# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:13:10 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: N-[2-(6-amino-9H-purin-9-yl)ethyl]-5-hydroxy-6-oxo-2-[2-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCNC(=O)C3=C(O)C(=O)NC(=N3)c4ccccc4C(F)(F)F)cnc12
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 QQP  QQP  N-[2-(6-amino-9H-purin-9-yl)ethyl]-5-hydroxy-6-oxo-2-[2-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide  ligand  48  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QQP
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 QQP  N12  N  N     0  -0.451   1.7834  34.9468  12.8005
 QQP  C13  C  CR56  0   0.005   3.0085  34.4010  12.5153
 QQP  C16  C  CR16  0   0.058   5.0605  32.8037  11.9934
 QQP  C18  C  CR6   0   0.457   4.2832  34.9524  12.2824
 QQP  C22  C  CR6   0   0.371   6.2606  30.7112  15.7593
 QQP  C24  C  CR16  0  -0.259   7.2538  32.5220  14.4441
 QQP  C25  C  CR16  0  -0.221   8.2036  33.0541  13.5857
 QQP  C27  C  CR16  0  -0.281   9.2752  30.9089  13.4583
 QQP  N33  N  NR16  0  -0.679   6.6501  30.3661  17.0182
 QQP  C02  C  CR6   0   0.508   5.7978  29.9369  18.0093
 QQP  C03  C  CR6   0   0.226   4.4007  29.9132  17.5816
 QQP  C05  C  CR6   0  -0.044   4.0943  30.2972  16.3065
 QQP  C06  C  C     0   0.612   2.6741  30.3117  15.8805
 QQP  C08  C  CH2   0  -0.260   1.0771  30.7752  14.1191
 QQP  C11  C  CR15  0   0.110   0.9899  33.9194  12.8979
 QQP  C14  C  CR56  0   0.489   2.9234  33.0204  12.4462
 QQP  C23  C  CR6   0   0.054   7.3095  31.1878  14.8251
 QQP  C26  C  CR16  0  -0.237   9.2186  32.2480  13.0993
 QQP  C28  C  CR6   0  -0.221   8.3259  30.3709  14.3171
 QQP  F30  F  F     0  -0.316   8.9631  28.7365  15.8896
 QQP  F31  F  F     0  -0.309   7.1987  28.3425  14.7230
 QQP  F32  F  F     0  -0.296   9.1417  28.2178  13.8141
 QQP  N07  N  NH1   0  -0.661   2.4296  30.6689  14.6250
 QQP  N10  N  NR5   0  -0.491   1.6172  32.7240  12.6900
 QQP  N15  N  N     0  -0.478   3.9181  32.1708  12.1962
 QQP  N17  N  N     0  -0.468   5.2914  34.1128  12.0176
 QQP  N19  N  NH2   0  -0.816   4.5205  36.2637  12.3186
 QQP  N21  N  N     0  -0.430   5.0318  30.6899  15.3953
 QQP  O04  O  OH1   0  -0.601   3.5328  29.5281  18.4992
 QQP  O20  O  O     0  -0.533   1.7814  30.0077  16.6849
 QQP  H1   H  HCR6  0   0.249   5.9211  32.1804  11.7788
 QQP  H2   H  HCR6  0   0.276   6.4582  33.1476  14.8257
 QQP  H3   H  HCR6  0   0.274   8.1361  34.0920  13.2913
 QQP  H4   H  HCR6  0   0.281  10.0625  30.2910  13.0499
 QQP  H5   H  HNR6  0   0.433   7.6244  30.4629  17.2790
 QQP  H6   H  HCH2  0   0.259   0.4775  31.3741  14.8073
 QQP  H7   H  HCH2  0   0.265   0.6080  29.7902  14.0540
 QQP  H8   H  HCH2  0   0.300   0.0055  31.4553  12.4063
 QQP  H9   H  HCH2  0   0.287   1.5743  30.7744  12.0161
 QQP  H10  H  HCR5  0   0.295  -0.0681  33.9654  13.1105
 QQP  H11  H  HCR6  0   0.277   9.9649  32.6526  12.4295
 QQP  H12  H  HNH1  0   0.430   3.2225  30.8487  14.0183
 QQP  H13  H  HNH2  0   0.403   5.4396  36.6189  12.1187
 QQP  H14  H  HNH2  0   0.412   3.7817  36.9218  12.4931
 QQP  H15  H  HOH1  0   0.483   2.6389  29.5991  18.0784
 QQP  C09  C  CH2   0  -0.378   1.0416  31.3964  12.7353
 QQP  O01  O  O     0  -0.447   6.1841  29.6313  19.1200
 QQP  C29  C  CT    0   1.065   8.4077  28.9169  14.6800

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 QQP  C16  N17  aromatic  1.330  0.020  1.330
 QQP  C16  N15  aromatic  1.322  0.020  1.322
 QQP  N17  C18  aromatic  1.338  0.020  1.338
 QQP  N15  C14  aromatic  1.332  0.020  1.332
 QQP  C18  N19  single    1.333  0.020  1.333
 QQP  C18  C13  aromatic  1.408  0.020  1.408
 QQP  C14  C13  aromatic  1.385  0.020  1.385
 QQP  C14  N10  aromatic  1.361  0.020  1.361
 QQP  C13  N12  aromatic  1.371  0.020  1.371
 QQP  N10  C09  single    1.448  0.020  1.448
 QQP  N10  C11  aromatic  1.366  0.020  1.366
 QQP  C09  C08  single    1.517  0.020  1.517
 QQP  N12  C11  aromatic  1.302  0.020  1.302
 QQP  C26  C27  aromatic  1.388  0.020  1.388
 QQP  C26  C25  aromatic  1.384  0.020  1.384
 QQP  F32  C29  single    1.333  0.020  1.333
 QQP  C27  C28  aromatic  1.389  0.020  1.389
 QQP  F31  C29  single    1.339  0.020  1.339
 QQP  C08  N07  single    1.448  0.020  1.448
 QQP  C25  C24  aromatic  1.386  0.020  1.386
 QQP  C28  C29  single    1.501  0.020  1.501
 QQP  C28  C23  aromatic  1.399  0.020  1.399
 QQP  C29  F30  single    1.343  0.020  1.343
 QQP  N07  C06  single    1.328  0.020  1.328
 QQP  C24  C23  aromatic  1.389  0.020  1.389
 QQP  C23  C22  single    1.483  0.020  1.483
 QQP  N21  C22  double    1.282  0.020  1.282
 QQP  N21  C05  single    1.365  0.020  1.365
 QQP  C06  C05  single    1.483  0.020  1.483
 QQP  C06  O20  double    1.240  0.020  1.240
 QQP  C22  N33  single    1.362  0.020  1.362
 QQP  C05  C03  double    1.366  0.020  1.366
 QQP  N33  C02  single    1.376  0.020  1.376
 QQP  C03  C02  single    1.461  0.020  1.461
 QQP  C03  O04  single    1.320  0.020  1.320
 QQP  C02  O01  double    1.215  0.020  1.215
 QQP  C16  H1   single    0.930  0.020  1.080
 QQP  C24  H2   single    0.930  0.020  1.080
 QQP  C25  H3   single    0.930  0.020  1.080
 QQP  C27  H4   single    0.930  0.020  1.080
 QQP  N33  H5   single    0.860  0.020  1.020
 QQP  C08  H6   single    0.970  0.020  1.090
 QQP  C08  H7   single    0.970  0.020  1.090
 QQP  C09  H8   single    0.970  0.020  1.090
 QQP  C09  H9   single    0.970  0.020  1.090
 QQP  C11  H10  single    0.930  0.020  1.080
 QQP  C26  H11  single    0.930  0.020  1.080
 QQP  N07  H12  single    0.860  0.020  1.020
 QQP  N19  H13  single    0.860  0.020  1.020
 QQP  N19  H14  single    0.860  0.020  1.020
 QQP  O04  H15  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 QQP  C11  N12  C13  104.24  3.000
 QQP  C14  C13  C18  115.96  3.000
 QQP  C14  C13  N12  110.62  3.000
 QQP  C18  C13  N12  133.42  3.000
 QQP  H1   C16  N17  115.58  3.000
 QQP  H1   C16  N15  116.18  3.000
 QQP  N17  C16  N15  128.23  3.000
 QQP  N19  C18  N17  119.23  3.000
 QQP  N19  C18  C13  122.80  3.000
 QQP  N17  C18  C13  117.97  3.000
 QQP  N21  C22  C23  120.29  3.000
 QQP  N21  C22  N33  122.16  3.000
 QQP  C23  C22  N33  117.47  3.000
 QQP  H2   C24  C23  119.24  3.000
 QQP  H2   C24  C25  120.02  3.000
 QQP  C23  C24  C25  120.74  3.000
 QQP  H3   C25  C26  120.60  3.000
 QQP  H3   C25  C24  119.63  3.000
 QQP  C26  C25  C24  119.76  3.000
 QQP  H4   C27  C28  120.68  3.000
 QQP  H4   C27  C26  118.92  3.000
 QQP  C28  C27  C26  120.40  3.000
 QQP  H5   N33  C02  116.11  3.000
 QQP  H5   N33  C22  119.25  3.000
 QQP  C02  N33  C22  124.59  3.000
 QQP  O01  C02  C03  124.57  3.000
 QQP  O01  C02  N33  122.69  3.000
 QQP  C03  C02  N33  112.73  3.000
 QQP  O04  C03  C05  125.66  3.000
 QQP  O04  C03  C02  115.45  3.000
 QQP  C05  C03  C02  118.88  3.000
 QQP  N21  C05  C06  117.60  3.000
 QQP  C06  C05  C03  119.05  3.000
 QQP  N21  C05  C03  123.34  3.000
 QQP  O20  C06  N07  123.15  3.000
 QQP  O20  C06  C05  120.07  3.000
 QQP  N07  C06  C05  116.78  3.000
 QQP  H7   C08  H6   107.23  3.000
 QQP  H7   C08  N07  110.83  3.000
 QQP  H6   C08  N07  109.45  3.000
 QQP  H7   C08  C09  107.74  3.000
 QQP  H6   C08  C09  109.72  3.000
 QQP  N07  C08  C09  111.75  3.000
 QQP  H10  C11  N10  121.13  3.000
 QQP  H10  C11  N12  125.32  3.000
 QQP  N10  C11  N12  113.54  3.000
 QQP  N15  C14  N10  127.68  3.000
 QQP  N10  C14  C13  105.49  3.000
 QQP  N15  C14  C13  126.83  3.000
 QQP  C28  C23  C24  119.36  3.000
 QQP  C24  C23  C22  116.95  3.000
 QQP  C28  C23  C22  123.69  3.000
 QQP  H11  C26  C27  119.55  3.000
 QQP  H11  C26  C25  120.38  3.000
 QQP  C27  C26  C25  120.06  3.000
 QQP  C23  C28  C29  121.15  3.000
 QQP  C23  C28  C27  119.67  3.000
 QQP  C29  C28  C27  119.18  3.000
 QQP  H12  N07  C08  120.54  3.000
 QQP  H12  N07  C06  117.98  3.000
 QQP  C08  N07  C06  121.47  3.000
 QQP  C14  N10  C11  106.10  3.000
 QQP  C11  N10  C09  127.97  3.000
 QQP  C14  N10  C09  125.92  3.000
 QQP  C14  N15  C16  111.64  3.000
 QQP  C18  N17  C16  119.37  3.000
 QQP  H14  N19  H13  118.38  3.000
 QQP  H14  N19  C18  121.21  3.000
 QQP  H13  N19  C18  120.32  3.000
 QQP  C05  N21  C22  118.27  3.000
 QQP  H15  O04  C03  106.08  3.000
 QQP  H9   C09  H8   107.26  3.000
 QQP  H9   C09  N10  107.96  3.000
 QQP  H8   C09  N10  108.62  3.000
 QQP  H9   C09  C08  110.90  3.000
 QQP  H8   C09  C08  108.66  3.000
 QQP  N10  C09  C08  113.24  3.000
 QQP  F32  C29  F31  107.04  3.000
 QQP  F31  C29  F30  106.66  3.000
 QQP  F32  C29  F30  106.67  3.000
 QQP  F30  C29  C28  111.74  3.000
 QQP  F31  C29  C28  111.97  3.000
 QQP  F32  C29  C28  112.40  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 QQP  CONST_01  N17  C18  C13  N12   180.00   0.0  0
 QQP  CONST_02  N15  C14  C13  N12   180.00   0.0  0
 QQP  CONST_03  N10  C14  C13  N12     0.00   0.0  0
 QQP  CONST_04  C14  N10  C11  N12     0.00   0.0  0
 QQP  CONST_05  C16  N17  C18  C13     0.00   0.0  0
 QQP  CONST_06  C16  N15  C14  C13     0.00   0.0  0
 QQP  CONST_07  C11  N10  C14  C13     0.00   0.0  0
 QQP  CONST_08  N10  C11  N12  C13     0.00   0.0  0
 QQP  CONST_09  N10  C14  N15  C16   180.00   0.0  0
 QQP  CONST_10  N15  C16  N17  C18     0.00   0.0  0
 QQP  CONST_11  N15  C14  C13  C18     0.00   0.0  0
 QQP  CONST_12  N10  C14  C13  C18   180.00   0.0  0
 QQP  CONST_13  C11  N12  C13  C18   180.00   0.0  0
 QQP  CONST_14  C27  C26  C25  C24     0.00   0.0  0
 QQP  CONST_15  C27  C28  C23  C24     0.00   0.0  0
 QQP  CONST_16  C28  C27  C26  C25     0.00   0.0  0
 QQP  CONST_17  C28  C23  C24  C25     0.00   0.0  0
 QQP  CONST_18  N15  C14  N10  C11   180.00   0.0  0
 QQP  CONST_19  C14  C13  N12  C11     0.00   0.0  0
 QQP  CONST_20  N17  C16  N15  C14     0.00   0.0  0
 QQP  CONST_21  N17  C18  C13  C14     0.00   0.0  0
 QQP  CONST_22  C26  C27  C28  C23     0.00   0.0  0
 QQP  CONST_23  C26  C25  C24  C23     0.00   0.0  0
 QQP  CONST_24  C27  C28  C23  C22   180.00   0.0  0
 QQP  CONST_25  C25  C24  C23  C22   180.00   0.0  0
 QQP  CONST_26  C03  C02  N33  C22     0.00   0.0  0
 QQP  CONST_27  C05  N21  C22  N33     0.00   0.0  0
 QQP  CONST_28  C23  C22  N33  C02   180.00   0.0  0
 QQP  CONST_29  N21  C22  N33  C02     0.00   0.0  0
 QQP  CONST_30  C23  C22  N21  C05   180.00   0.0  0
 QQP  CONST_31  N19  C18  C13  N12     0.00   0.0  0
 QQP  CONST_32  C09  N10  C11  N12   180.00   0.0  0
 QQP  CONST_33  C09  N10  C14  C13   180.00   0.0  0
 QQP  CONST_34  N19  C18  N17  C16   180.00   0.0  0
 QQP  CONST_35  C29  C28  C23  C22     0.00   0.0  0
 QQP  CONST_36  C29  C28  C23  C24   180.00   0.0  0
 QQP  CONST_37  C26  C27  C28  C29   180.00   0.0  0
 QQP  CONST_38  N15  C14  N10  C09     0.00   0.0  0
 QQP  CONST_39  N19  C18  C13  C14   180.00   0.0  0
 QQP  CONST_40  O01  C02  N33  C22   180.00   0.0  0
 QQP  CONST_41  H10  C11  N12  C13   180.00   0.0  0
 QQP  CONST_42  H1   C16  N17  C18   180.00   0.0  0
 QQP  CONST_43  H2   C24  C23  C22     0.00   0.0  0
 QQP  CONST_44  H11  C26  C25  C24   180.00   0.0  0
 QQP  CONST_45  H4   C27  C26  C25   180.00   0.0  0
 QQP  CONST_46  H3   C25  C26  C27   180.00   0.0  0
 QQP  CONST_47  H5   N33  C02  C03   180.00   0.0  0
 QQP  CONST_48  H13  N19  C18  C13   180.00   0.0  0
 QQP  CONST_49  H14  N19  C18  C13     0.00   0.0  0
 QQP  CONST_50  C08  N07  C06  C05   180.00   0.0  0
 QQP  CONST_51  H12  N07  C06  C05     0.00   0.0  0
 QQP  CONST_52  O20  C06  N07  C08     0.00   0.0  0
 QQP  Var_01    N21  C22  C23  C24    64.70  30.0  2
 QQP  Var_02    F32  C29  C28  C27   -19.53  30.0  2
 QQP  Var_03    N07  C06  C05  C03  -178.82  30.0  2
 QQP  Var_04    C14  N10  C09  C08    89.89  30.0  3
 QQP  Var_05    N10  C09  C08  N07   -59.01  30.0  2
 QQP  Var_06    C09  C08  N07  C06   171.37  30.0  1

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 QQP  plan-1  C22  0.020
 QQP  plan-1  C24  0.020
 QQP  plan-1  C25  0.020
 QQP  plan-1  C27  0.020
 QQP  plan-1  C23  0.020
 QQP  plan-1  C26  0.020
 QQP  plan-1  C28  0.020
 QQP  plan-1  H2   0.020
 QQP  plan-1  H3   0.020
 QQP  plan-1  H4   0.020
 QQP  plan-1  H11  0.020
 QQP  plan-1  C29  0.020
 QQP  plan-2  C22  0.020
 QQP  plan-2  N33  0.020
 QQP  plan-2  C02  0.020
 QQP  plan-2  C03  0.020
 QQP  plan-2  C05  0.020
 QQP  plan-2  C06  0.020
 QQP  plan-2  C23  0.020
 QQP  plan-2  N21  0.020
 QQP  plan-2  O04  0.020
 QQP  plan-2  H5   0.020
 QQP  plan-2  O01  0.020
 QQP  plan-3  N12  0.020
 QQP  plan-3  C13  0.020
 QQP  plan-3  C16  0.020
 QQP  plan-3  C18  0.020
 QQP  plan-3  C11  0.020
 QQP  plan-3  C14  0.020
 QQP  plan-3  N10  0.020
 QQP  plan-3  N15  0.020
 QQP  plan-3  N17  0.020
 QQP  plan-3  N19  0.020
 QQP  plan-3  H1   0.020
 QQP  plan-3  H10  0.020
 QQP  plan-3  C09  0.020
 QQP  plan-4  C05  0.020
 QQP  plan-4  C06  0.020
 QQP  plan-4  C08  0.020
 QQP  plan-4  N07  0.020
 QQP  plan-4  O20  0.020
 QQP  plan-4  H12  0.020
 QQP  plan-5  C18  0.020
 QQP  plan-5  N19  0.020
 QQP  plan-5  H13  0.020
 QQP  plan-5  H14  0.020

