# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 12:08:38 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 6-(cyclohexylmethyl)-4-hydroxy-3-phenylpyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(C(=O)NC(=C1)CC2CCCCC2)c3ccccc3
#
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
 3KX  3KX  6-(cyclohexylmethyl)-4-hydroxy-3-phenylpyridin-2(1H)-one  ligand  42  21  .  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_3KX
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
 3KX  O    O  O     0  -0.504  -1.4040  -1.7879  -1.5406
 3KX  C    C  CR6   0   0.500  -0.9543  -0.7373  -1.0851
 3KX  C11  C  CR6   0  -0.345  -1.6801   0.2032  -0.2816
 3KX  C12  C  CR6   0   0.132  -3.0906  -0.0886   0.0460
 3KX  C17  C  CR16  0  -0.288  -4.0430  -0.2238  -0.9641
 3KX  C16  C  CR16  0  -0.245  -5.3695  -0.4929  -0.6582
 3KX  C15  C  CR16  0  -0.270  -5.7670  -0.6353   0.6653
 3KX  C14  C  CR16  0  -0.244  -4.8270  -0.5086   1.6792
 3KX  C13  C  CR16  0  -0.291  -3.5002  -0.2401   1.3704
 3KX  C10  C  CR6   0   0.478  -1.0537   1.3490   0.1577
 3KX  O1   O  OH1   0  -0.601  -1.7594   2.2215   0.8802
 3KX  C9   C  CR16  0  -0.545   0.3025   1.6140  -0.1521
 3KX  C1   C  CR6   0   0.438   0.9952   0.7162  -0.9028
 3KX  N    N  NR16  0  -0.711   0.3654  -0.3960  -1.3416
 3KX  C2   C  CH2   0  -0.525   2.4448   0.8804  -1.2323
 3KX  C3   C  CH1   0  -0.226   3.3742   0.4515  -0.0868
 3KX  C8   C  CH2   0  -0.427   3.2336  -1.0284   0.2669
 3KX  C7   C  CH2   0  -0.429   4.1997  -1.4367   1.3756
 3KX  C6   C  CH2   0  -0.431   5.6421  -1.0955   1.0193
 3KX  C5   C  CH2   0  -0.433   5.7860   0.3812   0.6691
 3KX  C4   C  CH2   0  -0.420   4.8234   0.7805  -0.4440
 3KX  H1   H  HCR6  0   0.245  -3.7474  -0.1038  -1.9986
 3KX  H2   H  HCR6  0   0.253  -6.0952  -0.5893  -1.4555
 3KX  H3   H  HCR6  0   0.254  -6.8019  -0.8433   0.9045
 3KX  H4   H  HCR6  0   0.253  -5.1247  -0.6230   2.7137
 3KX  H5   H  HCR6  0   0.245  -2.7729  -0.1570   2.1682
 3KX  H6   H  HOH1  0   0.484  -1.2182   2.9831   1.1190
 3KX  H7   H  HCR6  0   0.285   0.7914   2.5129   0.2001
 3KX  H8   H  HNR6  0   0.411   0.8892  -1.0552  -1.9026
 3KX  H9   H  HCH2  0   0.261   2.6928   0.3165  -2.1368
 3KX  H10  H  HCH2  0   0.271   2.6299   1.9326  -1.4594
 3KX  H11  H  HCH1  0   0.228   3.1025   1.0399   0.7991
 3KX  H12  H  HCH2  0   0.233   2.2099  -1.2553   0.5762
 3KX  H13  H  HCH2  0   0.211   3.4271  -1.6317  -0.6285
 3KX  H14  H  HCH2  0   0.211   3.9220  -0.9190   2.3001
 3KX  H15  H  HCH2  0   0.229   4.1000  -2.5056   1.5788
 3KX  H16  H  HCH2  0   0.227   6.3084  -1.3575   1.8450
 3KX  H17  H  HCH2  0   0.209   5.9567  -1.7015   0.1624
 3KX  H18  H  HCH2  0   0.210   5.5828   0.9894   1.5572
 3KX  H19  H  HCH2  0   0.228   6.8135   0.6032   0.3706
 3KX  H20  H  HCH2  0   0.211   5.0954   0.2512  -1.3651
 3KX  H21  H  HCH2  0   0.230   4.9179   1.8484  -0.6610

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
 3KX  O1   C10  single    1.335  0.020  1.335
 3KX  C15  C14  aromatic  1.388  0.020  1.388
 3KX  C15  C16  aromatic  1.389  0.020  1.389
 3KX  C14  C13  aromatic  1.388  0.020  1.388
 3KX  C16  C17  aromatic  1.388  0.020  1.388
 3KX  C13  C12  aromatic  1.395  0.020  1.395
 3KX  C17  C12  aromatic  1.395  0.020  1.395
 3KX  C12  C11  single    1.477  0.020  1.477
 3KX  C10  C11  double    1.378  0.020  1.378
 3KX  C10  C9   single    1.416  0.020  1.416
 3KX  C11  C    single    1.434  0.020  1.434
 3KX  C9   C1   double    1.360  0.020  1.360
 3KX  C    O    double    1.230  0.020  1.230
 3KX  C    N    single    1.387  0.020  1.387
 3KX  C1   N    single    1.351  0.020  1.351
 3KX  C1   C2   single    1.496  0.020  1.496
 3KX  C2   C3   single    1.536  0.020  1.536
 3KX  C8   C3   single    1.528  0.020  1.528
 3KX  C8   C7   single    1.526  0.020  1.526
 3KX  C3   C4   single    1.528  0.020  1.528
 3KX  C7   C6   single    1.524  0.020  1.524
 3KX  C4   C5   single    1.525  0.020  1.525
 3KX  C6   C5   single    1.524  0.020  1.524
 3KX  C17  H1   single    0.930  0.020  1.080
 3KX  C16  H2   single    0.930  0.020  1.080
 3KX  C15  H3   single    0.930  0.020  1.080
 3KX  C14  H4   single    0.930  0.020  1.080
 3KX  C13  H5   single    0.930  0.020  1.080
 3KX  O1   H6   single    0.850  0.020  0.980
 3KX  C9   H7   single    0.930  0.020  1.080
 3KX  N    H8   single    0.860  0.020  1.020
 3KX  C2   H9   single    0.970  0.020  1.090
 3KX  C2   H10  single    0.970  0.020  1.090
 3KX  C3   H11  single    0.970  0.020  1.090
 3KX  C8   H12  single    0.970  0.020  1.090
 3KX  C8   H13  single    0.970  0.020  1.090
 3KX  C7   H14  single    0.970  0.020  1.090
 3KX  C7   H15  single    0.970  0.020  1.090
 3KX  C6   H16  single    0.970  0.020  1.090
 3KX  C6   H17  single    0.970  0.020  1.090
 3KX  C5   H18  single    0.970  0.020  1.090
 3KX  C5   H19  single    0.970  0.020  1.090
 3KX  C4   H20  single    0.970  0.020  1.090
 3KX  C4   H21  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
 3KX  N    C    C11  115.07  3.000
 3KX  N    C    O    119.30  3.000
 3KX  C11  C    O    125.62  3.000
 3KX  C10  C11  C12  121.85  3.000
 3KX  C10  C11  C    119.60  3.000
 3KX  C12  C11  C    118.55  3.000
 3KX  C13  C12  C17  118.47  3.000
 3KX  C17  C12  C11  120.70  3.000
 3KX  C13  C12  C11  120.83  3.000
 3KX  H1   C17  C16  119.54  3.000
 3KX  H1   C17  C12  119.66  3.000
 3KX  C16  C17  C12  120.79  3.000
 3KX  H2   C16  C15  120.05  3.000
 3KX  H2   C16  C17  119.72  3.000
 3KX  C15  C16  C17  120.23  3.000
 3KX  H3   C15  C14  120.23  3.000
 3KX  H3   C15  C16  120.26  3.000
 3KX  C14  C15  C16  119.51  3.000
 3KX  H4   C14  C13  119.72  3.000
 3KX  H4   C14  C15  120.13  3.000
 3KX  C13  C14  C15  120.15  3.000
 3KX  H5   C13  C14  119.53  3.000
 3KX  H5   C13  C12  119.61  3.000
 3KX  C14  C13  C12  120.86  3.000
 3KX  C9   C10  O1   120.17  3.000
 3KX  C9   C10  C11  121.42  3.000
 3KX  O1   C10  C11  118.41  3.000
 3KX  H6   O1   C10  110.71  3.000
 3KX  H7   C9   C1   119.86  3.000
 3KX  H7   C9   C10  121.12  3.000
 3KX  C1   C9   C10  119.02  3.000
 3KX  C2   C1   N    118.07  3.000
 3KX  C2   C1   C9   122.88  3.000
 3KX  N    C1   C9   119.02  3.000
 3KX  H8   N    C1   118.36  3.000
 3KX  H8   N    C    115.77  3.000
 3KX  C1   N    C    125.87  3.000
 3KX  H10  C2   H9   106.62  3.000
 3KX  H10  C2   C3   108.75  3.000
 3KX  H9   C2   C3   109.59  3.000
 3KX  H10  C2   C1   108.41  3.000
 3KX  H9   C2   C1   110.19  3.000
 3KX  C3   C2   C1   113.04  3.000
 3KX  H11  C3   C4   107.94  3.000
 3KX  H11  C3   C8   108.03  3.000
 3KX  C4   C3   C8   110.47  3.000
 3KX  H11  C3   C2   107.60  3.000
 3KX  C4   C3   C2   109.83  3.000
 3KX  C8   C3   C2   112.79  3.000
 3KX  H13  C8   H12  106.38  3.000
 3KX  H13  C8   C7   109.52  3.000
 3KX  H12  C8   C7   109.37  3.000
 3KX  H13  C8   C3   109.11  3.000
 3KX  H12  C8   C3   110.65  3.000
 3KX  C7   C8   C3   111.66  3.000
 3KX  H15  C7   H14  106.39  3.000
 3KX  H15  C7   C6   110.42  3.000
 3KX  H14  C7   C6   109.36  3.000
 3KX  H15  C7   C8   109.82  3.000
 3KX  H14  C7   C8   109.04  3.000
 3KX  C6   C7   C8   111.67  3.000
 3KX  H17  C6   H16  106.45  3.000
 3KX  H17  C6   C5   109.21  3.000
 3KX  H16  C6   C5   110.37  3.000
 3KX  H17  C6   C7   109.31  3.000
 3KX  H16  C6   C7   110.28  3.000
 3KX  C5   C6   C7   111.09  3.000
 3KX  H19  C5   H18  106.45  3.000
 3KX  H19  C5   C4   109.94  3.000
 3KX  H18  C5   C4   109.23  3.000
 3KX  H19  C5   C6   110.38  3.000
 3KX  H18  C5   C6   109.52  3.000
 3KX  C4   C5   C6   111.20  3.000
 3KX  H21  C4   H20  106.45  3.000
 3KX  H21  C4   C5   110.23  3.000
 3KX  H20  C4   C5   109.28  3.000
 3KX  H21  C4   C3   109.78  3.000
 3KX  H20  C4   C3   109.13  3.000
 3KX  C5   C4   C3   111.82  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
 3KX  CONST_01  C15  C14  C13  C12    0.00   0.0  0
 3KX  CONST_02  C15  C16  C17  C12    0.00   0.0  0
 3KX  CONST_03  C14  C15  C16  C17    0.00   0.0  0
 3KX  CONST_04  C14  C13  C12  C17    0.00   0.0  0
 3KX  CONST_05  C13  C14  C15  C16    0.00   0.0  0
 3KX  CONST_06  C13  C12  C17  C16    0.00   0.0  0
 3KX  CONST_07  C14  C13  C12  C11  180.00   0.0  0
 3KX  CONST_08  C16  C17  C12  C11  180.00   0.0  0
 3KX  CONST_09  C1   N    C    C11    0.00   0.0  0
 3KX  CONST_10  C1   N    C    O    180.00   0.0  0
 3KX  CONST_11  H5   C13  C12  C11    0.00   0.0  0
 3KX  CONST_12  H1   C17  C12  C11    0.00   0.0  0
 3KX  CONST_13  H4   C14  C13  C12  180.00   0.0  0
 3KX  CONST_14  H2   C16  C17  C12  180.00   0.0  0
 3KX  CONST_15  H3   C15  C16  C17  180.00   0.0  0
 3KX  CONST_16  H8   N    C    C11  180.00   0.0  0
 3KX  Var_01    C13  C12  C11  C    118.90  30.0  3
 3KX  Var_02    C6   C7   C8   C3   -55.10  30.0  1
 3KX  Var_03    C6   C5   C4   C3    55.83  30.0  1
 3KX  Var_04    C5   C6   C7   C8    54.86  30.0  1
 3KX  Var_05    C4   C5   C6   C7   -55.06  30.0  1
 3KX  Var_06    C3   C2   C1   C9    80.20  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
 3KX  chir_01  C3  C2  C8  C4  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
 3KX  plan-1  C11  0.020
 3KX  plan-1  C12  0.020
 3KX  plan-1  C17  0.020
 3KX  plan-1  C16  0.020
 3KX  plan-1  C15  0.020
 3KX  plan-1  C14  0.020
 3KX  plan-1  C13  0.020
 3KX  plan-1  H1   0.020
 3KX  plan-1  H2   0.020
 3KX  plan-1  H3   0.020
 3KX  plan-1  H4   0.020
 3KX  plan-1  H5   0.020
 3KX  plan-2  O    0.020
 3KX  plan-2  C    0.020
 3KX  plan-2  C11  0.020
 3KX  plan-2  C12  0.020
 3KX  plan-2  C10  0.020
 3KX  plan-2  O1   0.020
 3KX  plan-2  C9   0.020
 3KX  plan-2  C1   0.020
 3KX  plan-2  N    0.020
 3KX  plan-2  C2   0.020
 3KX  plan-2  H7   0.020
 3KX  plan-2  H8   0.020

