# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 12:43:56 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 6-[(4,4-dimethylcyclohexyl)methyl]-4-hydroxy-3-phenylpyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CCC(CC1)CC2=CC(=C(C(=O)N2)c3ccccc3)O
#
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
 3KY  3KY  6-[(4,4-dimethylcyclohexyl)methyl]-4-hydroxy-3-phenylpyridin-2(1H)-one  ligand  48  23  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3KY
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
 3KY  O1   O  O     0  -0.504   1.8481   1.4169  -1.7334
 3KY  C19  C  CR6   0   0.500   1.4991   0.4144  -1.1120
 3KY  C12  C  CR6   0  -0.341   2.3070  -0.3134  -0.1753
 3KY  C13  C  CR6   0   0.131   3.6837   0.1555   0.0818
 3KY  C18  C  CR16  0  -0.288   4.6018   0.2710  -0.9623
 3KY  C17  C  CR16  0  -0.245   5.8956   0.7130  -0.7258
 3KY  C16  C  CR16  0  -0.270   6.2949   1.0504   0.5611
 3KY  C15  C  CR16  0  -0.244   5.3894   0.9422   1.6081
 3KY  C14  C  CR16  0  -0.293   4.0952   0.5009   1.3689
 3KY  C    C  CR6   0   0.478   1.7873  -1.4287   0.4451
 3KY  O    O  OH1   0  -0.601   2.5691  -2.1131   1.2830
 3KY  N    N  NR16  0  -0.711   0.2222  -0.0900  -1.3029
 3KY  C2   C  CR6   0   0.439  -0.3065  -1.1698  -0.6839
 3KY  C1   C  CR16  0  -0.549   0.4613  -1.8627   0.1985
 3KY  C3   C  CH2   0  -0.525  -1.7267  -1.5223  -0.9908
 3KY  C4   C  CH1   0  -0.219  -2.7462  -0.8775  -0.0387
 3KY  C11  C  CH2   0  -0.428  -4.1513  -1.3568  -0.4040
 3KY  C10  C  CH2   0  -0.403  -5.2207  -0.7245   0.4797
 3KY  C7   C  CT    0  -0.086  -5.1880   0.8101   0.4742
 3KY  C9   C  CH3   0  -0.641  -6.1664   1.3387   1.5217
 3KY  C8   C  CH3   0  -0.650  -5.5987   1.3595  -0.8943
 3KY  C6   C  CH2   0  -0.395  -3.7673   1.2624   0.8379
 3KY  C5   C  CH2   0  -0.445  -2.6859   0.6490  -0.0462
 3KY  H1   H  HCR6  0   0.245   4.3057   0.0028  -1.9682
 3KY  H2   H  HCR6  0   0.253   6.5939   0.7930  -1.5489
 3KY  H3   H  HCR6  0   0.254   7.3036   1.3960   0.7468
 3KY  H4   H  HCR6  0   0.254   5.6896   1.2050   2.6144
 3KY  H5   H  HCR6  0   0.245   3.3940   0.4361   2.1912
 3KY  H6   H  HOH1  0   0.484   2.1029  -2.8806   1.6349
 3KY  H7   H  HNR6  0   0.411  -0.3525   0.4117  -1.9675
 3KY  H8   H  HCR6  0   0.285   0.0615  -2.7384   0.6928
 3KY  H9   H  HCH2  0   0.260  -1.9593  -1.2339  -2.0205
 3KY  H10  H  HCH2  0   0.270  -1.8328  -2.6075  -0.9379
 3KY  H11  H  HCH1  0   0.228  -2.5212  -1.2238   0.9780
 3KY  H12  H  HCH2  0   0.216  -4.3457  -1.1250  -1.4567
 3KY  H13  H  HCH2  0   0.232  -4.2028  -2.4461  -0.3193
 3KY  H14  H  HCH2  0   0.222  -6.2113  -1.0766   0.1742
 3KY  H15  H  HCH2  0   0.213  -5.0768  -1.0718   1.5099
 3KY  H16  H  HCH3  0   0.219  -5.9135   0.9731   2.5196
 3KY  H17  H  HCH3  0   0.220  -6.1544   2.4308   1.5553
 3KY  H18  H  HCH3  0   0.221  -7.1900   1.0250   1.3030
 3KY  H19  H  HCH3  0   0.222  -6.6098   1.0368  -1.1523
 3KY  H20  H  HCH3  0   0.221  -5.5931   2.4519  -0.8895
 3KY  H21  H  HCH3  0   0.226  -4.9376   1.0374  -1.7000
 3KY  H22  H  HCH2  0   0.222  -3.7042   2.3544   0.7962
 3KY  H23  H  HCH2  0   0.214  -3.5684   0.9837   1.8793
 3KY  H24  H  HCH2  0   0.237  -1.7091   0.9951   0.3005
 3KY  H25  H  HCH2  0   0.215  -2.7937   1.0099  -1.0758

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
 3KY  O    C    single    1.335  0.020  1.335
 3KY  C16  C15  aromatic  1.389  0.020  1.389
 3KY  C16  C17  aromatic  1.389  0.020  1.389
 3KY  C15  C14  aromatic  1.388  0.020  1.388
 3KY  C17  C18  aromatic  1.388  0.020  1.388
 3KY  C14  C13  aromatic  1.395  0.020  1.395
 3KY  C18  C13  aromatic  1.395  0.020  1.395
 3KY  C13  C12  single    1.477  0.020  1.477
 3KY  C    C12  double    1.378  0.020  1.378
 3KY  C    C1   single    1.417  0.020  1.417
 3KY  C12  C19  single    1.435  0.020  1.435
 3KY  C1   C2   double    1.360  0.020  1.360
 3KY  C2   N    single    1.352  0.020  1.352
 3KY  C2   C3   single    1.495  0.020  1.495
 3KY  C19  N    single    1.386  0.020  1.386
 3KY  C19  O1   double    1.230  0.020  1.230
 3KY  C3   C4   single    1.537  0.020  1.537
 3KY  C4   C11  single    1.529  0.020  1.529
 3KY  C4   C5   single    1.528  0.020  1.528
 3KY  C11  C10  single    1.525  0.020  1.525
 3KY  C9   C7   single    1.528  0.020  1.528
 3KY  C10  C7   single    1.535  0.020  1.535
 3KY  C5   C6   single    1.526  0.020  1.526
 3KY  C7   C6   single    1.535  0.020  1.535
 3KY  C7   C8   single    1.531  0.020  1.531
 3KY  C18  H1   single    0.930  0.020  1.080
 3KY  C17  H2   single    0.930  0.020  1.080
 3KY  C16  H3   single    0.930  0.020  1.080
 3KY  C15  H4   single    0.930  0.020  1.080
 3KY  C14  H5   single    0.930  0.020  1.080
 3KY  O    H6   single    0.850  0.020  0.980
 3KY  N    H7   single    0.860  0.020  1.020
 3KY  C1   H8   single    0.930  0.020  1.080
 3KY  C3   H9   single    0.970  0.020  1.090
 3KY  C3   H10  single    0.970  0.020  1.090
 3KY  C4   H11  single    0.970  0.020  1.090
 3KY  C11  H12  single    0.970  0.020  1.090
 3KY  C11  H13  single    0.970  0.020  1.090
 3KY  C10  H14  single    0.970  0.020  1.090
 3KY  C10  H15  single    0.970  0.020  1.090
 3KY  C9   H16  single    0.970  0.020  1.090
 3KY  C9   H17  single    0.970  0.020  1.090
 3KY  C9   H18  single    0.970  0.020  1.090
 3KY  C8   H19  single    0.970  0.020  1.090
 3KY  C8   H20  single    0.970  0.020  1.090
 3KY  C8   H21  single    0.970  0.020  1.090
 3KY  C6   H22  single    0.970  0.020  1.090
 3KY  C6   H23  single    0.970  0.020  1.090
 3KY  C5   H24  single    0.970  0.020  1.090
 3KY  C5   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
 3KY  N    C19  C12  115.08  3.000
 3KY  N    C19  O1   119.23  3.000
 3KY  C12  C19  O1   125.69  3.000
 3KY  C    C12  C13  122.02  3.000
 3KY  C    C12  C19  119.47  3.000
 3KY  C13  C12  C19  118.51  3.000
 3KY  C14  C13  C18  118.42  3.000
 3KY  C18  C13  C12  120.63  3.000
 3KY  C14  C13  C12  120.95  3.000
 3KY  H1   C18  C17  119.50  3.000
 3KY  H1   C18  C13  119.67  3.000
 3KY  C17  C18  C13  120.83  3.000
 3KY  H2   C17  C16  120.08  3.000
 3KY  H2   C17  C18  119.70  3.000
 3KY  C16  C17  C18  120.22  3.000
 3KY  H3   C16  C15  120.21  3.000
 3KY  H3   C16  C17  120.30  3.000
 3KY  C15  C16  C17  119.49  3.000
 3KY  H4   C15  C14  119.73  3.000
 3KY  H4   C15  C16  120.08  3.000
 3KY  C14  C15  C16  120.19  3.000
 3KY  H5   C14  C15  119.47  3.000
 3KY  H5   C14  C13  119.67  3.000
 3KY  C15  C14  C13  120.85  3.000
 3KY  C1   C    O    120.02  3.000
 3KY  C1   C    C12  121.50  3.000
 3KY  O    C    C12  118.47  3.000
 3KY  H6   O    C    110.73  3.000
 3KY  H7   N    C2   118.33  3.000
 3KY  H7   N    C19  115.68  3.000
 3KY  C2   N    C19  125.99  3.000
 3KY  C3   C2   C1   123.33  3.000
 3KY  C3   C2   N    117.76  3.000
 3KY  C1   C2   N    118.90  3.000
 3KY  H8   C1   C2   120.02  3.000
 3KY  H8   C1   C    120.94  3.000
 3KY  C2   C1   C    119.04  3.000
 3KY  H10  C3   H9   106.67  3.000
 3KY  H10  C3   C4   108.82  3.000
 3KY  H9   C3   C4   109.36  3.000
 3KY  H10  C3   C2   108.46  3.000
 3KY  H9   C3   C2   109.44  3.000
 3KY  C4   C3   C2   113.83  3.000
 3KY  H11  C4   C5   108.17  3.000
 3KY  H11  C4   C11  108.11  3.000
 3KY  C5   C4   C11  110.39  3.000
 3KY  H11  C4   C3   107.79  3.000
 3KY  C5   C4   C3   112.96  3.000
 3KY  C11  C4   C3   109.28  3.000
 3KY  H13  C11  H12  106.07  3.000
 3KY  H13  C11  C10  109.58  3.000
 3KY  H12  C11  C10  110.18  3.000
 3KY  H13  C11  C4   109.69  3.000
 3KY  H12  C11  C4   109.05  3.000
 3KY  C10  C11  C4   112.10  3.000
 3KY  H15  C10  H14  106.20  3.000
 3KY  H15  C10  C7   108.49  3.000
 3KY  H14  C10  C7   109.86  3.000
 3KY  H15  C10  C11  108.74  3.000
 3KY  H14  C10  C11  109.85  3.000
 3KY  C7   C10  C11  113.43  3.000
 3KY  C6   C7   C8   110.76  3.000
 3KY  C8   C7   C9   108.48  3.000
 3KY  C6   C7   C9   109.17  3.000
 3KY  C8   C7   C10  110.87  3.000
 3KY  C6   C7   C10  108.27  3.000
 3KY  C9   C7   C10  109.26  3.000
 3KY  H18  C9   H17  107.66  3.000
 3KY  H18  C9   H16  107.67  3.000
 3KY  H17  C9   H16  107.69  3.000
 3KY  H18  C9   C7   111.30  3.000
 3KY  H17  C9   C7   111.09  3.000
 3KY  H16  C9   C7   111.24  3.000
 3KY  H21  C8   H20  107.18  3.000
 3KY  H21  C8   H19  107.42  3.000
 3KY  H20  C8   H19  107.53  3.000
 3KY  H21  C8   C7   113.06  3.000
 3KY  H20  C8   C7   110.70  3.000
 3KY  H19  C8   C7   110.70  3.000
 3KY  H23  C6   H22  106.22  3.000
 3KY  H23  C6   C5   108.65  3.000
 3KY  H22  C6   C5   109.76  3.000
 3KY  H23  C6   C7   108.55  3.000
 3KY  H22  C6   C7   109.78  3.000
 3KY  C5   C6   C7   113.60  3.000
 3KY  H25  C5   H24  106.35  3.000
 3KY  H25  C5   C6   110.02  3.000
 3KY  H24  C5   C6   108.81  3.000
 3KY  H25  C5   C4   109.24  3.000
 3KY  H24  C5   C4   110.50  3.000
 3KY  C6   C5   C4   111.77  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
 3KY  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 3KY  CONST_02  C16  C17  C18  C13    0.00   0.0  0
 3KY  CONST_03  C15  C16  C17  C18    0.00   0.0  0
 3KY  CONST_04  C15  C14  C13  C18    0.00   0.0  0
 3KY  CONST_05  C14  C15  C16  C17    0.00   0.0  0
 3KY  CONST_06  C14  C13  C18  C17    0.00   0.0  0
 3KY  CONST_07  C15  C14  C13  C12  180.00   0.0  0
 3KY  CONST_08  C17  C18  C13  C12  180.00   0.0  0
 3KY  CONST_09  C2   N    C19  C12    0.00   0.0  0
 3KY  CONST_10  C2   N    C19  O1   180.00   0.0  0
 3KY  CONST_11  H5   C14  C13  C12    0.00   0.0  0
 3KY  CONST_12  H1   C18  C13  C12    0.00   0.0  0
 3KY  CONST_13  H4   C15  C14  C13  180.00   0.0  0
 3KY  CONST_14  H2   C17  C18  C13  180.00   0.0  0
 3KY  CONST_15  H3   C16  C17  C18  180.00   0.0  0
 3KY  CONST_16  H7   N    C19  C12  180.00   0.0  0
 3KY  Var_01    C14  C13  C12  C19  121.82  30.0  2
 3KY  Var_02    C7   C10  C11  C4    55.49  30.0  1
 3KY  Var_03    C7   C6   C5   C4   -55.80  30.0  1
 3KY  Var_04    C6   C7   C10  C11  -53.82  30.0  1
 3KY  Var_05    C5   C6   C7   C10   54.09  30.0  1
 3KY  Var_06    C4   C3   C2   N    -91.40  30.0  3
 3KY  Var_07    H16  C9   C7   C10   59.06  30.0  3
 3KY  Var_08    H19  C8   C7   C10   59.76  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
 3KY  chir_01  C4  C3  C11  C5  positiv

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
 3KY  plan-1  C12  0.020
 3KY  plan-1  C13  0.020
 3KY  plan-1  C18  0.020
 3KY  plan-1  C17  0.020
 3KY  plan-1  C16  0.020
 3KY  plan-1  C15  0.020
 3KY  plan-1  C14  0.020
 3KY  plan-1  H1   0.020
 3KY  plan-1  H2   0.020
 3KY  plan-1  H3   0.020
 3KY  plan-1  H4   0.020
 3KY  plan-1  H5   0.020
 3KY  plan-2  O1   0.020
 3KY  plan-2  C19  0.020
 3KY  plan-2  C12  0.020
 3KY  plan-2  C13  0.020
 3KY  plan-2  C    0.020
 3KY  plan-2  O    0.020
 3KY  plan-2  N    0.020
 3KY  plan-2  C2   0.020
 3KY  plan-2  C1   0.020
 3KY  plan-2  C3   0.020
 3KY  plan-2  H7   0.020
 3KY  plan-2  H8   0.020

