# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 13:04:54 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-(2-fluorophenyl)-5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CCNC(=O)C2=C(O)C(=O)N=C(N2)c3ccccc3F)ccc1O
#
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
 WTG  WTG  "2-(2-fluorophenyl)-5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide"
  ligand  47  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WTG
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
 WTG  C27  C  CR16  0  -0.328  40.9818  13.3947  10.4166
 WTG  C28  C  CR6   0   0.266  39.9011  12.5455  10.5864
 WTG  O13  O  OH1   0  -0.594  40.9999  16.1829  18.3360
 WTG  C01  C  CH3   0  -0.440  38.7330   9.9147  12.7916
 WTG  C03  C  CR6   0   0.312  39.8641  11.7037  11.7078
 WTG  C04  C  CR16  0  -0.438  40.9010  11.7340  12.6288
 WTG  C05  C  CR6   0   0.124  41.9897  12.5908  12.4579
 WTG  C06  C  CH2   0  -0.565  43.0982  12.6253  13.4764
 WTG  C07  C  CH2   0  -0.258  43.1473  13.9257  14.2707
 WTG  C09  C  C     0   0.531  41.6335  15.2744  15.6373
 WTG  C11  C  CR6   0   0.110  40.2752  15.3206  16.2656
 WTG  C12  C  CR6   0   0.189  40.0391  15.7596  17.5219
 WTG  C14  C  CR6   0   0.375  38.6708  15.7291  18.0490
 WTG  C17  C  CR6   0   0.489  37.9562  14.8707  16.0323
 WTG  C19  C  CR6   0  -0.204  36.8915  14.3586  15.1500
 WTG  C20  C  CR16  0  -0.269  37.1148  13.2424  14.3410
 WTG  C21  C  CR16  0  -0.259  36.1188  12.7458  13.5176
 WTG  C22  C  CR16  0  -0.227  34.8751  13.3613  13.4930
 WTG  C23  C  CR16  0  -0.402  34.6285  14.4727  14.2850
 WTG  C24  C  CR6   0   0.554  35.6340  14.9530  15.1003
 WTG  C26  C  CR16  0  -0.316  42.0167  13.4173  11.3436
 WTG  F25  F  F     0  -0.290  35.3863  16.0432  15.8299
 WTG  N08  N  NH1   0  -0.636  41.9012  14.1373  14.9806
 WTG  N16  N  N     0  -0.464  37.6817  15.2526  17.2451
 WTG  N18  N  NR16  0  -0.670  39.1960  14.8909  15.5249
 WTG  O02  O  O2    0  -0.492  38.7748  10.9060  11.7854
 WTG  O10  O  O     0  -0.454  42.4015  16.2156  15.7219
 WTG  O15  O  O     0  -0.478  38.4700  16.1161  19.1958
 WTG  O29  O  OH1   0  -0.630  38.9140  12.5385   9.6659
 WTG  H1   H  HCR6  0   0.260  41.0134  14.0369   9.5449
 WTG  H2   H  HOH1  0   0.472  40.5803  16.4026  19.1844
 WTG  H3   H  HCH3  0   0.262  37.8195   9.3477  12.6317
 WTG  H4   H  HCH3  0   0.238  39.5890   9.2381  12.7259
 WTG  H5   H  HCH3  0   0.232  38.7045  10.3525  13.7928
 WTG  H6   H  HCR6  0   0.278  40.8844  11.0822  13.4941
 WTG  H7   H  HCH2  0   0.259  42.9971  11.7825  14.1646
 WTG  H8   H  HCH2  0   0.269  44.0677  12.5085  12.9872
 WTG  H9   H  HCH2  0   0.253  43.9861  13.8929  14.9710
 WTG  H10  H  HCH2  0   0.249  43.3216  14.7673  13.5979
 WTG  H11  H  HCR6  0   0.285  38.0733  12.7381  14.3732
 WTG  H12  H  HCR6  0   0.274  36.3118  11.8793  12.9013
 WTG  H13  H  HCR6  0   0.278  34.0904  12.9798  12.8536
 WTG  H14  H  HCR6  0   0.288  33.6678  14.9705  14.2684
 WTG  H15  H  HCR6  0   0.246  42.8530  14.0874  11.1829
 WTG  H16  H  HNH1  0   0.414  41.2930  13.3417  15.1072
 WTG  H17  H  HNR6  0   0.443  39.3321  14.6750  14.5454
 WTG  H18  H  HOH1  0   0.468  38.2488  11.8787   9.8970

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
 WTG  O29  C28  single    1.350  0.020  1.350
 WTG  C27  C28  aromatic  1.385  0.020  1.385
 WTG  C27  C26  aromatic  1.390  0.020  1.390
 WTG  C28  C03  aromatic  1.403  0.020  1.403
 WTG  C26  C05  aromatic  1.388  0.020  1.388
 WTG  C03  O02  single    1.352  0.020  1.352
 WTG  C03  C04  aromatic  1.387  0.020  1.387
 WTG  O02  C01  single    1.413  0.020  1.413
 WTG  C05  C04  aromatic  1.396  0.020  1.396
 WTG  C05  C06  single    1.506  0.020  1.506
 WTG  C21  C22  aromatic  1.388  0.020  1.388
 WTG  C21  C20  aromatic  1.384  0.020  1.384
 WTG  C06  C07  single    1.525  0.020  1.525
 WTG  C22  C23  aromatic  1.387  0.020  1.387
 WTG  C20  C19  aromatic  1.397  0.020  1.397
 WTG  C07  N08  single    1.450  0.020  1.450
 WTG  C23  C24  aromatic  1.381  0.020  1.381
 WTG  N08  C09  single    1.340  0.020  1.340
 WTG  C19  C24  aromatic  1.392  0.020  1.392
 WTG  C19  C17  single    1.475  0.020  1.475
 WTG  C24  F25  single    1.335  0.020  1.335
 WTG  N18  C17  single    1.340  0.020  1.340
 WTG  N18  C11  single    1.378  0.020  1.378
 WTG  C09  O10  double    1.218  0.020  1.218
 WTG  C09  C11  single    1.497  0.020  1.497
 WTG  C17  N16  double    1.301  0.020  1.301
 WTG  C11  C12  double    1.352  0.020  1.352
 WTG  N16  C14  single    1.361  0.020  1.361
 WTG  C12  C14  single    1.467  0.020  1.467
 WTG  C12  O13  single    1.329  0.020  1.329
 WTG  C14  O15  double    1.227  0.020  1.227
 WTG  C27  H1   single    0.930  0.020  1.080
 WTG  O13  H2   single    0.850  0.020  0.980
 WTG  C01  H3   single    0.970  0.020  1.090
 WTG  C01  H4   single    0.970  0.020  1.090
 WTG  C01  H5   single    0.970  0.020  1.090
 WTG  C04  H6   single    0.930  0.020  1.080
 WTG  C06  H7   single    0.970  0.020  1.090
 WTG  C06  H8   single    0.970  0.020  1.090
 WTG  C07  H9   single    0.970  0.020  1.090
 WTG  C07  H10  single    0.970  0.020  1.090
 WTG  C20  H11  single    0.930  0.020  1.080
 WTG  C21  H12  single    0.930  0.020  1.080
 WTG  C22  H13  single    0.930  0.020  1.080
 WTG  C23  H14  single    0.930  0.020  1.080
 WTG  C26  H15  single    0.930  0.020  1.080
 WTG  N08  H16  single    0.860  0.020  1.020
 WTG  N18  H17  single    0.860  0.020  1.020
 WTG  O29  H18  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
 WTG  H1   C27  C26  120.37  3.000
 WTG  H1   C27  C28  119.01  3.000
 WTG  C26  C27  C28  120.62  3.000
 WTG  O29  C28  C03  121.53  3.000
 WTG  C03  C28  C27  119.12  3.000
 WTG  O29  C28  C27  119.35  3.000
 WTG  H2   O13  C12  107.15  3.000
 WTG  H5   C01  H4   108.86  3.000
 WTG  H5   C01  H3   108.77  3.000
 WTG  H4   C01  H3   109.05  3.000
 WTG  H5   C01  O02  111.84  3.000
 WTG  H4   C01  O02  111.61  3.000
 WTG  H3   C01  O02  106.62  3.000
 WTG  O02  C03  C04  125.23  3.000
 WTG  C04  C03  C28  119.87  3.000
 WTG  O02  C03  C28  114.90  3.000
 WTG  H6   C04  C05  118.62  3.000
 WTG  H6   C04  C03  120.37  3.000
 WTG  C05  C04  C03  121.00  3.000
 WTG  C26  C05  C06  121.01  3.000
 WTG  C06  C05  C04  120.36  3.000
 WTG  C26  C05  C04  118.63  3.000
 WTG  H8   C06  H7   106.36  3.000
 WTG  H8   C06  C07  107.22  3.000
 WTG  H7   C06  C07  109.43  3.000
 WTG  H8   C06  C05  110.37  3.000
 WTG  H7   C06  C05  109.89  3.000
 WTG  C07  C06  C05  113.31  3.000
 WTG  H10  C07  H9   107.18  3.000
 WTG  H10  C07  N08  109.06  3.000
 WTG  H9   C07  N08  110.50  3.000
 WTG  H10  C07  C06  109.98  3.000
 WTG  H9   C07  C06  109.44  3.000
 WTG  N08  C07  C06  110.61  3.000
 WTG  O10  C09  N08  124.32  3.000
 WTG  O10  C09  C11  121.28  3.000
 WTG  N08  C09  C11  114.39  3.000
 WTG  N18  C11  C12  117.66  3.000
 WTG  C12  C11  C09  123.95  3.000
 WTG  N18  C11  C09  118.39  3.000
 WTG  C14  C12  C11  119.36  3.000
 WTG  C14  C12  O13  117.46  3.000
 WTG  C11  C12  O13  123.14  3.000
 WTG  O15  C14  N16  122.93  3.000
 WTG  O15  C14  C12  118.82  3.000
 WTG  N16  C14  C12  118.24  3.000
 WTG  N18  C17  N16  122.95  3.000
 WTG  N16  C17  C19  120.49  3.000
 WTG  N18  C17  C19  116.54  3.000
 WTG  C24  C19  C20  117.72  3.000
 WTG  C24  C19  C17  121.70  3.000
 WTG  C20  C19  C17  120.58  3.000
 WTG  H11  C20  C21  119.15  3.000
 WTG  H11  C20  C19  119.75  3.000
 WTG  C21  C20  C19  121.08  3.000
 WTG  H12  C21  C22  120.36  3.000
 WTG  H12  C21  C20  119.89  3.000
 WTG  C22  C21  C20  119.75  3.000
 WTG  H13  C22  C23  119.42  3.000
 WTG  H13  C22  C21  120.27  3.000
 WTG  C23  C22  C21  120.30  3.000
 WTG  H14  C23  C24  119.70  3.000
 WTG  H14  C23  C22  121.18  3.000
 WTG  C24  C23  C22  119.11  3.000
 WTG  F25  C24  C23  118.14  3.000
 WTG  F25  C24  C19  119.79  3.000
 WTG  C23  C24  C19  122.04  3.000
 WTG  H15  C26  C05  120.16  3.000
 WTG  H15  C26  C27  119.07  3.000
 WTG  C05  C26  C27  120.77  3.000
 WTG  H16  N08  C09  119.14  3.000
 WTG  H16  N08  C07  117.66  3.000
 WTG  C09  N08  C07  122.38  3.000
 WTG  C17  N16  C14  120.01  3.000
 WTG  H17  N18  C17  119.19  3.000
 WTG  H17  N18  C11  118.78  3.000
 WTG  C17  N18  C11  121.74  3.000
 WTG  C03  O02  C01  118.59  3.000
 WTG  H18  O29  C28  110.14  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
 WTG  CONST_01  C04  C03  C28  C27     0.00   0.0  0
 WTG  CONST_02  C04  C05  C26  C27     0.00   0.0  0
 WTG  CONST_03  C05  C26  C27  C28     0.00   0.0  0
 WTG  CONST_04  C05  C04  C03  C28     0.00   0.0  0
 WTG  CONST_05  C26  C27  C28  C03     0.00   0.0  0
 WTG  CONST_06  C26  C05  C04  C03     0.00   0.0  0
 WTG  CONST_07  C22  C21  C20  C19     0.00   0.0  0
 WTG  CONST_08  C22  C23  C24  C19     0.00   0.0  0
 WTG  CONST_09  C23  C22  C21  C20     0.00   0.0  0
 WTG  CONST_10  C23  C24  C19  C20     0.00   0.0  0
 WTG  CONST_11  C24  C23  C22  C21     0.00   0.0  0
 WTG  CONST_12  C24  C19  C20  C21     0.00   0.0  0
 WTG  CONST_13  C21  C20  C19  C17   180.00   0.0  0
 WTG  CONST_14  C23  C24  C19  C17   180.00   0.0  0
 WTG  CONST_15  C19  C17  N18  C11   180.00   0.0  0
 WTG  CONST_16  N16  C17  N18  C11     0.00   0.0  0
 WTG  CONST_17  C19  C17  N16  C14   180.00   0.0  0
 WTG  CONST_18  N18  C17  N16  C14     0.00   0.0  0
 WTG  CONST_19  O02  C03  C28  C27   180.00   0.0  0
 WTG  CONST_20  C06  C05  C26  C27   180.00   0.0  0
 WTG  CONST_21  C06  C05  C04  C03   180.00   0.0  0
 WTG  CONST_22  O29  C28  C03  C04   180.00   0.0  0
 WTG  CONST_23  O02  C03  C04  C05   180.00   0.0  0
 WTG  CONST_24  F25  C24  C19  C17     0.00   0.0  0
 WTG  CONST_25  F25  C24  C19  C20   180.00   0.0  0
 WTG  CONST_26  F25  C24  C23  C22   180.00   0.0  0
 WTG  CONST_27  O29  C28  C27  C26   180.00   0.0  0
 WTG  CONST_28  H15  C26  C27  C28   180.00   0.0  0
 WTG  CONST_29  H6   C04  C03  C28   180.00   0.0  0
 WTG  CONST_30  H1   C27  C28  C03   180.00   0.0  0
 WTG  CONST_31  H15  C26  C05  C04   180.00   0.0  0
 WTG  CONST_32  H1   C27  C26  C05   180.00   0.0  0
 WTG  CONST_33  H11  C20  C19  C17     0.00   0.0  0
 WTG  CONST_34  H12  C21  C20  C19   180.00   0.0  0
 WTG  CONST_35  H14  C23  C24  C19   180.00   0.0  0
 WTG  CONST_36  H13  C22  C21  C20   180.00   0.0  0
 WTG  CONST_37  H14  C23  C22  C21   180.00   0.0  0
 WTG  CONST_38  H11  C20  C21  C22   180.00   0.0  0
 WTG  CONST_39  H12  C21  C22  C23   180.00   0.0  0
 WTG  CONST_40  H13  C22  C23  C24   180.00   0.0  0
 WTG  CONST_41  H11  C20  C19  C24   180.00   0.0  0
 WTG  CONST_42  H6   C04  C05  C26   180.00   0.0  0
 WTG  CONST_43  H17  N18  C17  C19     0.00   0.0  0
 WTG  CONST_44  H17  N18  C17  N16   180.00   0.0  0
 WTG  CONST_45  C11  C09  N08  C07   180.00   0.0  0
 WTG  CONST_46  H16  N08  C09  C11     0.00   0.0  0
 WTG  CONST_47  O10  C09  N08  C07     0.00   0.0  0
 WTG  CONST_48  H16  N08  C09  O10   180.00   0.0  0
 WTG  Var_01    N16  C14  C12  C11     0.12  30.0  1
 WTG  Var_02    C17  N18  C11  C12    -1.73  30.0  1
 WTG  Var_03    C17  N16  C14  C12    -1.72  30.0  1
 WTG  Var_04    N18  C11  C12  C14     1.52  30.0  1
 WTG  Var_05    N18  C17  C19  C20    40.85  30.0  2
 WTG  Var_06    N16  C17  C19  C20  -137.89  30.0  2
 WTG  Var_07    N18  C17  C19  C24  -139.79  30.0  2
 WTG  Var_08    N16  C17  C19  C24    41.47  30.0  2
 WTG  Var_09    N18  C11  C12  O13   179.17  30.0  1
 WTG  Var_10    N16  C14  C12  O13  -177.65  30.0  1
 WTG  Var_11    C17  N18  C11  C09   178.25  30.0  1
 WTG  Var_12    C14  C12  C11  C09  -178.45  30.0  1
 WTG  Var_13    O15  C14  C12  C11   179.20  30.0  1
 WTG  Var_14    O15  C14  N16  C17   179.25  30.0  1
 WTG  Var_15    H17  N18  C11  C12   171.99  30.0  1
 WTG  Var_16    C01  O02  C03  C28   172.45  30.0  2
 WTG  Var_17    C09  C11  C12  O13    -0.81  30.0  1
 WTG  Var_18    O15  C14  C12  O13     1.42  30.0  1
 WTG  Var_19    C04  C03  O02  C01    -7.38  30.0  2
 WTG  Var_20    C07  C06  C05  C04  -111.07  30.0  2
 WTG  Var_21    C26  C05  C06  C07    68.06  30.0  2
 WTG  Var_22    N08  C09  C11  C12   135.12  30.0  2
 WTG  Var_23    O10  C09  C11  C12   -45.66  30.0  2
 WTG  Var_24    N18  C11  C09  N08   -44.85  30.0  2
 WTG  Var_25    O10  C09  C11  N18   134.36  30.0  2
 WTG  Var_26    H7   C06  C05  C04    11.69  30.0  2
 WTG  Var_27    H8   C06  C05  C04   128.68  30.0  2
 WTG  Var_28    H17  N18  C11  C09    -8.03  30.0  1
 WTG  Var_29    H7   C06  C05  C26  -169.18  30.0  2
 WTG  Var_30    H8   C06  C05  C26   -52.19  30.0  2
 WTG  Var_31    N08  C07  C06  C05    59.41  30.0  3
 WTG  Var_32    H3   C01  O02  C03  -175.93  30.0  3
 WTG  Var_33    H4   C01  O02  C03   -56.94  30.0  3
 WTG  Var_34    H5   C01  O02  C03    65.29  30.0  3
 WTG  Var_35    H9   C07  C06  C05  -178.62  30.0  3
 WTG  Var_36    H10  C07  C06  C05   -61.12  30.0  3
 WTG  Var_37    C09  N08  C07  C06  -172.73  30.0  3
 WTG  Var_38    H16  N08  C07  C06    17.70  30.0  3
 WTG  Var_39    H9   C07  N08  C09    65.92  30.0  1
 WTG  Var_40    H10  C07  N08  C09   -51.66  30.0  1
 WTG  Var_41    H7   C06  C07  N08   -63.60  30.0  2
 WTG  Var_42    H8   C06  C07  N08  -178.56  30.0  2

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
 WTG  plan-1  C27  0.020
 WTG  plan-1  C28  0.020
 WTG  plan-1  C03  0.020
 WTG  plan-1  C04  0.020
 WTG  plan-1  C05  0.020
 WTG  plan-1  C06  0.020
 WTG  plan-1  C26  0.020
 WTG  plan-1  O02  0.020
 WTG  plan-1  O29  0.020
 WTG  plan-1  H1   0.020
 WTG  plan-1  H6   0.020
 WTG  plan-1  H15  0.020
 WTG  plan-2  C17  0.020
 WTG  plan-2  C19  0.020
 WTG  plan-2  C20  0.020
 WTG  plan-2  C21  0.020
 WTG  plan-2  C22  0.020
 WTG  plan-2  C23  0.020
 WTG  plan-2  C24  0.020
 WTG  plan-2  F25  0.020
 WTG  plan-2  H11  0.020
 WTG  plan-2  H12  0.020
 WTG  plan-2  H13  0.020
 WTG  plan-2  H14  0.020
 WTG  plan-3  C07  0.020
 WTG  plan-3  C09  0.020
 WTG  plan-3  C11  0.020
 WTG  plan-3  N08  0.020
 WTG  plan-3  O10  0.020
 WTG  plan-3  H16  0.020
 WTG  plan-4  C12  0.020
 WTG  plan-4  C14  0.020
 WTG  plan-4  N16  0.020
 WTG  plan-4  O15  0.020
 WTG  plan-5  C11  0.020
 WTG  plan-5  C14  0.020
 WTG  plan-5  C17  0.020
 WTG  plan-5  C19  0.020
 WTG  plan-5  N16  0.020
 WTG  plan-5  N18  0.020
 WTG  plan-5  H17  0.020

