# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:59:58 2021
#   Inital geometry file: a 141 line input string
#   Ligand name: 7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-[3-(trifluoromethyloxy)phenoxy]purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(CCCO)C(=O)c2n(Cc3ccc(Cl)cc3)c(Oc4cccc(OC(F)(F)F)c4)nc12
#
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
 PJQ  PJQ  7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-[3-(trifluoromethyloxy)phenoxy]purine-2,6-dione  ligand  56  36  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PJQ
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
 PJQ  C10  C   CR16  0  -0.256  118.1982  135.7782  157.4922
 PJQ  C11  C   CR16  0  -0.295  119.4288  135.9039  156.8634
 PJQ  C12  C   CR6   0   0.323  120.5783  135.6729  157.5990
 PJQ  C02  C   CR6   0   0.585  119.1723  136.9734  165.1361
 PJQ  C03  C   CR56  0   0.134  119.1823  136.6511  163.7557
 PJQ  C04  C   CR56  0   0.454  119.3025  137.6049  162.7835
 PJQ  C06  C   CR5   0   0.728  119.2391  135.7800  161.7768
 PJQ  C08  C   CR6   0   0.357  119.2904  135.2147  159.5333
 PJQ  C09  C   CR16  0  -0.291  118.1182  135.4311  158.8330
 PJQ  C14  C   CT    0   1.075  122.3734  134.7928  156.3881
 PJQ  C18  C   CR16  0  -0.349  120.5334  135.3293  158.9393
 PJQ  C21  C   CR6   0   0.134  117.4346  133.7840  163.6313
 PJQ  C22  C   CR16  0  -0.302  116.8313  133.1467  162.5514
 PJQ  C23  C   CR16  0  -0.196  115.4717  132.8709  162.5544
 PJQ  C24  C   CR6   0  -0.049  114.7125  133.2369  163.6544
 PJQ  C26  C   CR16  0  -0.195  115.2905  133.8655  164.7461
 PJQ  C27  C   CR16  0  -0.303  116.6506  134.1340  164.7263
 PJQ  C30  C   CR6   0   0.738  119.3453  139.3460  164.3777
 PJQ  C33  C   CH2   0  -0.465  117.8077  139.1255  167.2056
 PJQ  C34  C   CH2   0  -0.162  117.7498  139.5199  168.6678
 PJQ  F15  F   F     0  -0.298  122.5331  133.7492  157.2027
 PJQ  F16  F   F     0  -0.297  121.6527  134.3656  155.3500
 PJQ  F17  F   F     0  -0.274  123.5621  135.1664  155.9461
 PJQ  N05  N   N     0  -0.499  119.3382  137.0694  161.5479
 PJQ  N19  N   NR5   0  -0.543  119.1541  135.4426  163.0692
 PJQ  N28  N   NR6   0  -0.594  119.3817  138.9323  163.0668
 PJQ  N31  N   NR6   0  -0.612  119.2639  138.3558  165.3515
 PJQ  O01  O   O     0  -0.477  119.0987  136.1873  166.0682
 PJQ  O07  O   O2    0  -0.509  119.2233  134.8256  160.8590
 PJQ  O13  O   O2    0  -0.523  121.8192  135.8475  157.0026
 PJQ  O35  O   OH1   0  -0.674  118.4962  140.7027  168.8599
 PJQ  O36  O   O     0  -0.487  119.3895  140.5233  164.6778
 PJQ  CL1  CL  CL    0  -0.126  113.0143  132.8936  163.6687
 PJQ  H1   H   HCR6  0   0.283  117.2914  135.9552  156.9308
 PJQ  H2   H   HCR6  0   0.289  119.4878  136.1895  155.8221
 PJQ  H3   H   HCR6  0   0.285  117.1589  135.3290  159.3230
 PJQ  H4   H   HCR6  0   0.300  121.4398  135.1638  159.5073
 PJQ  H5   H   HCH2  0   0.302  119.4629  133.3902  163.0182
 PJQ  H6   H   HCH2  0   0.303  119.3199  134.0911  164.6152
 PJQ  H7   H   HCR6  0   0.267  117.4191  132.8466  161.6934
 PJQ  H8   H   HCR6  0   0.283  115.0153  132.3724  161.7103
 PJQ  H9   H   HCR6  0   0.282  114.6928  134.1415  165.6041
 PJQ  H10  H   HCR6  0   0.273  117.1025  134.6201  165.5814
 PJQ  H11  H   HCH3  0   0.273  119.5018  140.8923  162.3804
 PJQ  H12  H   HCH3  0   0.260  120.3967  139.7163  161.4089
 PJQ  H13  H   HCH3  0   0.260  118.6291  139.7874  161.3099
 PJQ  H14  H   HCH2  0   0.259  119.6582  138.0324  167.3600
 PJQ  H15  H   HCH2  0   0.267  119.8665  139.6877  166.8297
 PJQ  H16  H   HCH2  0   0.237  117.3744  139.9175  166.5901
 PJQ  H17  H   HCH2  0   0.239  117.1783  138.2420  167.0761
 PJQ  H18  H   HCH2  0   0.209  116.7000  139.6570  168.9551
 PJQ  H19  H   HCH2  0   0.195  118.1409  138.6957  169.2800
 PJQ  H20  H   HOH1  0   0.454  118.4806  140.9198  169.7960
 PJQ  C20  C   CH2   0  -0.438  118.9048  134.1127  163.6116
 PJQ  C29  C   CH3   0  -0.537  119.4837  139.8880  161.9757
 PJQ  C32  C   CH2   0  -0.298  119.2255  138.8159  166.7422

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
 PJQ  F16  C14  single    1.334  0.020  1.334
 PJQ  C11  C10  aromatic  1.388  0.020  1.388
 PJQ  C11  C12  aromatic  1.384  0.020  1.384
 PJQ  C10  C09  aromatic  1.387  0.020  1.387
 PJQ  F17  C14  single    1.322  0.020  1.322
 PJQ  O13  C14  single    1.340  0.020  1.340
 PJQ  O13  C12  single    1.388  0.020  1.388
 PJQ  C14  F15  single    1.333  0.020  1.333
 PJQ  C12  C18  aromatic  1.384  0.020  1.384
 PJQ  C09  C08  aromatic  1.383  0.020  1.383
 PJQ  C18  C08  aromatic  1.382  0.020  1.382
 PJQ  C08  O07  single    1.383  0.020  1.383
 PJQ  O07  C06  single    1.324  0.020  1.324
 PJQ  N05  C06  aromatic  1.313  0.020  1.313
 PJQ  N05  C04  aromatic  1.347  0.020  1.347
 PJQ  C06  N19  aromatic  1.338  0.020  1.338
 PJQ  C29  N28  single    1.454  0.020  1.454
 PJQ  C04  N28  single    1.360  0.020  1.360
 PJQ  C04  C03  aromatic  1.367  0.020  1.367
 PJQ  N19  C03  aromatic  1.390  0.020  1.390
 PJQ  N19  C20  single    1.458  0.020  1.458
 PJQ  N28  C30  single    1.375  0.020  1.375
 PJQ  C22  C23  aromatic  1.387  0.020  1.387
 PJQ  C22  C21  aromatic  1.391  0.020  1.391
 PJQ  C23  C24  aromatic  1.386  0.020  1.386
 PJQ  C03  C02  single    1.418  0.020  1.418
 PJQ  C20  C21  single    1.507  0.020  1.507
 PJQ  C21  C27  aromatic  1.392  0.020  1.392
 PJQ  C30  O36  double    1.216  0.020  1.216
 PJQ  C30  N31  single    1.391  0.020  1.391
 PJQ  C24  CL1  single    1.733  0.020  1.733
 PJQ  C24  C26  aromatic  1.386  0.020  1.386
 PJQ  C02  N31  single    1.402  0.020  1.402
 PJQ  C02  O01  double    1.222  0.020  1.222
 PJQ  N31  C32  single    1.465  0.020  1.465
 PJQ  C27  C26  aromatic  1.387  0.020  1.387
 PJQ  C32  C33  single    1.523  0.020  1.523
 PJQ  C33  C34  single    1.516  0.020  1.516
 PJQ  C34  O35  single    1.412  0.020  1.412
 PJQ  C10  H1   single    0.930  0.020  1.080
 PJQ  C11  H2   single    0.930  0.020  1.080
 PJQ  C09  H3   single    0.930  0.020  1.080
 PJQ  C18  H4   single    0.930  0.020  1.080
 PJQ  C20  H5   single    0.970  0.020  1.090
 PJQ  C20  H6   single    0.970  0.020  1.090
 PJQ  C22  H7   single    0.930  0.020  1.080
 PJQ  C23  H8   single    0.930  0.020  1.080
 PJQ  C26  H9   single    0.930  0.020  1.080
 PJQ  C27  H10  single    0.930  0.020  1.080
 PJQ  C29  H11  single    0.970  0.020  1.090
 PJQ  C29  H12  single    0.970  0.020  1.090
 PJQ  C29  H13  single    0.970  0.020  1.090
 PJQ  C32  H14  single    0.970  0.020  1.090
 PJQ  C32  H15  single    0.970  0.020  1.090
 PJQ  C33  H16  single    0.970  0.020  1.090
 PJQ  C33  H17  single    0.970  0.020  1.090
 PJQ  C34  H18  single    0.970  0.020  1.090
 PJQ  C34  H19  single    0.970  0.020  1.090
 PJQ  O35  H20  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
 PJQ  H1   C10  C09  119.63  3.000
 PJQ  H1   C10  C11  119.59  3.000
 PJQ  C09  C10  C11  120.78  3.000
 PJQ  H2   C11  C12  120.70  3.000
 PJQ  H2   C11  C10  120.57  3.000
 PJQ  C12  C11  C10  118.73  3.000
 PJQ  O13  C12  C18  118.45  3.000
 PJQ  C18  C12  C11  121.94  3.000
 PJQ  O13  C12  C11  119.55  3.000
 PJQ  O01  C02  N31  121.41  3.000
 PJQ  O01  C02  C03  126.67  3.000
 PJQ  N31  C02  C03  111.92  3.000
 PJQ  N19  C03  C04  104.90  3.000
 PJQ  N19  C03  C02  132.72  3.000
 PJQ  C04  C03  C02  122.31  3.000
 PJQ  N28  C04  N05  125.29  3.000
 PJQ  N28  C04  C03  122.55  3.000
 PJQ  N05  C04  C03  112.16  3.000
 PJQ  O07  C06  N19  119.13  3.000
 PJQ  N19  C06  N05  114.87  3.000
 PJQ  O07  C06  N05  125.99  3.000
 PJQ  O07  C08  C18  118.60  3.000
 PJQ  O07  C08  C09  119.23  3.000
 PJQ  C18  C08  C09  122.13  3.000
 PJQ  H3   C09  C08  120.50  3.000
 PJQ  H3   C09  C10  120.83  3.000
 PJQ  C08  C09  C10  118.67  3.000
 PJQ  O13  C14  F17  107.62  3.000
 PJQ  O13  C14  F16  112.66  3.000
 PJQ  F17  C14  F16  108.42  3.000
 PJQ  O13  C14  F15  112.66  3.000
 PJQ  F17  C14  F15  108.52  3.000
 PJQ  F16  C14  F15  106.82  3.000
 PJQ  H4   C18  C08  120.99  3.000
 PJQ  H4   C18  C12  121.25  3.000
 PJQ  C08  C18  C12  117.76  3.000
 PJQ  C27  C21  C22  118.80  3.000
 PJQ  C27  C21  C20  120.34  3.000
 PJQ  C22  C21  C20  120.86  3.000
 PJQ  H7   C22  C23  118.60  3.000
 PJQ  H7   C22  C21  120.44  3.000
 PJQ  C23  C22  C21  120.95  3.000
 PJQ  H8   C23  C24  120.67  3.000
 PJQ  H8   C23  C22  120.24  3.000
 PJQ  C24  C23  C22  119.09  3.000
 PJQ  CL1  C24  C26  119.48  3.000
 PJQ  C26  C24  C23  121.10  3.000
 PJQ  CL1  C24  C23  119.42  3.000
 PJQ  H9   C26  C27  120.27  3.000
 PJQ  H9   C26  C24  120.68  3.000
 PJQ  C27  C26  C24  119.06  3.000
 PJQ  H10  C27  C26  119.02  3.000
 PJQ  H10  C27  C21  119.97  3.000
 PJQ  C26  C27  C21  121.01  3.000
 PJQ  O36  C30  N31  121.23  3.000
 PJQ  N31  C30  N28  117.05  3.000
 PJQ  O36  C30  N28  121.72  3.000
 PJQ  H17  C33  H16  106.91  3.000
 PJQ  H17  C33  C34  107.63  3.000
 PJQ  H16  C33  C34  109.86  3.000
 PJQ  H17  C33  C32  109.62  3.000
 PJQ  H16  C33  C32  110.18  3.000
 PJQ  C34  C33  C32  112.46  3.000
 PJQ  H19  C34  H18  106.77  3.000
 PJQ  H19  C34  O35  111.37  3.000
 PJQ  H18  C34  O35  111.44  3.000
 PJQ  H19  C34  C33  109.20  3.000
 PJQ  H18  C34  C33  108.77  3.000
 PJQ  O35  C34  C33  109.21  3.000
 PJQ  C06  N05  C04  103.20  3.000
 PJQ  C20  N19  C06  126.88  3.000
 PJQ  C20  N19  C03  127.80  3.000
 PJQ  C06  N19  C03  104.86  3.000
 PJQ  C30  N28  C29  121.30  3.000
 PJQ  C30  N28  C04  119.39  3.000
 PJQ  C29  N28  C04  119.30  3.000
 PJQ  C32  N31  C30  116.26  3.000
 PJQ  C32  N31  C02  116.98  3.000
 PJQ  C30  N31  C02  126.73  3.000
 PJQ  C08  O07  C06  117.45  3.000
 PJQ  C14  O13  C12  117.88  3.000
 PJQ  H20  O35  C34  108.25  3.000
 PJQ  H6   C20  H5   107.12  3.000
 PJQ  H6   C20  N19  107.25  3.000
 PJQ  H5   C20  N19  108.35  3.000
 PJQ  H6   C20  C21  110.89  3.000
 PJQ  H5   C20  C21  111.26  3.000
 PJQ  N19  C20  C21  111.76  3.000
 PJQ  H13  C29  H12  109.00  3.000
 PJQ  H13  C29  H11  109.12  3.000
 PJQ  H12  C29  H11  109.08  3.000
 PJQ  H13  C29  N28  110.08  3.000
 PJQ  H12  C29  N28  110.24  3.000
 PJQ  H11  C29  N28  109.29  3.000
 PJQ  H15  C32  H14  107.33  3.000
 PJQ  H15  C32  N31  108.25  3.000
 PJQ  H14  C32  N31  107.61  3.000
 PJQ  H15  C32  C33  111.21  3.000
 PJQ  H14  C32  C33  110.11  3.000
 PJQ  N31  C32  C33  112.14  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
 PJQ  CONST_01  C18  C12  C11  C10    0.00   0.0  0
 PJQ  CONST_02  C18  C08  C09  C10    0.00   0.0  0
 PJQ  CONST_03  C08  C09  C10  C11    0.00   0.0  0
 PJQ  CONST_04  C08  C18  C12  C11    0.00   0.0  0
 PJQ  CONST_05  C09  C10  C11  C12    0.00   0.0  0
 PJQ  CONST_06  C09  C08  C18  C12    0.00   0.0  0
 PJQ  CONST_07  C06  N05  C04  C03    0.00   0.0  0
 PJQ  CONST_08  N05  C06  N19  C03    0.00   0.0  0
 PJQ  CONST_09  N19  C06  N05  C04    0.00   0.0  0
 PJQ  CONST_10  C06  N19  C03  C04    0.00   0.0  0
 PJQ  CONST_11  C24  C23  C22  C21    0.00   0.0  0
 PJQ  CONST_12  C24  C26  C27  C21    0.00   0.0  0
 PJQ  CONST_13  C26  C24  C23  C22    0.00   0.0  0
 PJQ  CONST_14  C26  C27  C21  C22    0.00   0.0  0
 PJQ  CONST_15  C27  C21  C22  C23    0.00   0.0  0
 PJQ  CONST_16  C27  C26  C24  C23    0.00   0.0  0
 PJQ  CONST_17  N19  C03  C04  N05    0.00   0.0  0
 PJQ  CONST_18  N28  C30  N31  C02    0.00   0.0  0
 PJQ  CONST_19  C30  N31  C02  C03    0.00   0.0  0
 PJQ  CONST_20  N31  C30  N28  C04    0.00   0.0  0
 PJQ  CONST_21  O13  C12  C11  C10  180.00   0.0  0
 PJQ  CONST_22  O07  C08  C09  C10  180.00   0.0  0
 PJQ  CONST_23  O07  C08  C18  C12  180.00   0.0  0
 PJQ  CONST_24  C20  N19  C03  C02    0.00   0.0  0
 PJQ  CONST_25  O07  C06  N19  C03  180.00   0.0  0
 PJQ  CONST_26  O07  C06  N05  C04  180.00   0.0  0
 PJQ  CONST_27  C20  N19  C03  C04  180.00   0.0  0
 PJQ  CONST_28  O13  C12  C18  C08  180.00   0.0  0
 PJQ  CONST_29  N05  C06  N19  C20  180.00   0.0  0
 PJQ  CONST_30  C23  C22  C21  C20  180.00   0.0  0
 PJQ  CONST_31  C26  C27  C21  C20  180.00   0.0  0
 PJQ  CONST_32  CL1  C24  C23  C22  180.00   0.0  0
 PJQ  CONST_33  CL1  C24  C26  C27  180.00   0.0  0
 PJQ  CONST_34  O36  C30  N31  C02  180.00   0.0  0
 PJQ  CONST_35  C32  N31  C02  C03  180.00   0.0  0
 PJQ  CONST_36  O36  C30  N28  C04  180.00   0.0  0
 PJQ  CONST_37  N31  C30  N28  C29  180.00   0.0  0
 PJQ  CONST_38  O01  C02  N31  C30  180.00   0.0  0
 PJQ  CONST_39  N28  C30  N31  C32  180.00   0.0  0
 PJQ  CONST_40  H3   C09  C10  C11  180.00   0.0  0
 PJQ  CONST_41  H4   C18  C12  C11  180.00   0.0  0
 PJQ  CONST_42  H1   C10  C11  C12  180.00   0.0  0
 PJQ  CONST_43  H2   C11  C10  C09  180.00   0.0  0
 PJQ  CONST_44  H8   C23  C22  C21  180.00   0.0  0
 PJQ  CONST_45  H9   C26  C27  C21  180.00   0.0  0
 PJQ  CONST_46  H10  C27  C21  C22  180.00   0.0  0
 PJQ  CONST_47  H7   C22  C23  C24  180.00   0.0  0
 PJQ  CONST_48  O36  C30  N28  C29    0.00   0.0  0
 PJQ  CONST_49  O36  C30  N31  C32    0.00   0.0  0
 PJQ  CONST_50  O01  C02  N31  C32    0.00   0.0  0
 PJQ  Var_01    C21  C20  N19  C03   88.11  30.0  2
 PJQ  Var_02    C09  C08  O07  C06  -91.72  30.0  3
 PJQ  Var_03    N05  C06  O07  C08   -1.37  30.0  2
 PJQ  Var_04    N19  C20  C21  C22   90.94  30.0  2
 PJQ  Var_05    C33  C32  N31  C02  -91.07  30.0  3
 PJQ  Var_06    C18  C12  O13  C14   92.89  30.0  2
 PJQ  Var_07    H11  C29  N28  C04  178.03  30.0  3
 PJQ  Var_08    F16  C14  O13  C12   63.10  30.0  3
 PJQ  Var_09    N31  C32  C33  C34  176.47  30.0  1
 PJQ  Var_10    O35  C34  C33  C32   62.27  30.0  3

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
 PJQ  plan-1  C10  0.020
 PJQ  plan-1  C11  0.020
 PJQ  plan-1  C12  0.020
 PJQ  plan-1  C08  0.020
 PJQ  plan-1  C09  0.020
 PJQ  plan-1  C18  0.020
 PJQ  plan-1  O07  0.020
 PJQ  plan-1  O13  0.020
 PJQ  plan-1  H1   0.020
 PJQ  plan-1  H2   0.020
 PJQ  plan-1  H3   0.020
 PJQ  plan-1  H4   0.020
 PJQ  plan-2  C21  0.020
 PJQ  plan-2  C22  0.020
 PJQ  plan-2  C23  0.020
 PJQ  plan-2  C24  0.020
 PJQ  plan-2  C26  0.020
 PJQ  plan-2  C27  0.020
 PJQ  plan-2  CL1  0.020
 PJQ  plan-2  H7   0.020
 PJQ  plan-2  H8   0.020
 PJQ  plan-2  H9   0.020
 PJQ  plan-2  H10  0.020
 PJQ  plan-2  C20  0.020
 PJQ  plan-3  C02  0.020
 PJQ  plan-3  C03  0.020
 PJQ  plan-3  C04  0.020
 PJQ  plan-3  C06  0.020
 PJQ  plan-3  C30  0.020
 PJQ  plan-3  N05  0.020
 PJQ  plan-3  N19  0.020
 PJQ  plan-3  N28  0.020
 PJQ  plan-3  N31  0.020
 PJQ  plan-3  O01  0.020
 PJQ  plan-3  O07  0.020
 PJQ  plan-3  O36  0.020
 PJQ  plan-3  C20  0.020
 PJQ  plan-3  C29  0.020
 PJQ  plan-3  C32  0.020

