# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 13:15:20 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: (5R)-2-amino-5-(2-cyclohexylethyl)-3-methyl-5-phenyl-3,5-dihydro-4H-imidazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@@](CCC2CCCCC2)(C1=O)c3ccccc3)N
#
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
 QKY  QKY  (5R)-2-amino-5-(2-cyclohexylethyl)-3-methyl-5-phenyl-3,5-dihydro-4H-imidazol-4-one  ligand  47  22  .  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_QKY
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
 QKY  N1   N  N     0  -0.467  12.3384  -47.6769  -16.3568
 QKY  C4   C  CR16  0  -0.301  11.6046  -47.5908  -20.0462
 QKY  C5   C  CR16  0  -0.243  10.8370  -48.3055  -20.9541
 QKY  C6   C  CR16  0  -0.268  10.0622  -49.3770  -20.5281
 QKY  C7   C  CR16  0  -0.237  10.0663  -49.7256  -19.1859
 QKY  C8   C  CR16  0  -0.319  10.8377  -49.0112  -18.2768
 QKY  C10  C  CH2   0  -0.425  12.9338  -44.7581  -16.8519
 QKY  C13  C  C     0  -0.431  12.6054  -41.1973  -15.3419
 QKY  C15  C  C     0  -0.429  11.5688  -41.1869  -17.6317
 QKY  C17  C  CH3   0  -0.555  15.8933  -48.2462  -16.8130
 QKY  O    O  O     0  -0.443  14.5188  -46.9791  -19.0620
 QKY  C    C  CR5   0   0.561  13.9399  -47.3046  -18.0503
 QKY  C16  C  C     0  -0.422  12.1486  -42.5727  -17.9022
 QKY  N2   N  NH2   0  -0.845  13.8104  -48.6989  -14.8493
 QKY  N    N  NR5   0  -0.518  14.5015  -47.8942  -16.9566
 QKY  C1   C  CR5   0  -0.169  12.4559  -47.1471  -17.6975
 QKY  C2   C  CR5   0   0.661  13.5020  -48.0804  -16.0062
 QKY  C3   C  CR6   0   0.168  11.6153  -47.9351  -18.6937
 QKY  C9   C  CH2   0  -0.392  12.0641  -45.6562  -17.7235
 QKY  C14  C  C     0  -0.429  12.4143  -40.4062  -16.6317
 QKY  C12  C  C     0  -0.413  13.1837  -42.5798  -15.6235
 QKY  C11  C  CR16  0  -0.224  12.3313  -43.3744  -16.6124
 QKY  H1   H  HCR6  0   0.249  12.2016  -46.7633  -20.4059
 QKY  H2   H  HCR6  0   0.253  10.8445  -48.0221  -21.9989
 QKY  H3   H  HCR6  0   0.254   9.4601  -49.9318  -21.2359
 QKY  H4   H  HCR6  0   0.252   9.4674  -50.5583  -18.8390
 QKY  H5   H  HCR6  0   0.251  10.8319  -49.2900  -17.2325
 QKY  H6   H  HCH2  0   0.227  13.0921  -45.2336  -15.8795
 QKY  H7   H  HCH2  0   0.215  13.9253  -44.6362  -17.3034
 QKY  H9   H  H     0   0.206  11.6385  -41.3035  -14.8372
 QKY  H10  H  H     0   0.224  11.4761  -40.6299  -18.5675
 QKY  H11  H  H     0   0.207  10.5530  -41.2965  -17.2354
 QKY  H12  H  HCH3  0   0.265  16.0045  -49.3062  -16.5890
 QKY  H13  H  HCH3  0   0.274  16.4020  -48.0354  -17.7493
 QKY  H14  H  HCH3  0   0.262  16.3682  -47.6604  -16.0261
 QKY  H15  H  H     0   0.230  11.5017  -43.1094  -18.6007
 QKY  H16  H  H     0   0.202  13.1229  -42.4738  -18.3973
 QKY  H17  H  HNH2  0   0.403  13.0984  -48.6749  -14.1377
 QKY  H18  H  HNH2  0   0.410  14.7510  -48.6445  -14.4947
 QKY  H19  H  HCH2  0   0.239  12.0810  -45.3066  -18.7568
 QKY  H20  H  HCH2  0   0.237  11.0222  -45.5967  -17.3936
 QKY  H21  H  H     0   0.206  13.3934  -40.1911  -17.0737
 QKY  H22  H  H     0   0.224  11.9525  -39.4386  -16.4187
 QKY  H23  H  H     0   0.221  13.2911  -43.1423  -14.6914
 QKY  H24  H  H     0   0.203  14.1941  -42.4702  -16.0369
 QKY  H25  H  HCR6  0   0.204  11.3381  -43.5170  -16.1626
 QKY  H8   H  H     0   0.223  13.2554  -40.6511  -14.6536

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
 QKY  C5   C4   aromatic  1.387  0.020  1.387
 QKY  C5   C6   aromatic  1.389  0.020  1.389
 QKY  C4   C3   aromatic  1.396  0.020  1.396
 QKY  C6   C7   aromatic  1.387  0.020  1.387
 QKY  O    C    double    1.210  0.020  1.210
 QKY  C3   C8   aromatic  1.392  0.020  1.392
 QKY  C3   C1   single    1.523  0.020  1.523
 QKY  C7   C8   aromatic  1.390  0.020  1.390
 QKY  C    C1   single    1.533  0.020  1.533
 QKY  C    N    single    1.364  0.020  1.364
 QKY  C9   C1   single    1.542  0.020  1.542
 QKY  C9   C10  single    1.524  0.020  1.524
 QKY  C16  C15  single    1.526  0.020  1.526
 QKY  C16  C11  single    1.530  0.020  1.530
 QKY  C1   N1   single    1.446  0.020  1.446
 QKY  C15  C14  single    1.525  0.020  1.525
 QKY  N    C17  single    1.443  0.020  1.443
 QKY  N    C2   single    1.392  0.020  1.392
 QKY  C10  C11  single    1.528  0.020  1.528
 QKY  C11  C12  single    1.528  0.020  1.528
 QKY  N1   C2   double    1.280  0.020  1.280
 QKY  C14  C13  single    1.525  0.020  1.525
 QKY  C2   N2   single    1.348  0.020  1.348
 QKY  C12  C13  single    1.525  0.020  1.525
 QKY  C4   H1   single    0.930  0.020  1.080
 QKY  C5   H2   single    0.930  0.020  1.080
 QKY  C6   H3   single    0.930  0.020  1.080
 QKY  C7   H4   single    0.930  0.020  1.080
 QKY  C8   H5   single    0.930  0.020  1.080
 QKY  C10  H6   single    0.970  0.020  1.090
 QKY  C10  H7   single    0.970  0.020  1.090
 QKY  C13  H8   single    0.970  0.020  1.090
 QKY  C13  H9   single    0.970  0.020  1.090
 QKY  C15  H10  single    0.970  0.020  1.090
 QKY  C15  H11  single    0.970  0.020  1.090
 QKY  C17  H12  single    0.970  0.020  1.090
 QKY  C17  H13  single    0.970  0.020  1.090
 QKY  C17  H14  single    0.970  0.020  1.090
 QKY  C16  H15  single    0.970  0.020  1.090
 QKY  C16  H16  single    0.970  0.020  1.090
 QKY  N2   H17  single    0.890  0.020  1.040
 QKY  N2   H18  single    0.890  0.020  1.040
 QKY  C9   H19  single    0.970  0.020  1.090
 QKY  C9   H20  single    0.970  0.020  1.090
 QKY  C14  H21  single    0.970  0.020  1.090
 QKY  C14  H22  single    0.970  0.020  1.090
 QKY  C12  H23  single    0.970  0.020  1.090
 QKY  C12  H24  single    0.970  0.020  1.090
 QKY  C11  H25  single    0.970  0.020  1.090

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
 QKY  C2   N1   C1   107.18  3.000
 QKY  H1   C4   C3   120.44  3.000
 QKY  H1   C4   C5   118.80  3.000
 QKY  C3   C4   C5   120.76  3.000
 QKY  H2   C5   C6   120.12  3.000
 QKY  H2   C5   C4   119.54  3.000
 QKY  C6   C5   C4   120.35  3.000
 QKY  H3   C6   C7   120.38  3.000
 QKY  H3   C6   C5   120.34  3.000
 QKY  C7   C6   C5   119.28  3.000
 QKY  H4   C7   C8   119.52  3.000
 QKY  H4   C7   C6   120.12  3.000
 QKY  C8   C7   C6   120.36  3.000
 QKY  H5   C8   C3   119.46  3.000
 QKY  H5   C8   C7   119.76  3.000
 QKY  C3   C8   C7   120.78  3.000
 QKY  H7   C10  H6   106.47  3.000
 QKY  H7   C10  C11  108.69  3.000
 QKY  H6   C10  C11  108.15  3.000
 QKY  H7   C10  C9   110.25  3.000
 QKY  H6   C10  C9   109.56  3.000
 QKY  C11  C10  C9   113.47  3.000
 QKY  H9   C13  H8   106.45  3.000
 QKY  H9   C13  C12  109.38  3.000
 QKY  H8   C13  C12  110.11  3.000
 QKY  H9   C13  C14  109.22  3.000
 QKY  H8   C13  C14  110.36  3.000
 QKY  C12  C13  C14  111.20  3.000
 QKY  H11  C15  H10  106.38  3.000
 QKY  H11  C15  C14  109.15  3.000
 QKY  H10  C15  C14  110.35  3.000
 QKY  H11  C15  C16  108.99  3.000
 QKY  H10  C15  C16  110.07  3.000
 QKY  C14  C15  C16  111.74  3.000
 QKY  H14  C17  H13  108.29  3.000
 QKY  H14  C17  H12  109.28  3.000
 QKY  H13  C17  H12  108.56  3.000
 QKY  H14  C17  N    111.17  3.000
 QKY  H13  C17  N    108.58  3.000
 QKY  H12  C17  N    110.89  3.000
 QKY  C1   C    N    104.98  3.000
 QKY  N    C    O    126.14  3.000
 QKY  C1   C    O    128.88  3.000
 QKY  H16  C16  H15  106.34  3.000
 QKY  H16  C16  C11  108.76  3.000
 QKY  H15  C16  C11  110.63  3.000
 QKY  H16  C16  C15  109.60  3.000
 QKY  H15  C16  C15  109.53  3.000
 QKY  C11  C16  C15  111.83  3.000
 QKY  H18  N2   H17  114.23  3.000
 QKY  H18  N2   C2   119.43  3.000
 QKY  H17  N2   C2   115.72  3.000
 QKY  C2   N    C    108.05  3.000
 QKY  C2   N    C17  126.31  3.000
 QKY  C    N    C17  125.64  3.000
 QKY  C9   C1   C3   110.42  3.000
 QKY  C9   C1   C    109.96  3.000
 QKY  C3   C1   C    109.29  3.000
 QKY  C9   C1   N1   110.44  3.000
 QKY  C    C1   N1   104.73  3.000
 QKY  C3   C1   N1   111.84  3.000
 QKY  N    C2   N2   118.90  3.000
 QKY  N2   C2   N1   125.99  3.000
 QKY  N    C2   N1   115.06  3.000
 QKY  C1   C3   C8   120.83  3.000
 QKY  C1   C3   C4   120.69  3.000
 QKY  C8   C3   C4   118.48  3.000
 QKY  H20  C9   H19  106.43  3.000
 QKY  H20  C9   C1   106.82  3.000
 QKY  H19  C9   C1   108.78  3.000
 QKY  H20  C9   C10  109.80  3.000
 QKY  H19  C9   C10  110.12  3.000
 QKY  C1   C9   C10  114.53  3.000
 QKY  H22  C14  H21  106.40  3.000
 QKY  H22  C14  C15  110.29  3.000
 QKY  H21  C14  C15  109.37  3.000
 QKY  H22  C14  C13  110.32  3.000
 QKY  H21  C14  C13  109.33  3.000
 QKY  C15  C14  C13  111.01  3.000
 QKY  H24  C12  H23  106.37  3.000
 QKY  H24  C12  C11  108.76  3.000
 QKY  H23  C12  C11  109.80  3.000
 QKY  H24  C12  C13  109.17  3.000
 QKY  H23  C12  C13  110.25  3.000
 QKY  C11  C12  C13  112.30  3.000
 QKY  H25  C11  C12  107.85  3.000
 QKY  H25  C11  C16  107.76  3.000
 QKY  C12  C11  C16  109.86  3.000
 QKY  H25  C11  C10  107.62  3.000
 QKY  C12  C11  C10  110.63  3.000
 QKY  C16  C11  C10  112.93  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
 QKY  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 QKY  CONST_02  C7   C8   C3   C4      0.00   0.0  0
 QKY  CONST_03  C8   C3   C4   C5      0.00   0.0  0
 QKY  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 QKY  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 QKY  CONST_06  C3   C8   C7   C6      0.00   0.0  0
 QKY  CONST_07  C1   C3   C4   C5    180.00   0.0  0
 QKY  CONST_08  C1   C3   C8   C7    180.00   0.0  0
 QKY  CONST_09  C    N    C2   N1      0.00   0.0  0
 QKY  CONST_10  C1   N1   C2   N       0.00   0.0  0
 QKY  CONST_11  C2   N    C    C1      0.00   0.0  0
 QKY  CONST_12  C17  N    C2   N1    180.00   0.0  0
 QKY  CONST_13  C1   C    N    C17   180.00   0.0  0
 QKY  CONST_14  C2   N    C    O     180.00   0.0  0
 QKY  CONST_15  N2   C2   N    C     180.00   0.0  0
 QKY  CONST_16  C1   N1   C2   N2    180.00   0.0  0
 QKY  CONST_17  H3   C6   C5   C4    180.00   0.0  0
 QKY  CONST_18  H5   C8   C3   C4    180.00   0.0  0
 QKY  CONST_19  H4   C7   C6   C5    180.00   0.0  0
 QKY  CONST_20  H1   C4   C5   C6    180.00   0.0  0
 QKY  CONST_21  H2   C5   C6   C7    180.00   0.0  0
 QKY  CONST_22  O    C    N    C17     0.00   0.0  0
 QKY  CONST_23  N2   C2   N    C17     0.00   0.0  0
 QKY  CONST_24  H17  N2   C2   N1      0.00   0.0  0
 QKY  Var_01    C16  C15  C14  C13   -54.66  30.0  1
 QKY  Var_02    C12  C13  C14  C15    54.55  30.0  1
 QKY  Var_03    C11  C16  C15  C14    55.47  30.0  1
 QKY  Var_04    C11  C12  C13  C14   -55.82  30.0  1
 QKY  Var_05    C11  C10  C9   C1   -165.49  30.0  3
 QKY  Var_06    H12  C17  N    C    -123.60  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
 QKY  chir_01  C1   C    C3   N1   negativ
 QKY  chir_02  C11  C16  C10  C12  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
 QKY  plan-1  C4   0.020
 QKY  plan-1  C5   0.020
 QKY  plan-1  C6   0.020
 QKY  plan-1  C7   0.020
 QKY  plan-1  C8   0.020
 QKY  plan-1  C1   0.020
 QKY  plan-1  C3   0.020
 QKY  plan-1  H1   0.020
 QKY  plan-1  H2   0.020
 QKY  plan-1  H3   0.020
 QKY  plan-1  H4   0.020
 QKY  plan-1  H5   0.020
 QKY  plan-2  N1   0.020
 QKY  plan-2  C17  0.020
 QKY  plan-2  O    0.020
 QKY  plan-2  C    0.020
 QKY  plan-2  N2   0.020
 QKY  plan-2  N    0.020
 QKY  plan-2  C1   0.020
 QKY  plan-2  C2   0.020
 QKY  plan-2  H17  0.020
 QKY  plan-2  H18  0.020

