data_5ZL
#

_chem_comp.id                                   5ZL
_chem_comp.name                                 "[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H17 N2 O18 P4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2021-09-07
_chem_comp.pdbx_modified_date                   2021-09-10
_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                       565.129
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    ?
_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       7DPT
_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
5ZL  C21  C1   C  0  1  N  N  S  118.226  131.633  145.028  -1.679  -3.406  -0.244  C21  5ZL   1  
5ZL  C22  C2   C  0  1  N  N  R  118.225  133.053  145.322  -2.988  -2.770   0.274  C22  5ZL   2  
5ZL  C24  C3   C  0  1  N  N  R  116.880  133.345  145.804  -2.520  -1.494   1.009  C24  5ZL   3  
5ZL  C26  C4   C  0  1  Y  N  N  116.133  135.575  146.286  -4.537  -0.301   1.575  C26  5ZL   4  
5ZL  C28  C5   C  0  1  Y  N  N  117.565  135.649  148.735  -4.162   1.497  -0.377  C28  5ZL   5  
5ZL  C23  C6   C  0  1  N  N  R  117.306  131.013  145.999  -0.575  -2.440   0.240  C23  5ZL   6  
5ZL  C25  C7   C  0  1  N  N  N  118.062  130.420  147.124   0.527  -2.320  -0.815  C25  5ZL   7  
5ZL  C27  C8   C  0  1  Y  N  N  117.616  134.486  147.921  -3.259   0.470  -0.180  C27  5ZL   8  
5ZL  C29  C9   C  0  1  Y  N  N  116.803  136.760  148.322  -5.272   1.576   0.462  C29  5ZL   9  
5ZL  N19  N1   N  1  1  Y  N  N  116.877  134.457  146.672  -3.474  -0.403   0.794  N19  5ZL  10  
5ZL  N20  N2   N  0  1  Y  N  N  116.085  136.729  147.088  -5.424   0.667   1.418  N20  5ZL  11  
5ZL  O04  O1   O  0  1  N  N  N  116.414  132.095  146.519  -1.245  -1.172   0.414  O04  5ZL  12  
5ZL  O05  O2   O  0  1  N  N  N  117.658  131.419  143.717  -1.494  -4.704   0.326  O05  5ZL  13  
5ZL  O06  O3   O  0  1  N  N  N  118.546  133.860  144.138  -3.651  -3.654   1.179  O06  5ZL  14  
5ZL  O07  O4   O  0  1  N  N  N  118.589  131.480  147.880   1.592  -1.516  -0.302  O07  5ZL  15  
5ZL  O08  O5   O  0  1  N  N  N  115.437  135.542  145.097  -4.725  -1.216   2.556  O08  5ZL  16  
5ZL  O09  O6   O  0  1  N  N  N  120.608  129.793  148.388   3.954  -0.367  -0.216  O09  5ZL  17  
5ZL  O10  O7   O  0  1  N  N  N  120.772  132.257  148.999   3.550  -2.440  -1.598  O10  5ZL  18  
5ZL  O11  O8   O  0  1  N  N  N  119.370  131.064  150.236   2.531  -0.284  -2.426  O11  5ZL  19  
5ZL  O12  O9   O  0  1  N  N  N  116.693  137.923  149.053  -6.183   2.567   0.305  O12  5ZL  20  
5ZL  O13  O10  O  0  1  N  N  N  121.946  128.136  150.066   5.885   1.155   0.717  O13  5ZL  21  
5ZL  O14  O11  O  0  1  N  N  N  120.315  127.238  148.343   5.823   0.447  -1.706  O14  5ZL  22  
5ZL  O15  O12  O  0  1  N  N  N  119.455  128.318  150.070   6.394  -1.323   0.001  O15  5ZL  23  
5ZL  O16  O13  O  0  1  N  N  N  123.470  129.501  151.596   7.352   2.817  -0.489  O16  5ZL  24  
5ZL  O17  O14  O  0  1  N  N  N  122.220  127.909  152.651   6.689   3.370   1.882  O17  5ZL  25  
5ZL  O18  O15  O  0  1  N  N  N  121.292  129.808  151.916   8.417   1.460   1.353  O18  5ZL  26  
5ZL  O31  O16  O  0  1  N  N  N  117.780  137.680  151.366  -8.327   3.487  -0.908  O31  5ZL  27  
5ZL  O32  O17  O  0  1  N  N  N  119.164  138.385  149.680  -6.828   1.778  -2.005  O32  5ZL  28  
5ZL  O33  O18  O  0  1  N  N  N  117.595  139.801  150.562  -8.255   0.994  -0.077  O33  5ZL  29  
5ZL  P01  P1   P  0  1  N  N  N  119.833  131.173  148.888   2.921  -1.179  -1.146  P01  5ZL  30  
5ZL  P02  P2   P  0  1  N  N  N  120.604  128.348  149.217   5.521  -0.012  -0.331  P02  5ZL  31  
5ZL  P03  P3   P  0  1  N  N  N  122.218  128.812  151.530   7.092   2.214   0.837  P03  5ZL  32  
5ZL  P30  P4   P  0  1  N  N  N  117.797  138.427  150.145  -7.386   2.197  -0.700  P30  5ZL  33  
5ZL  H1   H1   H  0  1  N  N  N  119.236  131.204  145.108  -1.687  -3.464  -1.332  H1   5ZL  34  
5ZL  H2   H2   H  0  1  N  N  N  118.954  133.266  146.117  -3.643  -2.512  -0.559  H2   5ZL  35  
5ZL  H3   H3   H  0  1  N  N  N  116.215  133.531  144.947  -2.403  -1.692   2.075  H3   5ZL  36  
5ZL  H4   H4   H  0  1  N  N  N  118.109  135.682  149.668  -4.011   2.222  -1.163  H4   5ZL  37  
5ZL  H5   H5   H  0  1  N  N  N  116.701  130.239  145.504  -0.159  -2.783   1.187  H5   5ZL  38  
5ZL  H6   H6   H  0  1  N  N  N  117.392  129.810  147.748   0.906  -3.313  -1.059  H6   5ZL  39  
5ZL  H7   H7   H  0  1  N  N  N  118.878  129.791  146.739   0.121  -1.855  -1.713  H7   5ZL  40  
5ZL  H8   H8   H  0  1  N  N  N  118.199  133.631  148.229  -2.388   0.379  -0.812  H8   5ZL  41  
5ZL  H9   H9   H  0  1  N  N  N  117.657  130.490  143.520  -2.192  -5.334   0.104  H9   5ZL  42  
5ZL  H10  H10  H  0  1  N  N  N  118.536  134.781  144.370  -3.914  -4.497   0.784  H10  5ZL  43  
5ZL  H11  H11  H  0  1  N  N  N  119.805  131.714  150.774   2.113   0.559  -2.203  H11  5ZL  44  
5ZL  H12  H12  H  0  1  N  N  N  118.883  127.607  149.807   6.246  -1.680   0.887  H12  5ZL  45  
5ZL  H13  H13  H  0  1  N  N  N  123.034  128.003  153.132   7.372   4.044   2.005  H13  5ZL  46  
5ZL  H14  H14  H  0  1  N  N  N  121.755  130.617  152.100   8.319   1.040   2.219  H14  5ZL  47  
5ZL  H15  H15  H  0  1  N  N  N  118.654  137.356  151.552  -9.074   3.337  -1.503  H15  5ZL  48  
5ZL  H16  H16  H  0  1  N  N  N  118.394  140.296  150.422  -8.653   1.199   0.780  H16  5ZL  49  
5ZL  H17  H17  H  0  1  N  N  N  114.984  136.368  144.971  -4.320  -0.975   3.401  H17  5ZL  50  
#   #
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
5ZL  O05  C21  SING  N  N   1  
5ZL  O06  C22  SING  N  N   2  
5ZL  C21  C22  SING  N  N   3  
5ZL  C21  C23  SING  N  N   4  
5ZL  O08  C26  SING  N  N   5  
5ZL  C22  C24  SING  N  N   6  
5ZL  C24  O04  SING  N  N   7  
5ZL  C24  N19  SING  N  N   8  
5ZL  C23  O04  SING  N  N   9  
5ZL  C23  C25  SING  N  N  10  
5ZL  C26  N19  SING  Y  N  11  
5ZL  C26  N20  DOUB  Y  N  12  
5ZL  N19  C27  DOUB  Y  N  13  
5ZL  N20  C29  SING  Y  N  14  
5ZL  C25  O07  SING  N  N  15  
5ZL  O07  P01  SING  N  N  16  
5ZL  C27  C28  SING  Y  N  17  
5ZL  C29  C28  DOUB  Y  N  18  
5ZL  C29  O12  SING  N  N  19  
5ZL  O14  P02  DOUB  N  N  20  
5ZL  O09  P01  SING  N  N  21  
5ZL  O09  P02  SING  N  N  22  
5ZL  P01  O10  DOUB  N  N  23  
5ZL  P01  O11  SING  N  N  24  
5ZL  O12  P30  SING  N  N  25  
5ZL  P02  O13  SING  N  N  26  
5ZL  P02  O15  SING  N  N  27  
5ZL  O32  P30  DOUB  N  N  28  
5ZL  O13  P03  SING  N  N  29  
5ZL  P30  O33  SING  N  N  30  
5ZL  P30  O31  SING  N  N  31  
5ZL  P03  O16  DOUB  N  N  32  
5ZL  P03  O18  SING  N  N  33  
5ZL  P03  O17  SING  N  N  34  
5ZL  C21  H1   SING  N  N  35  
5ZL  C22  H2   SING  N  N  36  
5ZL  C24  H3   SING  N  N  37  
5ZL  C28  H4   SING  N  N  38  
5ZL  C23  H5   SING  N  N  39  
5ZL  C25  H6   SING  N  N  40  
5ZL  C25  H7   SING  N  N  41  
5ZL  C27  H8   SING  N  N  42  
5ZL  O05  H9   SING  N  N  43  
5ZL  O06  H10  SING  N  N  44  
5ZL  O11  H11  SING  N  N  45  
5ZL  O15  H12  SING  N  N  46  
5ZL  O17  H13  SING  N  N  47  
5ZL  O18  H14  SING  N  N  48  
5ZL  O31  H15  SING  N  N  49  
5ZL  O33  H16  SING  N  N  50  
5ZL  O08  H17  SING  N  N  51  
#   #
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
5ZL  InChI             InChI                 1.03   "InChI=1S/C9H16N2O18P4/c12-6-4(3-25-32(21,22)29-33(23,24)28-31(18,19)20)26-8(7(6)13)11-2-1-5(10-9(11)14)27-30(15,16)17/h1-2,4,6-8,12-13H,3H2,(H6,15,16,17,18,19,20,21,22,23,24)/p+1/t4-,6-,7-,8-/m1/s1"  
5ZL  InChIKey          InChI                 1.03   RYGLMDXZXSWNKW-XVFCMESISA-O  
5ZL  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[n+]2ccc(O[P](O)(O)=O)nc2O"  
5ZL  SMILES            CACTVS                3.385  "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[n+]2ccc(O[P](O)(O)=O)nc2O"  
5ZL  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1c[n+](c(nc1OP(=O)(O)O)O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"  
5ZL  SMILES            "OpenEye OEToolkits"  2.0.7  "c1c[n+](c(nc1OP(=O)(O)O)O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          5ZL
_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~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-ium-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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
5ZL  "Create component"  2021-09-07  PDBJ  
5ZL  "Initial release"   2021-09-15  RCSB  
##
