# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 05:37:15 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 4,4'-{[(3S)-3-(methylsulfanyl)cyclohexylidene]methanediyl}diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@H]1CCCC(C1)=C(c2ccc(O)cc2)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
 5K1  5K1  4,4'-{[(3S)-3-(methylsulfanyl)cyclohexylidene]methanediyl}diphenol  ligand  45  23  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5K1
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
 5K1  O01  O  OH1   0  -0.632   5.8641   1.2889  -0.5426
 5K1  C02  C  CR6   0   0.339   4.5549   1.0276  -0.3531
 5K1  C03  C  CR16  0  -0.323   4.2114   0.0681   0.5979
 5K1  C04  C  CR16  0  -0.278   2.8805  -0.2377   0.8221
 5K1  C05  C  CR6   0   0.011   1.8532   0.4066   0.1298
 5K1  C06  C  C     0  -0.018   0.4340   0.0452   0.3750
 5K1  C07  C  CR6   0   0.016   0.1444  -1.4028   0.2258
 5K1  C08  C  CR16  0  -0.287  -0.4669  -2.1416   1.2394
 5K1  C09  C  CR16  0  -0.328  -0.7013  -3.5009   1.1094
 5K1  C10  C  CR6   0   0.341  -0.3184  -4.1639  -0.0536
 5K1  O11  O  OH1   0  -0.632  -0.5627  -5.4871  -0.1376
 5K1  C12  C  CR16  0  -0.370   0.3042  -3.4470  -1.0731
 5K1  C13  C  CR16  0  -0.279   0.5359  -2.0892  -0.9235
 5K1  C14  C  C     0   0.109  -0.4997   0.9526   0.7142
 5K1  C15  C  CH2   0  -0.504  -0.2040   2.3951   1.0202
 5K1  C16  C  CH2   0  -0.432  -0.9984   3.3306   0.1095
 5K1  C17  C  CH2   0  -0.411  -2.4915   3.0327   0.1941
 5K1  C18  C  CH1   0  -0.368  -2.7686   1.5681  -0.1150
 5K1  S19  S  S2    0  -0.032  -4.5283   1.1333   0.0742
 5K1  C20  C  CH3   0  -0.768  -5.2648   2.0211  -1.3159
 5K1  C21  C  CH2   0  -0.489  -1.9699   0.6379   0.8081
 5K1  C22  C  CR16  0  -0.283   2.2177   1.3521  -0.8258
 5K1  C23  C  CR16  0  -0.373   3.5472   1.6661  -1.0691
 5K1  H1   H  HOH1  0   0.474   5.9761   1.9653  -1.2198
 5K1  H2   H  HCR6  0   0.261   4.9885  -0.4377   1.1575
 5K1  H3   H  HCR6  0   0.247   2.6386  -0.9930   1.5605
 5K1  H5   H  HCR6  0   0.255  -0.7580  -1.6482   2.1586
 5K1  H6   H  HCR6  0   0.261  -1.1723  -4.0517   1.9142
 5K1  H7   H  HOH1  0   0.474  -0.2305  -5.8369  -0.9718
 5K1  H8   H  HCR6  0   0.269   0.6152  -3.9486  -1.9830
 5K1  H9   H  HCR6  0   0.250   1.0306  -1.5534  -1.7247
 5K1  H11  H  HCH2  0   0.237  -0.5138   2.5840   2.0561
 5K1  H12  H  HCH2  0   0.251   0.8603   2.6179   0.9700
 5K1  H13  H  HCH2  0   0.239  -0.8103   4.3697   0.3880
 5K1  H14  H  HCH2  0   0.222  -0.6565   3.2150  -0.9239
 5K1  H15  H  HCH2  0   0.221  -2.8562   3.2562   1.2019
 5K1  H16  H  HCH2  0   0.243  -3.0394   3.6798  -0.4942
 5K1  H17  H  HCH1  0   0.264  -2.4853   1.3524  -1.1512
 5K1  H18  H  HCH3  0   0.259  -5.1444   3.0988  -1.2220
 5K1  H19  H  HCH3  0   0.260  -4.8397   1.6903  -2.2624
 5K1  H20  H  HCH3  0   0.275  -6.3295   1.7947  -1.3161
 5K1  H21  H  HCH2  0   0.261  -2.1814  -0.3962   0.5422
 5K1  H22  H  HCH2  0   0.243  -2.3126   0.7852   1.8400
 5K1  H23  H  HCR6  0   0.255   1.4515   1.8496  -1.4076
 5K1  H24  H  HCR6  0   0.269   3.7935   2.4043  -1.8243

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
 5K1  O01  C02  single    1.348  0.020  1.348
 5K1  C02  C23  aromatic  1.391  0.020  1.391
 5K1  C02  C03  aromatic  1.394  0.020  1.394
 5K1  C23  C22  aromatic  1.388  0.020  1.388
 5K1  C03  C04  aromatic  1.384  0.020  1.384
 5K1  C22  C05  aromatic  1.393  0.020  1.393
 5K1  C04  C05  aromatic  1.396  0.020  1.396
 5K1  C05  C06  single    1.485  0.020  1.485
 5K1  C06  C07  single    1.484  0.020  1.484
 5K1  C06  C14  double    1.345  0.020  1.345
 5K1  C07  C13  aromatic  1.395  0.020  1.395
 5K1  C07  C08  aromatic  1.395  0.020  1.395
 5K1  C13  C12  aromatic  1.386  0.020  1.386
 5K1  C08  C09  aromatic  1.386  0.020  1.386
 5K1  C12  C10  aromatic  1.393  0.020  1.393
 5K1  C09  C10  aromatic  1.392  0.020  1.392
 5K1  C10  O11  single    1.348  0.020  1.348
 5K1  C15  C14  single    1.504  0.020  1.504
 5K1  C15  C16  single    1.528  0.020  1.528
 5K1  C14  C21  single    1.506  0.020  1.506
 5K1  C16  C17  single    1.525  0.020  1.525
 5K1  C21  C18  single    1.535  0.020  1.535
 5K1  C17  C18  single    1.522  0.020  1.522
 5K1  C18  S19  single    1.822  0.020  1.822
 5K1  S19  C20  single    1.806  0.020  1.806
 5K1  O01  H1   single    0.850  0.020  0.980
 5K1  C03  H2   single    0.930  0.020  1.080
 5K1  C04  H3   single    0.930  0.020  1.080
 5K1  C08  H5   single    0.930  0.020  1.080
 5K1  C09  H6   single    0.930  0.020  1.080
 5K1  O11  H7   single    0.850  0.020  0.980
 5K1  C12  H8   single    0.930  0.020  1.080
 5K1  C13  H9   single    0.930  0.020  1.080
 5K1  C15  H11  single    0.970  0.020  1.090
 5K1  C15  H12  single    0.970  0.020  1.090
 5K1  C16  H13  single    0.970  0.020  1.090
 5K1  C16  H14  single    0.970  0.020  1.090
 5K1  C17  H15  single    0.970  0.020  1.090
 5K1  C17  H16  single    0.970  0.020  1.090
 5K1  C18  H17  single    0.970  0.020  1.090
 5K1  C20  H18  single    0.970  0.020  1.090
 5K1  C20  H19  single    0.970  0.020  1.090
 5K1  C20  H20  single    0.970  0.020  1.090
 5K1  C21  H21  single    0.970  0.020  1.090
 5K1  C21  H22  single    0.970  0.020  1.090
 5K1  C22  H23  single    0.930  0.020  1.080
 5K1  C23  H24  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
 5K1  H1   O01  C02  110.34  3.000
 5K1  C23  C02  C03  119.24  3.000
 5K1  C03  C02  O01  117.94  3.000
 5K1  C23  C02  O01  122.82  3.000
 5K1  H2   C03  C04  120.21  3.000
 5K1  H2   C03  C02  119.81  3.000
 5K1  C04  C03  C02  119.97  3.000
 5K1  H3   C04  C05  119.69  3.000
 5K1  H3   C04  C03  118.62  3.000
 5K1  C05  C04  C03  121.69  3.000
 5K1  C22  C05  C06  121.91  3.000
 5K1  C06  C05  C04  120.59  3.000
 5K1  C22  C05  C04  117.44  3.000
 5K1  C14  C06  C07  123.22  3.000
 5K1  C14  C06  C05  122.73  3.000
 5K1  C07  C06  C05  114.04  3.000
 5K1  C13  C07  C08  117.45  3.000
 5K1  C08  C07  C06  121.94  3.000
 5K1  C13  C07  C06  120.54  3.000
 5K1  H5   C08  C09  118.76  3.000
 5K1  H5   C08  C07  119.54  3.000
 5K1  C09  C08  C07  121.70  3.000
 5K1  H6   C09  C10  119.88  3.000
 5K1  H6   C09  C08  120.18  3.000
 5K1  C10  C09  C08  119.93  3.000
 5K1  C12  C10  O11  122.71  3.000
 5K1  O11  C10  C09  118.01  3.000
 5K1  C12  C10  C09  119.28  3.000
 5K1  H7   O11  C10  110.35  3.000
 5K1  H8   C12  C13  119.73  3.000
 5K1  H8   C12  C10  120.27  3.000
 5K1  C13  C12  C10  120.00  3.000
 5K1  H9   C13  C12  118.76  3.000
 5K1  H9   C13  C07  119.62  3.000
 5K1  C12  C13  C07  121.62  3.000
 5K1  C21  C14  C15  112.31  3.000
 5K1  C21  C14  C06  123.51  3.000
 5K1  C15  C14  C06  124.17  3.000
 5K1  H12  C15  H11  106.52  3.000
 5K1  H12  C15  C16  110.82  3.000
 5K1  H11  C15  C16  108.08  3.000
 5K1  H12  C15  C14  112.29  3.000
 5K1  H11  C15  C14  107.55  3.000
 5K1  C16  C15  C14  111.32  3.000
 5K1  H14  C16  H13  106.70  3.000
 5K1  H14  C16  C17  109.73  3.000
 5K1  H13  C16  C17  109.90  3.000
 5K1  H14  C16  C15  109.61  3.000
 5K1  H13  C16  C15  109.94  3.000
 5K1  C17  C16  C15  110.87  3.000
 5K1  H16  C17  H15  106.98  3.000
 5K1  H16  C17  C18  110.54  3.000
 5K1  H15  C17  C18  108.83  3.000
 5K1  H16  C17  C16  109.91  3.000
 5K1  H15  C17  C16  109.71  3.000
 5K1  C18  C17  C16  110.79  3.000
 5K1  H17  C18  C21  108.36  3.000
 5K1  H17  C18  S19  107.50  3.000
 5K1  C21  C18  S19  107.19  3.000
 5K1  H17  C18  C17  109.54  3.000
 5K1  S19  C18  C17  112.59  3.000
 5K1  C21  C18  C17  111.49  3.000
 5K1  C20  S19  C18  101.34  3.000
 5K1  H20  C20  H19  108.56  3.000
 5K1  H20  C20  H18  108.31  3.000
 5K1  H19  C20  H18  109.43  3.000
 5K1  H20  C20  S19  107.26  3.000
 5K1  H19  C20  S19  111.13  3.000
 5K1  H18  C20  S19  112.03  3.000
 5K1  H22  C21  H21  107.25  3.000
 5K1  H22  C21  C18  108.77  3.000
 5K1  H21  C21  C18  109.13  3.000
 5K1  H22  C21  C14  109.60  3.000
 5K1  H21  C21  C14  111.89  3.000
 5K1  C18  C21  C14  110.11  3.000
 5K1  H23  C22  C23  118.67  3.000
 5K1  H23  C22  C05  119.68  3.000
 5K1  C23  C22  C05  121.65  3.000
 5K1  H24  C23  C22  119.59  3.000
 5K1  H24  C23  C02  120.41  3.000
 5K1  C22  C23  C02  119.99  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
 5K1  CONST_01  C05  C22  C23  C02    0.00   0.0  0
 5K1  CONST_02  C05  C04  C03  C02    0.00   0.0  0
 5K1  CONST_03  C22  C23  C02  C03    0.00   0.0  0
 5K1  CONST_04  C22  C05  C04  C03    0.00   0.0  0
 5K1  CONST_05  C23  C02  C03  C04    0.00   0.0  0
 5K1  CONST_06  C23  C22  C05  C04    0.00   0.0  0
 5K1  CONST_07  C10  C12  C13  C07    0.00   0.0  0
 5K1  CONST_08  C10  C09  C08  C07    0.00   0.0  0
 5K1  CONST_09  C12  C13  C07  C08    0.00   0.0  0
 5K1  CONST_10  C12  C10  C09  C08    0.00   0.0  0
 5K1  CONST_11  C13  C07  C08  C09    0.00   0.0  0
 5K1  CONST_12  C13  C12  C10  C09    0.00   0.0  0
 5K1  CONST_13  C22  C23  C02  O01  180.00   0.0  0
 5K1  CONST_14  C04  C03  C02  O01  180.00   0.0  0
 5K1  CONST_15  C06  C05  C04  C03  180.00   0.0  0
 5K1  CONST_16  C23  C22  C05  C06  180.00   0.0  0
 5K1  CONST_17  C12  C13  C07  C06  180.00   0.0  0
 5K1  CONST_18  C09  C08  C07  C06  180.00   0.0  0
 5K1  CONST_19  O11  C10  C09  C08  180.00   0.0  0
 5K1  CONST_20  C13  C12  C10  O11  180.00   0.0  0
 5K1  CONST_21  H23  C22  C23  C02  180.00   0.0  0
 5K1  CONST_22  H3   C04  C03  C02  180.00   0.0  0
 5K1  CONST_23  H24  C23  C02  C03  180.00   0.0  0
 5K1  CONST_24  H2   C03  C04  C05  180.00   0.0  0
 5K1  CONST_25  H8   C12  C13  C07  180.00   0.0  0
 5K1  CONST_26  H6   C09  C08  C07  180.00   0.0  0
 5K1  CONST_27  H9   C13  C07  C08  180.00   0.0  0
 5K1  CONST_28  H5   C08  C09  C10  180.00   0.0  0
 5K1  Var_01    C17  C16  C15  C14   55.08  30.0  1
 5K1  Var_02    C18  C21  C14  C15   55.90  30.0  1
 5K1  Var_03    C18  C17  C16  C15  -55.10  30.0  1
 5K1  Var_04    C21  C14  C15  C16  -56.13  30.0  1
 5K1  Var_05    C07  C06  C05  C04  -53.81  30.0  2
 5K1  Var_06    C13  C07  C06  C05  -51.32  30.0  2
 5K1  Var_07    C15  C14  C06  C05   -6.46  30.0  2
 5K1  Var_08    H18  C20  S19  C18  -63.34  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
 5K1  chir_01  C18  C21  C17  S19  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
 5K1  plan-1  O01  0.020
 5K1  plan-1  C02  0.020
 5K1  plan-1  C03  0.020
 5K1  plan-1  C04  0.020
 5K1  plan-1  C05  0.020
 5K1  plan-1  C06  0.020
 5K1  plan-1  C22  0.020
 5K1  plan-1  C23  0.020
 5K1  plan-1  H2   0.020
 5K1  plan-1  H3   0.020
 5K1  plan-1  H23  0.020
 5K1  plan-1  H24  0.020
 5K1  plan-2  C06  0.020
 5K1  plan-2  C07  0.020
 5K1  plan-2  C08  0.020
 5K1  plan-2  C09  0.020
 5K1  plan-2  C10  0.020
 5K1  plan-2  O11  0.020
 5K1  plan-2  C12  0.020
 5K1  plan-2  C13  0.020
 5K1  plan-2  H5   0.020
 5K1  plan-2  H6   0.020
 5K1  plan-2  H8   0.020
 5K1  plan-2  H9   0.020

