# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 07:56:22 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-[(4R)-4-(4-hydroxyphenyl)-3,4-dimethyl-2,5-dioxoimidazolidin-1-yl]-2-(trifluoromethyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(c2ccc(C#N)c(c2)C(F)(F)F)C(=O)[C@@]1(C)c3ccc(O)cc3
#
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
 PK0  PK0  4-[(4R)-4-(4-hydroxyphenyl)-3,4-dimethyl-2,5-dioxoimidazolidin-1-yl]-2-(trifluoromethyl)benzonitrile  ligand  42  28  .  2021-08-19  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PK0
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
 PK0  N4   N  NR5   0  -0.493   2.1662   1.8244   0.7440
 PK0  C31  C  CH3   0  -0.664   2.6198   0.2688   2.5911
 PK0  C4   C  CH3   0  -0.529   3.1641   2.8390   0.9779
 PK0  O2   O  O     0  -0.399   0.6923  -1.3274   0.8466
 PK0  C2   C  CR5   0   0.580   1.0144  -0.1735   0.7455
 PK0  O5   O  O     0  -0.463   0.4308   3.1447   0.0015
 PK0  C5   C  CR5   0   0.724   0.9218   2.0862   0.3151
 PK0  C3   C  CR5   0  -0.125   2.3719   0.4301   1.0921
 PK0  C1B  C  CR6   0   0.157   3.4298  -0.2162   0.2134
 PK0  C2B  C  CR16  0  -0.299   4.2427  -1.2454   0.6785
 PK0  C3B  C  CR16  0  -0.322   5.1728  -1.8571  -0.1455
 PK0  C4B  C  CR6   0   0.351   5.3077  -1.4493  -1.4696
 PK0  C5B  C  CR16  0  -0.369   4.4969  -0.4233  -1.9501
 PK0  C6B  C  CR16  0  -0.279   3.5704   0.1778  -1.1148
 PK0  O4   O  OH1   0  -0.627   6.2275  -2.0690  -2.2302
 PK0  N1   N  NR5   0  -0.685   0.2309   0.8547   0.2881
 PK0  C1A  C  CR6   0   0.398  -1.0966   0.7215  -0.1539
 PK0  C2A  C  CR16  0  -0.258  -1.4612   1.1942  -1.4050
 PK0  C3A  C  CR16  0  -0.244  -2.7687   1.0529  -1.8341
 PK0  C4A  C  CR6   0   0.048  -3.7069   0.4275  -1.0210
 PK0  C5A  C  CR6   0  -0.163  -3.3328  -0.0527   0.2395
 PK0  C6A  C  CR16  0  -0.335  -2.0302   0.1012   0.6707
 PK0  C41  C  CSP   0   0.024  -5.0413   0.2907  -1.5116
 PK0  N41  N  NS    0  -0.226  -6.1065   0.1989  -1.9382
 PK0  C51  C  CT    0   1.082  -4.3547  -0.7210   1.1135
 PK0  F1   F  F     0  -0.310  -4.8519  -1.8135   0.5232
 PK0  F2   F  F     0  -0.289  -3.8533  -1.0933   2.2880
 PK0  F3   F  F     0  -0.309  -5.3869   0.0939   1.3579
 PK0  H1   H  HCH3  0   0.266   1.8596   0.8080   3.1558
 PK0  H2   H  HCH3  0   0.263   2.5791  -0.7769   2.8882
 PK0  H3   H  HCH3  0   0.264   3.5982   0.6632   2.8634
 PK0  H4   H  HCH3  0   0.256   4.1301   2.4962   0.6097
 PK0  H5   H  HCH3  0   0.270   2.8938   3.7433   0.4401
 PK0  H6   H  HCH3  0   0.257   3.2555   3.0778   2.0379
 PK0  H7   H  HCR6  0   0.260   4.1676  -1.5894   1.7007
 PK0  H8   H  HCR6  0   0.268   5.7975  -2.6533   0.2395
 PK0  H9   H  HCR6  0   0.276   4.5871  -0.0892  -2.9774
 PK0  H10  H  HCR6  0   0.261   2.9607   0.9757  -1.5210
 PK0  H11  H  HOH1  0   0.477   6.2250  -1.7094  -3.1245
 PK0  H12  H  HCR6  0   0.300  -0.7340   1.6594  -2.0548
 PK0  H13  H  HCR6  0   0.303  -3.0592   1.4184  -2.8086
 PK0  H14  H  HCR6  0   0.301  -1.7304  -0.2436   1.6496

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
 PK0  O5   C5   double    1.208  0.020  1.208
 PK0  C4   N4   single    1.442  0.020  1.442
 PK0  C5   N4   single    1.342  0.020  1.342
 PK0  C5   N1   single    1.412  0.020  1.412
 PK0  F1   C51  single    1.338  0.020  1.338
 PK0  N4   C3   single    1.452  0.020  1.452
 PK0  N41  C41  triple    1.151  0.020  1.151
 PK0  C41  C4A  single    1.428  0.020  1.428
 PK0  C3A  C2A  aromatic  1.383  0.020  1.383
 PK0  C3A  C4A  aromatic  1.390  0.020  1.390
 PK0  C2A  C1A  aromatic  1.386  0.020  1.386
 PK0  C4A  C5A  aromatic  1.400  0.020  1.400
 PK0  F3   C51  single    1.338  0.020  1.338
 PK0  C1A  N1   single    1.405  0.020  1.405
 PK0  C1A  C6A  aromatic  1.392  0.020  1.392
 PK0  N1   C2   single    1.371  0.020  1.371
 PK0  C31  C3   single    1.528  0.020  1.528
 PK0  C5A  C6A  aromatic  1.381  0.020  1.381
 PK0  C5A  C51  single    1.502  0.020  1.502
 PK0  C51  F2   single    1.330  0.020  1.330
 PK0  C3   C2   single    1.526  0.020  1.526
 PK0  C3   C1B  single    1.520  0.020  1.520
 PK0  C2   O2   double    1.202  0.020  1.202
 PK0  C1B  C6B  aromatic  1.392  0.020  1.392
 PK0  C1B  C2B  aromatic  1.392  0.020  1.392
 PK0  C6B  C5B  aromatic  1.385  0.020  1.385
 PK0  C2B  C3B  aromatic  1.385  0.020  1.385
 PK0  C5B  C4B  aromatic  1.393  0.020  1.393
 PK0  C3B  C4B  aromatic  1.392  0.020  1.392
 PK0  C4B  O4   single    1.345  0.020  1.345
 PK0  C31  H1   single    0.970  0.020  1.090
 PK0  C31  H2   single    0.970  0.020  1.090
 PK0  C31  H3   single    0.970  0.020  1.090
 PK0  C4   H4   single    0.970  0.020  1.090
 PK0  C4   H5   single    0.970  0.020  1.090
 PK0  C4   H6   single    0.970  0.020  1.090
 PK0  C2B  H7   single    0.930  0.020  1.080
 PK0  C3B  H8   single    0.930  0.020  1.080
 PK0  C5B  H9   single    0.930  0.020  1.080
 PK0  C6B  H10  single    0.930  0.020  1.080
 PK0  O4   H11  single    0.850  0.020  0.980
 PK0  C2A  H12  single    0.930  0.020  1.080
 PK0  C3A  H13  single    0.930  0.020  1.080
 PK0  C6A  H14  single    0.930  0.020  1.080

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
 PK0  C3   N4   C5   113.29  3.000
 PK0  C3   N4   C4   122.60  3.000
 PK0  C5   N4   C4   123.79  3.000
 PK0  H3   C31  H2   108.26  3.000
 PK0  H3   C31  H1   108.53  3.000
 PK0  H2   C31  H1   107.94  3.000
 PK0  H3   C31  C3   110.65  3.000
 PK0  H2   C31  C3   111.31  3.000
 PK0  H1   C31  C3   110.06  3.000
 PK0  H6   C4   H5   108.66  3.000
 PK0  H6   C4   H4   108.86  3.000
 PK0  H5   C4   H4   108.39  3.000
 PK0  H6   C4   N4   111.69  3.000
 PK0  H5   C4   N4   109.46  3.000
 PK0  H4   C4   N4   109.72  3.000
 PK0  N1   C2   C3   106.71  3.000
 PK0  C3   C2   O2   126.80  3.000
 PK0  N1   C2   O2   126.48  3.000
 PK0  N1   C5   O5   124.06  3.000
 PK0  N1   C5   N4   106.84  3.000
 PK0  O5   C5   N4   129.10  3.000
 PK0  C1B  C3   C2   108.65  3.000
 PK0  C1B  C3   C31  114.17  3.000
 PK0  C2   C3   C31  109.00  3.000
 PK0  C1B  C3   N4   111.62  3.000
 PK0  C2   C3   N4   101.50  3.000
 PK0  C31  C3   N4   111.08  3.000
 PK0  C6B  C1B  C2B  117.97  3.000
 PK0  C2B  C1B  C3   121.87  3.000
 PK0  C6B  C1B  C3   120.10  3.000
 PK0  H7   C2B  C3B  117.95  3.000
 PK0  H7   C2B  C1B  120.71  3.000
 PK0  C3B  C2B  C1B  121.34  3.000
 PK0  H8   C3B  C4B  119.85  3.000
 PK0  H8   C3B  C2B  120.04  3.000
 PK0  C4B  C3B  C2B  120.11  3.000
 PK0  O4   C4B  C5B  122.84  3.000
 PK0  O4   C4B  C3B  117.99  3.000
 PK0  C5B  C4B  C3B  119.17  3.000
 PK0  H9   C5B  C6B  119.58  3.000
 PK0  H9   C5B  C4B  120.36  3.000
 PK0  C6B  C5B  C4B  120.06  3.000
 PK0  H10  C6B  C5B  118.04  3.000
 PK0  H10  C6B  C1B  120.61  3.000
 PK0  C5B  C6B  C1B  121.34  3.000
 PK0  H11  O4   C4B  110.55  3.000
 PK0  C1A  N1   C5   123.42  3.000
 PK0  C1A  N1   C2   125.00  3.000
 PK0  C5   N1   C2   111.58  3.000
 PK0  C6A  C1A  C2A  120.69  3.000
 PK0  C6A  C1A  N1   119.31  3.000
 PK0  C2A  C1A  N1   119.99  3.000
 PK0  H12  C2A  C3A  119.57  3.000
 PK0  H12  C2A  C1A  120.84  3.000
 PK0  C3A  C2A  C1A  119.58  3.000
 PK0  H13  C3A  C4A  119.89  3.000
 PK0  H13  C3A  C2A  119.95  3.000
 PK0  C4A  C3A  C2A  120.16  3.000
 PK0  C41  C4A  C5A  121.74  3.000
 PK0  C5A  C4A  C3A  120.05  3.000
 PK0  C41  C4A  C3A  118.21  3.000
 PK0  C51  C5A  C6A  120.66  3.000
 PK0  C51  C5A  C4A  119.66  3.000
 PK0  C6A  C5A  C4A  119.68  3.000
 PK0  H14  C6A  C5A  120.62  3.000
 PK0  H14  C6A  C1A  119.54  3.000
 PK0  C5A  C6A  C1A  119.84  3.000
 PK0  N41  C41  C4A  180.00  3.000
 PK0  F3   C51  F2   107.46  3.000
 PK0  F2   C51  F1   107.53  3.000
 PK0  F3   C51  F1   106.94  3.000
 PK0  F2   C51  C5A  112.45  3.000
 PK0  F3   C51  C5A  111.13  3.000
 PK0  F1   C51  C5A  111.07  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
 PK0  CONST_01  C4B  C5B  C6B  C1B     0.00   0.0  0
 PK0  CONST_02  C4B  C3B  C2B  C1B     0.00   0.0  0
 PK0  CONST_03  C5B  C6B  C1B  C2B     0.00   0.0  0
 PK0  CONST_04  C5B  C4B  C3B  C2B     0.00   0.0  0
 PK0  CONST_05  C6B  C1B  C2B  C3B     0.00   0.0  0
 PK0  CONST_06  C6B  C5B  C4B  C3B     0.00   0.0  0
 PK0  CONST_07  C4A  C3A  C2A  C1A     0.00   0.0  0
 PK0  CONST_08  C4A  C5A  C6A  C1A     0.00   0.0  0
 PK0  CONST_09  C5A  C4A  C3A  C2A     0.00   0.0  0
 PK0  CONST_10  C5A  C6A  C1A  C2A     0.00   0.0  0
 PK0  CONST_11  C6A  C1A  C2A  C3A     0.00   0.0  0
 PK0  CONST_12  C6A  C5A  C4A  C3A     0.00   0.0  0
 PK0  CONST_13  C5B  C6B  C1B  C3    180.00   0.0  0
 PK0  CONST_14  C3B  C2B  C1B  C3    180.00   0.0  0
 PK0  CONST_15  C3A  C2A  C1A  N1    180.00   0.0  0
 PK0  CONST_16  C5A  C6A  C1A  N1    180.00   0.0  0
 PK0  CONST_17  C1A  N1   C5   N4    180.00   0.0  0
 PK0  CONST_18  C2   N1   C5   N4      0.00   0.0  0
 PK0  CONST_19  C3   C2   N1   C5      0.00   0.0  0
 PK0  CONST_20  N1   C5   N4   C3      0.00   0.0  0
 PK0  CONST_21  C1A  N1   C2   C3    180.00   0.0  0
 PK0  CONST_22  O4   C4B  C3B  C2B   180.00   0.0  0
 PK0  CONST_23  O4   C4B  C5B  C6B   180.00   0.0  0
 PK0  CONST_24  C51  C5A  C6A  C1A   180.00   0.0  0
 PK0  CONST_25  C41  C4A  C3A  C2A   180.00   0.0  0
 PK0  CONST_26  C51  C5A  C4A  C3A   180.00   0.0  0
 PK0  CONST_27  C41  C4A  C5A  C6A   180.00   0.0  0
 PK0  CONST_28  N1   C5   N4   C4    180.00   0.0  0
 PK0  CONST_29  C5   N1   C2   O2    180.00   0.0  0
 PK0  CONST_30  C1A  N1   C2   O2      0.00   0.0  0
 PK0  CONST_31  O5   C5   N1   C2    180.00   0.0  0
 PK0  CONST_32  C3   N4   C5   O5    180.00   0.0  0
 PK0  CONST_33  C1A  N1   C5   O5      0.00   0.0  0
 PK0  CONST_34  H10  C6B  C1B  C3      0.00   0.0  0
 PK0  CONST_35  H7   C2B  C1B  C3      0.00   0.0  0
 PK0  CONST_36  H9   C5B  C6B  C1B   180.00   0.0  0
 PK0  CONST_37  H8   C3B  C2B  C1B   180.00   0.0  0
 PK0  CONST_38  H12  C2A  C1A  N1      0.00   0.0  0
 PK0  CONST_39  H14  C6A  C1A  N1      0.00   0.0  0
 PK0  CONST_40  H13  C3A  C2A  C1A   180.00   0.0  0
 PK0  CONST_41  O5   C5   N4   C4      0.00   0.0  0
 PK0  Var_01    C2A  C1A  N1   C2   -126.33  30.0  3
 PK0  Var_02    F1   C51  C5A  C4A    60.89  30.0  2
 PK0  Var_03    H4   C4   N4   C5   -138.74  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PK0  chir_01  C3  N4  C2  C1B  negativ

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
 PK0  plan-1  C3   0.020
 PK0  plan-1  C1B  0.020
 PK0  plan-1  C2B  0.020
 PK0  plan-1  C3B  0.020
 PK0  plan-1  C4B  0.020
 PK0  plan-1  C5B  0.020
 PK0  plan-1  C6B  0.020
 PK0  plan-1  O4   0.020
 PK0  plan-1  H7   0.020
 PK0  plan-1  H8   0.020
 PK0  plan-1  H9   0.020
 PK0  plan-1  H10  0.020
 PK0  plan-2  N1   0.020
 PK0  plan-2  C1A  0.020
 PK0  plan-2  C2A  0.020
 PK0  plan-2  C3A  0.020
 PK0  plan-2  C4A  0.020
 PK0  plan-2  C5A  0.020
 PK0  plan-2  C6A  0.020
 PK0  plan-2  C41  0.020
 PK0  plan-2  N41  0.020
 PK0  plan-2  C51  0.020
 PK0  plan-2  H12  0.020
 PK0  plan-2  H13  0.020
 PK0  plan-2  H14  0.020
 PK0  plan-3  N4   0.020
 PK0  plan-3  C4   0.020
 PK0  plan-3  O2   0.020
 PK0  plan-3  C2   0.020
 PK0  plan-3  O5   0.020
 PK0  plan-3  C5   0.020
 PK0  plan-3  C3   0.020
 PK0  plan-3  N1   0.020
 PK0  plan-3  C1A  0.020

