data_VQV
#

_chem_comp.id                                   VQV
_chem_comp.name                                 "1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H14 N2 O12 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-09-08
_chem_comp.pdbx_modified_date                   2020-09-18
_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                       404.161
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VQV
_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       7K1O
_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
VQV  O2     O1   O  0  1  N  N  N  33.757   1.712  -19.237  -4.037  -0.580  -2.179  O2     VQV   1  
VQV  N1     N1   N  0  1  N  N  N  34.996   2.101  -21.070  -2.753  -0.073  -0.448  N1     VQV   2  
VQV  C4     C1   C  0  1  N  N  N  35.791  -0.515  -20.976  -4.765  -0.930   1.165  C4     VQV   3  
VQV  C2     C2   C  0  1  N  N  N  34.548   1.280  -20.104  -3.901  -0.541  -0.971  C2     VQV   4  
VQV  C6     C3   C  0  1  N  N  N  35.840   1.641  -22.004  -2.576  -0.018   0.907  C6     VQV   5  
VQV  C5     C4   C  0  1  N  N  N  36.262   0.317  -21.980  -3.562  -0.439   1.728  C5     VQV   6  
VQV  "C1'"  C5   C  0  1  N  N  R  34.558   3.507  -21.113  -1.681   0.378  -1.339  "C1'"  VQV   7  
VQV  "C2'"  C6   C  0  1  N  N  S  35.332   4.389  -20.131  -1.137   1.748  -0.875  "C2'"  VQV   8  
VQV  "C3'"  C7   C  0  1  N  N  S  35.578   5.676  -20.888   0.084   1.389   0.002  "C3'"  VQV   9  
VQV  "C4'"  C8   C  0  1  N  N  S  35.628   5.199  -22.328   0.132  -0.154  -0.035  "C4'"  VQV  10  
VQV  "C5'"  C9   C  0  1  N  N  N  35.210   6.258  -23.332   1.583  -0.641  -0.068  "C5'"  VQV  11  
VQV  N3     N2   N  0  1  N  N  N  34.939  -0.017  -20.053  -4.900  -0.967  -0.176  N3     VQV  12  
VQV  O1P    O2   O  0  1  N  N  N  37.487   4.116  -24.712   2.623  -4.492  -0.017  O1P    VQV  13  
VQV  "O2'"  O3   O  0  1  N  N  N  36.609   3.805  -19.844  -2.120   2.443  -0.106  "O2'"  VQV  14  
VQV  O2A    O4   O  0  1  N  N  N  33.467   8.200  -19.054   2.870   2.217   1.522  O2A    VQV  15  
VQV  O2B    O5   O  0  1  N  N  N  34.680   9.072  -21.011   1.426   4.121   0.711  O2B    VQV  16  
VQV  O2C    O6   O  0  1  N  N  N  35.940   7.998  -19.177   3.404   3.481  -0.721  O2C    VQV  17  
VQV  O2P    O7   O  0  1  N  N  N  37.971   6.488  -24.257   3.826  -2.582   1.330  O2P    VQV  18  
VQV  "O3'"  O8   O  0  1  N  N  N  34.479   6.558  -20.688   1.279   1.941  -0.553  "O3'"  VQV  19  
VQV  O3P    O9   O  0  1  N  N  N  37.236   5.785  -26.520   3.766  -2.574  -1.193  O3P    VQV  20  
VQV  O4     O10  O  0  1  N  N  N  36.187  -1.818  -20.925  -5.668  -1.314   1.885  O4     VQV  21  
VQV  "O4'"  O11  O  0  1  N  N  N  34.759   4.068  -22.417  -0.549  -0.516  -1.256  "O4'"  VQV  22  
VQV  "O5'"  O12  O  0  1  N  N  N  35.556   5.792  -24.632   1.609  -2.067   0.015  "O5'"  VQV  23  
VQV  P      P1   P  0  1  N  N  N  37.096   5.535  -25.037   2.974  -2.921   0.007  P      VQV  24  
VQV  P2     P2   P  0  1  N  N  N  34.650   7.988  -19.965   2.227   2.966   0.250  P2     VQV  25  
VQV  H1     H1   H  0  1  N  N  N  36.194   2.303  -22.780  -1.651   0.359   1.319  H1     VQV  26  
VQV  H2     H2   H  0  1  N  N  N  36.944  -0.057  -22.729  -3.435  -0.401   2.800  H2     VQV  27  
VQV  H3     H3   H  0  1  N  N  N  33.490   3.557  -20.852  -2.042   0.441  -2.365  H3     VQV  28  
VQV  H4     H4   H  0  1  N  N  N  34.742   4.572  -19.221  -0.830   2.347  -1.733  H4     VQV  29  
VQV  H5     H5   H  0  1  N  N  N  36.536   6.129  -20.592  -0.062   1.744   1.022  H5     VQV  30  
VQV  H6     H6   H  0  1  N  N  N  36.659   4.891  -22.557  -0.387  -0.571   0.827  H6     VQV  31  
VQV  H7     H7   H  0  1  N  N  N  35.736   7.201  -23.121   2.052  -0.323  -1.000  H7     VQV  32  
VQV  H8     H8   H  0  1  N  N  N  34.124   6.422  -23.271   2.127  -0.218   0.776  H8     VQV  33  
VQV  H9     H9   H  0  1  N  N  N  34.594  -0.610  -19.326  -5.721  -1.301  -0.570  H9     VQV  34  
VQV  H10    H10  H  0  1  N  N  N  37.743   3.667  -25.509   3.400  -5.069  -0.023  H10    VQV  35  
VQV  H11    H11  H  0  1  N  N  N  37.081   4.359  -19.234  -2.932   2.639  -0.591  H11    VQV  36  
VQV  H12    H12  H  0  1  N  N  N  32.988   8.973  -19.330   3.410   1.447   1.294  H12    VQV  37  
VQV  H13    H13  H  0  1  N  N  N  36.506   8.687  -19.504   4.015   4.103  -0.303  H13    VQV  38  
VQV  H14    H14  H  0  1  N  N  N  38.436   7.056  -24.859   3.367  -2.785   2.157  H14    VQV  39  
#   #
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
VQV  O3P    P      DOUB  N  N   1  
VQV  P      O1P    SING  N  N   2  
VQV  P      "O5'"  SING  N  N   3  
VQV  P      O2P    SING  N  N   4  
VQV  "O5'"  "C5'"  SING  N  N   5  
VQV  "C5'"  "C4'"  SING  N  N   6  
VQV  "O4'"  "C4'"  SING  N  N   7  
VQV  "O4'"  "C1'"  SING  N  N   8  
VQV  "C4'"  "C3'"  SING  N  N   9  
VQV  C6     C5     DOUB  N  N  10  
VQV  C6     N1     SING  N  N  11  
VQV  C5     C4     SING  N  N  12  
VQV  "C1'"  N1     SING  N  N  13  
VQV  "C1'"  "C2'"  SING  N  N  14  
VQV  N1     C2     SING  N  N  15  
VQV  O2B    P2     DOUB  N  N  16  
VQV  C4     O4     DOUB  N  N  17  
VQV  C4     N3     SING  N  N  18  
VQV  "C3'"  "O3'"  SING  N  N  19  
VQV  "C3'"  "C2'"  SING  N  N  20  
VQV  "O3'"  P2     SING  N  N  21  
VQV  "C2'"  "O2'"  SING  N  N  22  
VQV  C2     N3     SING  N  N  23  
VQV  C2     O2     DOUB  N  N  24  
VQV  P2     O2C    SING  N  N  25  
VQV  P2     O2A    SING  N  N  26  
VQV  C6     H1     SING  N  N  27  
VQV  C5     H2     SING  N  N  28  
VQV  "C1'"  H3     SING  N  N  29  
VQV  "C2'"  H4     SING  N  N  30  
VQV  "C3'"  H5     SING  N  N  31  
VQV  "C4'"  H6     SING  N  N  32  
VQV  "C5'"  H7     SING  N  N  33  
VQV  "C5'"  H8     SING  N  N  34  
VQV  N3     H9     SING  N  N  35  
VQV  O1P    H10    SING  N  N  36  
VQV  "O2'"  H11    SING  N  N  37  
VQV  O2A    H12    SING  N  N  38  
VQV  O2C    H13    SING  N  N  39  
VQV  O2P    H14    SING  N  N  40  
#   #
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
VQV  SMILES            ACDLabs               12.01  "O=C1N(C=CC(=O)N1)C2C(O)C(OP(O)(=O)O)C(COP(O)(O)=O)O2"  
VQV  InChI             InChI                 1.03   "InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(14)10-5)8-6(13)7(23-25(18,19)20)4(22-8)3-21-24(15,16)17/h1-2,4,6-8,13H,3H2,(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7+,8+/m0/s1"  
VQV  InChIKey          InChI                 1.03   ZPVPRWPOZBXDKD-ZAKLUEHWSA-N  
VQV  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@H](O[P](O)(O)=O)[C@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O"  
VQV  SMILES            CACTVS                3.385  "O[CH]1[CH](O[P](O)(O)=O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O"  
VQV  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)NC1=O)[C@H]2[C@H]([C@@H]([C@@H](O2)COP(=O)(O)O)OP(=O)(O)O)O"  
VQV  SMILES            "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)OP(=O)(O)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
VQV  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione"  
VQV  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{S},3~{S},4~{S},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] 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
VQV  "Create component"  2020-09-08  RCSB  
VQV  "Initial release"   2020-09-23  RCSB  
##
