# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 05:42:00 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 4,4'-[(4-ethylcyclohexylidene)methanediyl]diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[CH]1CC[C](CC1)=[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
 5JY  5JY  4,4'-[(4-ethylcyclohexylidene)methanediyl]diphenol  ligand  47  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_5JY
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
 5JY  O01  O  OH1   0  -0.633   1.5995   5.3608  -0.5279
 5JY  C02  C  CR6   0   0.339   1.2423   4.0756  -0.3276
 5JY  C03  C  CR16  0  -0.323   1.9658   3.3352   0.6062
 5JY  C04  C  CR16  0  -0.280   1.6380   2.0114   0.8410
 5JY  C05  C  CR6   0   0.012   0.5796   1.3883   0.1766
 5JY  C06  C  C     0  -0.028   0.2612  -0.0396   0.4300
 5JY  C07  C  CR6   0   0.026   1.4067  -0.9634   0.2349
 5JY  C08  C  CR16  0  -0.280   2.1281  -0.9524  -0.9584
 5JY  C09  C  CR16  0  -0.371   3.2061  -1.7983  -1.1637
 5JY  C10  C  CR6   0   0.340   3.6059  -2.6748  -0.1573
 5JY  O11  O  OH1   0  -0.633   4.6500  -3.5173  -0.2976
 5JY  C12  C  CR16  0  -0.328   2.9134  -2.6854   1.0505
 5JY  C13  C  CR16  0  -0.287   1.8329  -1.8374   1.2354
 5JY  C14  C  C     0   0.110  -0.9647  -0.4589   0.7906
 5JY  C15  C  CH2   0  -0.502  -1.3793  -1.9022   0.8601
 5JY  C16  C  CH2   0  -0.408  -2.5431  -2.1528  -0.1064
 5JY  C17  C  CH1   0  -0.225  -3.7360  -1.2324   0.1454
 5JY  C18  C  CH2   0  -0.407  -4.8543  -1.5088  -0.8585
 5JY  C19  C  CH3   0  -0.670  -6.1494  -0.7560  -0.5831
 5JY  C20  C  CH2   0  -0.419  -3.2821   0.2264   0.1334
 5JY  C21  C  CH2   0  -0.506  -2.1146   0.4607   1.0949
 5JY  C22  C  CR16  0  -0.283  -0.1217   2.1414  -0.7625
 5JY  C23  C  CR16  0  -0.374   0.1967   3.4680  -1.0156
 5JY  H1   H  HOH1  0   0.473   1.0411   5.7625  -1.2026
 5JY  H2   H  HCR6  0   0.260   2.7849   3.7995   1.1417
 5JY  H3   H  HCR6  0   0.246   2.2170   1.4506   1.5652
 5JY  H5   H  HCR6  0   0.248   1.8409  -0.2733  -1.7524
 5JY  H6   H  HCR6  0   0.268   3.7373  -1.7728  -2.1087
 5JY  H7   H  HOH1  0   0.473   5.0343  -3.4290  -1.1767
 5JY  H8   H  HCR6  0   0.260   3.2257  -3.3518   1.8450
 5JY  H9   H  HCR6  0   0.253   1.3125  -1.8517   2.1855
 5JY  H11  H  HCH2  0   0.246  -0.5600  -2.5799   0.6252
 5JY  H12  H  HCH2  0   0.227  -1.7074  -2.1402   1.8786
 5JY  H13  H  HCH2  0   0.211  -2.1860  -2.0108  -1.1330
 5JY  H14  H  HCH2  0   0.227  -2.8599  -3.1967  -0.0276
 5JY  H15  H  HCH1  0   0.205  -4.1178  -1.4527   1.1529
 5JY  H16  H  HCH2  0   0.207  -4.4955  -1.2661  -1.8649
 5JY  H17  H  HCH2  0   0.217  -5.0616  -2.5835  -0.8630
 5JY  H18  H  HCH3  0   0.215  -6.5221  -0.9669   0.4216
 5JY  H19  H  HCH3  0   0.221  -6.0210   0.3237  -0.6669
 5JY  H20  H  HCH3  0   0.228  -6.9284  -1.0455  -1.2896
 5JY  H21  H  HCH2  0   0.211  -2.9763   0.4998  -0.8836
 5JY  H22  H  HCH2  0   0.233  -4.1081   0.8898   0.4013
 5JY  H23  H  HCH2  0   0.233  -2.4601   0.2388   2.1130
 5JY  H24  H  HCH2  0   0.246  -1.8180   1.5086   1.0885
 5JY  H25  H  HCR6  0   0.254  -0.9303   1.6840  -1.3202
 5JY  H26  H  HCR6  0   0.268  -0.3679   4.0254  -1.7549

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
 5JY  O01  C02  single    1.349  0.020  1.349
 5JY  C02  C03  aromatic  1.394  0.020  1.394
 5JY  C02  C23  aromatic  1.391  0.020  1.391
 5JY  C03  C04  aromatic  1.384  0.020  1.384
 5JY  C23  C22  aromatic  1.388  0.020  1.388
 5JY  C04  C05  aromatic  1.396  0.020  1.396
 5JY  C22  C05  aromatic  1.393  0.020  1.393
 5JY  C05  C06  single    1.485  0.020  1.485
 5JY  C06  C07  single    1.484  0.020  1.484
 5JY  C06  C14  double    1.345  0.020  1.345
 5JY  C13  C07  aromatic  1.395  0.020  1.395
 5JY  C13  C12  aromatic  1.386  0.020  1.386
 5JY  C07  C08  aromatic  1.394  0.020  1.394
 5JY  C12  C10  aromatic  1.392  0.020  1.392
 5JY  C08  C09  aromatic  1.386  0.020  1.386
 5JY  C10  C09  aromatic  1.393  0.020  1.393
 5JY  C10  O11  single    1.349  0.020  1.349
 5JY  C21  C14  single    1.504  0.020  1.504
 5JY  C21  C20  single    1.531  0.020  1.531
 5JY  C14  C15  single    1.503  0.020  1.503
 5JY  C20  C17  single    1.528  0.020  1.528
 5JY  C15  C16  single    1.533  0.020  1.533
 5JY  C17  C16  single    1.528  0.020  1.528
 5JY  C17  C18  single    1.528  0.020  1.528
 5JY  C18  C19  single    1.523  0.020  1.523
 5JY  O01  H1   single    0.850  0.020  0.980
 5JY  C03  H2   single    0.930  0.020  1.080
 5JY  C04  H3   single    0.930  0.020  1.080
 5JY  C08  H5   single    0.930  0.020  1.080
 5JY  C09  H6   single    0.930  0.020  1.080
 5JY  O11  H7   single    0.850  0.020  0.980
 5JY  C12  H8   single    0.930  0.020  1.080
 5JY  C13  H9   single    0.930  0.020  1.080
 5JY  C15  H11  single    0.970  0.020  1.090
 5JY  C15  H12  single    0.970  0.020  1.090
 5JY  C16  H13  single    0.970  0.020  1.090
 5JY  C16  H14  single    0.970  0.020  1.090
 5JY  C17  H15  single    0.970  0.020  1.090
 5JY  C18  H16  single    0.970  0.020  1.090
 5JY  C18  H17  single    0.970  0.020  1.090
 5JY  C19  H18  single    0.970  0.020  1.090
 5JY  C19  H19  single    0.970  0.020  1.090
 5JY  C19  H20  single    0.970  0.020  1.090
 5JY  C20  H21  single    0.970  0.020  1.090
 5JY  C20  H22  single    0.970  0.020  1.090
 5JY  C21  H23  single    0.970  0.020  1.090
 5JY  C21  H24  single    0.970  0.020  1.090
 5JY  C22  H25  single    0.930  0.020  1.080
 5JY  C23  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
 5JY  H1   O01  C02  110.35  3.000
 5JY  C23  C02  C03  119.30  3.000
 5JY  C23  C02  O01  122.80  3.000
 5JY  C03  C02  O01  117.91  3.000
 5JY  H2   C03  C04  120.35  3.000
 5JY  H2   C03  C02  119.73  3.000
 5JY  C04  C03  C02  119.92  3.000
 5JY  H3   C04  C05  119.48  3.000
 5JY  H3   C04  C03  118.81  3.000
 5JY  C05  C04  C03  121.71  3.000
 5JY  C22  C05  C06  121.80  3.000
 5JY  C06  C05  C04  120.69  3.000
 5JY  C22  C05  C04  117.46  3.000
 5JY  C14  C06  C07  123.00  3.000
 5JY  C14  C06  C05  122.76  3.000
 5JY  C07  C06  C05  114.24  3.000
 5JY  C13  C07  C08  117.42  3.000
 5JY  C08  C07  C06  120.45  3.000
 5JY  C13  C07  C06  122.09  3.000
 5JY  H5   C08  C09  118.70  3.000
 5JY  H5   C08  C07  119.66  3.000
 5JY  C09  C08  C07  121.63  3.000
 5JY  H6   C09  C10  120.25  3.000
 5JY  H6   C09  C08  119.73  3.000
 5JY  C10  C09  C08  120.02  3.000
 5JY  C12  C10  O11  118.06  3.000
 5JY  O11  C10  C09  122.68  3.000
 5JY  C12  C10  C09  119.26  3.000
 5JY  H7   O11  C10  110.26  3.000
 5JY  H8   C12  C13  120.23  3.000
 5JY  H8   C12  C10  119.85  3.000
 5JY  C13  C12  C10  119.93  3.000
 5JY  H9   C13  C12  118.91  3.000
 5JY  H9   C13  C07  119.37  3.000
 5JY  C12  C13  C07  121.72  3.000
 5JY  C21  C14  C15  111.52  3.000
 5JY  C15  C14  C06  124.28  3.000
 5JY  C21  C14  C06  124.10  3.000
 5JY  H12  C15  H11  106.89  3.000
 5JY  H12  C15  C16  108.84  3.000
 5JY  H11  C15  C16  109.48  3.000
 5JY  H12  C15  C14  109.51  3.000
 5JY  H11  C15  C14  112.33  3.000
 5JY  C16  C15  C14  109.70  3.000
 5JY  H14  C16  H13  106.59  3.000
 5JY  H14  C16  C17  109.70  3.000
 5JY  H13  C16  C17  109.31  3.000
 5JY  H14  C16  C15  109.29  3.000
 5JY  H13  C16  C15  108.78  3.000
 5JY  C17  C16  C15  112.97  3.000
 5JY  H15  C17  C20  107.56  3.000
 5JY  H15  C17  C18  108.15  3.000
 5JY  C20  C17  C18  112.64  3.000
 5JY  H15  C17  C16  107.54  3.000
 5JY  C18  C17  C16  110.75  3.000
 5JY  C20  C17  C16  110.00  3.000
 5JY  H17  C18  H16  106.00  3.000
 5JY  H17  C18  C19  108.97  3.000
 5JY  H16  C18  C19  109.58  3.000
 5JY  H17  C18  C17  108.60  3.000
 5JY  H16  C18  C17  108.89  3.000
 5JY  C19  C18  C17  114.47  3.000
 5JY  H20  C19  H19  107.28  3.000
 5JY  H20  C19  H18  107.51  3.000
 5JY  H19  C19  H18  107.58  3.000
 5JY  H20  C19  C18  111.04  3.000
 5JY  H19  C19  C18  112.04  3.000
 5JY  H18  C19  C18  111.17  3.000
 5JY  H22  C20  H21  106.66  3.000
 5JY  H22  C20  C21  109.24  3.000
 5JY  H21  C20  C21  109.37  3.000
 5JY  H22  C20  C17  110.69  3.000
 5JY  H21  C20  C17  109.16  3.000
 5JY  C21  C20  C17  111.59  3.000
 5JY  H24  C21  H23  106.60  3.000
 5JY  H24  C21  C20  110.57  3.000
 5JY  H23  C21  C20  108.16  3.000
 5JY  H24  C21  C14  112.27  3.000
 5JY  H23  C21  C14  107.74  3.000
 5JY  C20  C21  C14  111.26  3.000
 5JY  H25  C22  C23  118.75  3.000
 5JY  H25  C22  C05  119.63  3.000
 5JY  C23  C22  C05  121.62  3.000
 5JY  H26  C23  C22  119.75  3.000
 5JY  H26  C23  C02  120.26  3.000
 5JY  C22  C23  C02  119.98  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
 5JY  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 5JY  CONST_02  C05  C22  C23  C02    0.00   0.0  0
 5JY  CONST_03  C22  C23  C02  C03    0.00   0.0  0
 5JY  CONST_04  C22  C05  C04  C03    0.00   0.0  0
 5JY  CONST_05  C23  C02  C03  C04    0.00   0.0  0
 5JY  CONST_06  C23  C22  C05  C04    0.00   0.0  0
 5JY  CONST_07  C10  C12  C13  C07    0.00   0.0  0
 5JY  CONST_08  C10  C09  C08  C07    0.00   0.0  0
 5JY  CONST_09  C12  C13  C07  C08    0.00   0.0  0
 5JY  CONST_10  C12  C10  C09  C08    0.00   0.0  0
 5JY  CONST_11  C13  C07  C08  C09    0.00   0.0  0
 5JY  CONST_12  C13  C12  C10  C09    0.00   0.0  0
 5JY  CONST_13  C04  C03  C02  O01  180.00   0.0  0
 5JY  CONST_14  C22  C23  C02  O01  180.00   0.0  0
 5JY  CONST_15  C06  C05  C04  C03  180.00   0.0  0
 5JY  CONST_16  C23  C22  C05  C06  180.00   0.0  0
 5JY  CONST_17  C12  C13  C07  C06  180.00   0.0  0
 5JY  CONST_18  C09  C08  C07  C06  180.00   0.0  0
 5JY  CONST_19  O11  C10  C09  C08  180.00   0.0  0
 5JY  CONST_20  C13  C12  C10  O11  180.00   0.0  0
 5JY  CONST_21  H3   C04  C03  C02  180.00   0.0  0
 5JY  CONST_22  H25  C22  C23  C02  180.00   0.0  0
 5JY  CONST_23  H26  C23  C02  C03  180.00   0.0  0
 5JY  CONST_24  H2   C03  C04  C05  180.00   0.0  0
 5JY  CONST_25  H8   C12  C13  C07  180.00   0.0  0
 5JY  CONST_26  H6   C09  C08  C07  180.00   0.0  0
 5JY  CONST_27  H9   C13  C07  C08  180.00   0.0  0
 5JY  CONST_28  H5   C08  C09  C10  180.00   0.0  0
 5JY  Var_01    C17  C20  C21  C14   55.68  30.0  1
 5JY  Var_02    C17  C16  C15  C14  -55.81  30.0  1
 5JY  Var_03    C20  C21  C14  C15  -57.85  30.0  1
 5JY  Var_04    C21  C14  C15  C16   57.03  30.0  1
 5JY  Var_05    C07  C06  C05  C04  -54.60  30.0  2
 5JY  Var_06    C13  C07  C06  C05  124.82  30.0  2
 5JY  Var_07    H18  C19  C18  C17  -56.44  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
 5JY  chir_01  C17  C20  C16  C18  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
 5JY  plan-1  O01  0.020
 5JY  plan-1  C02  0.020
 5JY  plan-1  C03  0.020
 5JY  plan-1  C04  0.020
 5JY  plan-1  C05  0.020
 5JY  plan-1  C06  0.020
 5JY  plan-1  C22  0.020
 5JY  plan-1  C23  0.020
 5JY  plan-1  H2   0.020
 5JY  plan-1  H3   0.020
 5JY  plan-1  H25  0.020
 5JY  plan-1  H26  0.020
 5JY  plan-2  C06  0.020
 5JY  plan-2  C07  0.020
 5JY  plan-2  C08  0.020
 5JY  plan-2  C09  0.020
 5JY  plan-2  C10  0.020
 5JY  plan-2  O11  0.020
 5JY  plan-2  C12  0.020
 5JY  plan-2  C13  0.020
 5JY  plan-2  H5   0.020
 5JY  plan-2  H6   0.020
 5JY  plan-2  H8   0.020
 5JY  plan-2  H9   0.020

