data_QGJ
#

_chem_comp.id                                   QGJ
_chem_comp.name                                 "1-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-2,4-dioxo-N-(3-phenylpropyl)-1,2,3,4-tetrahydropyrimidine-5-carboxamide"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C19 H24 N3 O9 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-10-28
_chem_comp.pdbx_modified_date                   2021-10-29
_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                       469.382
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    QGJ
_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       6USL
_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
QGJ  "C1'"  C1   C  0  1  N  N  R  22.604  -29.791  -39.458    2.456   1.552  -0.885  "C1'"  QGJ   1  
QGJ  C2     C2   C  0  1  N  N  N  20.984  -28.022  -38.880    1.174   0.899   1.065  C2     QGJ   2  
QGJ  "C2'"  C3   C  0  1  N  N  N  22.594  -31.105  -40.231    3.024   2.848  -0.274  "C2'"  QGJ   3  
QGJ  "C3'"  C4   C  0  1  N  N  R  23.704  -31.617  -39.419    4.412   2.433   0.272  "C3'"  QGJ   4  
QGJ  C4     C5   C  0  1  N  N  N  20.160  -26.505  -40.650   -1.139   0.561   1.060  C4     QGJ   5  
QGJ  "C4'"  C6   C  0  1  N  N  R  24.717  -30.509  -39.403    4.710   1.148  -0.541  "C4'"  QGJ   6  
QGJ  C5     C7   C  0  1  N  N  N  21.058  -27.245  -41.634   -1.156   0.908  -0.370  C5     QGJ   7  
QGJ  "C5'"  C8   C  0  1  N  N  N  25.820  -30.485  -40.439    5.695   0.251   0.211  "C5'"  QGJ   8  
QGJ  C6     C9   C  0  1  N  N  N  21.806  -28.276  -41.239    0.043   1.226  -0.976  C6     QGJ   9  
QGJ  CAP    C10  C  0  1  N  N  N  21.233  -27.018  -43.127   -2.414   0.910  -1.133  CAP    QGJ  10  
QGJ  CAR    C11  C  0  1  N  N  N  19.801  -25.015  -43.872   -4.783   0.384  -1.344  CAR    QGJ  11  
QGJ  CAT    C12  C  0  1  N  N  N  19.186  -24.850  -45.282   -5.923  -0.115  -0.453  CAT    QGJ  12  
QGJ  CAU    C13  C  0  1  N  N  N  17.837  -25.621  -45.201   -7.206  -0.224  -1.279  CAU    QGJ  13  
QGJ  CAV    C14  C  0  1  Y  N  N  17.732  -26.726  -46.261   -8.328  -0.715  -0.401  CAV    QGJ  14  
QGJ  CAW    C15  C  0  1  Y  N  N  17.722  -26.375  -47.609   -8.563  -2.071  -0.273  CAW    QGJ  15  
QGJ  CAX    C16  C  0  1  Y  N  N  17.609  -27.359  -48.579   -9.589  -2.522   0.536  CAX    QGJ  16  
QGJ  CAY    C17  C  0  1  Y  N  N  17.491  -28.695  -48.179  -10.380  -1.616   1.218  CAY    QGJ  17  
QGJ  CAZ    C18  C  0  1  Y  N  N  17.472  -29.040  -46.818  -10.145  -0.260   1.091  CAZ    QGJ  18  
QGJ  CBA    C19  C  0  1  Y  N  N  17.598  -28.049  -45.846   -9.119   0.191   0.281  CBA    QGJ  19  
QGJ  N1     N1   N  0  1  N  N  N  21.792  -28.738  -39.860    1.185   1.214  -0.240  N1     QGJ  20  
QGJ  N3     N2   N  0  1  N  N  N  20.157  -26.916  -39.296    0.042   0.575   1.712  N3     QGJ  21  
QGJ  NAQ    N3   N  0  1  N  N  N  20.709  -26.086  -44.097   -3.555   0.488  -0.553  NAQ    QGJ  22  
QGJ  O2     O1   O  0  1  N  N  N  21.000  -28.421  -37.758    2.223   0.902   1.679  O2     QGJ  23  
QGJ  "O3'"  O2   O  0  1  N  N  N  24.250  -32.978  -39.652    4.346   2.148   1.670  "O3'"  QGJ  24  
QGJ  O4     O3   O  0  1  N  N  N  19.505  -25.587  -40.990   -2.168   0.268   1.641  O4     QGJ  25  
QGJ  "O4'"  O4   O  0  1  N  N  N  24.004  -29.216  -39.471    3.419   0.511  -0.650  "O4'"  QGJ  26  
QGJ  "O5'"  O5   O  0  1  N  N  N  25.360  -29.999  -41.637    6.042  -0.868  -0.609  "O5'"  QGJ  27  
QGJ  OAS    O6   O  0  1  N  N  N  21.971  -27.761  -43.617   -2.424   1.292  -2.288  OAS    QGJ  28  
QGJ  OP1    O7   O  0  1  N  N  N  25.641  -29.976  -44.165    6.597  -2.590   1.151  OP1    QGJ  29  
QGJ  OP2    O8   O  0  1  N  N  N  26.783  -31.786  -42.954    7.116  -3.181  -1.248  OP2    QGJ  30  
QGJ  P      P1   P  0  1  N  N  N  26.274  -30.400  -42.970    7.061  -2.020  -0.134  P      QGJ  31  
QGJ  O1     O9   O  0  1  N  Y  N  27.463  -29.454  -42.971    8.531  -1.391   0.058  O1     QGJ  32  
QGJ  H1     H1   H  0  1  N  N  N  22.367  -30.035  -38.412    2.305   1.683  -1.956  H1     QGJ  33  
QGJ  H2     H2   H  0  1  N  N  N  21.661  -31.678  -40.123    3.129   3.616  -1.040  H2     QGJ  34  
QGJ  H3     H3   H  0  1  N  N  N  22.836  -30.996  -41.298    2.385   3.200   0.536  H3     QGJ  35  
QGJ  H4     H4   H  0  1  N  N  N  23.312  -31.646  -38.392    5.156   3.203   0.068  H4     QGJ  36  
QGJ  H5     H5   H  0  1  N  N  N  25.212  -30.550  -38.421    5.098   1.399  -1.528  H5     QGJ  37  
QGJ  H6     H6   H  0  1  N  N  N  26.197  -31.508  -40.587    6.594   0.819   0.449  H6     QGJ  38  
QGJ  H7     H7   H  0  1  N  N  N  26.637  -29.842  -40.080    5.234  -0.103   1.132  H7     QGJ  39  
QGJ  H8     H8   H  0  1  N  N  N  22.436  -28.779  -41.958    0.073   1.487  -2.024  H8     QGJ  40  
QGJ  H9     H9   H  0  1  N  N  N  20.324  -24.103  -43.550   -4.629  -0.319  -2.164  H9     QGJ  41  
QGJ  H10    H10  H  0  1  N  N  N  19.037  -25.282  -43.127   -5.040   1.363  -1.748  H10    QGJ  42  
QGJ  H11    H11  H  0  1  N  N  N  19.842  -25.290  -46.048   -5.666  -1.094  -0.049  H11    QGJ  43  
QGJ  H12    H12  H  0  1  N  N  N  19.015  -23.788  -45.512   -6.077   0.587   0.366  H12    QGJ  44  
QGJ  H13    H13  H  0  1  N  N  N  17.013  -24.908  -45.351   -7.462   0.755  -1.683  H13    QGJ  45  
QGJ  H14    H14  H  0  1  N  N  N  17.750  -26.078  -44.204   -7.052  -0.926  -2.098  H14    QGJ  46  
QGJ  H15    H15  H  0  1  N  N  N  17.802  -25.338  -47.898   -7.945  -2.779  -0.806  H15    QGJ  47  
QGJ  H16    H16  H  0  1  N  N  N  17.612  -27.099  -49.627   -9.773  -3.581   0.635  H16    QGJ  48  
QGJ  H17    H17  H  0  1  N  N  N  17.414  -29.470  -48.927  -11.182  -1.968   1.849  H17    QGJ  49  
QGJ  H18    H18  H  0  1  N  N  N  17.360  -30.073  -46.524  -10.762   0.448   1.623  H18    QGJ  50  
QGJ  H19    H19  H  0  1  N  N  N  17.592  -28.301  -44.796   -8.933   1.250   0.184  H19    QGJ  51  
QGJ  H20    H20  H  0  1  N  N  N  19.583  -26.441  -38.629    0.074   0.349   2.655  H20    QGJ  52  
QGJ  H21    H21  H  0  1  N  N  N  21.022  -26.208  -45.039   -3.562   0.254   0.388  H21    QGJ  53  
QGJ  H22    H22  H  0  1  N  N  N  24.959  -33.144  -39.042    4.074   2.901   2.213  H22    QGJ  54  
QGJ  H23    H23  H  0  1  N  N  N  26.599  -32.201  -43.788    7.712  -3.910  -1.028  H23    QGJ  55  
QGJ  H24    H24  H  0  1  N  N  N  27.421  -28.893  -43.737    8.899  -0.998  -0.745  H24    QGJ  56  
#   #
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
QGJ  CAX    CAY    DOUB  Y  N   1  
QGJ  CAX    CAW    SING  Y  N   2  
QGJ  CAY    CAZ    SING  Y  N   3  
QGJ  CAW    CAV    DOUB  Y  N   4  
QGJ  CAZ    CBA    DOUB  Y  N   5  
QGJ  CAV    CBA    SING  Y  N   6  
QGJ  CAV    CAU    SING  N  N   7  
QGJ  CAT    CAU    SING  N  N   8  
QGJ  CAT    CAR    SING  N  N   9  
QGJ  OP1    P      DOUB  N  N  10  
QGJ  NAQ    CAR    SING  N  N  11  
QGJ  NAQ    CAP    SING  N  N  12  
QGJ  OAS    CAP    DOUB  N  N  13  
QGJ  CAP    C5     SING  N  N  14  
QGJ  P      OP2    SING  N  N  15  
QGJ  P      "O5'"  SING  N  N  16  
QGJ  "O5'"  "C5'"  SING  N  N  17  
QGJ  C5     C6     DOUB  N  N  18  
QGJ  C5     C4     SING  N  N  19  
QGJ  C6     N1     SING  N  N  20  
QGJ  O4     C4     DOUB  N  N  21  
QGJ  C4     N3     SING  N  N  22  
QGJ  "C5'"  "C4'"  SING  N  N  23  
QGJ  "C2'"  "C1'"  SING  N  N  24  
QGJ  "C2'"  "C3'"  SING  N  N  25  
QGJ  N1     "C1'"  SING  N  N  26  
QGJ  N1     C2     SING  N  N  27  
QGJ  "O3'"  "C3'"  SING  N  N  28  
QGJ  "O4'"  "C1'"  SING  N  N  29  
QGJ  "O4'"  "C4'"  SING  N  N  30  
QGJ  "C3'"  "C4'"  SING  N  N  31  
QGJ  N3     C2     SING  N  N  32  
QGJ  C2     O2     DOUB  N  N  33  
QGJ  P      O1     SING  N  N  34  
QGJ  "C1'"  H1     SING  N  N  35  
QGJ  "C2'"  H2     SING  N  N  36  
QGJ  "C2'"  H3     SING  N  N  37  
QGJ  "C3'"  H4     SING  N  N  38  
QGJ  "C4'"  H5     SING  N  N  39  
QGJ  "C5'"  H6     SING  N  N  40  
QGJ  "C5'"  H7     SING  N  N  41  
QGJ  C6     H8     SING  N  N  42  
QGJ  CAR    H9     SING  N  N  43  
QGJ  CAR    H10    SING  N  N  44  
QGJ  CAT    H11    SING  N  N  45  
QGJ  CAT    H12    SING  N  N  46  
QGJ  CAU    H13    SING  N  N  47  
QGJ  CAU    H14    SING  N  N  48  
QGJ  CAW    H15    SING  N  N  49  
QGJ  CAX    H16    SING  N  N  50  
QGJ  CAY    H17    SING  N  N  51  
QGJ  CAZ    H18    SING  N  N  52  
QGJ  CBA    H19    SING  N  N  53  
QGJ  N3     H20    SING  N  N  54  
QGJ  NAQ    H21    SING  N  N  55  
QGJ  "O3'"  H22    SING  N  N  56  
QGJ  OP2    H23    SING  N  N  57  
QGJ  O1     H24    SING  N  N  58  
#   #
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
QGJ  SMILES            ACDLabs               12.01  "C1(CC(C(COP(=O)(O)O)O1)O)N2C(=O)NC(C(=C2)C(NCCCc3ccccc3)=O)=O"  
QGJ  InChI             InChI                 1.03   "InChI=1S/C19H24N3O9P/c23-14-9-16(31-15(14)11-30-32(27,28)29)22-10-13(18(25)21-19(22)26)17(24)20-8-4-7-12-5-2-1-3-6-12/h1-3,5-6,10,14-16,23H,4,7-9,11H2,(H,20,24)(H,21,25,26)(H2,27,28,29)/t14-,15-,16-/m1/s1"  
QGJ  InChIKey          InChI                 1.03   HDAALGCFEARBOF-BZUAXINKSA-N  
QGJ  SMILES_CANONICAL  CACTVS                3.385  "O[C@@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCCCc3ccccc3)C(=O)NC2=O"  
QGJ  SMILES            CACTVS                3.385  "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCCCc3ccccc3)C(=O)NC2=O"  
QGJ  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)CCCNC(=O)C2=CN(C(=O)NC2=O)[C@H]3C[C@H]([C@H](O3)COP(=O)(O)O)O"  
QGJ  SMILES            "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)CCCNC(=O)C2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=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
QGJ  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-2,4-dioxo-N-(3-phenylpropyl)-1,2,3,4-tetrahydropyrimidine-5-carboxamide"  
QGJ  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{R},5~{R})-5-[2,4-bis(oxidanylidene)-5-(3-phenylpropylcarbamoyl)pyrimidin-1-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
QGJ  "Create component"  2019-10-28  RCSB  
QGJ  "Initial release"   2021-11-03  RCSB  
##
