data_P5E
#

_chem_comp.id                                   P5E
_chem_comp.name                                 "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H15 N2 O14 P3 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-04-15
_chem_comp.pdbx_modified_date                   2020-12-04
_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                       500.207
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    P5E
_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       6YMW
_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
P5E  PA     P1   P  0  1  N  N  S  45.603  61.322  69.959  -1.504  -1.568   0.612  PA     P5E   1  
P5E  O2A    O1   O  0  1  N  N  N  44.606  60.373  70.521  -1.401  -1.250   2.054  O2A    P5E   2  
P5E  O3A    O2   O  0  1  N  N  N  44.793  62.476  69.124  -2.547  -0.560  -0.087  O3A    P5E   3  
P5E  "O5'"  O3   O  0  1  N  N  N  46.393  62.017  71.224  -0.058  -1.408  -0.077  "O5'"  P5E   4  
P5E  PB     P2   P  0  1  N  N  N  43.304  62.966  69.592  -4.109  -0.238   0.132  PB     P5E   5  
P5E  O1B    O4   O  0  1  N  N  N  43.324  64.399  69.910  -4.388  -0.110   1.579  O1B    P5E   6  
P5E  O2B    O5   O  0  1  N  N  N  42.904  62.194  70.784  -4.994  -1.435  -0.481  O2B    P5E   7  
P5E  O3B    O6   O  0  1  N  N  N  42.201  62.665  68.392  -4.482   1.140  -0.612  O3B    P5E   8  
P5E  PG     P3   P  0  1  N  N  N  41.051  61.489  68.561  -5.684   2.201  -0.464  PG     P5E   9  
P5E  O1G    O7   O  0  1  N  N  N  39.917  62.015  69.390  -7.022   1.590  -1.120  O1G    P5E  10  
P5E  O2G    O8   O  0  1  N  N  N  40.535  61.094  67.210  -5.922   2.480   0.970  O2G    P5E  11  
P5E  O3G    O9   O  0  1  N  N  N  41.647  60.337  69.211  -5.291   3.567  -1.220  O3G    P5E  12  
P5E  "C5'"  C1   C  0  1  N  N  N  45.716  62.063  72.419   1.107  -2.092   0.389  "C5'"  P5E  13  
P5E  "C4'"  C2   C  0  1  N  N  R  46.514  62.908  73.486   2.304  -1.717  -0.487  "C4'"  P5E  14  
P5E  "O4'"  O10  O  0  1  N  N  N  47.959  63.251  72.974   2.681  -0.341  -0.261  "O4'"  P5E  15  
P5E  "C1'"  C3   C  0  1  N  N  R  47.994  64.764  72.883   4.048  -0.242  -0.717  "C1'"  P5E  16  
P5E  "C2'"  C4   C  0  1  N  N  R  46.720  65.125  72.789   4.720  -1.546  -0.235  "C2'"  P5E  17  
P5E  "O2'"  O11  O  0  1  N  N  N  46.549  66.404  73.408   5.651  -2.019  -1.210  "O2'"  P5E  18  
P5E  "C3'"  C5   C  0  1  N  N  S  45.926  64.046  73.679   3.547  -2.539  -0.080  "C3'"  P5E  19  
P5E  "O3'"  O12  O  0  1  N  N  N  46.046  64.415  75.085   3.717  -3.656  -0.955  "O3'"  P5E  20  
P5E  N1     N1   N  0  1  N  N  N  48.752  65.158  71.671   4.701   0.924  -0.117  N1     P5E  21  
P5E  C6     C6   C  0  1  N  N  N  48.613  64.449  70.549   4.698   1.078   1.243  C6     P5E  22  
P5E  C2     C7   C  0  1  N  N  N  49.590  66.222  71.704   5.305   1.830  -0.908  C2     P5E  23  
P5E  O2     O13  O  0  1  N  N  N  49.721  66.845  72.698   5.300   1.671  -2.113  O2     P5E  24  
P5E  N3     N2   N  0  1  N  N  N  50.278  66.569  70.602   5.913   2.910  -0.383  N3     P5E  25  
P5E  C4     C8   C  0  1  N  N  N  50.137  65.882  69.505   5.928   3.101   0.952  C4     P5E  26  
P5E  O4     O14  O  0  1  N  N  N  50.730  66.182  68.557   6.478   4.077   1.427  O4     P5E  27  
P5E  C5     C9   C  0  1  N  N  N  49.284  64.786  69.468   5.305   2.150   1.796  C5     P5E  28  
P5E  S1A    S1   S  0  1  N  N  N  46.590  60.753  68.978  -2.183  -3.563   0.376  S1A    P5E  29  
P5E  H1     H1   H  0  1  N  N  N  42.743  62.788  71.508  -4.862  -1.577  -1.429  H1     P5E  30  
P5E  H2     H2   H  0  1  N  N  N  39.114  61.986  68.883  -6.939   1.382  -2.061  H2     P5E  31  
P5E  H3     H3   H  0  1  N  N  N  41.581  59.581  68.639  -5.971   4.252  -1.172  H3     P5E  32  
P5E  H4     H4   H  0  1  N  N  N  44.731  62.525  72.257   1.308  -1.804   1.421  H4     P5E  33  
P5E  H5     H5   H  0  1  N  N  N  45.583  61.039  72.797   0.942  -3.168   0.338  H5     P5E  34  
P5E  H6     H6   H  0  1  N  N  N  46.601  62.313  74.407   2.069  -1.880  -1.539  H6     P5E  35  
P5E  H7     H7   H  0  1  N  N  N  48.481  65.174  73.780   4.081  -0.177  -1.804  H7     P5E  36  
P5E  H8     H8   H  0  1  N  N  N  46.329  65.110  71.761   5.218  -1.388   0.722  H8     P5E  37  
P5E  H9     H9   H  0  1  N  N  N  45.639  66.668  73.344   6.103  -2.836  -0.958  H9     P5E  38  
P5E  H10    H10  H  0  1  N  N  N  44.870  64.047  73.369   3.462  -2.872   0.954  H10    P5E  39  
P5E  H11    H11  H  0  1  N  N  N  45.580  63.783  75.620   4.484  -4.207  -0.745  H11    P5E  40  
P5E  H12    H12  H  0  1  N  N  N  47.949  63.597  70.528   4.211   0.347   1.870  H12    P5E  41  
P5E  H13    H13  H  0  1  N  N  N  50.897  67.354  70.625   6.344   3.553  -0.968  H13    P5E  42  
P5E  H14    H14  H  0  1  N  N  N  49.172  64.214  68.558   5.306   2.286   2.867  H14    P5E  43  
P5E  H15    H15  H  0  1  N  N  N  46.230  59.505  68.926  -2.228  -3.711  -0.960  H15    P5E  44  
#   #
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
P5E  O2G    PG     DOUB  N  N   1  
P5E  O3B    PG     SING  N  N   2  
P5E  O3B    PB     SING  N  N   3  
P5E  O4     C4     DOUB  N  N   4  
P5E  PG     O3G    SING  N  N   5  
P5E  PG     O1G    SING  N  N   6  
P5E  S1A    PA     SING  N  N   7  
P5E  O3A    PB     SING  N  N   8  
P5E  O3A    PA     SING  N  N   9  
P5E  C5     C4     SING  N  N  10  
P5E  C5     C6     DOUB  N  N  11  
P5E  C4     N3     SING  N  N  12  
P5E  PB     O1B    DOUB  N  N  13  
P5E  PB     O2B    SING  N  N  14  
P5E  PA     O2A    DOUB  N  N  15  
P5E  PA     "O5'"  SING  N  N  16  
P5E  C6     N1     SING  N  N  17  
P5E  N3     C2     SING  N  N  18  
P5E  "O5'"  "C5'"  SING  N  N  19  
P5E  N1     C2     SING  N  N  20  
P5E  N1     "C1'"  SING  N  N  21  
P5E  C2     O2     DOUB  N  N  22  
P5E  "C5'"  "C4'"  SING  N  N  23  
P5E  "C2'"  "C1'"  SING  N  N  24  
P5E  "C2'"  "O2'"  SING  N  N  25  
P5E  "C2'"  "C3'"  SING  N  N  26  
P5E  "C1'"  "O4'"  SING  N  N  27  
P5E  "O4'"  "C4'"  SING  N  N  28  
P5E  "C4'"  "C3'"  SING  N  N  29  
P5E  "C3'"  "O3'"  SING  N  N  30  
P5E  O2B    H1     SING  N  N  31  
P5E  O1G    H2     SING  N  N  32  
P5E  O3G    H3     SING  N  N  33  
P5E  "C5'"  H4     SING  N  N  34  
P5E  "C5'"  H5     SING  N  N  35  
P5E  "C4'"  H6     SING  N  N  36  
P5E  "C1'"  H7     SING  N  N  37  
P5E  "C2'"  H8     SING  N  N  38  
P5E  "O2'"  H9     SING  N  N  39  
P5E  "C3'"  H10    SING  N  N  40  
P5E  "O3'"  H11    SING  N  N  41  
P5E  C6     H12    SING  N  N  42  
P5E  N3     H13    SING  N  N  43  
P5E  C5     H14    SING  N  N  44  
P5E  S1A    H15    SING  N  N  45  
#   #
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
P5E  InChI             InChI                 1.03   "InChI=1S/C9H15N2O14P3S/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(23-8)3-22-28(21,29)25-27(19,20)24-26(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,29)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-,28+/m1/s1"  
P5E  InChIKey          InChI                 1.03   BWPNYQWDXHLOGU-KWWYXVLOSA-N  
P5E  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@@](S)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"  
P5E  SMILES            CACTVS                3.385  "O[CH]1[CH](O)[CH](O[CH]1CO[P](S)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"  
P5E  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(OP(=O)(O)OP(=O)(O)O)S)O)O"  
P5E  SMILES            "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(OP(=O)(O)OP(=O)(O)O)S)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          P5E
_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})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-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
P5E  "Create component"  2020-04-15  PDBE  
P5E  "Initial release"   2020-12-09  RCSB  
##
