data_A7R
#

_chem_comp.id                                   A7R
_chem_comp.name                                 "[[(2S,3S,4R,5S)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H28 N5 O15 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2018-10-12
_chem_comp.pdbx_modified_date                   2019-03-08
_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                       640.408
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    A7R
_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       6IH3
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
A7R  C01  C1   C  0  1  N  N  S  18.858  40.250  10.754  -6.261   0.724   2.187  C01  A7R   1  
A7R  C02  C2   C  0  1  N  N  R  19.588  41.328  11.545  -6.937  -0.582   1.715  C02  A7R   2  
A7R  C03  C3   C  0  1  N  N  S  17.966  39.805  11.664  -4.776   0.538   1.806  C03  A7R   3  
A7R  C04  C4   C  0  1  N  N  S  18.568  41.564  12.769  -5.780  -1.404   1.104  C04  A7R   4  
A7R  C05  C5   C  0  1  N  N  S  13.148  35.864  15.611   4.993   0.586  -2.771  C05  A7R   5  
A7R  C06  C6   C  0  1  N  N  R  12.062  35.250  15.646   6.054  -0.357  -2.161  C06  A7R   6  
A7R  C07  C7   C  0  1  N  N  S  14.261  34.759  15.803   3.786   0.461  -1.815  C07  A7R   7  
A7R  C08  C8   C  0  1  N  N  S  12.291  33.886  16.557   5.362  -0.940  -0.909  C08  A7R   8  
A7R  C09  C9   C  0  1  N  N  N  16.953  38.977  10.986  -4.178   1.863   1.331  C09  A7R   9  
A7R  C10  C10  C  0  1  N  N  N  14.727  34.276  14.552   3.093   1.816  -1.652  C10  A7R  10  
A7R  C11  C11  C  0  1  Y  N  N  10.399  32.393  16.660   6.918  -2.253   0.359  C11  A7R  11  
A7R  C12  C12  C  0  1  Y  N  N  12.003  32.040  15.044   6.578  -0.056   0.963  C12  A7R  12  
A7R  C13  C13  C  0  1  Y  N  N   9.648  31.289  16.239   7.847  -2.430   1.386  C13  A7R  13  
A7R  C14  C14  C  0  1  Y  N  N  11.323  30.930  14.551   7.482  -0.151   2.006  C14  A7R  14  
A7R  C15  C15  C  0  1  Y  N  N  10.132  30.553  15.168   8.135  -1.350   2.229  C15  A7R  15  
A7R  C16  C16  C  0  1  N  N  N   8.324  30.871  16.912   8.515  -3.734   1.579  C16  A7R  16  
A7R  C17  C17  C  0  1  N  N  N  19.320  42.601  14.760  -5.666  -1.910  -1.288  C17  A7R  17  
A7R  C18  C18  C  0  1  N  N  N  17.854  43.851  13.502  -7.238  -3.038   0.045  C18  A7R  18  
A7R  C19  C19  C  0  1  N  N  N  19.386  43.623  15.704  -6.103  -2.596  -2.370  C19  A7R  19  
A7R  C20  C20  C  0  1  N  N  N  18.625  44.758  15.453  -7.151  -3.526  -2.212  C20  A7R  20  
A7R  N01  N1   N  1  1  Y  N  N  11.537  32.743  16.063   6.327  -1.090   0.183  N01  A7R  21  
A7R  N02  N2   N  0  1  N  N  N   7.415  31.863  17.473   9.410  -3.892   2.575  N02  A7R  22  
A7R  N03  N3   N  0  1  N  N  N  18.577  42.740  13.663  -6.244  -2.139  -0.075  N03  A7R  23  
A7R  N04  N4   N  0  1  N  N  N  18.622  45.884  16.371  -7.615  -4.237  -3.294  N04  A7R  24  
A7R  N05  N5   N  0  1  N  N  N  17.886  44.839  14.366  -7.687  -3.713  -1.012  N05  A7R  25  
A7R  O01  O1   O  0  1  N  N  N  17.397  41.144  12.339  -4.790  -0.423   0.727  O01  A7R  26  
A7R  O02  O2   O  0  1  N  N  N  13.589  33.664  16.627   4.353   0.032  -0.558  O02  A7R  27  
A7R  O03  O3   O  0  1  N  N  N  18.145  40.755   9.553  -6.816   1.850   1.504  O03  A7R  28  
A7R  O04  O4   O  0  1  N  N  N  19.943  42.351  10.730  -7.930  -0.304   0.725  O04  A7R  29  
A7R  O05  O5   O  0  1  N  N  N  13.291  36.483  14.248   5.474   1.931  -2.797  O05  A7R  30  
A7R  O06  O6   O  0  1  N  N  N  11.666  34.921  14.268   7.223   0.377  -1.791  O06  A7R  31  
A7R  O07  O7   O  0  1  N  N  N  16.795  37.800  11.732  -2.778   1.697   1.094  O07  A7R  32  
A7R  O08  O8   O  0  1  N  N  N  14.069  34.896  13.428   1.915   1.656  -0.859  O08  A7R  33  
A7R  O09  O9   O  0  1  N  N  N  16.378  35.405  12.363  -0.350   2.317   0.301  O09  A7R  34  
A7R  O10  O10  O  0  1  N  N  N  17.225  35.745   9.939  -2.380   3.464  -0.664  O10  A7R  35  
A7R  O11  O11  O  0  1  N  N  N  18.763  36.098  11.854  -1.751   4.036   1.713  O11  A7R  36  
A7R  O12  O12  O  0  1  N  N  N  14.139  35.720  10.953   0.500   3.559  -1.725  O12  A7R  37  
A7R  O13  O13  O  0  1  N  N  N  15.001  33.434  11.468   1.723   3.927   0.452  O13  A7R  38  
A7R  O14  O14  O  0  1  N  N  N   8.021  29.718  16.984   8.257  -4.665   0.841  O14  A7R  39  
A7R  O15  O15  O  0  1  N  N  N  17.162  44.022  12.563  -7.744  -3.231   1.138  O15  A7R  40  
A7R  P01  P1   P  0  1  N  N  N  17.347  36.268  11.354  -1.827   2.891   0.584  P01  A7R  41  
A7R  P02  P2   P  0  1  N  N  N  14.858  34.854  11.970   0.938   2.880  -0.485  P02  A7R  42  
A7R  H1   H1   H  0  1  N  N  N  19.572  39.466  10.462  -6.367   0.841   3.266  H1   A7R  43  
A7R  H2   H2   H  0  1  N  N  N  20.490  40.867  11.975  -7.377  -1.112   2.560  H2   A7R  44  
A7R  H3   H3   H  0  1  N  N  N  18.457  39.213  12.451  -4.213   0.148   2.653  H3   A7R  45  
A7R  H4   H4   H  0  1  N  N  N  18.883  40.763  13.454  -5.372  -2.093   1.844  H4   A7R  46  
A7R  H5   H5   H  0  1  N  N  N  13.264  36.632  16.390   4.721   0.257  -3.774  H5   A7R  47  
A7R  H6   H6   H  0  1  N  N  N  11.259  35.828  16.127   6.307  -1.152  -2.863  H6   A7R  48  
A7R  H7   H7   H  0  1  N  N  N  15.088  35.193  16.384   3.082  -0.283  -2.188  H7   A7R  49  
A7R  H8   H8   H  0  1  N  N  N  11.905  34.133  17.557   4.900  -1.899  -1.143  H8   A7R  50  
A7R  H9   H9   H  0  1  N  N  N  15.998  39.520  10.936  -4.668   2.173   0.408  H9   A7R  51  
A7R  H10  H10  H  0  1  N  N  N  17.289  38.733   9.968  -4.329   2.625   2.096  H10  A7R  52  
A7R  H11  H11  H  0  1  N  N  N  14.550  33.191  14.507   3.771   2.513  -1.159  H11  A7R  53  
A7R  H12  H12  H  0  1  N  N  N  15.806  34.475  14.480   2.822   2.206  -2.633  H12  A7R  54  
A7R  H13  H13  H  0  1  N  N  N  10.044  32.979  17.495   6.686  -3.077  -0.300  H13  A7R  55  
A7R  H14  H14  H  0  1  N  N  N  12.934  32.335  14.583   6.070   0.880   0.784  H14  A7R  56  
A7R  H15  H15  H  0  1  N  N  N  11.710  30.374  13.710   7.679   0.703   2.637  H15  A7R  57  
A7R  H16  H16  H  0  1  N  N  N   9.588  29.690  14.813   8.848  -1.451   3.034  H16  A7R  58  
A7R  H17  H17  H  0  1  N  N  N  19.876  41.689  14.919  -4.865  -1.192  -1.383  H17  A7R  59  
A7R  H18  H18  H  0  1  N  N  N  19.999  43.537  16.589  -5.657  -2.433  -3.340  H18  A7R  60  
A7R  H19  H19  H  0  1  N  N  N   6.562  31.571  17.905   9.616  -3.149   3.164  H19  A7R  61  
A7R  H20  H20  H  0  1  N  N  N   7.645  32.835  17.426   9.848  -4.748   2.702  H20  A7R  62  
A7R  H21  H21  H  0  1  N  N  N  18.069  46.692  16.169  -7.220  -4.099  -4.170  H21  A7R  63  
A7R  H22  H22  H  0  1  N  N  N  19.173  45.851  17.205  -8.335  -4.877  -3.182  H22  A7R  64  
A7R  H23  H23  H  0  1  N  N  N  17.715  40.032   9.112  -7.762   1.978   1.660  H23  A7R  65  
A7R  H24  H24  H  0  1  N  N  N  20.397  43.016  11.235  -8.651   0.260   1.039  H24  A7R  66  
A7R  H25  H25  H  0  1  N  N  N  14.113  36.957  14.199   6.268   2.055  -3.334  H25  A7R  67  
A7R  H26  H26  H  0  1  N  N  N  10.840  34.453  14.279   7.663   0.814  -2.533  H26  A7R  68  
A7R  H27  H27  H  0  1  N  N  N  19.293  35.695  11.176  -1.396   3.731   2.559  H27  A7R  69  
A7R  H28  H28  H  0  1  N  N  N  14.609  33.361  10.606   2.040   3.550   1.284  H28  A7R  70  
#   #
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
A7R  O03  C01  SING  N  N   1  
A7R  O10  P01  DOUB  N  N   2  
A7R  O04  C02  SING  N  N   3  
A7R  C01  C02  SING  N  N   4  
A7R  C01  C03  SING  N  N   5  
A7R  O12  P02  DOUB  N  N   6  
A7R  C09  C03  SING  N  N   7  
A7R  C09  O07  SING  N  N   8  
A7R  P01  O07  SING  N  N   9  
A7R  P01  O11  SING  N  N  10  
A7R  P01  O09  SING  N  N  11  
A7R  O13  P02  SING  N  N  12  
A7R  C02  C04  SING  N  N  13  
A7R  C03  O01  SING  N  N  14  
A7R  P02  O09  SING  N  N  15  
A7R  P02  O08  SING  N  N  16  
A7R  O01  C04  SING  N  N  17  
A7R  O15  C18  DOUB  N  N  18  
A7R  C04  N03  SING  N  N  19  
A7R  O08  C10  SING  N  N  20  
A7R  C18  N03  SING  N  N  21  
A7R  C18  N05  SING  N  N  22  
A7R  N03  C17  SING  N  N  23  
A7R  O05  C05  SING  N  N  24  
A7R  O06  C06  SING  N  N  25  
A7R  N05  C20  DOUB  N  N  26  
A7R  C14  C12  DOUB  Y  N  27  
A7R  C14  C15  SING  Y  N  28  
A7R  C10  C07  SING  N  N  29  
A7R  C17  C19  DOUB  N  N  30  
A7R  C12  N01  SING  Y  N  31  
A7R  C15  C13  DOUB  Y  N  32  
A7R  C20  C19  SING  N  N  33  
A7R  C20  N04  SING  N  N  34  
A7R  C05  C06  SING  N  N  35  
A7R  C05  C07  SING  N  N  36  
A7R  C06  C08  SING  N  N  37  
A7R  C07  O02  SING  N  N  38  
A7R  N01  C08  SING  N  N  39  
A7R  N01  C11  DOUB  Y  N  40  
A7R  C13  C11  SING  Y  N  41  
A7R  C13  C16  SING  N  N  42  
A7R  C08  O02  SING  N  N  43  
A7R  C16  O14  DOUB  N  N  44  
A7R  C16  N02  SING  N  N  45  
A7R  C01  H1   SING  N  N  46  
A7R  C02  H2   SING  N  N  47  
A7R  C03  H3   SING  N  N  48  
A7R  C04  H4   SING  N  N  49  
A7R  C05  H5   SING  N  N  50  
A7R  C06  H6   SING  N  N  51  
A7R  C07  H7   SING  N  N  52  
A7R  C08  H8   SING  N  N  53  
A7R  C09  H9   SING  N  N  54  
A7R  C09  H10  SING  N  N  55  
A7R  C10  H11  SING  N  N  56  
A7R  C10  H12  SING  N  N  57  
A7R  C11  H13  SING  N  N  58  
A7R  C12  H14  SING  N  N  59  
A7R  C14  H15  SING  N  N  60  
A7R  C15  H16  SING  N  N  61  
A7R  C17  H17  SING  N  N  62  
A7R  C19  H18  SING  N  N  63  
A7R  N02  H19  SING  N  N  64  
A7R  N02  H20  SING  N  N  65  
A7R  N04  H21  SING  N  N  66  
A7R  N04  H22  SING  N  N  67  
A7R  O03  H23  SING  N  N  68  
A7R  O04  H24  SING  N  N  69  
A7R  O05  H25  SING  N  N  70  
A7R  O06  H26  SING  N  N  71  
A7R  O11  H27  SING  N  N  72  
A7R  O13  H28  SING  N  N  73  
#   #
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
A7R  InChI             InChI                 1.03   "InChI=1S/C20H27N5O15P2/c21-12-3-5-25(20(31)23-12)19-16(29)14(27)11(39-19)8-37-42(34,35)40-41(32,33)36-7-10-13(26)15(28)18(38-10)24-4-1-2-9(6-24)17(22)30/h1-6,10-11,13-16,18-19,26-29H,7-8H2,(H5-,21,22,23,30,31,32,33,34,35)/p+1/t10-,11-,13+,14+,15+,16+,18-,19-/m0/s1"  
A7R  InChIKey          InChI                 1.03   CRWNYXSXULHVKY-JKHXZYGESA-O  
A7R  SMILES_CANONICAL  CACTVS                3.385  "NC(=O)c1ccc[n+](c1)[C@H]2O[C@@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H]3O[C@@H]([C@H](O)[C@@H]3O)N4C=CC(=NC4=O)N)[C@@H](O)[C@H]2O"  
A7R  SMILES            CACTVS                3.385  "NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=NC4=O)N)[CH](O)[CH]2O"  
A7R  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "c1cc(c[n+](c1)[C@@H]2[C@@H]([C@@H]([C@@H](O2)COP(=O)(O)OP(=O)(O)OC[C@H]3[C@H]([C@H]([C@H](O3)N4C=CC(=NC4=O)N)O)O)O)O)C(=O)N"  
A7R  SMILES            "OpenEye OEToolkits"  2.0.6  "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=NC4=O)N)O)O)O)O)C(=O)N"  
#
_pdbx_chem_comp_identifier.comp_id          A7R
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       "[[(2~{S},3~{S},4~{R},5~{S})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{R},5~{S})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen 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
A7R  "Create component"  2018-10-12  PDBJ  
A7R  "Initial release"   2019-03-13  RCSB  
##
