data_XY7
#

_chem_comp.id                                   XY7
_chem_comp.name                                 "1-[2-deoxy-5-O-(dihydroxyphosphanyl)-2-fluoro-beta-L-ribofuranosyl]pyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H12 F N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-01-19
_chem_comp.pdbx_modified_date                   2021-08-27
_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                       310.173
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XY7
_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       7KW4
_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
XY7  C4     C1   C  0  1  N  N  N  -19.769   7.333  11.815   4.242  -1.705   0.189  C4     XY7   1  
XY7  N3     N1   N  0  1  N  N  N  -20.048   8.141  12.903   2.969  -2.143   0.120  N3     XY7   2  
XY7  C2     C2   C  0  1  N  N  N  -19.119   8.446  13.876   1.968  -1.280  -0.137  C2     XY7   3  
XY7  N1     N2   N  0  1  N  N  N  -17.860   7.925  13.760   2.215   0.028  -0.329  N1     XY7   4  
XY7  C6     C3   C  0  1  N  N  N  -17.541   7.084  12.671   3.493   0.513  -0.267  C6     XY7   5  
XY7  C5     C4   C  0  1  N  N  N  -18.467   6.795  11.706   4.516  -0.330  -0.011  C5     XY7   6  
XY7  O4     O1   O  0  1  N  N  N  -20.657   7.104  11.018   5.148  -2.484   0.426  O4     XY7   7  
XY7  O2     O2   O  0  1  N  N  N  -19.374   9.219  14.785   0.825  -1.690  -0.197  O2     XY7   8  
XY7  "C1'"  C5   C  0  1  N  N  S  -16.905   8.212  14.837   1.105   0.943  -0.606  "C1'"  XY7   9  
XY7  "O4'"  O3   O  0  1  N  N  N  -15.832   7.240  14.772  -0.157   0.244  -0.545  "O4'"  XY7  10  
XY7  "C2'"  C6   C  0  1  N  N  S  -16.286   9.555  14.701   0.985   2.012   0.510  "C2'"  XY7  11  
XY7  "F2'"  F1   F  0  1  N  N  N  -15.898   9.993  15.916   1.822   3.102   0.249  "F2'"  XY7  12  
XY7  "C3'"  C7   C  0  1  N  N  S  -15.084   9.237  13.793  -0.504   2.421   0.409  "C3'"  XY7  13  
XY7  "O3'"  O4   O  0  1  N  N  N  -14.095  10.266  13.787  -0.643   3.619  -0.358  "O3'"  XY7  14  
XY7  "C4'"  C8   C  0  1  N  N  S  -14.596   7.959  14.500  -1.174   1.234  -0.317  "C4'"  XY7  15  
XY7  "C5'"  C9   C  0  1  N  N  N  -13.665   7.084  13.639  -2.284   0.648   0.559  "C5'"  XY7  16  
XY7  "O5'"  O5   O  0  1  N  N  N  -14.251   6.908  12.354  -2.974  -0.372  -0.166  "O5'"  XY7  17  
XY7  P      P1   P  0  1  N  N  N  -13.492   6.096  11.234  -4.206  -1.205   0.451  P      XY7  18  
XY7  OP1    O6   O  0  1  N  N  N  -14.274   6.324  10.002  -5.468  -0.299   0.029  OP1    XY7  19  
XY7  OP2    O7   O  0  1  N  N  N  -12.067   6.438  11.259  -4.322  -2.440  -0.575  OP2    XY7  20  
XY7  H1     H1   H  0  1  N  N  N  -20.968   8.523  12.988   2.773  -3.083   0.255  H1     XY7  21  
XY7  H2     H2   H  0  1  N  N  N  -16.550   6.662  12.599   3.682   1.565  -0.422  H2     XY7  22  
XY7  H3     H3   H  0  1  N  N  N  -18.206   6.163  10.870   5.530   0.039   0.041  H3     XY7  23  
XY7  H4     H4   H  0  1  N  N  N  -17.414   8.142  15.810   1.234   1.417  -1.579  H4     XY7  24  
XY7  H5     H5   H  0  1  N  N  N  -16.969  10.250  14.191   1.205   1.580   1.487  H5     XY7  25  
XY7  H6     H6   H  0  1  N  N  N  -15.430   8.998  12.777  -0.933   2.552   1.403  H6     XY7  26  
XY7  H7     H7   H  0  1  N  N  N  -14.438  11.033  13.343  -0.240   4.397   0.051  H7     XY7  27  
XY7  H8     H8   H  0  1  N  N  N  -14.087   8.228  15.437  -1.588   1.567  -1.269  H8     XY7  28  
XY7  H9     H9   H  0  1  N  N  N  -13.531   6.104  14.120  -1.847   0.221   1.461  H9     XY7  29  
XY7  H10    H10  H  0  1  N  N  N  -12.688   7.578  13.534  -2.985   1.437   0.833  H10    XY7  30  
XY7  H11    H11  H  0  1  N  N  N  -15.174   6.054  10.143  -5.564   0.509   0.551  H11    XY7  31  
XY7  H12    H12  H  0  1  N  N  N  -11.707   6.235  12.114  -5.028  -3.065  -0.360  H12    XY7  32  
#   #
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
XY7  OP1    P      SING  N  N   1  
XY7  O4     C4     DOUB  N  N   2  
XY7  P      OP2    SING  N  N   3  
XY7  P      "O5'"  SING  N  N   4  
XY7  C5     C4     SING  N  N   5  
XY7  C5     C6     DOUB  N  N   6  
XY7  C4     N3     SING  N  N   7  
XY7  "O5'"  "C5'"  SING  N  N   8  
XY7  C6     N1     SING  N  N   9  
XY7  N3     C2     SING  N  N  10  
XY7  "C5'"  "C4'"  SING  N  N  11  
XY7  N1     C2     SING  N  N  12  
XY7  N1     "C1'"  SING  N  N  13  
XY7  "O3'"  "C3'"  SING  N  N  14  
XY7  "C3'"  "C4'"  SING  N  N  15  
XY7  "C3'"  "C2'"  SING  N  N  16  
XY7  C2     O2     DOUB  N  N  17  
XY7  "C4'"  "O4'"  SING  N  N  18  
XY7  "C2'"  "C1'"  SING  N  N  19  
XY7  "C2'"  "F2'"  SING  N  N  20  
XY7  "O4'"  "C1'"  SING  N  N  21  
XY7  N3     H1     SING  N  N  22  
XY7  C6     H2     SING  N  N  23  
XY7  C5     H3     SING  N  N  24  
XY7  "C1'"  H4     SING  N  N  25  
XY7  "C2'"  H5     SING  N  N  26  
XY7  "C3'"  H6     SING  N  N  27  
XY7  "O3'"  H7     SING  N  N  28  
XY7  "C4'"  H8     SING  N  N  29  
XY7  "C5'"  H9     SING  N  N  30  
XY7  "C5'"  H10    SING  N  N  31  
XY7  OP1    H11    SING  N  N  32  
XY7  OP2    H12    SING  N  N  33  
#   #
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
XY7  SMILES            ACDLabs               12.01  "C2(NC(=O)N(C1OC(C(C1F)O)COP(O)O)C=C2)=O"  
XY7  InChI             InChI                 1.03   "InChI=1S/C9H12FN2O7P/c10-6-7(14)4(3-18-20(16)17)19-8(6)12-2-1-5(13)11-9(12)15/h1-2,4,6-8,14,16-17H,3H2,(H,11,13,15)/t4-,6-,7-,8-/m0/s1"  
XY7  InChIKey          InChI                 1.03   SAPVPALVILMUHE-PSQAKQOGSA-N  
XY7  SMILES_CANONICAL  CACTVS                3.385  "O[C@@H]1[C@H](F)[C@H](O[C@H]1COP(O)O)N2C=CC(=O)NC2=O"  
XY7  SMILES            CACTVS                3.385  "O[CH]1[CH](F)[CH](O[CH]1COP(O)O)N2C=CC(=O)NC2=O"  
XY7  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)F"  
XY7  SMILES            "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(O)O)O)F"  
#   #
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
XY7  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-[2-deoxy-5-O-(dihydroxyphosphanyl)-2-fluoro-beta-L-ribofuranosyl]pyrimidine-2,4(1H,3H)-dione"  
XY7  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{S},3~{S},4~{S},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XY7  "Create component"  2021-01-19  RCSB  
XY7  "Initial release"   2021-09-01  RCSB  
##
