data_YRJ
#

_chem_comp.id                                   YRJ
_chem_comp.name                                 "3-({[(4-nitrophenyl)carbamoyl]amino}methyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-1-ium"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H22 N4 O10 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2021-03-26
_chem_comp.pdbx_modified_date                   2022-01-28
_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                       485.362
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YRJ
_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       7M6K
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
YRJ  C15   C1   C   0  1  Y  N  N  -1.596   5.210  -14.142    2.149  -1.325   1.255  C15   YRJ   1  
YRJ  C17   C2   C   0  1  Y  N  N  -1.794   3.370  -12.691    0.050  -2.462   1.281  C17   YRJ   2  
YRJ  C20   C3   C   0  1  N  N  N  -0.098   1.515  -12.738   -1.769  -1.715  -0.283  C20   YRJ   3  
YRJ  C22   C4   C   0  1  N  N  N   1.664  -0.148  -13.046   -3.990  -0.820   0.166  C22   YRJ   4  
YRJ  C26   C5   C   0  1  Y  N  N   3.318  -2.624  -12.427   -6.833  -0.990  -0.087  C26   YRJ   5  
YRJ  C28   C6   C   0  1  Y  N  N   4.996  -4.099  -13.231   -8.809   0.347  -0.297  C28   YRJ   6  
YRJ  C02   C7   C   0  1  N  N  S   2.053   6.846  -16.037    4.098   2.213   0.693  C02   YRJ   7  
YRJ  C03   C8   C   0  1  N  N  R   0.862   6.607  -15.136    2.630   1.733   0.745  C03   YRJ   8  
YRJ  C05   C9   C   0  1  N  N  R   0.215   5.506  -15.677    2.597   0.522  -0.214  C05   YRJ   9  
YRJ  C07   C10  C   0  1  N  N  R   2.458   5.353  -16.364    4.778   1.234  -0.290  C07   YRJ  10  
YRJ  C08   C11  C   0  1  N  N  N   3.479   4.990  -15.263    6.201   0.916   0.174  C08   YRJ  11  
YRJ  C16   C12  C   0  1  Y  N  N  -2.266   4.542  -13.160    1.338  -2.317   1.772  C16   YRJ  12  
YRJ  C18   C13  C   0  1  Y  N  N  -0.615   2.900  -13.252   -0.377  -1.599   0.283  C18   YRJ  13  
YRJ  C19   C14  C   0  1  Y  N  N   0.019   3.601  -14.248    0.487  -0.623  -0.178  C19   YRJ  14  
YRJ  C25   C15  C   0  1  Y  N  N   3.740  -1.667  -13.344   -6.167   0.087   0.482  C25   YRJ  15  
YRJ  C27   C16  C   0  1  Y  N  N   3.944  -3.853  -12.391   -8.152  -0.857  -0.477  C27   YRJ  16  
YRJ  C29   C17  C   0  1  Y  N  N   5.441  -3.127  -14.103   -8.146   1.423   0.265  C29   YRJ  17  
YRJ  C30   C18  C   0  1  Y  N  N   4.822  -1.888  -14.132   -6.828   1.295   0.657  C30   YRJ  18  
YRJ  N14   N1   N   1  1  Y  N  N  -0.480   4.709  -14.667    1.708  -0.518   0.309  N14   YRJ  19  
YRJ  N21   N2   N   0  1  N  N  N   1.285   1.259  -12.992   -2.683  -0.874   0.493  N21   YRJ  20  
YRJ  N24   N3   N   0  1  N  N  N   3.113  -0.364  -13.313   -4.831  -0.045   0.879  N24   YRJ  21  
YRJ  N31   N4   N   1  1  N  N  N   5.668  -5.352  -13.195  -10.222   0.486  -0.716  N31   YRJ  22  
YRJ  O01   O1   O   0  1  N  N  N   1.701   7.517  -17.241    4.170   3.552   0.202  O01   YRJ  23  
YRJ  O04   O2   O   0  1  N  N  N   0.050   7.704  -15.081    1.751   2.761   0.283  O04   YRJ  24  
YRJ  O06   O3   O   0  1  N  N  N   1.376   4.610  -16.271    3.960   0.045  -0.253  O06   YRJ  25  
YRJ  O09   O4   O   0  1  N  N  N   3.897   3.686  -15.533    6.827   0.045  -0.770  O09   YRJ  26  
YRJ  O11   O5   O   0  1  N  N  N   5.875   3.559  -13.881    8.751  -1.341  -1.905  O11   YRJ  27  
YRJ  O12   O6   O   0  1  N  N  N   4.763   1.455  -14.664    9.255   0.651  -0.439  O12   YRJ  28  
YRJ  O13   O7   O   0  1  N  N  N   3.577   3.048  -13.092    8.421  -1.440   0.701  O13   YRJ  29  
YRJ  O23   O8   O   0  1  N  N  N   0.878  -1.004  -12.932   -4.409  -1.469  -0.773  O23   YRJ  30  
YRJ  O32   O9   O  -1  1  N  N  N   6.948  -5.430  -13.719  -10.802   1.546  -0.558  O32   YRJ  31  
YRJ  O33   O10  O   0  1  N  N  N   5.169  -6.273  -12.680  -10.804  -0.457  -1.220  O33   YRJ  32  
YRJ  P10   P1   P   0  1  N  N  N   4.546   2.894  -14.245    8.333  -0.496  -0.600  P10   YRJ  33  
YRJ  H151  H1   H   0  0  N  N  N  -1.975   6.157  -14.498    3.154  -1.205   1.632  H151  YRJ  34  
YRJ  H171  H2   H   0  0  N  N  N  -2.309   2.823  -11.915   -0.606  -3.229   1.666  H171  YRJ  35  
YRJ  H202  H3   H   0  0  N  N  N  -0.260   1.471  -11.651   -1.767  -1.387  -1.323  H202  YRJ  36  
YRJ  H201  H4   H   0  0  N  N  N  -0.688   0.726  -13.228   -2.097  -2.753  -0.230  H201  YRJ  37  
YRJ  H261  H5   H   0  0  N  N  N   2.506  -2.407  -11.748   -6.320  -1.930  -0.228  H261  YRJ  38  
YRJ  H021  H6   H   0  0  N  N  N   2.866   7.350  -15.495    4.557   2.144   1.680  H021  YRJ  39  
YRJ  H031  H7   H   0  0  N  N  N   1.237   6.363  -14.131    2.363   1.429   1.757  H031  YRJ  40  
YRJ  H051  H8   H   0  0  N  N  N  -0.471   5.791  -16.488    2.274   0.833  -1.207  H051  YRJ  41  
YRJ  H071  H9   H   0  0  N  N  N   2.939   5.311  -17.352    4.791   1.655  -1.295  H071  YRJ  42  
YRJ  H082  H10  H   0  0  N  N  N   4.336   5.679  -15.295    6.774   1.841   0.250  H082  YRJ  43  
YRJ  H081  H11  H   0  0  N  N  N   3.005   5.041  -14.272    6.165   0.430   1.149  H081  YRJ  44  
YRJ  H161  H12  H   0  0  N  N  N  -3.179   4.954  -12.756    1.704  -2.972   2.549  H161  YRJ  45  
YRJ  H191  H13  H   0  0  N  N  N   0.934   3.222  -14.678    0.160   0.058  -0.950  H191  YRJ  46  
YRJ  H271  H14  H   0  0  N  N  N   3.606  -4.615  -11.705   -8.669  -1.692  -0.924  H271  YRJ  47  
YRJ  H291  H15  H   0  0  N  N  N   6.271  -3.332  -14.763   -8.660   2.363   0.397  H291  YRJ  48  
YRJ  H301  H16  H   0  0  N  N  N   5.197  -1.106  -14.775   -6.311   2.136   1.096  H301  YRJ  49  
YRJ  H211  H17  H   0  0  N  N  N   1.948   1.996  -13.124   -2.349  -0.356   1.241  H211  YRJ  50  
YRJ  H241  H18  H   0  0  N  N  N   3.686   0.438  -13.481   -4.511   0.420   1.668  H241  YRJ  51  
YRJ  H011  H19  H   0  0  N  N  N   1.458   8.414  -17.045    3.707   4.199   0.752  H011  YRJ  52  
YRJ  H041  H20  H   0  0  N  N  N  -0.687   7.525  -14.509    1.777   3.569   0.814  H041  YRJ  53  
YRJ  H1    H21  H   0  1  N  N  N   6.582   2.934  -13.990    9.649  -1.698  -1.872  H1    YRJ  54  
YRJ  H2    H22  H   0  1  N  N  N   3.265   2.192  -12.824    7.842  -2.214   0.665  H2    YRJ  55  
#   #
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
YRJ  O01  C02   SING  N  N   1  
YRJ  C07  O06   SING  N  N   2  
YRJ  C07  C02   SING  N  N   3  
YRJ  C07  C08   SING  N  N   4  
YRJ  O06  C05   SING  N  N   5  
YRJ  C02  C03   SING  N  N   6  
YRJ  C05  C03   SING  N  N   7  
YRJ  C05  N14   SING  N  N   8  
YRJ  O09  C08   SING  N  N   9  
YRJ  O09  P10   SING  N  N  10  
YRJ  C03  O04   SING  N  N  11  
YRJ  N14  C19   DOUB  Y  N  12  
YRJ  N14  C15   SING  Y  N  13  
YRJ  O12  P10   DOUB  N  N  14  
YRJ  C19  C18   SING  Y  N  15  
YRJ  P10  O11   SING  N  N  16  
YRJ  P10  O13   SING  N  N  17  
YRJ  C15  C16   DOUB  Y  N  18  
YRJ  C30  C29   DOUB  Y  N  19  
YRJ  C30  C25   SING  Y  N  20  
YRJ  C29  C28   SING  Y  N  21  
YRJ  O32  N31   SING  N  N  22  
YRJ  C25  N24   SING  N  N  23  
YRJ  C25  C26   DOUB  Y  N  24  
YRJ  N24  C22   SING  N  N  25  
YRJ  C18  C20   SING  N  N  26  
YRJ  C18  C17   DOUB  Y  N  27  
YRJ  C28  N31   SING  N  N  28  
YRJ  C28  C27   DOUB  Y  N  29  
YRJ  N31  O33   DOUB  N  N  30  
YRJ  C16  C17   SING  Y  N  31  
YRJ  C22  N21   SING  N  N  32  
YRJ  C22  O23   DOUB  N  N  33  
YRJ  N21  C20   SING  N  N  34  
YRJ  C26  C27   SING  Y  N  35  
YRJ  C15  H151  SING  N  N  36  
YRJ  C17  H171  SING  N  N  37  
YRJ  C20  H202  SING  N  N  38  
YRJ  C20  H201  SING  N  N  39  
YRJ  C26  H261  SING  N  N  40  
YRJ  C02  H021  SING  N  N  41  
YRJ  C03  H031  SING  N  N  42  
YRJ  C05  H051  SING  N  N  43  
YRJ  C07  H071  SING  N  N  44  
YRJ  C08  H082  SING  N  N  45  
YRJ  C08  H081  SING  N  N  46  
YRJ  C16  H161  SING  N  N  47  
YRJ  C19  H191  SING  N  N  48  
YRJ  C27  H271  SING  N  N  49  
YRJ  C29  H291  SING  N  N  50  
YRJ  C30  H301  SING  N  N  51  
YRJ  N21  H211  SING  N  N  52  
YRJ  N24  H241  SING  N  N  53  
YRJ  O01  H011  SING  N  N  54  
YRJ  O04  H041  SING  N  N  55  
YRJ  O11  H1    SING  N  N  56  
YRJ  O13  H2    SING  N  N  57  
#   #
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
YRJ  SMILES            ACDLabs               12.01  "[O-][N+](=O)c1ccc(cc1)NC(=O)NCc1ccc[n+](c1)C1OC(COP(=O)(O)O)C(O)C1O"  
YRJ  InChI             InChI                 1.03   "InChI=1S/C18H21N4O10P/c23-15-14(10-31-33(28,29)30)32-17(16(15)24)21-7-1-2-11(9-21)8-19-18(25)20-12-3-5-13(6-4-12)22(26)27/h1-7,9,14-17,23-24H,8,10H2,(H3-,19,20,25,28,29,30)/p+1/t14-,15-,16-,17-/m1/s1"  
YRJ  InChIKey          InChI                 1.03   OCUAXUHZRNUDEK-QBPKDAKJSA-O  
YRJ  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)[n+]2cccc(CNC(=O)Nc3ccc(cc3)[N+]([O-])=O)c2"  
YRJ  SMILES            CACTVS                3.385  "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)[n+]2cccc(CNC(=O)Nc3ccc(cc3)[N+]([O-])=O)c2"  
YRJ  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)CNC(=O)Nc3ccc(cc3)[N+](=O)[O-]"  
YRJ  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)O)O)O)CNC(=O)Nc3ccc(cc3)[N+](=O)[O-]"  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
YRJ  "SYSTEMATIC NAME"  ACDLabs               12.01  "3-({[(4-nitrophenyl)carbamoyl]amino}methyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-1-ium"  
YRJ  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{S},4~{R},5~{R})-5-[3-[[(4-nitrophenyl)carbamoylamino]methyl]pyridin-1-ium-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YRJ  "Create component"  2021-03-26  RCSB  
YRJ  "Initial release"   2022-02-02  RCSB  
##
