data_XC
#

_chem_comp.id                                   XC
_chem_comp.name                                 "[(2~{R},3~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-4,5-dihydropyrimidin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H16 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-01-12
_chem_comp.pdbx_modified_date                   2021-01-22
_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                       309.213
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XC
_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       7BFS
_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
XC  P       P1   P  0  1  N  N  N  38.977  33.367  16.850   4.012  -0.931  -0.007  P       XC   1  
XC  O1P     O1   O  0  1  N  N  N  40.117  33.925  16.239   5.077   0.062   0.257  O1P     XC   2  
XC  O2P     O2   O  0  1  N  N  N  37.641  33.976  16.702   3.637  -1.692   1.362  O2P     XC   3  
XC  "O5'"   O3   O  0  1  N  N  N  38.931  31.857  16.376   2.707  -0.181  -0.579  "O5'"   XC   4  
XC  "C5'"   C1   C  0  1  N  N  N  37.874  30.958  16.727   2.070   0.900   0.104  "C5'"   XC   5  
XC  "C4'"   C2   C  0  1  N  N  R  38.126  29.580  16.081   0.866   1.379  -0.710  "C4'"   XC   6  
XC  "O4'"   O4   O  0  1  N  N  N  39.111  28.899  16.886  -0.181   0.384  -0.693  "O4'"   XC   7  
XC  "C1'"   C3   C  0  1  N  N  R  38.942  27.477  16.705  -1.389   1.098  -1.032  "C1'"   XC   8  
XC  N1      N1   N  0  1  N  N  N  39.467  26.821  17.956  -2.566   0.350  -0.584  N1      XC   9  
XC  C6      C4   C  0  1  N  N  N  38.607  26.492  19.030  -3.632   0.029  -1.537  C6      XC  10  
XC  C5      C5   C  0  1  N  N  N  39.064  25.772  20.071  -4.208  -1.350  -1.202  C5      XC  11  
XC  C4      C6   C  0  1  N  N  N  40.402  25.372  20.069  -4.455  -1.439   0.282  C4      XC  12  
XC  N4      N2   N  0  1  N  N  N  40.920  24.675  21.052  -5.489  -2.174   0.747  N4      XC  13  
XC  N3      N3   N  0  1  N  N  N  41.212  25.605  19.067  -3.678  -0.809   1.122  N3      XC  14  
XC  C2      C7   C  0  1  N  N  N  40.762  26.330  18.045  -2.660  -0.044   0.698  C2      XC  15  
XC  O2      O5   O  0  1  N  N  N  41.688  26.737  17.282  -1.806   0.305   1.492  O2      XC  16  
XC  "C3'"   C8   C  0  1  N  N  R  36.869  28.678  16.154   0.235   2.628  -0.055  "C3'"   XC  17  
XC  "C2'"   C9   C  0  1  N  N  N  37.430  27.252  16.317  -1.283   2.438  -0.271  "C2'"   XC  18  
XC  "O3'"   O6   O  0  1  N  N  N  36.094  28.955  17.335   0.541   2.669   1.340  "O3'"   XC  19  
XC  O1      O7   O  0  1  N  Y  N  39.305  33.203  18.409   4.534  -2.001  -1.090  O1      XC  20  
XC  H1      H1   H  0  1  N  N  N  37.705  34.752  16.158   2.944  -2.359   1.263  H1      XC  21  
XC  "H5'2"  H2   H  0  0  N  N  N  36.916  31.361  16.366   1.733   0.563   1.085  "H5'2"  XC  22  
XC  "H5'1"  H3   H  0  0  N  N  N  37.836  30.847  17.821   2.776   1.721   0.225  "H5'1"  XC  23  
XC  "H4'"   H4   H  0  1  N  N  N  38.455  29.697  15.038   1.166   1.599  -1.735  "H4'"   XC  24  
XC  "H1'"   H5   H  0  1  N  N  N  39.556  27.144  15.855  -1.438   1.273  -2.107  "H1'"   XC  25  
XC  H6      H6   H  0  1  N  N  N  38.238  27.443  19.442  -4.420   0.779  -1.468  H6      XC  26  
XC  H2      H7   H  0  1  N  N  N  37.767  25.927  18.600  -3.226   0.018  -2.548  H2      XC  27  
XC  H3      H8   H  0  1  N  N  N  38.907  26.376  20.977  -5.147  -1.492  -1.737  H3      XC  28  
XC  H5      H9   H  0  1  N  N  N  38.452  24.859  20.128  -3.499  -2.122  -1.501  H5      XC  29  
XC  H41     H10  H  0  1  N  N  N  41.869  24.364  20.999  -6.069  -2.642   0.126  H41     XC  30  
XC  H42     H11  H  0  1  N  N  N  40.366  24.454  21.855  -5.651  -2.233   1.701  H42     XC  31  
XC  "H3'"   H12  H  0  1  N  N  N  36.274  28.762  15.232   0.582   3.535  -0.550  "H3'"   XC  32  
XC  "H2'2"  H13  H  0  0  N  N  N  36.898  26.712  17.114  -1.687   3.252  -0.873  "H2'2"  XC  33  
XC  "H2'1"  H14  H  0  0  N  N  N  37.348  26.690  15.375  -1.800   2.376   0.686  "H2'1"  XC  34  
XC  H4      H15  H  0  1  N  N  N  35.331  28.389  17.354   0.169   3.433   1.802  H4      XC  35  
XC  H7      H16  H  0  1  N  N  N  40.186  33.514  18.582   5.319  -2.492  -0.812  H7      XC  36  
#   #
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
XC  "C4'"  "C3'"   SING  N  N   1  
XC  "C4'"  "C5'"   SING  N  N   2  
XC  "C4'"  "O4'"   SING  N  N   3  
XC  "C3'"  "C2'"   SING  N  N   4  
XC  "C3'"  "O3'"   SING  N  N   5  
XC  O1P    P       DOUB  N  N   6  
XC  "C2'"  "C1'"   SING  N  N   7  
XC  "O5'"  "C5'"   SING  N  N   8  
XC  "O5'"  P       SING  N  N   9  
XC  O2P    P       SING  N  N  10  
XC  "C1'"  "O4'"   SING  N  N  11  
XC  "C1'"  N1      SING  N  N  12  
XC  O2     C2      DOUB  N  N  13  
XC  N1     C2      SING  N  N  14  
XC  N1     C6      SING  N  N  15  
XC  C2     N3      SING  N  N  16  
XC  C6     C5      SING  N  N  17  
XC  N3     C4      DOUB  N  N  18  
XC  C4     C5      SING  N  N  19  
XC  C4     N4      SING  N  N  20  
XC  P      O1      SING  N  N  21  
XC  O2P    H1      SING  N  N  22  
XC  "C5'"  "H5'2"  SING  N  N  23  
XC  "C5'"  "H5'1"  SING  N  N  24  
XC  "C4'"  "H4'"   SING  N  N  25  
XC  "C1'"  "H1'"   SING  N  N  26  
XC  C6     H6      SING  N  N  27  
XC  C6     H2      SING  N  N  28  
XC  C5     H3      SING  N  N  29  
XC  C5     H5      SING  N  N  30  
XC  N4     H41     SING  N  N  31  
XC  N4     H42     SING  N  N  32  
XC  "C3'"  "H3'"   SING  N  N  33  
XC  "C2'"  "H2'2"  SING  N  N  34  
XC  "C2'"  "H2'1"  SING  N  N  35  
XC  "O3'"  H4      SING  N  N  36  
XC  O1     H7      SING  N  N  37  
#   #
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
XC  InChI             InChI                 1.03   "InChI=1S/C9H16N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h5-6,8,13H,1-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6-,8-/m1/s1"  
XC  InChIKey          InChI                 1.03   RARHVLRQJXIMCB-ATRFCDNQSA-N  
XC  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)N(CC1)[C@H]2C[C@@H](O)[C@@H](CO[P](O)(O)=O)O2"  
XC  SMILES            CACTVS                3.385  "NC1=NC(=O)N(CC1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"  
XC  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1CN(C(=O)N=C1N)[C@H]2C[C@H]([C@H](O2)COP(=O)(O)O)O"  
XC  SMILES            "OpenEye OEToolkits"  2.0.7  "C1CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          XC
_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~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-4,5-dihydropyrimidin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl 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
XC  "Create component"  2021-01-12  PDBE  
XC  "Initial release"   2021-01-27  RCSB  
##
