data_V2V
#

_chem_comp.id                                   V2V
_chem_comp.name                                 CDP-ribitol
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C14 H25 N3 O15 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-06-19
_chem_comp.pdbx_modified_date                   2021-04-16
_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                       537.307
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    V2V
_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       6XHQ
_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
V2V  C01  C1   C  0  1  N  N  N  -26.254  12.515  20.833  -6.781   3.461  -0.049  C01  V2V   1  
V2V  C02  C2   C  0  1  N  N  N  -25.617  11.477  19.980  -6.167   2.631   0.826  C02  V2V   2  
V2V  C04  C3   C  0  1  N  N  N  -27.701  11.488  18.516  -5.698   1.146  -0.933  C04  V2V   3  
V2V  C07  C4   C  0  1  N  N  N  -27.606  13.037  20.488  -6.842   3.096  -1.410  C07  V2V   4  
V2V  C09  C5   C  0  1  N  N  R  -25.783   9.955  17.946  -4.955   0.560   1.308  C09  V2V   5  
V2V  C10  C6   C  0  1  N  N  R  -24.558  10.620  17.210  -5.726  -0.781   1.413  C10  V2V   6  
V2V  C11  C7   C  0  1  N  N  S  -23.697   9.361  16.814  -4.615  -1.758   1.870  C11  V2V   7  
V2V  C12  C8   C  0  1  N  N  R  -24.060   8.412  17.618  -3.305  -1.057   1.464  C12  V2V   8  
V2V  C14  C9   C  0  1  N  N  N  -22.954   8.042  18.540  -2.508  -1.952   0.512  C14  V2V   9  
V2V  C24  C10  C  0  1  N  N  N  -22.328   5.498  21.675   5.116  -0.387  -0.578  C24  V2V  10  
V2V  C25  C11  C  0  1  N  N  R  -21.985   4.009  22.069   5.737   0.737   0.255  C25  V2V  11  
V2V  C26  C12  C  0  1  N  N  S  -22.420   3.031  20.997   7.248   0.772   0.017  C26  V2V  12  
V2V  C27  C13  C  0  1  N  N  S  -22.000   1.583  21.318   7.869   1.895   0.850  C27  V2V  13  
V2V  C28  C14  C  0  1  N  N  N  -22.910   0.988  22.373   9.380   1.931   0.613  C28  V2V  14  
V2V  N03  N1   N  0  1  N  N  N  -26.356  10.976  18.844  -5.624   1.467   0.371  N03  V2V  15  
V2V  N06  N2   N  0  1  N  N  N  -28.310  12.525  19.362  -6.299   1.953  -1.806  N06  V2V  16  
V2V  N08  N3   N  0  1  N  N  N  -28.251  14.065  21.288  -7.461   3.921  -2.320  N08  V2V  17  
V2V  O05  O1   O  0  1  N  N  N  -28.279  11.065  17.544  -5.206   0.100  -1.323  O05  V2V  18  
V2V  O13  O2   O  0  1  N  N  N  -25.261   8.995  18.637  -3.662   0.167   0.799  O13  V2V  19  
V2V  O15  O3   O  0  1  N  N  N  -22.716   9.159  19.408  -1.245  -1.346   0.234  O15  V2V  20  
V2V  O17  O4   O  0  1  N  N  N  -20.163   9.155  18.830   0.159  -3.385  -0.263  O17  V2V  21  
V2V  O18  O5   O  0  1  N  N  N  -21.046  10.817  20.427  -0.723  -2.081  -2.237  O18  V2V  22  
V2V  O19  O6   O  0  1  N  N  N  -20.821   8.369  21.161   1.198  -1.129  -0.715  O19  V2V  23  
V2V  O21  O7   O  0  1  N  N  N  -21.102   8.624  23.709   3.111  -2.770  -0.846  O21  V2V  24  
V2V  O22  O8   O  0  1  N  N  N  -23.146   8.626  22.312   2.820  -1.178  -2.783  O22  V2V  25  
V2V  O23  O9   O  0  1  N  N  N  -21.745   6.373  22.667   3.693  -0.346  -0.447  O23  V2V  26  
V2V  O29  O10  O  0  1  N  N  N  -23.327  -0.326  22.045   9.944   3.050   1.298  O29  V2V  27  
V2V  O30  O11  O  0  1  N  N  N  -20.644   1.538  21.760   7.610   1.659   2.236  O30  V2V  28  
V2V  O31  O12  O  0  1  N  N  N  -21.831   3.398  19.763   7.506   1.008  -1.368  O31  V2V  29  
V2V  O32  O13  O  0  1  N  N  N  -22.527   3.710  23.340   5.478   0.501   1.640  O32  V2V  30  
V2V  O33  O14  O  0  1  N  N  N  -23.989   9.027  15.392  -4.665  -1.945   3.286  O33  V2V  31  
V2V  O34  O15  O  0  1  N  N  N  -24.886  11.361  16.160  -6.765  -0.697   2.390  O34  V2V  32  
V2V  P16  P1   P  0  1  N  N  N  -21.142   9.407  19.947  -0.146  -2.015  -0.735  P16  V2V  33  
V2V  P20  P2   P  0  1  N  N  N  -21.746   8.027  22.474   2.714  -1.386  -1.190  P20  V2V  34  
V2V  H1   H1   H  0  1  N  N  N  -25.736  12.891  21.703  -7.222   4.387   0.290  H1   V2V  35  
V2V  H2   H2   H  0  1  N  N  N  -24.627  11.107  20.204  -6.107   2.889   1.873  H2   V2V  36  
V2V  H3   H3   H  0  1  N  N  N  -26.524   9.623  17.203  -4.859   1.025   2.289  H3   V2V  37  
V2V  H4   H4   H  0  1  N  N  N  -23.990  11.200  17.952  -6.128  -1.075   0.444  H4   V2V  38  
V2V  H5   H5   H  0  1  N  N  N  -22.633   9.620  16.920  -4.712  -2.714   1.354  H5   V2V  39  
V2V  H6   H6   H  0  1  N  N  N  -24.450   7.521  17.105  -2.711  -0.839   2.351  H6   V2V  40  
V2V  H8   H8   H  0  1  N  N  N  -23.240   7.161  19.133  -2.350  -2.926   0.976  H8   V2V  41  
V2V  H9   H9   H  0  1  N  N  N  -22.045   7.816  17.963  -3.063  -2.079  -0.417  H9   V2V  42  
V2V  H10  H10  H  0  1  N  N  N  -21.909   5.727  20.684   5.388  -0.255  -1.625  H10  V2V  43  
V2V  H11  H11  H  0  1  N  N  N  -23.419   5.635  21.652   5.486  -1.349  -0.225  H11  V2V  44  
V2V  H12  H12  H  0  1  N  N  N  -20.889   3.950  22.136   5.300   1.691  -0.039  H12  V2V  45  
V2V  H13  H13  H  0  1  N  N  N  -23.516   3.063  20.915   7.685  -0.182   0.311  H13  V2V  46  
V2V  H14  H14  H  0  1  N  N  N  -22.105   0.989  20.398   7.432   2.850   0.557  H14  V2V  47  
V2V  H15  H15  H  0  1  N  N  N  -22.370   0.959  23.331   9.828   1.011   0.988  H15  V2V  48  
V2V  H16  H16  H  0  1  N  N  N  -23.800   1.627  22.474   9.578   2.022  -0.456  H16  V2V  49  
V2V  H17  H17  H  0  1  N  N  N  -29.163  14.392  21.041  -7.857   4.756  -2.027  H17  V2V  50  
V2V  H18  H18  H  0  1  N  N  N  -27.783  14.445  22.086  -7.501   3.667  -3.256  H18  V2V  51  
V2V  H20  H20  H  0  1  N  N  N  -20.381  11.277  19.928  -0.946  -1.217  -2.611  H20  V2V  52  
V2V  H21  H21  H  0  1  N  N  N  -23.311   9.241  23.017   2.574  -0.292  -3.081  H21  V2V  53  
V2V  H22  H22  H  0  1  N  N  N  -23.894  -0.659  22.731  10.901   3.136   1.192  H22  V2V  54  
V2V  H23  H23  H  0  1  N  N  N  -20.403   0.640  21.953   7.971   0.825   2.567  H23  V2V  55  
V2V  H24  H24  H  0  1  N  N  N  -22.102   2.787  19.088   7.146   1.842  -1.699  H24  V2V  56  
V2V  H25  H25  H  0  1  N  N  N  -22.317   2.813  23.571   5.839  -0.333   1.972  H25  V2V  57  
V2V  H26  H26  H  0  1  N  N  N  -23.479   8.269  15.133  -5.493  -2.330   3.603  H26  V2V  58  
V2V  H27  H27  H  0  1  N  N  N  -24.100  11.726  15.771  -7.275  -1.511   2.493  H27  V2V  59  
#   #
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
V2V  C01  C02  DOUB  N  N   1  
V2V  C01  C07  SING  N  N   2  
V2V  C02  N03  SING  N  N   3  
V2V  C04  N03  SING  N  N   4  
V2V  C04  N06  SING  N  N   5  
V2V  C04  O05  DOUB  N  N   6  
V2V  C07  N06  DOUB  N  N   7  
V2V  C07  N08  SING  N  N   8  
V2V  C09  C10  SING  N  N   9  
V2V  C09  N03  SING  N  N  10  
V2V  C09  O13  SING  N  N  11  
V2V  C10  C11  SING  N  N  12  
V2V  C10  O34  SING  N  N  13  
V2V  C11  C12  SING  N  N  14  
V2V  C11  O33  SING  N  N  15  
V2V  C12  C14  SING  N  N  16  
V2V  C14  O15  SING  N  N  17  
V2V  C24  C25  SING  N  N  18  
V2V  C24  O23  SING  N  N  19  
V2V  C25  C26  SING  N  N  20  
V2V  C25  O32  SING  N  N  21  
V2V  C26  C27  SING  N  N  22  
V2V  C26  O31  SING  N  N  23  
V2V  C27  C28  SING  N  N  24  
V2V  C27  O30  SING  N  N  25  
V2V  C28  O29  SING  N  N  26  
V2V  O15  P16  SING  N  N  27  
V2V  O17  P16  DOUB  N  N  28  
V2V  O18  P16  SING  N  N  29  
V2V  O19  P16  SING  N  N  30  
V2V  O19  P20  SING  N  N  31  
V2V  O21  P20  DOUB  N  N  32  
V2V  O22  P20  SING  N  N  33  
V2V  O23  P20  SING  N  N  34  
V2V  C01  H1   SING  N  N  35  
V2V  C02  H2   SING  N  N  36  
V2V  C09  H3   SING  N  N  37  
V2V  C10  H4   SING  N  N  38  
V2V  C11  H5   SING  N  N  39  
V2V  C12  H6   SING  N  N  40  
V2V  C14  H8   SING  N  N  41  
V2V  C14  H9   SING  N  N  42  
V2V  C24  H10  SING  N  N  43  
V2V  C24  H11  SING  N  N  44  
V2V  C25  H12  SING  N  N  45  
V2V  C26  H13  SING  N  N  46  
V2V  C27  H14  SING  N  N  47  
V2V  C28  H15  SING  N  N  48  
V2V  C28  H16  SING  N  N  49  
V2V  N08  H17  SING  N  N  50  
V2V  N08  H18  SING  N  N  51  
V2V  O18  H20  SING  N  N  52  
V2V  O22  H21  SING  N  N  53  
V2V  O29  H22  SING  N  N  54  
V2V  O30  H23  SING  N  N  55  
V2V  O31  H24  SING  N  N  56  
V2V  O32  H25  SING  N  N  57  
V2V  O33  H26  SING  N  N  58  
V2V  O34  H27  SING  N  N  59  
V2V  C12  O13  SING  N  N  60  
#   #
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
V2V  SMILES            ACDLabs               12.01  "C1=CN(C(N=C1N)=O)C2C(C(C(COP(=O)(O)OP(=O)(O)OCC(C(C(CO)O)O)O)O2)O)O"  
V2V  InChI             InChI                 1.03   "InChI=1S/C14H25N3O15P2/c15-9-1-2-17(14(24)16-9)13-12(23)11(22)8(31-13)5-30-34(27,28)32-33(25,26)29-4-7(20)10(21)6(19)3-18/h1-2,6-8,10-13,18-23H,3-5H2,(H,25,26)(H,27,28)(H2,15,16,24)/t6-,7+,8+,10-,11+,12+,13+/m0/s1"  
V2V  InChIKey          InChI                 1.03   DPJKHFICSGCNIR-HRENORGGSA-N  
V2V  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@@H](O)CO)[C@@H](O)[C@H]2O"  
V2V  SMILES            CACTVS                3.385  "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH](O)[CH](O)[CH](O)CO)[CH](O)[CH]2O"  
V2V  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H](C(O2)COP(=O)(O)OP(=O)(O)OC[C@H]([C@H]([C@H](CO)O)O)O)O)O"  
V2V  SMILES            "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC(C(C(CO)O)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
V2V  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate (non-preferred name)"  
V2V  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[[(3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate"  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     V2V
_pdbx_chem_comp_synonyms.name        "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate"
_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
V2V  "Create component"  2020-06-19  RCSB  
V2V  "Modify synonyms"   2021-03-13  RCSB  
V2V  "Initial release"   2021-04-21  RCSB  
##
