# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 01:01:39 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (5R)-3-(3,4-dichlorophenyl)-5-(4-hydroxyphenyl)-1,5-dimethyl-2-thioxoimidazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=S)N(C(=O)[C@@]1(C)c2ccc(O)cc2)c3ccc(Cl)c(Cl)c3
#
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
 PK1  PK1  (5R)-3-(3,4-dichlorophenyl)-5-(4-hydroxyphenyl)-1,5-dimethyl-2-thioxoimidazolidin-4-one  ligand  38  24  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PK1
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
 PK1  N4   N   NR5   0  -0.435   1.6369   1.7898  -0.0484
 PK1  C31  C   CH3   0  -0.661   2.3031   1.4597   2.2979
 PK1  C4   C   CH3   0  -0.524   2.4869   2.8597  -0.5135
 PK1  O2   O   O     0  -0.394   0.6854  -1.0488   1.7207
 PK1  C2   C   CR5   0   0.579   0.8399  -0.0851   1.0203
 PK1  S5   S   S1    0  -0.307  -0.4076   2.4283  -1.6498
 PK1  C5   C   CR5   0   0.408   0.4115   1.5636  -0.5093
 PK1  C3   C   CR5   0  -0.155   2.0709   0.8080   0.9366
 PK1  C1B  C   CR6   0   0.171   3.2442  -0.0040   0.4168
 PK1  C2B  C   CR16  0  -0.298   4.2573  -0.4525   1.2545
 PK1  C3B  C   CR16  0  -0.367   5.3012  -1.2254   0.7677
 PK1  C4B  C   CR6   0   0.353   5.3477  -1.5682  -0.5799
 PK1  C5B  C   CR16  0  -0.321   4.3346  -1.1277  -1.4306
 PK1  C6B  C   CR16  0  -0.286   3.3006  -0.3584  -0.9314
 PK1  O4   O   OH1   0  -0.626   6.3347  -2.3104  -1.1110
 PK1  N1   N   NR5   0  -0.640  -0.0775   0.4321   0.1368
 PK1  C1A  C   CR6   0   0.329  -1.3645  -0.1186  -0.0593
 PK1  C2A  C   CR16  0  -0.263  -1.4984  -1.3543  -0.6708
 PK1  C3A  C   CR16  0  -0.222  -2.7587  -1.9055  -0.8280
 PK1  C4A  C   CR6   0   0.002  -3.8783  -1.2205  -0.3817
 PK1  C5A  C   CR6   0  -0.002  -3.7348   0.0227   0.2287
 PK1  C6A  C   CR16  0  -0.206  -2.4753   0.5722   0.3965
 PK1  CL1  CL  CL    0  -0.085  -5.1099   0.8871   0.7932
 PK1  CL2  CL  CL    0  -0.083  -5.4362  -1.9168  -0.5881
 PK1  H1   H   HCH3  0   0.270   1.4409   2.0637   2.5781
 PK1  H2   H   HCH3  0   0.264   2.4499   0.7041   3.0674
 PK1  H3   H   HCH3  0   0.265   3.1840   2.1004   2.2775
 PK1  H4   H   HCH3  0   0.261   2.8142   2.6892  -1.5389
 PK1  H5   H   HCH3  0   0.269   1.9586   3.8098  -0.4679
 PK1  H6   H   HCH3  0   0.265   3.3629   2.9131   0.1266
 PK1  H7   H   HCR6  0   0.263   4.2569  -0.2051   2.3069
 PK1  H8   H   HCR6  0   0.277   6.0795  -1.5578   1.4449
 PK1  H9   H   HCR6  0   0.271   4.3617  -1.3860  -2.4815
 PK1  H10  H   HCR6  0   0.263   2.5350  -0.0260  -1.6229
 PK1  H11  H   HOH1  0   0.477   6.9819  -2.5438  -0.4360
 PK1  H12  H   HCR6  0   0.287  -0.6292  -1.8861  -1.0335
 PK1  H13  H   HCR6  0   0.299  -2.8732  -2.8687  -1.3050
 PK1  H14  H   HCR6  0   0.302  -2.3631   1.5321   0.8814

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
 PK1  S5   C5   double    1.649  0.020  1.649
 PK1  C4   N4   single    1.443  0.020  1.443
 PK1  C5   N4   single    1.329  0.020  1.329
 PK1  C5   N1   single    1.392  0.020  1.392
 PK1  N4   C3   single    1.457  0.020  1.457
 PK1  C2A  C3A  aromatic  1.385  0.020  1.385
 PK1  C2A  C1A  aromatic  1.385  0.020  1.385
 PK1  C3A  C4A  aromatic  1.386  0.020  1.386
 PK1  C31  C3   single    1.527  0.020  1.527
 PK1  C4A  CL2  single    1.719  0.020  1.719
 PK1  C4A  C5A  aromatic  1.392  0.020  1.392
 PK1  C1A  N1   single    1.414  0.020  1.414
 PK1  C1A  C6A  aromatic  1.385  0.020  1.385
 PK1  N1   C2   single    1.375  0.020  1.375
 PK1  C6A  C5A  aromatic  1.384  0.020  1.384
 PK1  C5A  CL1  single    1.720  0.020  1.720
 PK1  C3   C2   single    1.523  0.020  1.523
 PK1  C3   C1B  single    1.519  0.020  1.519
 PK1  C2   O2   double    1.201  0.020  1.201
 PK1  C1B  C6B  aromatic  1.395  0.020  1.395
 PK1  C1B  C2B  aromatic  1.389  0.020  1.389
 PK1  C6B  C5B  aromatic  1.382  0.020  1.382
 PK1  C2B  C3B  aromatic  1.387  0.020  1.387
 PK1  C5B  C4B  aromatic  1.394  0.020  1.394
 PK1  C3B  C4B  aromatic  1.391  0.020  1.391
 PK1  C4B  O4   single    1.344  0.020  1.344
 PK1  C31  H1   single    0.970  0.020  1.090
 PK1  C31  H2   single    0.970  0.020  1.090
 PK1  C31  H3   single    0.970  0.020  1.090
 PK1  C4   H4   single    0.970  0.020  1.090
 PK1  C4   H5   single    0.970  0.020  1.090
 PK1  C4   H6   single    0.970  0.020  1.090
 PK1  C2B  H7   single    0.930  0.020  1.080
 PK1  C3B  H8   single    0.930  0.020  1.080
 PK1  C5B  H9   single    0.930  0.020  1.080
 PK1  C6B  H10  single    0.930  0.020  1.080
 PK1  O4   H11  single    0.850  0.020  0.980
 PK1  C2A  H12  single    0.930  0.020  1.080
 PK1  C3A  H13  single    0.930  0.020  1.080
 PK1  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
 PK1  C3   N4   C5   113.24  3.000
 PK1  C3   N4   C4   122.82  3.000
 PK1  C5   N4   C4   123.89  3.000
 PK1  H3   C31  H2   108.21  3.000
 PK1  H3   C31  H1   108.58  3.000
 PK1  H2   C31  H1   108.05  3.000
 PK1  H3   C31  C3   110.93  3.000
 PK1  H2   C31  C3   110.76  3.000
 PK1  H1   C31  C3   110.22  3.000
 PK1  H6   C4   H5   108.91  3.000
 PK1  H6   C4   H4   108.66  3.000
 PK1  H5   C4   H4   108.77  3.000
 PK1  H6   C4   N4   108.75  3.000
 PK1  H5   C4   N4   110.35  3.000
 PK1  H4   C4   N4   111.35  3.000
 PK1  N1   C2   C3   106.47  3.000
 PK1  C3   C2   O2   127.32  3.000
 PK1  N1   C2   O2   126.21  3.000
 PK1  N1   C5   S5   124.95  3.000
 PK1  N1   C5   N4   107.54  3.000
 PK1  S5   C5   N4   127.51  3.000
 PK1  C1B  C3   C2   109.25  3.000
 PK1  C1B  C3   C31  114.57  3.000
 PK1  C2   C3   C31  108.91  3.000
 PK1  C1B  C3   N4   111.04  3.000
 PK1  C2   C3   N4   101.04  3.000
 PK1  C31  C3   N4   111.12  3.000
 PK1  C6B  C1B  C2B  118.12  3.000
 PK1  C2B  C1B  C3   121.99  3.000
 PK1  C6B  C1B  C3   119.86  3.000
 PK1  H7   C2B  C3B  118.00  3.000
 PK1  H7   C2B  C1B  120.86  3.000
 PK1  C3B  C2B  C1B  121.14  3.000
 PK1  H8   C3B  C4B  120.37  3.000
 PK1  H8   C3B  C2B  119.47  3.000
 PK1  C4B  C3B  C2B  120.16  3.000
 PK1  O4   C4B  C5B  117.83  3.000
 PK1  O4   C4B  C3B  122.90  3.000
 PK1  C5B  C4B  C3B  119.27  3.000
 PK1  H9   C5B  C6B  120.14  3.000
 PK1  H9   C5B  C4B  119.92  3.000
 PK1  C6B  C5B  C4B  119.94  3.000
 PK1  H10  C6B  C5B  117.95  3.000
 PK1  H10  C6B  C1B  120.67  3.000
 PK1  C5B  C6B  C1B  121.38  3.000
 PK1  H11  O4   C4B  110.49  3.000
 PK1  C1A  N1   C5   124.91  3.000
 PK1  C1A  N1   C2   123.38  3.000
 PK1  C5   N1   C2   111.70  3.000
 PK1  C6A  C1A  C2A  120.84  3.000
 PK1  C6A  C1A  N1   119.35  3.000
 PK1  C2A  C1A  N1   119.79  3.000
 PK1  H12  C2A  C3A  119.85  3.000
 PK1  H12  C2A  C1A  120.59  3.000
 PK1  C3A  C2A  C1A  119.55  3.000
 PK1  H13  C3A  C4A  119.79  3.000
 PK1  H13  C3A  C2A  120.08  3.000
 PK1  C4A  C3A  C2A  120.13  3.000
 PK1  CL2  C4A  C5A  120.52  3.000
 PK1  C5A  C4A  C3A  119.94  3.000
 PK1  CL2  C4A  C3A  119.55  3.000
 PK1  CL1  C5A  C6A  119.23  3.000
 PK1  CL1  C5A  C4A  120.68  3.000
 PK1  C6A  C5A  C4A  120.09  3.000
 PK1  H14  C6A  C5A  120.08  3.000
 PK1  H14  C6A  C1A  120.47  3.000
 PK1  C5A  C6A  C1A  119.45  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
 PK1  CONST_01  C4B  C5B  C6B  C1B    0.00   0.0  0
 PK1  CONST_02  C4B  C3B  C2B  C1B    0.00   0.0  0
 PK1  CONST_03  C5B  C6B  C1B  C2B    0.00   0.0  0
 PK1  CONST_04  C5B  C4B  C3B  C2B    0.00   0.0  0
 PK1  CONST_05  C6B  C1B  C2B  C3B    0.00   0.0  0
 PK1  CONST_06  C6B  C5B  C4B  C3B    0.00   0.0  0
 PK1  CONST_07  C4A  C3A  C2A  C1A    0.00   0.0  0
 PK1  CONST_08  C4A  C5A  C6A  C1A    0.00   0.0  0
 PK1  CONST_09  C5A  C4A  C3A  C2A    0.00   0.0  0
 PK1  CONST_10  C5A  C6A  C1A  C2A    0.00   0.0  0
 PK1  CONST_11  C6A  C1A  C2A  C3A    0.00   0.0  0
 PK1  CONST_12  C6A  C5A  C4A  C3A    0.00   0.0  0
 PK1  CONST_13  C5B  C6B  C1B  C3   180.00   0.0  0
 PK1  CONST_14  C3B  C2B  C1B  C3   180.00   0.0  0
 PK1  CONST_15  C3A  C2A  C1A  N1   180.00   0.0  0
 PK1  CONST_16  C5A  C6A  C1A  N1   180.00   0.0  0
 PK1  CONST_17  C1A  N1   C5   N4   180.00   0.0  0
 PK1  CONST_18  C2   N1   C5   N4     0.00   0.0  0
 PK1  CONST_19  C3   C2   N1   C5     0.00   0.0  0
 PK1  CONST_20  N1   C5   N4   C3     0.00   0.0  0
 PK1  CONST_21  C1A  N1   C2   C3   180.00   0.0  0
 PK1  CONST_22  O4   C4B  C3B  C2B  180.00   0.0  0
 PK1  CONST_23  O4   C4B  C5B  C6B  180.00   0.0  0
 PK1  CONST_24  CL1  C5A  C6A  C1A  180.00   0.0  0
 PK1  CONST_25  CL2  C4A  C3A  C2A  180.00   0.0  0
 PK1  CONST_26  CL1  C5A  C4A  C3A  180.00   0.0  0
 PK1  CONST_27  CL2  C4A  C5A  C6A  180.00   0.0  0
 PK1  CONST_28  N1   C5   N4   C4   180.00   0.0  0
 PK1  CONST_29  C5   N1   C2   O2   180.00   0.0  0
 PK1  CONST_30  C1A  N1   C2   O2     0.00   0.0  0
 PK1  CONST_31  S5   C5   N1   C2   180.00   0.0  0
 PK1  CONST_32  C3   N4   C5   S5   180.00   0.0  0
 PK1  CONST_33  C1A  N1   C5   S5     0.00   0.0  0
 PK1  CONST_34  H10  C6B  C1B  C3     0.00   0.0  0
 PK1  CONST_35  H7   C2B  C1B  C3     0.00   0.0  0
 PK1  CONST_36  H9   C5B  C6B  C1B  180.00   0.0  0
 PK1  CONST_37  H8   C3B  C2B  C1B  180.00   0.0  0
 PK1  CONST_38  H12  C2A  C1A  N1     0.00   0.0  0
 PK1  CONST_39  H14  C6A  C1A  N1     0.00   0.0  0
 PK1  CONST_40  H13  C3A  C2A  C1A  180.00   0.0  0
 PK1  CONST_41  S5   C5   N4   C4     0.00   0.0  0
 PK1  Var_01    C2A  C1A  N1   C2   -68.91  30.0  2
 PK1  Var_02    H4   C4   N4   C5   -68.84  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
 PK1  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
 PK1  plan-1  C3   0.020
 PK1  plan-1  C1B  0.020
 PK1  plan-1  C2B  0.020
 PK1  plan-1  C3B  0.020
 PK1  plan-1  C4B  0.020
 PK1  plan-1  C5B  0.020
 PK1  plan-1  C6B  0.020
 PK1  plan-1  O4   0.020
 PK1  plan-1  H7   0.020
 PK1  plan-1  H8   0.020
 PK1  plan-1  H9   0.020
 PK1  plan-1  H10  0.020
 PK1  plan-2  N1   0.020
 PK1  plan-2  C1A  0.020
 PK1  plan-2  C2A  0.020
 PK1  plan-2  C3A  0.020
 PK1  plan-2  C4A  0.020
 PK1  plan-2  C5A  0.020
 PK1  plan-2  C6A  0.020
 PK1  plan-2  CL1  0.020
 PK1  plan-2  CL2  0.020
 PK1  plan-2  H12  0.020
 PK1  plan-2  H13  0.020
 PK1  plan-2  H14  0.020
 PK1  plan-3  N4   0.020
 PK1  plan-3  C4   0.020
 PK1  plan-3  O2   0.020
 PK1  plan-3  C2   0.020
 PK1  plan-3  S5   0.020
 PK1  plan-3  C5   0.020
 PK1  plan-3  C3   0.020
 PK1  plan-3  N1   0.020
 PK1  plan-3  C1A  0.020

