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                    2024-09-27 
_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 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 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 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 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 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 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 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 N N N -6.741  -8.368  54.216 4.307  -1.075 -0.153 C4A   JGC 7  
JGC N5    N3  N 0 1 N N N 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 N 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 N 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 N 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 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 N 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 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 N 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 N 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 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 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 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 N N N -10.002 -8.901  57.517 -0.255 -0.163 -0.241 "C2'" JGC 20 
JGC "O2'" O3  O 0 1 N N N 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 N N N -11.124 -8.542  58.514 -1.646 -0.105 -0.875 "C3'" JGC 22 
JGC "O3'" O4  O 0 1 N N N 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 N N N -10.629 -7.860  59.791 -2.710 -0.147 0.225  "C4'" JGC 24 
JGC "O4'" O5  O 0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 
JGC "Modify PCM"        2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            JGC 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C4A 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
