from HEMC CO group C1 C1N ; cyano exclusions from HEMC CO group C4 C1N ; cyano exclusions from HEMC CO group C6 C1N ; cyano exclusions from HEMC CO group C9 C1N ; cyano exclusions from HEMC CO group C11 C1N ; cyano exclusions from HEMC CO group C14 C1N ; cyano exclusions from HEMC CO group C16 C1N ; cyano exclusions from HEMC CO group C19 C1N ; cyano exclusions from HEMC CO group N3B N1C ; cyano exclusion unique to 6-coordinate iron C1N C9B ; additional cyano exclusion at Fe 6-center C1N C2B ; additional cyano exclusion at Fe 6-center [ angles ] ; ai aj ak gromos type C2 C26 C27 ga_15 ; from GLN, fragment 1 C26 C27 O28 ga_30 ; from GLN C26 C27 N29 ga_19 ; from GLN O28 C27 N29 ga_33 ; from GLN C27 N29 HAE ga_23 ; from GLN C27 N29 HAD ga_23 ; from GLN HAE N29 HAD ga_24 ; from GLN C30 C31 C32 ga_15 ; from GLN, fragment 2 C31 C32 O34 ga_30 ; from GLN C31 C32 N33 ga_19 ; from GLN O34 C32 N33 ga_33 ; from GLN C32 N33 HAG ga_23 ; from GLN C32 N33 HAF ga_23 ; from GLN HAG N33 HAF ga_24 ; from GLN C7 C37 C38 ga_15 ; from GLN, fragment 3 C37 C38 O39 ga_30 ; from GLN C37 C38 N40 ga_19 ; from GLN O39 C38 N40 ga_33 ; from GLN C38 N40 HAI ga_23 ; from GLN C38 N40 HAH ga_23 ; from GLN HAI N40 HAH ga_24 ; from GLN C41 C42 C43 ga_15 ; from GLN, fragment 4 C42 C43 O44 ga_30 ; from GLN C42 C43 N45 ga_19 ; from GLN O44 C43 N45 ga_33 ; from GLN C43 N45 HAK ga_23 ; from GLN C43 N45 HAJ ga_23 ; from GLN HAK N45 HAJ ga_24 ; from GLN C48 C49 C50 ga_15 ; from GLN, fragment 5 C49 C50 O51 ga_30 ; from GLN C49 C50 N52 ga_19 ; from GLN O51 C50 N52 ga_33 ; from GLN C50 N52 HAM ga_23 ; from GLN C50 N52 HAL ga_23 ; from GLN HAM N52 HAL ga_24 ; from GLN C18 C60 C61 ga_15 ; from GLN, fragment 6 C60 C61 O63 ga_30 ; from GLN C60 C61 N62 ga_19 ; from GLN O63 C61 N62 ga_33 ; from GLN C61 N62 HAO ga_23 ; from GLN C61 N62 HAN ga_23 ; from GLN HAO N62 HAN ga_24 ; from GLN N21 FE N22 ga_2 ; corrin ring Fe-N angle N21 FE N24 ga_2 ; corrin ring Fe-N angle N22 FE N23 ga_2 ; corrin ring Fe-N angle N23 FE N24 ga_2 ; corrin ring Fe-N angle N21 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N22 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N23 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N24 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole FE N21 C1 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N21 C4 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N22 C6 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N22 C9 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N23 C11 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N23 C14 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N24 C16 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N24 C19 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N3B C9B ga_34 ; Fe-dimethylbenzimidazole-N,C angle FE N3B C2B ga_34 ; Fe-dimethylbenzimidazole-N,C angle C8B N1B C2B ga_7 ; angle containing C8B, see minimization issues discussion N1B C8B C9B ga_7 ; angle containing C8B, see minimization issues discussion C8B C9B N3B ga_7 ; angle containing C8B, see minimization issues discussion C7B C8B N1B ga_39 ; angle containing C8B, see minimization issues discussion C8B N1B C1R ga_37 ; angle containing C8B, see minimization issues discussion C4B C9B C8B ga_27 ; angle containing C8B, see minimization issues discussion C6B C7B C8B ga_27 ; angle containing C8B, see minimization issues discussion C7B C8B C9B ga_27 ; angle containing C8B, see minimization issues discussion N21 C1 C2 ga_13 ; corrin ring-specific but HEMC-derived angles N21 C1 C20 ga_13 ; corrin ring-specific but HEMC-derived angles N21 C4 C3 ga_33 ; corrin ring-specific but HEMC-derived angles C4 N21 C1 ga_6 ; corrin ring-specific but HEMC-derived angles C5 C4 N21 ga_33 ; corrin ring-specific but HEMC-derived angles C19 C1 N21 ga_13 ; corrin ring-specific but HEMC-derived angles N22 C6 C5 ga_33 ; corrin ring-specific but HEMC-derived angles N22 C6 C7 ga_33 ; corrin ring-specific but HEMC-derived angles N22 C9 C8 ga_33 ; corrin ring-specific but HEMC-derived angles C9 N22 C6 ga_6 ; corrin ring-specific but HEMC-derived angles C10 C9 N22 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C11 C10 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C11 C12 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C14 C13 ga_33 ; corrin ring-specific but HEMC-derived angles C14 N23 C11 ga_6 ; corrin ring-specific but HEMC-derived angles C15 C14 N23 ga_33 ; corrin ring-specific but HEMC-derived angles N24 C16 C15 ga_33 ; corrin ring-specific but HEMC-derived angles N24 C19 C1 ga_13 ; corrin ring-specific but HEMC-derived angles C19 N24 C16 ga_6 ; corrin ring-specific but HEMC-derived angles C17 C16 N24 ga_33 ; corrin ring-specific but HEMC-derived angles C18 C19 N24 ga_13 ; corrin ring-specific but HEMC-derived angles C3R O2 P ga_26 ; phosphate angle from ADE O2 P O3 ga_5 ; phosphate angle from ADE O2 P O4 ga_14 ; phosphate angle from ADE O2 P O5 ga_14 ; phosphate angle from ADE O3 P O4 ga_14 ; phosphate angle from ADE O3 P O5 ga_14 ; phosphate angle from ADE O4 P O5 ga_29 ; phosphate angle from ADE P O3 C2P ga_26 ; phosphate angle from ADE O2 C3R C2R ga_9 ; phosphate oxygen to CHn carbons from ADE O2 C3R C4R ga_9 ; phosphate oxygen to CHn carbons from ADE O3 C2P C1P ga_9 ; phosphate oxygen to CHn carbons from ADE O3 C2P C3P ga_9 ; phosphate oxygen to CHn carbons from ADE C1 C2 C26 ga_13 ; CHn-CHn-CHn angles C1 C2 C25 ga_13 ; CHn-CHn-CHn angles C1 C2 C3 ga_13 ; CHn-CHn-CHn angles C1 C19 C18 ga_13 ; CHn-CHn-CHn angles C2 C1 C19 ga_13 ; CHn-CHn-CHn angles C2 C1 C20 ga_13 ; CHn-CHn-CHn angles C2 C3 C30 ga_13 ; CHn-CHn-CHn angles C3 C2 C25 ga_13 ; CHn-CHn-CHn angles C3 C2 C26 ga_13 ; CHn-CHn-CHn angles C3 C30 C31 ga_13 ; CHn-CHn-CHn angles C7 C8 C41 ga_13 ; CHn-CHn-CHn angles C8 C41 C42 ga_13 ; CHn-CHn-CHn angles C12 C13 C48 ga_13 ; CHn-CHn-CHn angles C13 C12 C46 ga_13 ; CHn-CHn-CHn angles C13 C12 C47 ga_13 ; CHn-CHn-CHn angles C13 C48 C49 ga_13 ; CHn-CHn-CHn angles C17 C18 C19 ga_13 ; CHn-CHn-CHn angles C17 C18 C60 ga_13 ; CHn-CHn-CHn angles C17 C55 C56 ga_13 ; CHn-CHn-CHn angles C18 C17 C54 ga_13 ; CHn-CHn-CHn angles C18 C17 C55 ga_13 ; CHn-CHn-CHn angles C19 C1 C20 ga_13 ; CHn-CHn-CHn angles C19 C18 C60 ga_13 ; CHn-CHn-CHn angles C25 C2 C26 ga_13 ; CHn-CHn-CHn angles C46 C12 C47 ga_13 ; CHn-CHn-CHn angles C54 C17 C55 ga_13 ; CHn-CHn-CHn angles C36 C7 C37 ga_13 ; CHn-CHn-CHn angles C2 C3 C4 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C4 C3 C30 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C8 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C36 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C37 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C7 C8 C9 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C8 C7 C36 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C8 C7 C37 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C9 C8 C41 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C13 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C46 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C47 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C12 C13 C14 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C14 C13 C48 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C18 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C54 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C55 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C4 C5 C6 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C9 C10 C11 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C14 C15 C16 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C3 C4 C5 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C4 C5 C35 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C5 C6 C7 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C6 C5 C35 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C8 C9 C10 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C10 C11 C12 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C13 C14 C15 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C14 C15 C53 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C15 C16 C17 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C16 C15 C53 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C5M C5B C4B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C5M C5B C6B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C6M C6B C5B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C6M C6B C7B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C4B C5B C6B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle C5B C4B C9B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle C5B C6B C7B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle N1B C1R C2R ga_9 ; from ADE Nsp2-containing dimethylbenzimidazole angle N1B C1R O6R ga_9 ; from ADE Nsp2-containing dimethylbenzimidazole angle N1B C2B N3B ga_7 ; from ADE Nsp2-containing dimethylbenzimidazole angle C2B N1B C1R ga_37 ; from ADE Nsp2-containing dimethylbenzimidazole angle N3B C9B C4B ga_39 ; from ADE Nsp2-containing dimethylbenzimidazole angle C9B N3B C2B ga_7 ; from ADE Nsp2-containing dimethylbenzimidazole angle C1R C2R C3R ga_8 ; from ADE sugar angle C1R C2R O7R ga_9 ; from ADE sugar angle C1R O6R C4R ga_10 ; from ADE sugar angle C2R C1R O6R ga_9 ; from ADE sugar angle C2R C3R C4R ga_8 ; from ADE sugar angle C2R O7R HAA ga_12 ; from ADE sugar angle C3R C2R O7R ga_9 ; from ADE sugar angle C3R C4R C5R ga_8 ; from ADE sugar angle C3R C4R O6R ga_9 ; from ADE sugar angle C4R C5R O8R ga_9 ; from ADE sugar angle C5R O8R HAB ga_12 ; from ADE sugar angle C5R C4R O6R ga_9 ; from ADE sugar angle C1P C2P C3P ga_13 ; amide linkage angle C57 C56 C55 ga_13 ; amide linkage angle C57 N59 HAC ga_23 ; from GLN angle N59 C57 O58 ga_33 ; from GLN angle C56 C57 N59 ga_19 ; from GLN angle O58 C57 C56 ga_30 ; from GLN angle C1P N59 C57 ga_31 ; from force field angle definitions C1P N59 HAC ga_18 ; from force field angle definitions C2P C1P N59 ga_15 ; from force field angle definitions C5B C4B H4B ga_25 ; from PHE C-C-H angle C9B C4B H4B ga_25 ; from PHE C-C-H angle C6B C7B H7B ga_25 ; from PHE C-C-H angle C8B C7B H7B ga_25 ; from PHE C-C-H angle N1B C2B H2B ga_36 ; from ADE N-C-H angle N3B C2B H2B ga_36 ; from ADE N-C-H angle C9 C10 H10 ga_25 ; corrin ring C-C10-H angle C11 C10 H10 ga_20 ; corrin ring C-C10-H angle ; ; cyano group addition to the original B12 topology ; N21 FE C1N ga_1 ; cyano group from HEMC CO group N22 FE C1N ga_1 ; cyano group from HEMC CO group N23 FE C1N ga_1 ; cyano group from HEMC CO group N24 FE C1N ga_1 ; cyano group from HEMC CO group FE C1N N1C ga_41 ; cyano group from HEMC CO group N3B FE C1N ga_41 ; cyano group from HEMC CO group (found during pdb2gmx) [ impropers ] ; ai aj ak al gromos type C1R C8B C2B N1B gi_1 ; dimethylbenzimidazole improper for planarity N1B C8B C9B N3B gi_1 ; dimethylbenzimidazole improper for planarity C8B N1B C7B C9B gi_1 ; dimethylbenzimidazole improper for planarity C8B N1B C2B N3B gi_1 ; dimethylbenzimidazole improper for planarity C8B C7B C6B C5B gi_1 ; dimethylbenzimidazole improper for planarity C8B C9B N3B C2B gi_1 ; dimethylbenzimidazole improper for planarity C7B C8B C9B C4B gi_1 ; dimethylbenzimidazole improper for planarity C7B C6B C5B C4B gi_1 ; dimethylbenzimidazole improper for planarity C6B C5B C4B C9B gi_1 ; dimethylbenzimidazole improper for planarity C5B C4B C9B C8B gi_1 ; dimethylbenzimidazole improper for planarity C9B C8B C7B C6B gi_1 ; dimethylbenzimidazole improper for planarity C9B C4B N3B C8B gi_1 ; dimethylbenzimidazole improper for planarity C9B N3B C2B N1B gi_1 ; dimethylbenzimidazole improper for planarity C2B N1B C8B C9B gi_1 ; dimethylbenzimidazole improper for planarity C5M C4B C6B C5B gi_1 ; dimethylbenzimidazole methyl groups C6M C7B C5B C6B gi_1 ; dimethylbenzimidazole methyl groups C2B N1B N3B H2B gi_1 ; dimethylbenzimidazole H atom-containing planarity C4B C9B C5B H4B gi_1 ; dimethylbenzimidazole H atom-containing planarity C7B C8B C6B H7B gi_1 ; dimethylbenzimidazole H atom-containing planarity N3B FE C2B C9B gi_1 ; Fe-dimethylbenzimidazole planarity N21 C4 C5 C6 gi_1 ; HEMC-based conjugated corrin ring improper planarity N22 C6 C5 C4 gi_1 ; HEMC-based conjugated corrin ring improper planarity N22 C9 C10 C11 gi_1 ; HEMC-based conjugated corrin ring improper planarity N23 C11 C10 C9 gi_1 ; HEMC-based conjugated corrin ring improper planarity N23 C14 C15 C16 gi_1 ; HEMC-based conjugated corrin ring improper planarity N24 C16 C15 C14 gi_1 ; HEMC-based conjugated corrin ring improper planarity C5 C4 C6 C35 gi_1 ; corrin ring on-Csp2 methyl group improper planarity C15 C16 C14 C53 gi_1 ; corrin ring on-Csp2 methyl group improper planarity C27 O28 N29 C26 gi_1 ; from GLN improper torsion definition N29 HAE HAD C27 gi_1 ; from GLN improper torsion definition C32 O34 N33 C31 gi_1 ; from GLN improper torsion definition N33 HAG HAF C32 gi_1 ; from GLN improper torsion definition C38 O39 N40 C37 gi_1 ; from GLN improper torsion definition N40 HAI HAH C38 gi_1 ; from GLN improper torsion definition C43 O44 N45 C42 gi_1 ; from GLN improper torsion definition N45 HAK HAJ C43 gi_1 ; from GLN improper torsion definition C50 O51 N52 C49 gi_1 ; from GLN improper torsion definition N52 HAM HAL C50 gi_1 ; from GLN improper torsion definition C61 O63 N62 C60 gi_1 ; from GLN improper torsion definition N62 HAO HAN C61 gi_1 ; from GLN improper torsion definition C57 C56 O58 N59 gi_1 ; amide linkage C57 planarity N59 C57 C1P HAC gi_1 ; amide linkage N59 planarity C4 N21 C3 C5 gi_1 ; corrin ring C sp2 planarity C5 C4 C6 C35 gi_1 ; corrin ring C sp2 planarity C6 N22 C5 C7 gi_1 ; corrin ring C sp2 planarity C9 N22 C10 C8 gi_1 ; corrin ring C sp2 planarity C11 N23 C10 C12 gi_1 ; corrin ring C sp2 planarity C14 N23 C15 C13 gi_1 ; corrin ring C sp2 planarity C15 C14 C16 C53 gi_1 ; corrin ring C sp2 planarity C16 N24 C15 C17 gi_1 ; corrin ring C sp2 planarity C10 C9 C11 H10 gi_1 ; corrin ring C10 planarity C18 C17 C19 C60 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C19 N24 C18 C1 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C3 C2 C30 C4 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C8 C9 C7 C41 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C13 C14 C12 C48 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C2P C1P O3 C3P gi_2 ; corrin ring C atom sp3 tetrahedral geometry C1R N1B C2R O6R gi_2 ; sugar C atom tetrahedral geometry C2R O7R C3R C1R gi_2 ; sugar C atom tetrahedral geometry C3R C5R O6R C4R gi_2 ; sugar C atom tetrahedral geometry C3R C2R O2 C4R gi_2 ; sugar C atom tetrahedral geometry FE C1 C4 N21 gi_3 ; HEMC improper definition FE C6 C9 N22 gi_3 ; HEMC improper definition FE C11 C14 N23 gi_3 ; HEMC improper definition FE C16 C19 N24 gi_3 ; HEMC improper definition [ dihedrals ] ; ai aj ak al gromos type C3R O2 P O3 gd_20 ; from ADE phosphate definition C3R O2 P O3 gd_27 ; from ADE phosphate definition C2P O3 P O2 gd_20 ; from ADE phosphate definition C2P O3 P O2 gd_27 ; from ADE phosphate definition P O3 C2P C1P gd_7 ; from ADE phosphate definition C2R C3R O2 P gd_29 ; from ADE phosphate definition O8R C5R C4R O6R gd_8 ; from ADE sugar dihedrals O8R C5R C4R O6R gd_25 ; from ADE sugar dihedrals O8R C5R C4R C3R gd_17 ; from ADE sugar dihedrals O8R C5R C4R C3R gd_34 ; from ADE sugar dihedrals C3R C4R O6R C1R gd_29 ; from ADE sugar dihedrals C5R C4R C3R C2R gd_34 ; from ADE sugar dihedrals C5R C4R C3R O2 gd_17 ; from ADE sugar dihedrals O6R C4R C3R C2R gd_17 ; from ADE sugar dihedrals O6R C4R C3R O2 gd_18 ; from ADE sugar dihedrals C4R O6R C1R C2R gd_29 ; from ADE sugar dihedrals O6R C1R C2R O7R gd_18 ; from ADE sugar dihedrals O6R C1R C2R C3R gd_17 ; from ADE sugar dihedrals O6R C1R C2R C3R gd_34 ; from ADE sugar dihedrals C1R C2R C3R C4R gd_34 ; from ADE sugar dihedrals C1R C2R C3R O2 gd_17 ; from ADE sugar dihedrals O7R C2R C3R C4R gd_17 ; from ADE sugar dihedrals O7R C2R C3R O2 gd_18 ; from ADE sugar dihedrals C1R C2R O7R HAA gd_23 ; from ADE sugar dihedrals N1B C1R C2R O7R gd_17 ; from ADE sugar dihedrals O6R C1R N1B C8B gd_16 ; from ADE sugar dihedrals C4R C5R O8R HAB gd_2 ; additional ADE-based sugar dihedral N1B C1R C2R C3R gd_17 ; additional ADE-based sugar dihedral N1B C1R O6R C4R gd_17 ; additional ADE-based sugar dihedral C2 C26 C27 N29 gd_40 ; from GLN dihedral C26 C27 N29 HAD gd_14 ; from GLN dihedral C30 C31 C32 N33 gd_40 ; from GLN dihedral C31 C32 N33 HAF gd_14 ; from GLN dihedral C7 C37 C38 N40 gd_40 ; from GLN dihedral C37 C38 N40 HAH gd_14 ; from GLN dihedral C41 C42 C43 N45 gd_40 ; from GLN dihedral C42 C43 N45 HAJ gd_14 ; from GLN dihedral C48 C49 C50 N52 gd_40 ; from GLN dihedral C49 C50 N52 HAL gd_14 ; from GLN dihedral C18 C60 C61 N62 gd_40 ; from GLN dihedral C60 C61 N62 HAN gd_14 ; from GLN dihedral C5M C5B C6B C6M gd_33 ; dimethylbenzimidazole methyl dihedral fix C4B C5B C6B C6M gd_10 ; dimethylbenzimidazole methyl dihedral fix C8B C7B C6B C6M gd_10 ; dimethylbenzimidazole methyl dihedral fix C7B C6B C5B C5M gd_10 ; dimethylbenzimidazole methyl dihedral fix C9B C4B C5B C5M gd_10 ; dimethylbenzimidazole methyl dihedral fix C35 C5 C4 N21 gd_10 ; corrin ring methyl planarity C35 C5 C6 N22 gd_10 ; corrin ring methyl planarity C53 C15 C14 N23 gd_10 ; corrin ring methyl planarity C53 C1 C16 N24 gd_10 ; corrin ring methyl planarity N24 C19 C1 N21 gd_34 ; corrin ring but HEMC-derived N,C torsions N24 C19 C1 N21 gd_34 ; corrin ring but HEMC-derived N,C torsions N21 C4 C5 C6 gd_15 ; corrin ring but HEMC-derived N,C torsions C4 C5 C6 N22 gd_15 ; corrin ring but HEMC-derived N,C torsions N22 C9 C10 C11 gd_15 ; corrin ring but HEMC-derived N,C torsions C9 C10 C11 N23 gd_15 ; corrin ring but HEMC-derived N,C torsions N23 C14 C15 C16 gd_15 ; corrin ring but HEMC-derived N,C torsions C14 C15 C16 N24 gd_15 ; corrin ring but HEMC-derived N,C torsions C1 C2 C26 C27 gd_40 ; corrin ring HEMC derived CHn torsions C25 C2 C26 C27 gd_34 ; corrin ring HEMC derived CHn torsions C2 C26 C27 O28 gd_34 ; corrin ring HEMC derived CHn torsions C2 C3 C30 C31 gd_9 ; corrin ring HEMC derived CHn torsions C3 C30 C31 C32 gd_40 ; corrin ring HEMC derived CHn torsions C30 C31 C32 O34 gd_40 ; corrin ring HEMC derived CHn torsions C6 C7 C37 C38 gd_40 ; corrin ring HEMC derived CHn torsions C36 C7 C37 C38 gd_40 ; corrin ring HEMC derived CHn torsions C7 C37 C38 O39 gd_40 ; corrin ring HEMC derived CHn torsions C7 C8 C41 C42 gd_9 ; corrin ring HEMC derived CHn torsions C8 C41 C42 C43 gd_34 ; corrin ring HEMC derived CHn torsions C41 C42 C43 O44 gd_40 ; corrin ring HEMC derived CHn torsions C12 C13 C48 C49 gd_9 ; corrin ring HEMC derived CHn torsions C13 C48 C49 C50 gd_34 ; corrin ring HEMC derived CHn torsions C48 C49 C50 O51 gd_40 ; corrin ring HEMC derived CHn torsions C16 C17 C55 C56 gd_40 ; corrin ring HEMC derived CHn torsions C54 C17 C56 C57 gd_40 ; corrin ring HEMC derived CHn torsions C17 C55 C56 C57 gd_34 ; corrin ring HEMC derived CHn torsions C55 C56 C57 O58 gd_40 ; corrin ring HEMC derived CHn torsions C17 C18 C60 C61 gd_9 ; corrin ring HEMC derived CHn torsions C18 C60 C61 O63 gd_34 ; corrin ring HEMC derived CHn torsions C18 C17 C55 C56 gd_9 ; corrin ring HEMC derived CHn torsions N59 C1P C2P O3 gd_34 ; amide linkage torsion terms N59 C1P C2P C3P gd_34 ; amide linkage torsion terms C2P C1P N59 C57 gd_34 ; amide linkage torsion terms C56 C57 N59 C1P gd_14 ; amide linkage torsion terms C55 C56 C57 N59 gd_40 ; amide linkage torsion terms C17 C55 C56 C57 gd_40 ; amide linkage torsion terms C5 C4 N21 C1 gd_14 ; corrin ring sp3-containing torsions C10 C9 N22 C6 gd_14 ; corrin ring sp3-containing torsions C5 C6 N22 C9 gd_14 ; corrin ring sp3-containing torsions C15 C14 N23 C11 gd_14 ; corrin ring sp3-containing torsions C10 C11 N23 C14 gd_14 ; corrin ring sp3-containing torsions C15 C16 N24 C19 gd_14 ; corrin ring sp3-containing torsions C4 N21 C1 C2 gd_40 ; corrin ring sp3-containing torsions C18 C19 N24 C16 gd_40 ; corrin ring sp3-containing torsions N22 C6 C5 C4 gd_33 ; corrin ring sp3-containing torsions N23 C11 C10 C9 gd_33 ; corrin ring sp3-containing torsions C19 C18 C17 C55 gd_34 ; corrin ring sp3-containing torsions C55 C17 C16 C15 gd_40 ; corrin ring sp3-containing torsions C17 C18 C19 C1 gd_34 ; corrin ring sp3-containing torsions C18 C19 C1 C2 gd_34 ; corrin ring sp3-containing torsions C17 C16 C15 C14 gd_10 ; corrin ring sp3-containing torsions C16 C15 C14 C13 gd_10 ; corrin ring sp3-containing torsions C15 C14 C13 C12 gd_40 ; corrin ring sp3-containing torsions C6 C7 C8 C9 gd_34 ; corrin ring sp3-containing torsions C8 C7 C6 C5 gd_34 ; corrin ring sp3-containing torsions C30 C3 C2 C1 gd_34 ; corrin ring sp3-containing torsions C11 C12 C13 C14 gd_34 ; corrin ring sp3-containing torsions C13 C12 C11 C10 gd_34 ; corrin ring sp3-containing torsions C10 C9 C8 C7 gd_10 ; corrin ring sp3-containing torsions C5 C4 C3 C30 gd_34 ; corrin ring sp3-containing torsions C3 C2 C1 C19 gd_34 ; corrin ring sp3-containing torsions ; ; cyano group dihedral. imidazole-Fe-CN group torsion ; C9B N3B FE N21 gd_38 ; THIS IS NEW!!! N3B FE N21 C1 gd_38 ; THIS IS NEW!!! N3B FE N22 C6 gd_38 ; THIS IS NEW!!! N3B FE N23 C11 gd_38 ; THIS IS NEW!!! N3B FE N24 C16 gd_38 ; THIS IS NEW!!! N3B FE C1N N1C gd_38 ; corrin ring sp3-containing torsions [ LCB ] ; ; lysine-cyanocobalamin residue file based on the HEMC CO parameters ; [ atoms ] C27 C 0.38000 0 ; from GLN residue O28 O -0.38000 0 ; from GLN residue N29 NT -0.83000 0 ; from GLN residue HAE H 0.41500 0 ; from GLN residue HAD H 0.41500 0 ; from GLN residue C32 C 0.38000 1 ; from GLN residue O34 O -0.38000 1 ; from GLN residue N33 NT -0.83000 1 ; from GLN residue HAG H 0.41500 1 ; from GLN residue HAF H 0.41500 1 ; from GLN residue C38 C 0.38000 2 ; from GLN residue O39 O -0.38000 2 ; from GLN residue N40 NT -0.83000 2 ; from GLN residue HAI H 0.41500 2 ; from GLN residue HAH H 0.41500 2 ; from GLN residue C43 C 0.38000 3 ; from GLN residue O44 O -0.38000 3 ; from GLN residue N45 NT -0.83000 3 ; from GLN residue HAK H 0.41500 3 ; from GLN residue HAJ H 0.41500 3 ; from GLN residue C50 C 0.38000 4 ; from GLN residue O51 O -0.38000 4 ; from GLN residue N52 NT -0.83000 4 ; from GLN residue HAM H 0.41500 4 ; from GLN residue HAL H 0.41500 4 ; from GLN residue C61 C 0.38000 5 ; from GLN residue O63 O -0.38000 5 ; from GLN residue N62 NT -0.83000 5 ; from GLN residue HAO H 0.41500 5 ; from GLN residue HAN H 0.41500 5 ; from GLN residue C20 CH3 0.00000 6 ; methyl group C25 CH3 0.00000 7 ; methyl group C36 CH3 0.00000 8 ; methyl group C46 CH3 0.00000 9 ; methyl group C47 CH3 0.00000 10 ; methyl group C54 CH3 0.00000 11 ; methyl group C26 CH2 0.00000 12 ; non-polar CHn fragments C30 CH2 0.00000 13 ; non-polar CHn fragments C31 CH2 0.00000 13 ; non-polar CHn fragments C37 CH2 0.00000 14 ; non-polar CHn fragments C41 CH2 0.00000 15 ; non-polar CHn fragments C42 CH2 0.00000 15 ; non-polar CHn fragments C48 CH2 0.00000 16 ; non-polar CHn fragments C49 CH2 0.00000 16 ; non-polar CHn fragments C56 CH2 0.00000 17 ; non-polar CHn fragments C55 CH2 0.00000 17 ; non-polar CHn fragments C60 CH2 0.00000 18 ; non-polar CHn fragments C2R CH1 0.15000 19 ; C2*-O2*-H2* from ADE O7R OA -0.54800 19 ; C2*-O2*-H2* from ADE HAA H 0.39800 19 ; C2*-O2*-H2* from ADE C1R CH1 0.20000 20 ; C1*-O4*-C4* from ADE O6R OA -0.36000 20 ; C1*-O4*-C4* from ADE C4R CH1 0.16000 20 ; C1*-O4*-C4* from ADE C3R CH1 0.00000 21 ; C3* from ADE C5R CH2 0.15000 22 ; C2*-O2*-H2* from ADE O8R OA -0.54800 22 ; C2*-O2*-H2* from ADE ; O8R OA -0.54800 22 ; C2*-O2*-H2* from ADE ; ; HAB from B12 is gone in LYB, where the lysine fragment is added via CLB ; HAB H 0.39800 22 ; C2*-O2*-H2* from ADE ; HAB from B12 is gone in LYB, where the lysine fragment is added via CLB ; P P 2.20000 23 ; PO3+O3* fragment from ADE ; ; the O2P is a special mod to the PDB file. The O2 (fine in B12) is a "special" label ; that pdb2gmx has some kind of structure prep issue with. This, like the CO to FE, is a ; by-hand hack of the PDB file (for now) ; O2P OA -0.80000 23 ; PO3+O3* fragment from ADE O4 OM -1.00000 23 ; PO3+O3* fragment from ADE O5 OM -1.00000 23 ; PO3+O3* fragment from ADE O3 OA -0.80000 23 ; PO3+O3* fragment from ADE C2P CH1 0.35000 24 ; non-polar CHn fragment C3P CH3 0.00000 24 ; non-polar CHn fragment C1P CH2 0.00000 24 ; non-polar CHn fragment N59 N -0.28000 25 ; tempered GLN fragment charges HAC H 0.28000 25 ; tempered GLN fragment charges C57 C 0.38000 25 ; tempered GLN fragment charges O58 O -0.38000 25 ; tempered GLN fragment charges C5B C 0.00000 26 ; dimethylbenzimidazole C-CH3 group (non-polar) C5M CH3 0.00000 26 ; dimethylbenzimidazole C-CH3 group (non-polar) C6B C 0.00000 27 ; dimethylbenzimidazole C-CH3 group (non-polar) C6M CH3 0.00000 27 ; dimethylbenzimidazole C-CH3 group (non-polar) C4B C -0.14000 28 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H4B H 0.14000 28 ; dimethylbenzimidazole aromatic C-H from TRP, PHE C7B C -0.14000 29 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H7B H 0.14000 29 ; dimethylbenzimidazole aromatic C-H from TRP, PHE N3B NR -0.55000 30 ; dimethylbenzimidazole polar aromatic NC fragment C9B C 0.20000 30 ; dimethylbenzimidazole polar aromatic NC fragment N1B NR -0.30000 31 ; dimethylbenzimidazole polar aromatic NC fragment C8B C 0.20000 31 ; dimethylbenzimidazole polar aromatic NC fragment C2B C 0.23000 32 ; dimethylbenzimidazole aromatic C-H from TRP, PHE H2B H 0.23000 32 ; dimethylbenzimidazole aromatic C-H from TRP, PHE C5 C -0.05000 33 ; C-CH3 group (non-polar) C35 CH3 0.00000 33 ; C-CH3 group (non-polar) C15 C -0.05000 34 ; C-CH3 group (non-polar) C53 CH3 0.00000 34 ; C-CH3 group (non-polar) FE FE 1.00000 35 ; HEMC Fe-N group N21 NR -0.44000 35 ; HEMC Fe-N group N22 NR -0.50000 35 ; HEMC Fe-N group N23 NR -0.50000 35 ; HEMC Fe-N group N24 NR -0.44000 35 ; HEMC Fe-N group C1 CH0 0.22000 36 ; non-polar HEMC-derived corrin atoms C2 CH0 0.00000 36 ; non-polar HEMC-derived corrin atoms C3 CH1 0.00000 36 ; non-polar HEMC-derived corrin atoms C4 C 0.38000 36 ; non-polar HEMC-derived corrin atoms C6 C 0.29000 37 ; non-polar HEMC-derived corrin atoms C7 CH0 0.00000 37 ; non-polar HEMC-derived corrin atoms C8 CH1 0.00000 37 ; non-polar HEMC-derived corrin atoms C9 C 0.35000 37 ; non-polar HEMC-derived corrin atoms C16 C 0.38000 38 ; non-polar HEMC-derived corrin atoms C17 CH0 0.00000 38 ; non-polar HEMC-derived corrin atoms C18 CH1 0.00000 38 ; non-polar HEMC-derived corrin atoms C19 CH1 0.24000 38 ; non-polar HEMC-derived corrin atoms C11 C 0.35000 39 ; non-polar HEMC-derived corrin atoms C12 CH0 0.00000 39 ; non-polar HEMC-derived corrin atoms C13 CH1 0.00000 39 ; non-polar HEMC-derived corrin atoms C14 C 0.29000 39 ; non-polar HEMC-derived corrin atoms C10 C -0.24000 40 ; aromatic C-H from TRP, PHE H10 H 0.14000 40 ; aromatic C-H from TRP, PHE ; ; Since CO is not defined as an atom in GROMOSxx, CO is converted to FE and the HEME ; values are employed. This is a workaround due for proper implementation. ; N N -0.31000 41 ; standard LYS (lysine) atom information H H 0.31000 41 ; standard LYS (lysine) atom information CA CH1 0.00000 42 ; standard LYS (lysine) atom information CB CH2 0.00000 42 ; standard LYS (lysine) atom information CG CH2 0.00000 43 ; standard LYS (lysine) atom information CD CH2 0.00000 43 ; standard LYS (lysine) atom information CE CH2 0.00000 44 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information NZ NT -0.34000 44 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information HZ1 H 0.34000 44 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information ; CE CH2 -0.24000 44 ; standard LYS (lysine) atom information ; NZ NT -0.64000 44 ; standard LYS (lysine) atom information ; HZ1 H 0.44000 44 ; standard LYS (lysine) atom information ; ; this H atom is gone, replaced by the linkage CLB atom. ; HZ2 H 0.44000 44 ; standard LYS (lysine) atom information ; this H atom is gone, replaced by the linkage CLB atom. ; C C 0.20000 45 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information O O -0.20000 45 ; NEW CHARGE FROM B12 standard LYS (lysine) atom information ; C C 0.45000 45 ; standard LYS (lysine) atom information ; O O -0.45000 45 ; standard LYS (lysine) atom information ; ; linkage atoms (added new) ; CLB C 0.00000 46 ; this is the linkage carbon atom between LYS and B12 OLB O 0.00000 46 ; this is the additional =O at the linkage position ; ; cyano group addition to the original B12 topology ; C1N C 0.04000 41 ; CN group on Fe N1C N -0.42000 41 ; CN group on Fe ; [ bonds ] ; ai aj gromos type C26 C27 gb_27 ; from GLN fragment 0 C27 O28 gb_5 ; from GLN C27 N29 gb_9 ; from GLN N29 HAE gb_2 ; from GLN N29 HAD gb_2 ; from GLN C31 C32 gb_27 ; from GLN fragment 1 C32 O34 gb_5 ; from GLN C32 N33 gb_9 ; from GLN N33 HAG gb_2 ; from GLN N33 HAF gb_2 ; from GLN C37 C38 gb_27 ; from GLN fragment 2 C38 O39 gb_5 ; from GLN C38 N40 gb_9 ; from GLN N40 HAI gb_2 ; from GLN N40 HAH gb_2 ; from GLN C42 C43 gb_27 ; from GLN fragment 3 C43 O44 gb_5 ; from GLN C43 N45 gb_9 ; from GLN N45 HAK gb_2 ; from GLN N45 HAJ gb_2 ; from GLN C49 C50 gb_27 ; from GLN fragment 4 C50 O51 gb_5 ; from GLN C50 N52 gb_9 ; from GLN N52 HAM gb_2 ; from GLN N52 HAL gb_2 ; from GLN C60 C61 gb_27 ; from GLN fragment 5 C61 O63 gb_5 ; from GLN C61 N62 gb_9 ; from GLN N62 HAO gb_2 ; from GLN N62 HAN gb_2 ; from GLN FE N21 gb_35 ; FE-N bond from HEMC FE N22 gb_35 ; FE-N bond from HEMC FE N23 gb_35 ; FE-N bond from HEMC FE N24 gb_35 ; FE-N bond from HEMC FE N3B gb_37 ; FE-N3B bond from HEMC not in corrin ring P O2P gb_28 ; from ADE phosphate P O4 gb_24 ; from ADE phosphate P O5 gb_24 ; from ADE phosphate P O3 gb_28 ; from ADE phosphate N21 C1 gb_21 ; corrin ring N-CHn bonds N21 C4 gb_14 ; corrin ring N-C bonds N22 C6 gb_14 ; corrin ring N-C bonds N22 C9 gb_14 ; corrin ring N-C bonds N23 C11 gb_14 ; corrin ring N-C bonds N23 C14 gb_14 ; corrin ring N-C bonds N24 C16 gb_14 ; corrin ring N-C bonds N24 C19 gb_21 ; corrin ring N-CHn bonds C30 C31 gb_27 ; CH2-CH2 bonds C41 C42 gb_27 ; CH2-CH2 bonds C48 C49 gb_27 ; CH2-CH2 bonds C55 C56 gb_27 ; CH2-CH2 bonds C56 C57 gb_27 ; CH2-CH2 bonds N1B C1R gb_22 ; sugar bonds from ADE C1R C2R gb_26 ; sugar bonds from ADE C2R O7R gb_20 ; sugar bonds from ADE O7R HAA gb_1 ; sugar bonds from ADE C2R C3R gb_26 ; sugar bonds from ADE C3R C4R gb_26 ; sugar bonds from ADE C3R O2P gb_20 ; sugar bonds from ADE C4R C5R gb_26 ; sugar bonds from ADE C5R O8R gb_20 ; sugar bonds from ADE ; ; HAB is deleted from B12 for LYB O8R HAB gb_1 ; sugar bonds from ADE ; C4R O6R gb_20 ; sugar bonds from ADE O6R C1R gb_20 ; sugar bonds from ADE C1P N59 gb_9 ; amide corrin - phosphate linkage C1P C2P gb_27 ; amide corrin - phosphate linkage C2P C3P gb_27 ; amide corrin - phosphate linkage C2P O3 gb_20 ; amide corrin - phosphate linkage N59 HAC gb_2 ; amide corrin - phosphate linkage N59 C57 gb_9 ; amide corrin - phosphate linkage C57 O58 gb_5 ; amide corrin - phosphate linkage N1B C2B gb_10 ; dimethylbenzimidazole ring C2B N3B gb_10 ; dimethylbenzimidazole ring C2B H2B gb_3 ; dimethylbenzimidazole ring N3B C9B gb_10 ; dimethylbenzimidazole ring C9B C4B gb_16 ; dimethylbenzimidazole ring C4B C5B gb_16 ; dimethylbenzimidazole ring C4B H4B gb_3 ; dimethylbenzimidazole ring C5B C6B gb_16 ; dimethylbenzimidazole ring C5B C5M gb_27 ; dimethylbenzimidazole ring C6B C7B gb_16 ; dimethylbenzimidazole ring C6B C6M gb_27 ; dimethylbenzimidazole ring C7B C8B gb_16 ; dimethylbenzimidazole ring C7B H7B gb_3 ; dimethylbenzimidazole ring C8B N1B gb_10 ; dimethylbenzimidazole ring C8B C9B gb_16 ; dimethylbenzimidazole ring C1 C20 gb_27 ; corrin ring carbon framework C1 C2 gb_27 ; corrin ring carbon framework C2 C3 gb_27 ; corrin ring carbon framework C2 C25 gb_27 ; corrin ring carbon framework C2 C26 gb_27 ; corrin ring carbon framework C3 C4 gb_27 ; corrin ring carbon framework C3 C30 gb_27 ; corrin ring carbon framework C4 C5 gb_17 ; corrin ring carbon framework C5 C6 gb_17 ; corrin ring carbon framework C5 C35 gb_27 ; corrin ring carbon framework C6 C7 gb_27 ; corrin ring carbon framework C7 C8 gb_27 ; corrin ring carbon framework C7 C37 gb_27 ; corrin ring carbon framework C7 C36 gb_27 ; corrin ring carbon framework C8 C9 gb_27 ; corrin ring carbon framework C8 C41 gb_27 ; corrin ring carbon framework C9 C10 gb_17 ; corrin ring carbon framework C10 C11 gb_17 ; corrin ring carbon framework C11 C12 gb_27 ; corrin ring carbon framework C12 C46 gb_27 ; corrin ring carbon framework C12 C47 gb_27 ; corrin ring carbon framework C12 C13 gb_27 ; corrin ring carbon framework C13 C14 gb_27 ; corrin ring carbon framework C13 C48 gb_27 ; corrin ring carbon framework C14 C15 gb_17 ; corrin ring carbon framework C15 C16 gb_17 ; corrin ring carbon framework C15 C53 gb_27 ; corrin ring carbon framework C16 C17 gb_27 ; corrin ring carbon framework C17 C18 gb_27 ; corrin ring carbon framework C17 C54 gb_27 ; corrin ring carbon framework C17 C55 gb_27 ; corrin ring carbon framework C18 C19 gb_27 ; corrin ring carbon framework C18 C60 gb_27 ; corrin ring carbon framework C19 C1 gb_27 ; corrin ring carbon framework C10 H10 gb_3 ; corrin ring C10-H10 bond ; ; linker bond from B12 to CLB ; O8R CLB gb_5 ; LYS B12 linker (CLB replaces H) ; ; Lysine bond topology ; N H gb_2 ; standard LYS (lysine) N CA gb_21 ; standard LYS (lysine) CA CB gb_27 ; standard LYS (lysine) CA C gb_27 ; standard LYS (lysine) CB CG gb_27 ; standard LYS (lysine) CG CD gb_27 ; standard LYS (lysine) CD CE gb_27 ; standard LYS (lysine) CE NZ gb_21 ; standard LYS (lysine) NZ HZ1 gb_2 ; standard LYS (lysine) ; ; this replaces the HZ2 with CLB for the B12-LYS connection ; NZ CLB gb_9 ; standard LYS (lysine) C O gb_5 ; standard LYS (lysine) C +N gb_10 ; standard LYS (lysine) ; ; below is the C=O bond on the B12-LYS linkage (OLB is only connected to CLB) ; CLB OLB gb_27 ; CLB-OLB linkage bond (previously nowhere in the structure) ; ; cyano group addition to the original B12 topology ; FE C1N gb_30 ; cyano group on the Fe C1N N1C gb_4 ; cyano group on the Fe [ exclusions ] ; ai aj FE C2 FE C3 FE C5 FE C7 FE C8 FE C10 FE C12 FE C13 FE C15 FE C17 FE C18 FE C20 N21 C25 N21 C26 N21 C30 N21 C35 N21 C6 N21 C9 N21 C11 N21 C14 N21 C16 N21 C19 N21 C10 N22 C1 N22 C4 N22 C36 N22 C37 N22 C11 N22 C14 N22 C16 N22 C19 N22 C15 N23 C16 N23 C19 N23 C1 N23 C4 N23 C6 N23 C9 N23 C46 N23 C47 N23 C48 N23 C5 N24 C4 N24 C5 N24 C6 N24 C9 N24 C10 N24 C11 N24 C14 N24 C55 N24 C54 N24 C60 C1R C7B C1R C9B C1R N3B N1B C6B N1B C4B C8B C5B C8B C5M C8B C6M C7B C4B C7B N3B C7B C2B C2B C9B C5B C2B C5M C6M C1 C30 ; HEMC-based C framework exclusions C1 C5 ; HEMC-based C framework exclusions C2 C5 ; HEMC-based C framework exclusions C3 C35 ; HEMC-based C framework exclusions C3 C6 ; HEMC-based C framework exclusions C4 C26 ; HEMC-based C framework exclusions C4 C7 ; HEMC-based C framework exclusions C30 C26 ; HEMC-based C framework exclusions C30 C5 ; HEMC-based C framework exclusions C5 C8 ; HEMC-based C framework exclusions C5 C9 ; HEMC-based C framework exclusions C5 C36 ; HEMC-based C framework exclusions C5 C37 ; HEMC-based C framework exclusions C35 C7 ; HEMC-based C framework exclusions C6 C41 ; HEMC-based C framework exclusions C6 C10 ; HEMC-based C framework exclusions C7 C10 ; HEMC-based C framework exclusions C8 H10 ; HEMC-based C framework exclusions C8 C11 ; HEMC-based C framework exclusions C9 C36 ; HEMC-based C framework exclusions C9 C37 ; HEMC-based C framework exclusions C9 C12 ; HEMC-based C framework exclusions C36 C41 ; HEMC-based C framework exclusions C37 C10 ; HEMC-based C framework exclusions C10 C13 ; HEMC-based C framework exclusions C10 C14 ; HEMC-based C framework exclusions C10 C46 ; HEMC-based C framework exclusions C10 C47 ; HEMC-based C framework exclusions H10 C12 ; HEMC-based C framework exclusions C11 C48 ; HEMC-based C framework exclusions C11 C15 ; HEMC-based C framework exclusions C12 C15 ; HEMC-based C framework exclusions C13 C53 ; HEMC-based C framework exclusions C13 C16 ; HEMC-based C framework exclusions C14 C46 ; HEMC-based C framework exclusions C14 C47 ; HEMC-based C framework exclusions C14 C17 ; HEMC-based C framework exclusions C46 C48 ; HEMC-based C framework exclusions C47 C48 ; HEMC-based C framework exclusions C48 C15 ; HEMC-based C framework exclusions C15 C18 ; HEMC-based C framework exclusions C15 C19 ; HEMC-based C framework exclusions C15 C54 ; HEMC-based C framework exclusions C15 C55 ; HEMC-based C framework exclusions C53 C17 ; HEMC-based C framework exclusions C16 C60 ; HEMC-based C framework exclusions C19 C54 ; HEMC-based C framework exclusions C19 C55 ; HEMC-based C framework exclusions C54 C60 ; HEMC-based C framework exclusions C55 C60 ; HEMC-based C framework exclusions ; ; cyano group addition to the original B12 topology ; N21 N1C ; cyano exclusions from HEMC CO group N22 N1C ; cyano exclusions from HEMC CO group N23 N1C ; cyano exclusions from HEMC CO group N24 N1C ; cyano exclusions from HEMC CO group C1 C1N ; cyano exclusions from HEMC CO group C4 C1N ; cyano exclusions from HEMC CO group C6 C1N ; cyano exclusions from HEMC CO group C9 C1N ; cyano exclusions from HEMC CO group C11 C1N ; cyano exclusions from HEMC CO group C14 C1N ; cyano exclusions from HEMC CO group C16 C1N ; cyano exclusions from HEMC CO group C19 C1N ; cyano exclusions from HEMC CO group N3B N1C ; cyano exclusion unique to 6-coordinate iron C1N C9B ; additional cyano exclusion at Fe 6-center C1N C2B ; additional cyano exclusion at Fe 6-center [ angles ] ; ai aj ak gromos type C2 C26 C27 ga_15 ; from GLN, fragment 1 C26 C27 O28 ga_30 ; from GLN C26 C27 N29 ga_19 ; from GLN O28 C27 N29 ga_33 ; from GLN C27 N29 HAE ga_23 ; from GLN C27 N29 HAD ga_23 ; from GLN HAE N29 HAD ga_24 ; from GLN C30 C31 C32 ga_15 ; from GLN, fragment 2 C31 C32 O34 ga_30 ; from GLN C31 C32 N33 ga_19 ; from GLN O34 C32 N33 ga_33 ; from GLN C32 N33 HAG ga_23 ; from GLN C32 N33 HAF ga_23 ; from GLN HAG N33 HAF ga_24 ; from GLN C7 C37 C38 ga_15 ; from GLN, fragment 3 C37 C38 O39 ga_30 ; from GLN C37 C38 N40 ga_19 ; from GLN O39 C38 N40 ga_33 ; from GLN C38 N40 HAI ga_23 ; from GLN C38 N40 HAH ga_23 ; from GLN HAI N40 HAH ga_24 ; from GLN C41 C42 C43 ga_15 ; from GLN, fragment 4 C42 C43 O44 ga_30 ; from GLN C42 C43 N45 ga_19 ; from GLN O44 C43 N45 ga_33 ; from GLN C43 N45 HAK ga_23 ; from GLN C43 N45 HAJ ga_23 ; from GLN HAK N45 HAJ ga_24 ; from GLN C48 C49 C50 ga_15 ; from GLN, fragment 5 C49 C50 O51 ga_30 ; from GLN C49 C50 N52 ga_19 ; from GLN O51 C50 N52 ga_33 ; from GLN C50 N52 HAM ga_23 ; from GLN C50 N52 HAL ga_23 ; from GLN HAM N52 HAL ga_24 ; from GLN C18 C60 C61 ga_15 ; from GLN, fragment 6 C60 C61 O63 ga_30 ; from GLN C60 C61 N62 ga_19 ; from GLN O63 C61 N62 ga_33 ; from GLN C61 N62 HAO ga_23 ; from GLN C61 N62 HAN ga_23 ; from GLN HAO N62 HAN ga_24 ; from GLN N21 FE N22 ga_2 ; corrin ring Fe-N angle N21 FE N24 ga_2 ; corrin ring Fe-N angle N22 FE N23 ga_2 ; corrin ring Fe-N angle N23 FE N24 ga_2 ; corrin ring Fe-N angle N21 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N22 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N23 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole N24 FE N3B ga_2 ; corrin-Fe-dimethylbenzimidazole FE N21 C1 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N21 C4 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N22 C6 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N22 C9 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N23 C11 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N23 C14 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N24 C16 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N24 C19 ga_34 ; corrin Fe-N-C angles (based on HEMC) FE N3B C9B ga_34 ; Fe-dimethylbenzimidazole-N,C angle FE N3B C2B ga_34 ; Fe-dimethylbenzimidazole-N,C angle C8B N1B C2B ga_7 ; angle containing C8B, see minimization issues discussion N1B C8B C9B ga_7 ; angle containing C8B, see minimization issues discussion C8B C9B N3B ga_7 ; angle containing C8B, see minimization issues discussion C7B C8B N1B ga_39 ; angle containing C8B, see minimization issues discussion C8B N1B C1R ga_37 ; angle containing C8B, see minimization issues discussion C4B C9B C8B ga_27 ; angle containing C8B, see minimization issues discussion C6B C7B C8B ga_27 ; angle containing C8B, see minimization issues discussion C7B C8B C9B ga_27 ; angle containing C8B, see minimization issues discussion N21 C1 C2 ga_13 ; corrin ring-specific but HEMC-derived angles N21 C1 C20 ga_13 ; corrin ring-specific but HEMC-derived angles N21 C4 C3 ga_33 ; corrin ring-specific but HEMC-derived angles C4 N21 C1 ga_6 ; corrin ring-specific but HEMC-derived angles C5 C4 N21 ga_33 ; corrin ring-specific but HEMC-derived angles C19 C1 N21 ga_13 ; corrin ring-specific but HEMC-derived angles N22 C6 C5 ga_33 ; corrin ring-specific but HEMC-derived angles N22 C6 C7 ga_33 ; corrin ring-specific but HEMC-derived angles N22 C9 C8 ga_33 ; corrin ring-specific but HEMC-derived angles C9 N22 C6 ga_6 ; corrin ring-specific but HEMC-derived angles C10 C9 N22 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C11 C10 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C11 C12 ga_33 ; corrin ring-specific but HEMC-derived angles N23 C14 C13 ga_33 ; corrin ring-specific but HEMC-derived angles C14 N23 C11 ga_6 ; corrin ring-specific but HEMC-derived angles C15 C14 N23 ga_33 ; corrin ring-specific but HEMC-derived angles N24 C16 C15 ga_33 ; corrin ring-specific but HEMC-derived angles N24 C19 C1 ga_13 ; corrin ring-specific but HEMC-derived angles C19 N24 C16 ga_6 ; corrin ring-specific but HEMC-derived angles C17 C16 N24 ga_33 ; corrin ring-specific but HEMC-derived angles C18 C19 N24 ga_13 ; corrin ring-specific but HEMC-derived angles C3R O2P P ga_26 ; phosphate angle from ADE O2P P O3 ga_5 ; phosphate angle from ADE O2P P O4 ga_14 ; phosphate angle from ADE O2P P O5 ga_14 ; phosphate angle from ADE O3 P O4 ga_14 ; phosphate angle from ADE O3 P O5 ga_14 ; phosphate angle from ADE O4 P O5 ga_29 ; phosphate angle from ADE P O3 C2P ga_26 ; phosphate angle from ADE O2P C3R C2R ga_9 ; phosphate oxygen to CHn carbons from ADE O2P C3R C4R ga_9 ; phosphate oxygen to CHn carbons from ADE O3 C2P C1P ga_9 ; phosphate oxygen to CHn carbons from ADE O3 C2P C3P ga_9 ; phosphate oxygen to CHn carbons from ADE C1 C2 C26 ga_13 ; CHn-CHn-CHn angles C1 C2 C25 ga_13 ; CHn-CHn-CHn angles C1 C2 C3 ga_13 ; CHn-CHn-CHn angles C1 C19 C18 ga_13 ; CHn-CHn-CHn angles C2 C1 C19 ga_13 ; CHn-CHn-CHn angles C2 C1 C20 ga_13 ; CHn-CHn-CHn angles C2 C3 C30 ga_13 ; CHn-CHn-CHn angles C3 C2 C25 ga_13 ; CHn-CHn-CHn angles C3 C2 C26 ga_13 ; CHn-CHn-CHn angles C3 C30 C31 ga_13 ; CHn-CHn-CHn angles C7 C8 C41 ga_13 ; CHn-CHn-CHn angles C8 C41 C42 ga_13 ; CHn-CHn-CHn angles C12 C13 C48 ga_13 ; CHn-CHn-CHn angles C13 C12 C46 ga_13 ; CHn-CHn-CHn angles C13 C12 C47 ga_13 ; CHn-CHn-CHn angles C13 C48 C49 ga_13 ; CHn-CHn-CHn angles C17 C18 C19 ga_13 ; CHn-CHn-CHn angles C17 C18 C60 ga_13 ; CHn-CHn-CHn angles C17 C55 C56 ga_13 ; CHn-CHn-CHn angles C18 C17 C54 ga_13 ; CHn-CHn-CHn angles C18 C17 C55 ga_13 ; CHn-CHn-CHn angles C19 C1 C20 ga_13 ; CHn-CHn-CHn angles C19 C18 C60 ga_13 ; CHn-CHn-CHn angles C25 C2 C26 ga_13 ; CHn-CHn-CHn angles C46 C12 C47 ga_13 ; CHn-CHn-CHn angles C54 C17 C55 ga_13 ; CHn-CHn-CHn angles C36 C7 C37 ga_13 ; CHn-CHn-CHn angles C2 C3 C4 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C4 C3 C30 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C8 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C36 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C6 C7 C37 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C7 C8 C9 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C8 C7 C36 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C8 C7 C37 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C9 C8 C41 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C13 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C46 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C11 C12 C47 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C12 C13 C14 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C14 C13 C48 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C18 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C54 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C16 C17 C55 ga_15 ; sp3-sp3-sp2 corrin ring carbon angle C4 C5 C6 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C9 C10 C11 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C14 C15 C16 ga_27 ; sp2-sp2-sp2 corrin ring carbon angle C3 C4 C5 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C4 C5 C35 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C5 C6 C7 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C6 C5 C35 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C8 C9 C10 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C10 C11 C12 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C13 C14 C15 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C14 C15 C53 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C15 C16 C17 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C16 C15 C53 ga_37 ; sp3-sp2-sp2 corrin ring carbon angle C5M C5B C4B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C5M C5B C6B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C6M C6B C5B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C6M C6B C7B ga_37 ; sp2-sp2-methyl dimethylbenzimidazole angle C4B C5B C6B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle C5B C4B C9B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle C5B C6B C7B ga_27 ; Csp2-Csp2-Csp2 dimethylbenzimidazole angle N1B C1R C2R ga_9 ; from ADE Nsp2-containing dimethylbenzimidazole angle N1B C1R O6R ga_9 ; from ADE Nsp2-containing dimethylbenzimidazole angle N1B C2B N3B ga_7 ; from ADE Nsp2-containing dimethylbenzimidazole angle C2B N1B C1R ga_37 ; from ADE Nsp2-containing dimethylbenzimidazole angle N3B C9B C4B ga_39 ; from ADE Nsp2-containing dimethylbenzimidazole angle C9B N3B C2B ga_7 ; from ADE Nsp2-containing dimethylbenzimidazole angle C1R C2R C3R ga_8 ; from ADE sugar angle C1R C2R O7R ga_9 ; from ADE sugar angle C1R O6R C4R ga_10 ; from ADE sugar angle C2R C1R O6R ga_9 ; from ADE sugar angle C2R C3R C4R ga_8 ; from ADE sugar angle C2R O7R HAA ga_12 ; from ADE sugar angle C3R C2R O7R ga_9 ; from ADE sugar angle C3R C4R C5R ga_8 ; from ADE sugar angle C3R C4R O6R ga_9 ; from ADE sugar angle C4R C5R O8R ga_9 ; from ADE sugar angle ; ; HAB angle is gone from B12 for LYB C5R O8R HAB ga_12 ; from ADE sugar angle ; C5R C4R O6R ga_9 ; from ADE sugar angle C1P C2P C3P ga_13 ; amide linkage angle C57 C56 C55 ga_13 ; amide linkage angle C57 N59 HAC ga_23 ; from GLN angle N59 C57 O58 ga_33 ; from GLN angle C56 C57 N59 ga_19 ; from GLN angle O58 C57 C56 ga_30 ; from GLN angle C1P N59 C57 ga_31 ; from force field angle definitions C1P N59 HAC ga_18 ; from force field angle definitions C2P C1P N59 ga_15 ; from force field angle definitions C5B C4B H4B ga_25 ; from PHE C-C-H angle C9B C4B H4B ga_25 ; from PHE C-C-H angle C6B C7B H7B ga_25 ; from PHE C-C-H angle C8B C7B H7B ga_25 ; from PHE C-C-H angle N1B C2B H2B ga_36 ; from ADE N-C-H angle N3B C2B H2B ga_36 ; from ADE N-C-H angle C9 C10 H10 ga_25 ; corrin ring C-C10-H angle C11 C10 H10 ga_20 ; corrin ring C-C10-H angle C5R O8R CLB ga_12 ; for LYS-B12 bridge (just replaces O8R H atom with CLB) ; ; standard Lysine angle topology ; -C N H ga_32 ; Standard LYS (lysine) -C N CA ga_31 ; Standard LYS (lysine) H N CA ga_18 ; Standard LYS (lysine) N CA CB ga_13 ; Standard LYS (lysine) N CA C ga_13 ; Standard LYS (lysine) CB CA C ga_13 ; Standard LYS (lysine) CA CB CG ga_15 ; Standard LYS (lysine) CB CG CD ga_15 ; Standard LYS (lysine) CG CD CE ga_15 ; Standard LYS (lysine) CD CE NZ ga_15 ; Standard LYS (lysine) CE NZ HZ1 ga_11 ; Standard LYS (lysine) CE NZ CLB ga_6 ; Modification from LYS (CLB from NZ H atom) HZ1 NZ CLB ga_23 ; Modification from LYS (CLB from NZ H atom) CA C O ga_30 ; Standard LYS (lysine) CA C +N ga_19 ; Standard LYS (lysine) O C +N ga_33 ; Standard LYS (lysine) ; ; additional CLB-OLB angle linkages ; OLB CLB O8R ga_33 ; new OLB-CLB linkage angles OLB CLB NZ ga_33 ; new OLB-CLB linkage angles O8R CLB NZ ga_33 ; new OLB-CLB linkage angles ; ; cyano group addition to the original B12 topology ; FE C1N N1C ga_41 ; cyano group from HEMC CO group N21 FE C1N ga_1 ; cyano group from HEMC CO group N22 FE C1N ga_1 ; cyano group from HEMC CO group N23 FE C1N ga_1 ; cyano group from HEMC CO group N24 FE C1N ga_1 ; cyano group from HEMC CO group N3B FE C1N ga_1 ; cyano group from HEMC CO group (found during pdb2gmx) ; N3B FE C1N ga_41 ; cyano group from HEMC CO group (found during pdb2gmx) [ impropers ] ; ai aj ak al gromos type C1R C8B C2B N1B gi_1 ; dimethylbenzimidazole improper for planarity N1B C8B C9B N3B gi_1 ; dimethylbenzimidazole improper for planarity C8B N1B C7B C9B gi_1 ; dimethylbenzimidazole improper for planarity C8B N1B C2B N3B gi_1 ; dimethylbenzimidazole improper for planarity C8B C7B C6B C5B gi_1 ; dimethylbenzimidazole improper for planarity C8B C9B N3B C2B gi_1 ; dimethylbenzimidazole improper for planarity C7B C8B C9B C4B gi_1 ; dimethylbenzimidazole improper for planarity C7B C6B C5B C4B gi_1 ; dimethylbenzimidazole improper for planarity C6B C5B C4B C9B gi_1 ; dimethylbenzimidazole improper for planarity C5B C4B C9B C8B gi_1 ; dimethylbenzimidazole improper for planarity C9B C8B C7B C6B gi_1 ; dimethylbenzimidazole improper for planarity C9B C4B N3B C8B gi_1 ; dimethylbenzimidazole improper for planarity C9B N3B C2B N1B gi_1 ; dimethylbenzimidazole improper for planarity C2B N1B C8B C9B gi_1 ; dimethylbenzimidazole improper for planarity C5M C4B C6B C5B gi_1 ; dimethylbenzimidazole methyl groups C6M C7B C5B C6B gi_1 ; dimethylbenzimidazole methyl groups C2B N1B N3B H2B gi_1 ; dimethylbenzimidazole H atom-containing planarity C4B C9B C5B H4B gi_1 ; dimethylbenzimidazole H atom-containing planarity C7B C8B C6B H7B gi_1 ; dimethylbenzimidazole H atom-containing planarity N3B FE C2B C9B gi_1 ; Fe-dimethylbenzimidazole planarity N21 C4 C5 C6 gi_1 ; HEMC-based conjugated corrin ring improper planarity N22 C6 C5 C4 gi_1 ; HEMC-based conjugated corrin ring improper planarity N22 C9 C10 C11 gi_1 ; HEMC-based conjugated corrin ring improper planarity N23 C11 C10 C9 gi_1 ; HEMC-based conjugated corrin ring improper planarity N23 C14 C15 C16 gi_1 ; HEMC-based conjugated corrin ring improper planarity N24 C16 C15 C14 gi_1 ; HEMC-based conjugated corrin ring improper planarity C5 C4 C6 C35 gi_1 ; corrin ring on-Csp2 methyl group improper planarity C15 C16 C14 C53 gi_1 ; corrin ring on-Csp2 methyl group improper planarity C27 O28 N29 C26 gi_1 ; from GLN improper torsion definition N29 HAE HAD C27 gi_1 ; from GLN improper torsion definition C32 O34 N33 C31 gi_1 ; from GLN improper torsion definition N33 HAG HAF C32 gi_1 ; from GLN improper torsion definition C38 O39 N40 C37 gi_1 ; from GLN improper torsion definition N40 HAI HAH C38 gi_1 ; from GLN improper torsion definition C43 O44 N45 C42 gi_1 ; from GLN improper torsion definition N45 HAK HAJ C43 gi_1 ; from GLN improper torsion definition C50 O51 N52 C49 gi_1 ; from GLN improper torsion definition N52 HAM HAL C50 gi_1 ; from GLN improper torsion definition C61 O63 N62 C60 gi_1 ; from GLN improper torsion definition N62 HAO HAN C61 gi_1 ; from GLN improper torsion definition C57 C56 O58 N59 gi_1 ; amide linkage C57 planarity N59 C57 C1P HAC gi_1 ; amide linkage N59 planarity C4 N21 C3 C5 gi_1 ; corrin ring C sp2 planarity C5 C4 C6 C35 gi_1 ; corrin ring C sp2 planarity C6 N22 C5 C7 gi_1 ; corrin ring C sp2 planarity C9 N22 C10 C8 gi_1 ; corrin ring C sp2 planarity C11 N23 C10 C12 gi_1 ; corrin ring C sp2 planarity C14 N23 C15 C13 gi_1 ; corrin ring C sp2 planarity C15 C14 C16 C53 gi_1 ; corrin ring C sp2 planarity C16 N24 C15 C17 gi_1 ; corrin ring C sp2 planarity C10 C9 C11 H10 gi_1 ; corrin ring C10 planarity C18 C17 C19 C60 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C19 N24 C18 C1 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C3 C2 C30 C4 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C8 C9 C7 C41 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C13 C14 C12 C48 gi_2 ; corrin ring C atom sp3 tetrahedral geometry C2P C1P O3 C3P gi_2 ; corrin ring C atom sp3 tetrahedral geometry C1R N1B C2R O6R gi_2 ; sugar C atom tetrahedral geometry C2R O7R C3R C1R gi_2 ; sugar C atom tetrahedral geometry C3R C5R O6R C4R gi_2 ; sugar C atom tetrahedral geometry C3R C2R O2P C4R gi_2 ; sugar C atom tetrahedral geometry FE C1 C4 N21 gi_3 ; HEMC improper definition FE C6 C9 N22 gi_3 ; HEMC improper definition FE C11 C14 N23 gi_3 ; HEMC improper definition FE C16 C19 N24 gi_3 ; HEMC improper definition ; ; standard Lysine improper torsions ; N -C CA H gi_1 ; Standard LYS (lysine) CA N C CB gi_2 ; Standard LYS (lysine) C CA +N O gi_1 ; Standard LYS (lysine) CLB O8R OLB NZ gi_1 ; Linkage improper torsion to maintain planarity at CLB [ dihedrals ] ; ai aj ak al gromos type C3R O2P P O3 gd_20 ; from ADE phosphate definition C3R O2P P O3 gd_27 ; from ADE phosphate definition C2P O3 P O2P gd_20 ; from ADE phosphate definition C2P O3 P O2P gd_27 ; from ADE phosphate definition P O3 C2P C1P gd_7 ; from ADE phosphate definition C2R C3R O2P P gd_29 ; from ADE phosphate definition O8R C5R C4R O6R gd_8 ; from ADE sugar dihedrals O8R C5R C4R O6R gd_25 ; from ADE sugar dihedrals O8R C5R C4R C3R gd_17 ; from ADE sugar dihedrals O8R C5R C4R C3R gd_34 ; from ADE sugar dihedrals C3R C4R O6R C1R gd_29 ; from ADE sugar dihedrals C5R C4R C3R C2R gd_34 ; from ADE sugar dihedrals C5R C4R C3R O2P gd_17 ; from ADE sugar dihedrals O6R C4R C3R C2R gd_17 ; from ADE sugar dihedrals O6R C4R C3R O2P gd_18 ; from ADE sugar dihedrals C4R O6R C1R C2R gd_29 ; from ADE sugar dihedrals O6R C1R C2R O7R gd_18 ; from ADE sugar dihedrals O6R C1R C2R C3R gd_17 ; from ADE sugar dihedrals O6R C1R C2R C3R gd_34 ; from ADE sugar dihedrals C1R C2R C3R C4R gd_34 ; from ADE sugar dihedrals C1R C2R C3R O2P gd_17 ; from ADE sugar dihedrals O7R C2R C3R C4R gd_17 ; from ADE sugar dihedrals O7R C2R C3R O2P gd_18 ; from ADE sugar dihedrals C1R C2R O7R HAA gd_23 ; from ADE sugar dihedrals N1B C1R C2R O7R gd_17 ; from ADE sugar dihedrals O6R C1R N1B C8B gd_16 ; from ADE sugar dihedrals ; ; HAB-based torsion gone for LYB C4R C5R O8R HAB gd_2 ; additional ADE-based sugar dihedral ; N1B C1R C2R C3R gd_17 ; additional ADE-based sugar dihedral N1B C1R O6R C4R gd_17 ; additional ADE-based sugar dihedral C2 C26 C27 N29 gd_40 ; from GLN dihedral C26 C27 N29 HAD gd_14 ; from GLN dihedral C30 C31 C32 N33 gd_40 ; from GLN dihedral C31 C32 N33 HAF gd_14 ; from GLN dihedral C7 C37 C38 N40 gd_40 ; from GLN dihedral C37 C38 N40 HAH gd_14 ; from GLN dihedral C41 C42 C43 N45 gd_40 ; from GLN dihedral C42 C43 N45 HAJ gd_14 ; from GLN dihedral C48 C49 C50 N52 gd_40 ; from GLN dihedral C49 C50 N52 HAL gd_14 ; from GLN dihedral C18 C60 C61 N62 gd_40 ; from GLN dihedral C60 C61 N62 HAN gd_14 ; from GLN dihedral C5M C5B C6B C6M gd_33 ; dimethylbenzimidazole methyl dihedral fix C4B C5B C6B C6M gd_10 ; dimethylbenzimidazole methyl dihedral fix C8B C7B C6B C6M gd_10 ; dimethylbenzimidazole methyl dihedral fix C7B C6B C5B C5M gd_10 ; dimethylbenzimidazole methyl dihedral fix C9B C4B C5B C5M gd_10 ; dimethylbenzimidazole methyl dihedral fix C35 C5 C4 N21 gd_10 ; corrin ring methyl planarity C35 C5 C6 N22 gd_10 ; corrin ring methyl planarity C53 C15 C14 N23 gd_10 ; corrin ring methyl planarity C53 C1 C16 N24 gd_10 ; corrin ring methyl planarity N24 C19 C1 N21 gd_34 ; corrin ring but HEMC-derived N,C torsions N24 C19 C1 N21 gd_34 ; corrin ring but HEMC-derived N,C torsions N21 C4 C5 C6 gd_15 ; corrin ring but HEMC-derived N,C torsions C4 C5 C6 N22 gd_15 ; corrin ring but HEMC-derived N,C torsions N22 C9 C10 C11 gd_15 ; corrin ring but HEMC-derived N,C torsions C9 C10 C11 N23 gd_15 ; corrin ring but HEMC-derived N,C torsions N23 C14 C15 C16 gd_15 ; corrin ring but HEMC-derived N,C torsions C14 C15 C16 N24 gd_15 ; corrin ring but HEMC-derived N,C torsions C1 C2 C26 C27 gd_40 ; corrin ring HEMC derived CHn torsions C25 C2 C26 C27 gd_34 ; corrin ring HEMC derived CHn torsions C2 C26 C27 O28 gd_34 ; corrin ring HEMC derived CHn torsions C2 C3 C30 C31 gd_9 ; corrin ring HEMC derived CHn torsions C3 C30 C31 C32 gd_40 ; corrin ring HEMC derived CHn torsions C30 C31 C32 O34 gd_40 ; corrin ring HEMC derived CHn torsions C6 C7 C37 C38 gd_40 ; corrin ring HEMC derived CHn torsions C36 C7 C37 C38 gd_40 ; corrin ring HEMC derived CHn torsions C7 C37 C38 O39 gd_40 ; corrin ring HEMC derived CHn torsions C7 C8 C41 C42 gd_9 ; corrin ring HEMC derived CHn torsions C8 C41 C42 C43 gd_34 ; corrin ring HEMC derived CHn torsions C41 C42 C43 O44 gd_40 ; corrin ring HEMC derived CHn torsions C12 C13 C48 C49 gd_9 ; corrin ring HEMC derived CHn torsions C13 C48 C49 C50 gd_34 ; corrin ring HEMC derived CHn torsions C48 C49 C50 O51 gd_40 ; corrin ring HEMC derived CHn torsions C16 C17 C55 C56 gd_40 ; corrin ring HEMC derived CHn torsions C54 C17 C56 C57 gd_40 ; corrin ring HEMC derived CHn torsions C17 C55 C56 C57 gd_34 ; corrin ring HEMC derived CHn torsions C55 C56 C57 O58 gd_40 ; corrin ring HEMC derived CHn torsions C17 C18 C60 C61 gd_9 ; corrin ring HEMC derived CHn torsions C18 C60 C61 O63 gd_34 ; corrin ring HEMC derived CHn torsions C18 C17 C55 C56 gd_9 ; corrin ring HEMC derived CHn torsions N59 C1P C2P O3 gd_34 ; amide linkage torsion terms N59 C1P C2P C3P gd_34 ; amide linkage torsion terms C2P C1P N59 C57 gd_34 ; amide linkage torsion terms C56 C57 N59 C1P gd_14 ; amide linkage torsion terms C55 C56 C57 N59 gd_40 ; amide linkage torsion terms C17 C55 C56 C57 gd_40 ; amide linkage torsion terms C5 C4 N21 C1 gd_14 ; corrin ring sp3-containing torsions C10 C9 N22 C6 gd_14 ; corrin ring sp3-containing torsions C5 C6 N22 C9 gd_14 ; corrin ring sp3-containing torsions C15 C14 N23 C11 gd_14 ; corrin ring sp3-containing torsions C10 C11 N23 C14 gd_14 ; corrin ring sp3-containing torsions C15 C16 N24 C19 gd_14 ; corrin ring sp3-containing torsions C4 N21 C1 C2 gd_40 ; corrin ring sp3-containing torsions C18 C19 N24 C16 gd_40 ; corrin ring sp3-containing torsions N22 C6 C5 C4 gd_33 ; corrin ring sp3-containing torsions N23 C11 C10 C9 gd_33 ; corrin ring sp3-containing torsions C19 C18 C17 C55 gd_34 ; corrin ring sp3-containing torsions C55 C17 C16 C15 gd_40 ; corrin ring sp3-containing torsions C17 C18 C19 C1 gd_34 ; corrin ring sp3-containing torsions C18 C19 C1 C2 gd_34 ; corrin ring sp3-containing torsions C17 C16 C15 C14 gd_10 ; corrin ring sp3-containing torsions C16 C15 C14 C13 gd_10 ; corrin ring sp3-containing torsions C15 C14 C13 C12 gd_40 ; corrin ring sp3-containing torsions C6 C7 C8 C9 gd_34 ; corrin ring sp3-containing torsions C8 C7 C6 C5 gd_34 ; corrin ring sp3-containing torsions C30 C3 C2 C1 gd_34 ; corrin ring sp3-containing torsions C11 C12 C13 C14 gd_34 ; corrin ring sp3-containing torsions C13 C12 C11 C10 gd_34 ; corrin ring sp3-containing torsions C10 C9 C8 C7 gd_10 ; corrin ring sp3-containing torsions C5 C4 C3 C30 gd_34 ; corrin ring sp3-containing torsions C3 C2 C1 C19 gd_34 ; corrin ring sp3-containing torsions ; ; standard Lysine torsion topology ; -CA -C N CA gd_14 ; Standard LYS (lysine) -C N CA C gd_39 ; Standard LYS (lysine) N CA CB CG gd_34 ; Standard LYS (lysine) N CA C +N gd_40 ; Standard LYS (lysine) CA CB CG CD gd_34 ; Standard LYS (lysine) CB CG CD CE gd_34 ; Standard LYS (lysine) CG CD CE NZ gd_34 ; Standard LYS (lysine) CD CE NZ HZ1 gd_29 ; Standard LYS (lysine) C4R C5R O8R CLB gd_23 ; LYS-B12 linkage dihedral terms C5R O8R CLB OLB gd_12 ; LYS-B12 linkage dihedral terms O8R CLB NZ CE gd_14 ; LYS-B12 linkage dihedral terms OLB CLB NZ CE gd_14 ; LYS-B12 linkage dihedral terms ; ; Use of LYB, which employs the pdb2gmx method for sewing the peptide chain together, ; requires the addition of this very new, bulky amino acid to aminoacids.dat. ; ; cyano group dihedral. imidazole-Fe-CN group torsion ; C9B N3B FE N21 gd_38 ; THIS IS NEW!!! N3B FE N21 C1 gd_38 ; THIS IS NEW!!! N3B FE N22 C6 gd_38 ; THIS IS NEW!!! N3B FE N23 C11 gd_38 ; THIS IS NEW!!! N3B FE N24 C16 gd_38 ; THIS IS NEW!!! N3B FE C1N N1C gd_38 ; imidazole-Fe-CN torsion to 0