data_JGC # _chem_comp.id JGC _chem_comp.name "Flavin mononucleotide (semi-quinone intermediate)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H23 N4 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(2R,3S,4S)-5-[(4aR)-7,8-dimethyl-2,4-bis(oxidanylidene)-4a,5-dihydrobenzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-04-27 _chem_comp.pdbx_modified_date 2023-05-19 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 458.360 _chem_comp.one_letter_code ? _chem_comp.three_letter_code JGC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 7YX0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal JGC N1 N1 N 0 1 N N N -6.860 -8.671 56.669 2.273 -2.346 -0.645 N1 JGC 1 JGC C2 C1 C 0 1 N N N -5.484 -8.772 56.754 2.884 -3.485 -0.297 C2 JGC 2 JGC O2 O1 O 0 1 N N N -4.883 -9.138 57.762 2.338 -4.545 -0.538 O2 JGC 3 JGC N3 N2 N 0 1 N N N -4.720 -8.436 55.606 4.082 -3.491 0.310 N3 JGC 4 JGC C4 C2 C 0 1 N N N -5.218 -8.225 54.347 4.800 -2.360 0.436 C4 JGC 5 JGC O4 O2 O 0 1 N N N -4.528 -7.946 53.376 5.855 -2.381 1.033 O4 JGC 6 JGC C4A C3 C 0 1 N N R -6.741 -8.368 54.216 4.307 -1.075 -0.153 C4A JGC 7 JGC N5 N3 N 0 1 N N N -7.247 -7.401 53.302 4.464 0.045 0.782 N5 JGC 8 JGC C5A C4 C 0 1 Y N N -8.639 -7.341 53.176 3.820 1.245 0.438 C5A JGC 9 JGC C6 C5 C 0 1 Y N N -9.293 -7.062 51.975 4.318 2.465 0.860 C6 JGC 10 JGC C7 C6 C 0 1 Y N N -10.688 -7.011 51.898 3.672 3.633 0.495 C7 JGC 11 JGC C7M C7 C 0 1 N N N -11.346 -6.709 50.578 4.211 4.964 0.953 C7M JGC 12 JGC C8 C8 C 0 1 Y N N -11.449 -7.248 53.059 2.534 3.582 -0.289 C8 JGC 13 JGC C8M C9 C 0 1 N N N -12.954 -7.213 53.035 1.842 4.859 -0.689 C8M JGC 14 JGC C9 C10 C 0 1 Y N N -10.801 -7.527 54.259 2.029 2.366 -0.710 C9 JGC 15 JGC C9A C11 C 0 1 Y N N -9.406 -7.572 54.330 2.663 1.189 -0.343 C9A JGC 16 JGC N10 N4 N 0 1 N N N -8.730 -7.841 55.547 2.138 -0.049 -0.731 N10 JGC 17 JGC C10 C12 C 0 1 N N N -7.421 -8.231 55.562 2.859 -1.182 -0.545 C10 JGC 18 JGC "C1'" C13 C 0 1 N N N -9.410 -7.646 56.853 0.808 -0.121 -1.341 "C1'" JGC 19 JGC "C2'" C14 C 0 1 N N S -10.002 -8.901 57.517 -0.255 -0.163 -0.241 "C2'" JGC 20 JGC "O2'" O3 O 0 1 N N N -10.557 -9.730 56.481 -0.122 -1.375 0.504 "O2'" JGC 21 JGC "C3'" C15 C 0 1 N N S -11.124 -8.542 58.514 -1.646 -0.105 -0.875 "C3'" JGC 22 JGC "O3'" O4 O 0 1 N N N -12.062 -7.666 57.876 -1.780 1.107 -1.620 "O3'" JGC 23 JGC "C4'" C16 C 0 1 N N R -10.629 -7.860 59.791 -2.710 -0.147 0.225 "C4'" JGC 24 JGC "O4'" O5 O 0 1 N N N -9.751 -8.738 60.507 -2.576 -1.359 0.970 "O4'" JGC 25 JGC "C5'" C17 C 0 1 N N N -11.796 -7.451 60.716 -4.101 -0.089 -0.408 "C5'" JGC 26 JGC "O5'" O6 O 0 1 N N N -12.814 -8.409 60.866 -5.090 -0.011 0.620 "O5'" JGC 27 JGC P P1 P 0 1 N N N -12.629 -9.716 61.990 -6.669 0.066 0.315 P JGC 28 JGC O1P O7 O 0 1 N N N -11.472 -10.569 61.461 -6.941 1.203 -0.592 O1P JGC 29 JGC O2P O8 O 0 1 N N N -14.011 -10.358 61.795 -7.148 -1.304 -0.383 O2P JGC 30 JGC O3P O9 O 0 1 N N N -12.431 -9.018 63.340 -7.473 0.275 1.694 O3P JGC 31 JGC H2 H2 H 0 1 N N N -3.731 -8.345 55.727 4.436 -4.323 0.662 H2 JGC 32 JGC H3 H3 H 0 1 N N N -6.951 -9.376 53.830 4.894 -0.852 -1.044 H3 JGC 33 JGC H4 H4 H 0 1 N N N -6.867 -7.606 52.400 4.985 -0.039 1.596 H4 JGC 34 JGC H5 H5 H 0 1 N N N -8.708 -6.881 51.085 5.207 2.505 1.472 H5 JGC 35 JGC H6 H6 H 0 1 N N N -11.530 -7.648 50.036 4.921 5.341 0.217 H6 JGC 36 JGC H7 H7 H 0 1 N N N -12.302 -6.194 50.754 3.388 5.671 1.060 H7 JGC 37 JGC H8 H8 H 0 1 N N N -10.687 -6.063 49.979 4.712 4.842 1.913 H8 JGC 38 JGC H9 H9 H 0 1 N N N -13.341 -8.217 52.807 2.256 5.218 -1.631 H9 JGC 39 JGC H10 H10 H 0 1 N N N -13.329 -6.890 54.018 0.775 4.672 -0.809 H10 JGC 40 JGC H11 H11 H 0 1 N N N -13.292 -6.506 52.263 1.994 5.612 0.085 H11 JGC 41 JGC H12 H12 H 0 1 N N N -11.385 -7.711 55.149 1.140 2.333 -1.323 H12 JGC 42 JGC H14 H14 H 0 1 N N N -8.676 -7.215 57.550 0.648 0.757 -1.967 H14 JGC 43 JGC H15 H15 H 0 1 N N N -10.232 -6.932 56.698 0.736 -1.021 -1.951 H15 JGC 44 JGC H16 H16 H 0 1 N N N -9.204 -9.436 58.052 -0.123 0.689 0.425 H16 JGC 45 JGC H17 H17 H 0 1 N N N -10.930 -10.514 56.868 -0.210 -2.177 -0.030 H17 JGC 46 JGC H18 H18 H 0 1 N N N -11.633 -9.474 58.800 -1.779 -0.957 -1.541 H18 JGC 47 JGC H19 H19 H 0 1 N N N -12.754 -7.443 58.487 -1.674 1.909 -1.089 H19 JGC 48 JGC H20 H20 H 0 1 N N N -10.084 -6.948 59.505 -2.578 0.705 0.891 H20 JGC 49 JGC H21 H21 H 0 1 N N N -10.256 -9.442 60.898 -2.682 -2.161 0.439 H21 JGC 50 JGC H22 H22 H 0 1 N N N -11.381 -7.239 61.712 -4.172 0.791 -1.048 H22 JGC 51 JGC H23 H23 H 0 1 N N N -12.249 -6.536 60.306 -4.267 -0.986 -1.005 H23 JGC 52 JGC H24 H24 H 0 1 N N N -13.912 -11.200 61.367 -6.999 -2.093 0.156 H24 JGC 53 JGC H25 H25 H 0 1 N N N -11.568 -9.224 63.680 -8.432 0.330 1.586 H25 JGC 54 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal JGC C7M C7 SING N N 1 JGC C7 C6 DOUB Y N 2 JGC C7 C8 SING Y N 3 JGC C6 C5A SING Y N 4 JGC C8M C8 SING N N 5 JGC C8 C9 DOUB Y N 6 JGC C5A N5 SING N N 7 JGC C5A C9A DOUB Y N 8 JGC N5 C4A SING N N 9 JGC O4 C4 DOUB N N 10 JGC C4A C4 SING N N 11 JGC C4A C10 SING N N 12 JGC C9 C9A SING Y N 13 JGC C9A N10 SING N N 14 JGC C4 N3 SING N N 15 JGC N10 C10 SING N N 16 JGC N10 "C1'" SING N N 17 JGC C10 N1 DOUB N N 18 JGC N3 C2 SING N N 19 JGC "O2'" "C2'" SING N N 20 JGC N1 C2 SING N N 21 JGC C2 O2 DOUB N N 22 JGC "C1'" "C2'" SING N N 23 JGC "C2'" "C3'" SING N N 24 JGC "O3'" "C3'" SING N N 25 JGC "C3'" "C4'" SING N N 26 JGC "C4'" "O4'" SING N N 27 JGC "C4'" "C5'" SING N N 28 JGC "C5'" "O5'" SING N N 29 JGC "O5'" P SING N N 30 JGC O1P P DOUB N N 31 JGC O2P P SING N N 32 JGC P O3P SING N N 33 JGC N3 H2 SING N N 34 JGC C4A H3 SING N N 35 JGC N5 H4 SING N N 36 JGC C6 H5 SING N N 37 JGC C7M H6 SING N N 38 JGC C7M H7 SING N N 39 JGC C7M H8 SING N N 40 JGC C8M H9 SING N N 41 JGC C8M H10 SING N N 42 JGC C8M H11 SING N N 43 JGC C9 H12 SING N N 44 JGC "C1'" H14 SING N N 45 JGC "C1'" H15 SING N N 46 JGC "C2'" H16 SING N N 47 JGC "O2'" H17 SING N N 48 JGC "C3'" H18 SING N N 49 JGC "O3'" H19 SING N N 50 JGC "C4'" H20 SING N N 51 JGC "O4'" H21 SING N N 52 JGC "C5'" H22 SING N N 53 JGC "C5'" H23 SING N N 54 JGC O2P H24 SING N N 55 JGC O3P H25 SING N N 56 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor JGC InChI InChI 1.06 "InChI=1S/C17H23N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-14,18,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,13+,14-/m0/s1" JGC InChIKey InChI 1.06 JNFNEOXSUODPSY-DGAVXFQQSA-N JGC SMILES_CANONICAL CACTVS 3.385 "Cc1cc2N[C@H]3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C" JGC SMILES CACTVS 3.385 "Cc1cc2N[CH]3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C" JGC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@@H]3N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O" JGC SMILES "OpenEye OEToolkits" 2.0.7 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3N2)CC(C(C(COP(=O)(O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id JGC _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydrobenzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id JGC _pdbx_chem_comp_synonyms.name "[(2R,3S,4S)-5-[(4aR)-7,8-dimethyl-2,4-bis(oxidanylidene)-4a,5-dihydrobenzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site JGC "Create component" 2022-04-27 PDBE JGC "Modify formula" 2022-04-27 PDBE JGC "Modify name" 2022-04-27 PDBE JGC "Modify descriptor" 2022-08-22 RCSB JGC "Initial release" 2023-05-24 RCSB #