data_O5W
#

_chem_comp.id                                   O5W
_chem_comp.name                                 "[(3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C21 H28 N7 O13 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "[(1~{R},3~{R})-1-(6-azanyl-1-methyl-purin-9-yl)-1-oxidanyl-5-phosphonooxy-pentan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate"
_chem_comp.pdbx_formal_charge                   -1
_chem_comp.pdbx_initial_date                    2020-02-10
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       648.434
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    O5W
_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       6Y0Q
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
O5W  C31   C1   C   0  1  N  N  N  -16.868   -9.152   3.575   7.403  -0.918   1.695  C31   O5W   1  
O5W  C32   C2   C   0  1  N  N  N  -17.951   -9.320   4.602   7.933  -2.105   2.060  C32   O5W   2  
O5W  C01   C3   C   0  1  N  N  N   -1.186   -4.128   4.709  -7.392  -6.099   0.182  C01   O5W   3  
O5W  C03   C4   C   0  1  Y  N  N   -2.935   -4.852   6.239  -7.187  -3.788  -0.484  C03   O5W   4  
O5W  C04   C5   C   0  1  Y  N  N   -4.274   -5.273   6.475  -6.506  -2.560  -0.440  C04   O5W   5  
O5W  C05   C6   C   0  1  Y  N  N   -5.114   -5.350   5.397  -5.340  -2.475   0.339  C05   O5W   6  
O5W  C07   C7   C   0  1  Y  N  N   -6.228   -5.945   7.189  -5.751  -0.535  -0.624  C07   O5W   7  
O5W  C09   C8   C   0  1  N  N  R   -7.470   -5.953   5.012  -3.693  -0.618   0.834  C09   O5W   8  
O5W  C10   C9   C   0  1  N  N  N   -8.082   -7.407   5.125  -2.451  -0.924  -0.025  C10   O5W   9  
O5W  C11   C10  C   0  1  N  N  S   -9.595   -7.108   4.873  -1.874   0.471  -0.368  C11   O5W  10  
O5W  C12   C11  C   0  1  N  N  R   -9.832   -5.941   5.415  -2.492   1.360   0.741  C12   O5W  11  
O5W  C14   C12  C   0  1  N  N  N  -10.322   -6.053   6.821  -2.567   2.818   0.284  C14   O5W  12  
O5W  C24   C13  C   0  1  N  N  N  -12.414   -9.300   2.182   3.138   1.174  -1.849  C24   O5W  13  
O5W  C25   C14  C   0  1  N  N  R  -13.701   -9.310   1.333   4.394   1.452  -1.020  C25   O5W  14  
O5W  C26   C15  C   0  1  N  N  S  -14.452   -7.901   1.376   5.618   1.637  -1.943  C26   O5W  15  
O5W  C27   C16  C   0  1  N  N  N  -15.857   -8.271   0.938   6.777   0.972  -1.167  C27   O5W  16  
O5W  C28   C17  C   0  1  N  N  R  -16.011   -9.567   1.260   6.115   0.464   0.134  C28   O5W  17  
O5W  C33   C18  C   0  1  N  N  N  -19.187  -10.082   4.260   7.741  -3.231   1.225  C33   O5W  18  
O5W  C35   C19  C   0  1  N  N  N  -18.265  -10.488   1.911   6.516  -1.902  -0.255  C35   O5W  19  
O5W  C38   C20  C   0  1  N  N  N  -17.790   -8.710   6.012   8.720  -2.228   3.339  C38   O5W  20  
O5W  C42   C21  C   0  1  Y  N  N   -3.432   -4.648   3.961  -5.597  -4.681   0.932  C42   O5W  21  
O5W  N02   N1   N   1  1  Y  N  N   -2.578   -4.560   4.980  -6.698  -4.809   0.213  N02   O5W  22  
O5W  N06   N2   N   0  1  Y  N  N   -6.302   -5.772   5.868  -4.887  -1.188   0.204  N06   O5W  23  
O5W  N08   N3   N   0  1  Y  N  N   -4.982   -5.647   7.579  -6.701  -1.342  -1.001  N08   O5W  24  
O5W  N30   N4   N   0  1  N  N  N  -17.026   -9.726   2.246   6.691  -0.824   0.530  N30   O5W  25  
O5W  N34   N5   N   0  1  N  N  N  -19.340  -10.658   2.933   7.034  -3.097   0.085  N34   O5W  26  
O5W  N41   N6   N   0  1  Y  N  N   -4.689   -5.036   4.130  -4.927  -3.551   1.002  N41   O5W  27  
O5W  N43   N7   N   0  1  N  N  N   -1.997   -4.751   7.344  -8.344  -3.930  -1.230  N43   O5W  28  
O5W  O13   O1   O   0  1  N  N  N   -8.376   -5.120   5.412  -3.817   0.812   0.912  O13   O5W  29  
O5W  O15   O2   O   0  1  N  N  N   -9.368   -6.767   7.567  -3.031   3.632   1.363  O15   O5W  30  
O5W  O17   O3   O   0  1  N  N  N  -10.053   -6.625  10.054  -3.921   5.536  -0.036  O17   O5W  31  
O5W  O18   O4   O   0  1  N  N  N   -8.829   -8.774   9.318  -4.118   5.754   2.471  O18   O5W  32  
O5W  O19   O5   O   0  1  N  N  N  -11.229   -8.077   8.762  -1.910   5.891   1.257  O19   O5W  33  
O5W  O20   O6   O   0  1  N  N  N   -9.774   -6.998   3.393  -0.447   0.468  -0.282  O20   O5W  34  
O5W  O22   O7   O   0  1  N  N  N  -11.684   -5.648   2.188  -0.010   2.062  -2.190  O22   O5W  35  
O5W  O23   O8   O   0  1  N  N  N  -11.583   -8.218   1.726   2.000   1.122  -0.987  O23   O5W  36  
O5W  O29   O9   O   0  1  N  N  N  -14.564  -10.100   1.839   4.719   0.309  -0.199  O29   O5W  37  
O5W  O36   O10  O   0  1  N  N  N  -18.394  -10.956   0.829   5.880  -1.796  -1.286  O36   O5W  38  
O5W  O37   O11  O   0  1  N  N  N  -20.040  -10.216   5.071   8.210  -4.312   1.533  O37   O5W  39  
O5W  O39   O12  O   0  1  N  N  N  -13.892   -7.024   0.522   5.886   3.025  -2.148  O39   O5W  40  
O5W  O40   O13  O   0  1  N  N  N  -12.304   -6.947   3.877   0.528  -0.275  -2.489  O40   O5W  41  
O5W  P16   P1   P  -1  1  N  N  N   -9.873   -7.560   8.944  -3.231   5.225   1.236  P16   O5W  42  
O5W  P21   P2   P  -1  1  N  N  N  -11.343   -6.935   2.781   0.507   0.846  -1.523  P21   O5W  43  
O5W  H311  H1   H   0  0  N  N  N  -15.971   -8.605   3.823   7.535  -0.048   2.322  H311  O5W  44  
O5W  H012  H2   H   0  0  N  N  N   -1.066   -3.930   3.634  -7.001  -6.702  -0.637  H012  O5W  45  
O5W  H011  H3   H   0  0  N  N  N   -0.970   -3.211   5.277  -7.232  -6.620   1.126  H011  O5W  46  
O5W  H013  H4   H   0  0  N  N  N   -0.489   -4.922   5.016  -8.459  -5.934   0.035  H013  O5W  47  
O5W  H071  H5   H   0  0  N  N  N   -7.033   -6.269   7.832  -5.662   0.499  -0.923  H071  O5W  48  
O5W  H091  H6   H   0  0  N  N  N   -7.186   -5.785   3.963  -3.566  -1.036   1.832  H091  O5W  49  
O5W  H101  H7   H   0  0  N  N  N   -7.669   -8.081   4.359  -1.727  -1.507   0.545  H101  O5W  50  
O5W  H102  H8   H   0  0  N  N  N   -7.916   -7.840   6.122  -2.736  -1.452  -0.935  H102  O5W  51  
O5W  H111  H9   H   0  0  N  N  N  -10.210   -7.923   5.282  -2.202   0.796  -1.355  H111  O5W  52  
O5W  H1    H11  H   0  1  N  N  N  -10.544   -5.345   4.826  -1.918   1.277   1.664  H1    O5W  53  
O5W  H141  H12  H   0  0  N  N  N  -10.453   -5.049   7.250  -1.577   3.154  -0.025  H141  O5W  54  
O5W  H142  H13  H   0  0  N  N  N  -11.283   -6.588   6.838  -3.257   2.901  -0.556  H142  O5W  55  
O5W  H242  H14  H   0  0  N  N  N  -12.668   -9.153   3.242   3.004   1.969  -2.582  H242  O5W  56  
O5W  H241  H15  H   0  0  N  N  N  -11.881  -10.255   2.062   3.248   0.219  -2.364  H241  O5W  57  
O5W  H251  H16  H   0  0  N  N  N  -13.448   -9.543   0.288   4.249   2.337  -0.400  H251  O5W  58  
O5W  H261  H17  H   0  0  N  N  N  -14.465   -7.534   2.413   5.458   1.133  -2.896  H261  O5W  59  
O5W  H272  H18  H   0  0  N  N  N  -16.598   -7.654   1.467   7.189   0.138  -1.736  H272  O5W  60  
O5W  H271  H19  H   0  0  N  N  N  -15.970   -8.130  -0.147   7.554   1.702  -0.940  H271  O5W  61  
O5W  H281  H20  H   0  0  N  N  N  -16.250  -10.173   0.373   6.238   1.195   0.932  H281  O5W  62  
O5W  H383  H21  H   0  0  N  N  N  -18.681   -8.939   6.615   8.047  -2.487   4.157  H383  O5W  63  
O5W  H382  H22  H   0  0  N  N  N  -16.900   -9.137   6.497   9.474  -3.007   3.229  H382  O5W  64  
O5W  H381  H23  H   0  0  N  N  N  -17.674   -7.619   5.928   9.209  -1.278   3.558  H381  O5W  65  
O5W  H421  H24  H   0  0  N  N  N   -3.090   -4.396   2.968  -5.234  -5.536   1.483  H421  O5W  66  
O5W  H341  H25  H   0  0  N  N  N  -20.168  -11.170   2.704   6.898  -3.864  -0.493  H341  O5W  67  
O5W  H431  H26  H   0  0  N  N  N   -1.056   -4.457   7.176  -8.694  -3.177  -1.730  H431  O5W  68  
O5W  H432  H27  H   0  0  N  N  N   -2.292   -4.976   8.273  -8.806  -4.783  -1.252  H432  O5W  69  
O5W  H181  H29  H   0  0  N  N  N   -9.300   -9.599   9.348  -4.279   6.708   2.460  H181  O5W  70  
O5W  H391  H31  H   0  0  N  N  N  -14.356   -6.197   0.567   6.645   3.199  -2.721  H391  O5W  71  
#   #
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
O5W  C31  C32   DOUB  N  N   1  
O5W  C31  N30   SING  N  N   2  
O5W  C32  C33   SING  N  N   3  
O5W  C32  C38   SING  N  N   4  
O5W  C01  N02   SING  N  N   5  
O5W  C03  C04   SING  Y  N   6  
O5W  C03  N02   DOUB  Y  N   7  
O5W  C03  N43   SING  N  N   8  
O5W  C04  C05   DOUB  Y  N   9  
O5W  C04  N08   SING  Y  N  10  
O5W  C05  N06   SING  Y  N  11  
O5W  C05  N41   SING  Y  N  12  
O5W  C07  N06   SING  Y  N  13  
O5W  C07  N08   DOUB  Y  N  14  
O5W  C09  C10   SING  N  N  15  
O5W  C09  N06   SING  N  N  16  
O5W  C09  O13   SING  N  N  17  
O5W  C10  C11   SING  N  N  18  
O5W  C11  C12   SING  N  N  19  
O5W  C11  O20   SING  N  N  20  
O5W  C12  C14   SING  N  N  21  
O5W  C14  O15   SING  N  N  22  
O5W  C24  C25   SING  N  N  23  
O5W  C24  O23   SING  N  N  24  
O5W  C25  C26   SING  N  N  25  
O5W  C25  O29   SING  N  N  26  
O5W  C26  C27   SING  N  N  27  
O5W  C26  O39   SING  N  N  28  
O5W  C27  C28   SING  N  N  29  
O5W  C28  N30   SING  N  N  30  
O5W  C28  O29   SING  N  N  31  
O5W  C33  N34   SING  N  N  32  
O5W  C33  O37   DOUB  N  N  33  
O5W  C35  N30   SING  N  N  34  
O5W  C35  N34   SING  N  N  35  
O5W  C35  O36   DOUB  N  N  36  
O5W  C42  N02   SING  Y  N  37  
O5W  C42  N41   DOUB  Y  N  38  
O5W  O15  P16   SING  N  N  39  
O5W  O17  P16   DOUB  N  N  40  
O5W  O18  P16   SING  N  N  41  
O5W  O19  P16   DOUB  N  N  42  
O5W  O20  P21   SING  N  N  43  
O5W  O22  P21   DOUB  N  N  44  
O5W  O23  P21   SING  N  N  45  
O5W  O40  P21   DOUB  N  N  46  
O5W  C31  H311  SING  N  N  47  
O5W  C01  H012  SING  N  N  48  
O5W  C01  H011  SING  N  N  49  
O5W  C01  H013  SING  N  N  50  
O5W  C07  H071  SING  N  N  51  
O5W  C09  H091  SING  N  N  52  
O5W  C10  H101  SING  N  N  53  
O5W  C10  H102  SING  N  N  54  
O5W  C11  H111  SING  N  N  55  
O5W  C12  H1    SING  N  N  56  
O5W  C14  H141  SING  N  N  57  
O5W  C14  H142  SING  N  N  58  
O5W  C24  H242  SING  N  N  59  
O5W  C24  H241  SING  N  N  60  
O5W  C25  H251  SING  N  N  61  
O5W  C26  H261  SING  N  N  62  
O5W  C27  H272  SING  N  N  63  
O5W  C27  H271  SING  N  N  64  
O5W  C28  H281  SING  N  N  65  
O5W  C38  H383  SING  N  N  66  
O5W  C38  H382  SING  N  N  67  
O5W  C38  H381  SING  N  N  68  
O5W  C42  H421  SING  N  N  69  
O5W  N34  H341  SING  N  N  70  
O5W  N43  H431  SING  N  N  71  
O5W  N43  H432  SING  N  N  72  
O5W  O18  H181  SING  N  N  73  
O5W  O39  H391  SING  N  N  74  
O5W  C12  O13   SING  N  N  75  
#   #
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
O5W  InChI             InChI                 1.03   "InChI=1S/C21H27N7O13P2/c1-10-5-27(21(31)25-20(10)30)15-3-11(29)13(39-15)6-38-43(35,36)41-12-4-16(40-14(12)7-37-42(32,33)34)28-9-23-17-18(22)26(2)8-24-19(17)28/h5,8-9,11-16,22,29H,3-4,6-7H2,1-2H3,(H2,25,30,31,32,33,34)/q-2/p+1/t11-,12-,13+,14+,15+,16+/m0/s1"  
O5W  InChIKey          InChI                 1.03   AESRSXSUEFZXFW-KPRKPIBOSA-O  
O5W  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P-](=O)(=O)O[C@H]3C[C@@H](O[C@@H]3CO[P-](O)(=O)=O)n4cnc5c(N)[n+](C)cnc45)O2)C(=O)NC1=O"  
O5W  SMILES            CACTVS                3.385  "CC1=CN([CH]2C[CH](O)[CH](CO[P-](=O)(=O)O[CH]3C[CH](O[CH]3CO[P-](O)(=O)=O)n4cnc5c(N)[n+](C)cnc45)O2)C(=O)NC1=O"  
O5W  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P-](=O)(=O)O[C@H]3C[C@@H](O[C@@H]3CO[P-](=O)(=O)O)n4cnc5c4nc[n+](c5N)C)O"  
O5W  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO[P-](=O)(=O)OC3CC(OC3CO[P-](=O)(=O)O)n4cnc5c4nc[n+](c5N)C)O"  
#
_pdbx_chem_comp_identifier.comp_id          O5W
_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       "1-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-1-ium-9-yl)-2-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]oxolan-3-yl]oxy-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
O5W  "Create component"  2020-02-10  PDBE  
O5W  "Initial release"   2020-09-09  RCSB  
O5W  "Modify synonyms"   2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     O5W
_pdbx_chem_comp_synonyms.name        "[(1~{R},3~{R})-1-(6-azanyl-1-methyl-purin-9-yl)-1-oxidanyl-5-phosphonooxy-pentan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
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