# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:07:55 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4,4'-{[(3S)-3-(2-hydroxyethyl)cyclohexylidene]methanediyl}diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC[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
 5KF  5KF  4,4'-{[(3S)-3-(2-hydroxyethyl)cyclohexylidene]methanediyl}diphenol  ligand  48  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5KF
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
 5KF  O01  O  OH1   0  -0.633   5.7651   1.7358  -0.8521
 5KF  C02  C  CR6   0   0.339   4.5258   1.3139  -0.5275
 5KF  C03  C  CR16  0  -0.370   4.2923   0.3435   0.4444
 5KF  C04  C  CR16  0  -0.280   2.9961  -0.0561   0.7284
 5KF  C05  C  CR6   0   0.010   1.8993   0.5048   0.0757
 5KF  C06  C  C     0  -0.025   0.5192   0.0486   0.3798
 5KF  C07  C  CR6   0   0.021   0.3188  -1.4154   0.2422
 5KF  C08  C  CR16  0  -0.288  -0.2181  -2.1863   1.2740
 5KF  C09  C  CR16  0  -0.328  -0.3742  -3.5578   1.1543
 5KF  C10  C  CR6   0   0.339   0.0163  -4.2018  -0.0166
 5KF  O11  O  OH1   0  -0.633  -0.1512  -5.5381  -0.0911
 5KF  C12  C  CR16  0  -0.370   0.5686  -3.4532  -1.0536
 5KF  C13  C  CR16  0  -0.282   0.7214  -2.0830  -0.9144
 5KF  C14  C  C     0   0.113  -0.4586   0.8940   0.7549
 5KF  C15  C  CH2   0  -0.504  -0.2402   2.3519   1.0515
 5KF  C16  C  CH2   0  -0.427  -1.1128   3.2367   0.1620
 5KF  C17  C  CH2   0  -0.428  -2.5824   2.8525   0.2756
 5KF  C18  C  CH1   0  -0.235  -2.8039   1.3673  -0.0090
 5KF  C19  C  CH2   0  -0.443  -4.2602   0.9393   0.1590
 5KF  C20  C  CH2   0  -0.143  -5.2179   1.6307  -0.7936
 5KF  O21  O  OH1   0  -0.677  -6.4984   1.0509  -0.6439
 5KF  C22  C  CH2   0  -0.486  -1.9042   0.5031   0.8916
 5KF  C23  C  CR16  0  -0.282   2.1555   1.4656  -0.9025
 5KF  C24  C  CR16  0  -0.327   3.4453   1.8719  -1.2053
 5KF  H1   H  HOH1  0   0.473   6.4240   1.2829  -0.3141
 5KF  H2   H  HCR6  0   0.268   5.1226  -0.1036   0.9796
 5KF  H3   H  HCR6  0   0.249   2.8398  -0.8200   1.4805
 5KF  H5   H  HCR6  0   0.254  -0.5133  -1.7071   2.1993
 5KF  H6   H  HCR6  0   0.260  -0.7893  -4.1319   1.9736
 5KF  H7   H  HOH1  0   0.473   0.1743  -5.8697  -0.9352
 5KF  H8   H  HCR6  0   0.268   0.8862  -3.9393  -1.9695
 5KF  H9   H  HCR6  0   0.249   1.1626  -1.5239  -1.7309
 5KF  H11  H  HCH2  0   0.234  -0.5337   2.5235   2.0953
 5KF  H12  H  HCH2  0   0.247   0.8072   2.6397   0.9730
 5KF  H13  H  HCH2  0   0.232  -0.9753   4.2857   0.4342
 5KF  H14  H  HCH2  0   0.217  -0.7885   3.1386  -0.8792
 5KF  H15  H  HCH2  0   0.209  -2.9422   3.0769   1.2872
 5KF  H16  H  HCH2  0   0.234  -3.1742   3.4658  -0.4078
 5KF  H17  H  HCH1  0   0.217  -2.5051   1.1736  -1.0482
 5KF  H18  H  HCH2  0   0.226  -4.3309  -0.1411  -0.0055
 5KF  H19  H  HCH2  0   0.216  -4.5755   1.1214   1.1929
 5KF  H20  H  HCH2  0   0.193  -5.2491   2.7072  -0.5850
 5KF  H21  H  HCH2  0   0.186  -4.8480   1.5171  -1.8223
 5KF  H22  H  HOH1  0   0.451  -7.1030   1.5050  -1.2372
 5KF  H23  H  HCH2  0   0.246  -2.0657  -0.5464   0.6470
 5KF  H24  H  HCH2  0   0.226  -2.2244   0.6383   1.9331
 5KF  H25  H  HCR6  0   0.252   1.3286   1.8994  -1.4512
 5KF  H26  H  HCR6  0   0.260   3.6151   2.6159  -1.9738

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
 5KF  O01  C02  single    1.349  0.020  1.349
 5KF  C09  C08  aromatic  1.386  0.020  1.386
 5KF  C09  C10  aromatic  1.392  0.020  1.392
 5KF  C03  C02  aromatic  1.393  0.020  1.393
 5KF  C03  C04  aromatic  1.386  0.020  1.386
 5KF  C02  C24  aromatic  1.392  0.020  1.392
 5KF  O11  C10  single    1.349  0.020  1.349
 5KF  C08  C07  aromatic  1.395  0.020  1.395
 5KF  C10  C12  aromatic  1.393  0.020  1.393
 5KF  C04  C05  aromatic  1.394  0.020  1.394
 5KF  C24  C23  aromatic  1.386  0.020  1.386
 5KF  C05  C23  aromatic  1.395  0.020  1.395
 5KF  C05  C06  single    1.485  0.020  1.485
 5KF  C07  C06  single    1.484  0.020  1.484
 5KF  C07  C13  aromatic  1.395  0.020  1.395
 5KF  C12  C13  aromatic  1.386  0.020  1.386
 5KF  C06  C14  double    1.346  0.020  1.346
 5KF  O21  C20  single    1.414  0.020  1.414
 5KF  C14  C15  single    1.504  0.020  1.504
 5KF  C14  C22  single    1.504  0.020  1.504
 5KF  C16  C15  single    1.528  0.020  1.528
 5KF  C16  C17  single    1.523  0.020  1.523
 5KF  C18  C22  single    1.539  0.020  1.539
 5KF  C18  C17  single    1.528  0.020  1.528
 5KF  C18  C19  single    1.527  0.020  1.527
 5KF  C20  C19  single    1.517  0.020  1.517
 5KF  O01  H1   single    0.850  0.020  0.980
 5KF  C03  H2   single    0.930  0.020  1.080
 5KF  C04  H3   single    0.930  0.020  1.080
 5KF  C08  H5   single    0.930  0.020  1.080
 5KF  C09  H6   single    0.930  0.020  1.080
 5KF  O11  H7   single    0.850  0.020  0.980
 5KF  C12  H8   single    0.930  0.020  1.080
 5KF  C13  H9   single    0.930  0.020  1.080
 5KF  C15  H11  single    0.970  0.020  1.090
 5KF  C15  H12  single    0.970  0.020  1.090
 5KF  C16  H13  single    0.970  0.020  1.090
 5KF  C16  H14  single    0.970  0.020  1.090
 5KF  C17  H15  single    0.970  0.020  1.090
 5KF  C17  H16  single    0.970  0.020  1.090
 5KF  C18  H17  single    0.970  0.020  1.090
 5KF  C19  H18  single    0.970  0.020  1.090
 5KF  C19  H19  single    0.970  0.020  1.090
 5KF  C20  H20  single    0.970  0.020  1.090
 5KF  C20  H21  single    0.970  0.020  1.090
 5KF  O21  H22  single    0.850  0.020  0.980
 5KF  C22  H23  single    0.970  0.020  1.090
 5KF  C22  H24  single    0.970  0.020  1.090
 5KF  C23  H25  single    0.930  0.020  1.080
 5KF  C24  H26  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
 5KF  H1   O01  C02  110.30  3.000
 5KF  C24  C02  C03  119.26  3.000
 5KF  C24  C02  O01  118.07  3.000
 5KF  C03  C02  O01  122.67  3.000
 5KF  H2   C03  C04  119.74  3.000
 5KF  H2   C03  C02  120.21  3.000
 5KF  C04  C03  C02  120.04  3.000
 5KF  H3   C04  C05  119.68  3.000
 5KF  H3   C04  C03  118.73  3.000
 5KF  C05  C04  C03  121.59  3.000
 5KF  C23  C05  C06  121.73  3.000
 5KF  C06  C05  C04  120.77  3.000
 5KF  C23  C05  C04  117.45  3.000
 5KF  C14  C06  C07  123.19  3.000
 5KF  C14  C06  C05  122.63  3.000
 5KF  C07  C06  C05  114.17  3.000
 5KF  C13  C07  C08  117.37  3.000
 5KF  C13  C07  C06  120.67  3.000
 5KF  C08  C07  C06  121.89  3.000
 5KF  H5   C08  C09  118.75  3.000
 5KF  H5   C08  C07  119.49  3.000
 5KF  C09  C08  C07  121.76  3.000
 5KF  H6   C09  C10  119.90  3.000
 5KF  H6   C09  C08  120.17  3.000
 5KF  C10  C09  C08  119.93  3.000
 5KF  C12  C10  O11  122.72  3.000
 5KF  C12  C10  C09  119.25  3.000
 5KF  O11  C10  C09  118.03  3.000
 5KF  H7   O11  C10  110.33  3.000
 5KF  H8   C12  C13  119.72  3.000
 5KF  H8   C12  C10  120.26  3.000
 5KF  C13  C12  C10  120.02  3.000
 5KF  H9   C13  C12  118.65  3.000
 5KF  H9   C13  C07  119.70  3.000
 5KF  C12  C13  C07  121.65  3.000
 5KF  C22  C14  C15  111.95  3.000
 5KF  C22  C14  C06  124.09  3.000
 5KF  C15  C14  C06  123.95  3.000
 5KF  H12  C15  H11  106.52  3.000
 5KF  H12  C15  C16  110.75  3.000
 5KF  H11  C15  C16  108.07  3.000
 5KF  H12  C15  C14  112.44  3.000
 5KF  H11  C15  C14  107.47  3.000
 5KF  C16  C15  C14  111.32  3.000
 5KF  H14  C16  H13  106.60  3.000
 5KF  H14  C16  C17  109.51  3.000
 5KF  H13  C16  C17  110.19  3.000
 5KF  H14  C16  C15  109.42  3.000
 5KF  H13  C16  C15  109.82  3.000
 5KF  C17  C16  C15  111.19  3.000
 5KF  H16  C17  H15  106.52  3.000
 5KF  H16  C17  C18  110.52  3.000
 5KF  H15  C17  C18  108.85  3.000
 5KF  H16  C17  C16  109.54  3.000
 5KF  H15  C17  C16  109.49  3.000
 5KF  C18  C17  C16  111.78  3.000
 5KF  H17  C18  C22  107.19  3.000
 5KF  H17  C18  C19  108.30  3.000
 5KF  C22  C18  C19  109.62  3.000
 5KF  H17  C18  C17  107.94  3.000
 5KF  C19  C18  C17  112.96  3.000
 5KF  C22  C18  C17  110.62  3.000
 5KF  H19  C19  H18  106.68  3.000
 5KF  H19  C19  C20  109.57  3.000
 5KF  H18  C19  C20  108.33  3.000
 5KF  H19  C19  C18  109.36  3.000
 5KF  H18  C19  C18  108.75  3.000
 5KF  C20  C19  C18  113.90  3.000
 5KF  H21  C20  H20  106.79  3.000
 5KF  H21  C20  O21  111.20  3.000
 5KF  H20  C20  O21  110.89  3.000
 5KF  H21  C20  C19  109.15  3.000
 5KF  H20  C20  C19  110.22  3.000
 5KF  O21  C20  C19  108.56  3.000
 5KF  H22  O21  C20  108.10  3.000
 5KF  H24  C22  H23  106.76  3.000
 5KF  H24  C22  C18  108.40  3.000
 5KF  H23  C22  C18  108.84  3.000
 5KF  H24  C22  C14  109.54  3.000
 5KF  H23  C22  C14  111.87  3.000
 5KF  C18  C22  C14  111.28  3.000
 5KF  H25  C23  C24  118.84  3.000
 5KF  H25  C23  C05  119.41  3.000
 5KF  C24  C23  C05  121.75  3.000
 5KF  H26  C24  C23  120.16  3.000
 5KF  H26  C24  C02  119.94  3.000
 5KF  C23  C24  C02  119.89  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
 5KF  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 5KF  CONST_02  C05  C23  C24  C02    0.00   0.0  0
 5KF  CONST_03  C23  C24  C02  C03    0.00   0.0  0
 5KF  CONST_04  C23  C05  C04  C03    0.00   0.0  0
 5KF  CONST_05  C24  C02  C03  C04    0.00   0.0  0
 5KF  CONST_06  C24  C23  C05  C04    0.00   0.0  0
 5KF  CONST_07  C10  C09  C08  C07    0.00   0.0  0
 5KF  CONST_08  C10  C12  C13  C07    0.00   0.0  0
 5KF  CONST_09  C12  C10  C09  C08    0.00   0.0  0
 5KF  CONST_10  C12  C13  C07  C08    0.00   0.0  0
 5KF  CONST_11  C13  C07  C08  C09    0.00   0.0  0
 5KF  CONST_12  C13  C12  C10  C09    0.00   0.0  0
 5KF  CONST_13  C04  C03  C02  O01  180.00   0.0  0
 5KF  CONST_14  C23  C24  C02  O01  180.00   0.0  0
 5KF  CONST_15  C06  C05  C04  C03  180.00   0.0  0
 5KF  CONST_16  C24  C23  C05  C06  180.00   0.0  0
 5KF  CONST_17  C09  C08  C07  C06  180.00   0.0  0
 5KF  CONST_18  C12  C13  C07  C06  180.00   0.0  0
 5KF  CONST_19  O11  C10  C09  C08  180.00   0.0  0
 5KF  CONST_20  C13  C12  C10  O11  180.00   0.0  0
 5KF  CONST_21  H3   C04  C03  C02  180.00   0.0  0
 5KF  CONST_22  H25  C23  C24  C02  180.00   0.0  0
 5KF  CONST_23  H26  C24  C02  C03  180.00   0.0  0
 5KF  CONST_24  H2   C03  C04  C05  180.00   0.0  0
 5KF  CONST_25  H6   C09  C08  C07  180.00   0.0  0
 5KF  CONST_26  H8   C12  C13  C07  180.00   0.0  0
 5KF  CONST_27  H9   C13  C07  C08  180.00   0.0  0
 5KF  CONST_28  H5   C08  C09  C10  180.00   0.0  0
 5KF  Var_01    C17  C16  C15  C14   54.74  30.0  1
 5KF  Var_02    C18  C22  C14  C15   56.28  30.0  1
 5KF  Var_03    C18  C17  C16  C15  -54.27  30.0  1
 5KF  Var_04    C22  C14  C15  C16  -56.14  30.0  1
 5KF  Var_05    C07  C06  C05  C04  -54.35  30.0  2
 5KF  Var_06    C08  C07  C06  C05  126.65  30.0  2
 5KF  Var_07    C15  C14  C06  C05   -6.86  30.0  2
 5KF  Var_08    O21  C20  C19  C18  173.69  30.0  1

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
 5KF  chir_01  C18  C22  C17  C19  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
 5KF  plan-1  O01  0.020
 5KF  plan-1  C02  0.020
 5KF  plan-1  C03  0.020
 5KF  plan-1  C04  0.020
 5KF  plan-1  C05  0.020
 5KF  plan-1  C06  0.020
 5KF  plan-1  C23  0.020
 5KF  plan-1  C24  0.020
 5KF  plan-1  H2   0.020
 5KF  plan-1  H3   0.020
 5KF  plan-1  H25  0.020
 5KF  plan-1  H26  0.020
 5KF  plan-2  C06  0.020
 5KF  plan-2  C07  0.020
 5KF  plan-2  C08  0.020
 5KF  plan-2  C09  0.020
 5KF  plan-2  C10  0.020
 5KF  plan-2  O11  0.020
 5KF  plan-2  C12  0.020
 5KF  plan-2  C13  0.020
 5KF  plan-2  H5   0.020
 5KF  plan-2  H6   0.020
 5KF  plan-2  H8   0.020
 5KF  plan-2  H9   0.020

