# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 06:36:16 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 4,4'-{[4-(fluoromethyl)cyclohexylidene]methanediyl}diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)[C](=[C]2CC[CH](CF)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
 5JX  5JX  4,4'-{[4-(fluoromethyl)cyclohexylidene]methanediyl}diphenol  ligand  44  23  .  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_5JX
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
 5JX  O01  O  OH1   0  -0.633   1.8010   5.2406  -0.7660
 5JX  C02  C  CR6   0   0.340   1.4589   3.9709  -0.4671
 5JX  C03  C  CR16  0  -0.370   2.1559   3.2013   0.4618
 5JX  C04  C  CR16  0  -0.279   1.7570   1.8998   0.7210
 5JX  C05  C  CR6   0   0.013   0.6529   1.3327   0.0856
 5JX  C06  C  C     0  -0.024   0.2561  -0.0701   0.3678
 5JX  C07  C  CR6   0   0.022   1.3467  -1.0608   0.1870
 5JX  C08  C  CR16  0  -0.286   1.7298  -1.9346   1.2048
 5JX  C09  C  CR16  0  -0.328   2.7614  -2.8440   1.0337
 5JX  C10  C  CR6   0   0.340   3.4472  -2.8974  -0.1768
 5JX  O11  O  OH1   0  -0.633   4.4432  -3.7983  -0.3010
 5JX  C12  C  CR16  0  -0.371   3.0904  -2.0227  -1.2007
 5JX  C13  C  CR16  0  -0.279   2.0610  -1.1152  -1.0095
 5JX  C14  C  C     0   0.108  -0.9874  -0.4132   0.7475
 5JX  C15  C  CH2   0  -0.511  -2.0832   0.5730   1.0447
 5JX  C16  C  CH2   0  -0.415  -3.2715   0.3807   0.1008
 5JX  C17  C  CH1   0  -0.322  -3.7945  -1.0524   0.1639
 5JX  C18  C  CH2   0   0.019  -4.9091  -1.3052  -0.8255
 5JX  F19  F  F     0  -0.384  -5.9825  -0.4410  -0.6016
 5JX  C20  C  CH2   0  -0.427  -2.6635  -2.0484  -0.0896
 5JX  C21  C  CH2   0  -0.500  -1.4762  -1.8315   0.8551
 5JX  C22  C  CR16  0  -0.286  -0.0207   2.1147  -0.8533
 5JX  C23  C  CR16  0  -0.327   0.3674   3.4157  -1.1297
 5JX  H1   H  HOH1  0   0.474   2.5620   5.5155  -0.2429
 5JX  H2   H  HCR6  0   0.268   3.0126   3.6150   0.9826
 5JX  H3   H  HCR6  0   0.249   2.3169   1.3158   1.4415
 5JX  H5   H  HCR6  0   0.253   1.2147  -1.9011   2.1573
 5JX  H6   H  HCR6  0   0.260   3.0411  -3.5096   1.8411
 5JX  H7   H  HOH1  0   0.473   4.8311  -3.7496  -1.1817
 5JX  H8   H  HCR6  0   0.268   3.6175  -2.0451  -2.1482
 5JX  H9   H  HCR6  0   0.248   1.8066  -0.4387  -1.8167
 5JX  H11  H  HCH2  0   0.237  -2.4277   0.3928   2.0712
 5JX  H12  H  HCH2  0   0.251  -1.7334   1.6036   1.0112
 5JX  H13  H  HCH2  0   0.238  -4.0621   1.0886   0.3576
 5JX  H14  H  HCH2  0   0.217  -2.9616   0.6087  -0.9258
 5JX  H15  H  HCH1  0   0.231  -4.1797  -1.2349   1.1755
 5JX  H16  H  HCH2  0   0.196  -4.5602  -1.1443  -1.8490
 5JX  H17  H  HCH2  0   0.211  -5.2841  -2.3278  -0.7409
 5JX  H18  H  HCH2  0   0.238  -3.0323  -3.0716   0.0235
 5JX  H19  H  HCH2  0   0.222  -2.3128  -1.9527  -1.1232
 5JX  H20  H  HCH2  0   0.251  -0.6969  -2.5557   0.6242
 5JX  H21  H  HCH2  0   0.232  -1.8005  -2.0308   1.8830
 5JX  H22  H  HCR6  0   0.253  -0.8626   1.6966  -1.3923
 5JX  H23  H  HCR6  0   0.260  -0.1699   4.0016  -1.8652

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
 5JX  O01  C02  single    1.349  0.020  1.349
 5JX  C23  C02  aromatic  1.392  0.020  1.392
 5JX  C23  C22  aromatic  1.386  0.020  1.386
 5JX  C02  C03  aromatic  1.393  0.020  1.393
 5JX  C22  C05  aromatic  1.395  0.020  1.395
 5JX  C03  C04  aromatic  1.386  0.020  1.386
 5JX  C05  C04  aromatic  1.394  0.020  1.394
 5JX  C05  C06  single    1.485  0.020  1.485
 5JX  C06  C07  single    1.484  0.020  1.484
 5JX  C06  C14  double    1.345  0.020  1.345
 5JX  C08  C07  aromatic  1.395  0.020  1.395
 5JX  C08  C09  aromatic  1.386  0.020  1.386
 5JX  C07  C13  aromatic  1.394  0.020  1.394
 5JX  C09  C10  aromatic  1.392  0.020  1.392
 5JX  C13  C12  aromatic  1.386  0.020  1.386
 5JX  C10  C12  aromatic  1.393  0.020  1.393
 5JX  C10  O11  single    1.349  0.020  1.349
 5JX  C15  C14  single    1.504  0.020  1.504
 5JX  C15  C16  single    1.530  0.020  1.530
 5JX  C14  C21  single    1.504  0.020  1.504
 5JX  C16  C17  single    1.527  0.020  1.527
 5JX  C21  C20  single    1.533  0.020  1.533
 5JX  C20  C17  single    1.528  0.020  1.528
 5JX  C17  C18  single    1.512  0.020  1.512
 5JX  F19  C18  single    1.396  0.020  1.396
 5JX  O01  H1   single    0.850  0.020  0.980
 5JX  C03  H2   single    0.930  0.020  1.080
 5JX  C04  H3   single    0.930  0.020  1.080
 5JX  C08  H5   single    0.930  0.020  1.080
 5JX  C09  H6   single    0.930  0.020  1.080
 5JX  O11  H7   single    0.850  0.020  0.980
 5JX  C12  H8   single    0.930  0.020  1.080
 5JX  C13  H9   single    0.930  0.020  1.080
 5JX  C15  H11  single    0.970  0.020  1.090
 5JX  C15  H12  single    0.970  0.020  1.090
 5JX  C16  H13  single    0.970  0.020  1.090
 5JX  C16  H14  single    0.970  0.020  1.090
 5JX  C17  H15  single    0.970  0.020  1.090
 5JX  C18  H16  single    0.970  0.020  1.090
 5JX  C18  H17  single    0.970  0.020  1.090
 5JX  C20  H18  single    0.970  0.020  1.090
 5JX  C20  H19  single    0.970  0.020  1.090
 5JX  C21  H20  single    0.970  0.020  1.090
 5JX  C21  H21  single    0.970  0.020  1.090
 5JX  C22  H22  single    0.930  0.020  1.080
 5JX  C23  H23  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
 5JX  H1   O01  C02  110.41  3.000
 5JX  C23  C02  C03  119.29  3.000
 5JX  C03  C02  O01  122.75  3.000
 5JX  C23  C02  O01  117.96  3.000
 5JX  H2   C03  C04  119.72  3.000
 5JX  H2   C03  C02  120.31  3.000
 5JX  C04  C03  C02  119.97  3.000
 5JX  H3   C04  C05  119.54  3.000
 5JX  H3   C04  C03  118.81  3.000
 5JX  C05  C04  C03  121.65  3.000
 5JX  C22  C05  C06  121.89  3.000
 5JX  C06  C05  C04  120.61  3.000
 5JX  C22  C05  C04  117.45  3.000
 5JX  C14  C06  C07  122.93  3.000
 5JX  C14  C06  C05  122.81  3.000
 5JX  C07  C06  C05  114.27  3.000
 5JX  C13  C07  C08  117.44  3.000
 5JX  C13  C07  C06  120.46  3.000
 5JX  C08  C07  C06  122.06  3.000
 5JX  H5   C08  C09  118.87  3.000
 5JX  H5   C08  C07  119.44  3.000
 5JX  C09  C08  C07  121.69  3.000
 5JX  H6   C09  C10  119.82  3.000
 5JX  H6   C09  C08  120.23  3.000
 5JX  C10  C09  C08  119.95  3.000
 5JX  C12  C10  O11  122.74  3.000
 5JX  O11  C10  C09  118.00  3.000
 5JX  C12  C10  C09  119.26  3.000
 5JX  H7   O11  C10  110.35  3.000
 5JX  H8   C12  C13  119.68  3.000
 5JX  H8   C12  C10  120.31  3.000
 5JX  C13  C12  C10  120.00  3.000
 5JX  H9   C13  C12  118.72  3.000
 5JX  H9   C13  C07  119.64  3.000
 5JX  C12  C13  C07  121.64  3.000
 5JX  C21  C14  C15  111.56  3.000
 5JX  C21  C14  C06  124.15  3.000
 5JX  C15  C14  C06  124.21  3.000
 5JX  H12  C15  H11  106.56  3.000
 5JX  H12  C15  C16  110.46  3.000
 5JX  H11  C15  C16  108.22  3.000
 5JX  H12  C15  C14  112.36  3.000
 5JX  H11  C15  C14  107.81  3.000
 5JX  C16  C15  C14  111.20  3.000
 5JX  H14  C16  H13  106.86  3.000
 5JX  H14  C16  C17  109.32  3.000
 5JX  H13  C16  C17  110.53  3.000
 5JX  H14  C16  C15  109.40  3.000
 5JX  H13  C16  C15  109.62  3.000
 5JX  C17  C16  C15  111.01  3.000
 5JX  H15  C17  C20  107.71  3.000
 5JX  H15  C17  C18  108.46  3.000
 5JX  C20  C17  C18  109.15  3.000
 5JX  H15  C17  C16  108.33  3.000
 5JX  C18  C17  C16  112.49  3.000
 5JX  C20  C17  C16  110.57  3.000
 5JX  H17  C18  H16  108.65  3.000
 5JX  H17  C18  F19  107.64  3.000
 5JX  H16  C18  F19  107.72  3.000
 5JX  H17  C18  C17  111.04  3.000
 5JX  H16  C18  C17  110.66  3.000
 5JX  F19  C18  C17  111.00  3.000
 5JX  H19  C20  H18  106.69  3.000
 5JX  H19  C20  C21  108.73  3.000
 5JX  H18  C20  C21  109.27  3.000
 5JX  H19  C20  C17  109.66  3.000
 5JX  H18  C20  C17  110.06  3.000
 5JX  C21  C20  C17  112.26  3.000
 5JX  H21  C21  H20  106.84  3.000
 5JX  H21  C21  C20  108.85  3.000
 5JX  H20  C21  C20  109.25  3.000
 5JX  H21  C21  C14  109.56  3.000
 5JX  H20  C21  C14  112.30  3.000
 5JX  C20  C21  C14  109.94  3.000
 5JX  H22  C22  C23  118.73  3.000
 5JX  H22  C22  C05  119.58  3.000
 5JX  C23  C22  C05  121.69  3.000
 5JX  H23  C23  C22  120.30  3.000
 5JX  H23  C23  C02  119.76  3.000
 5JX  C22  C23  C02  119.94  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
 5JX  CONST_01  C05  C22  C23  C02    0.00   0.0  0
 5JX  CONST_02  C05  C04  C03  C02    0.00   0.0  0
 5JX  CONST_03  C22  C23  C02  C03    0.00   0.0  0
 5JX  CONST_04  C22  C05  C04  C03    0.00   0.0  0
 5JX  CONST_05  C23  C02  C03  C04    0.00   0.0  0
 5JX  CONST_06  C23  C22  C05  C04    0.00   0.0  0
 5JX  CONST_07  C10  C09  C08  C07    0.00   0.0  0
 5JX  CONST_08  C10  C12  C13  C07    0.00   0.0  0
 5JX  CONST_09  C12  C13  C07  C08    0.00   0.0  0
 5JX  CONST_10  C12  C10  C09  C08    0.00   0.0  0
 5JX  CONST_11  C13  C07  C08  C09    0.00   0.0  0
 5JX  CONST_12  C13  C12  C10  C09    0.00   0.0  0
 5JX  CONST_13  C22  C23  C02  O01  180.00   0.0  0
 5JX  CONST_14  C04  C03  C02  O01  180.00   0.0  0
 5JX  CONST_15  C06  C05  C04  C03  180.00   0.0  0
 5JX  CONST_16  C23  C22  C05  C06  180.00   0.0  0
 5JX  CONST_17  C09  C08  C07  C06  180.00   0.0  0
 5JX  CONST_18  C12  C13  C07  C06  180.00   0.0  0
 5JX  CONST_19  O11  C10  C09  C08  180.00   0.0  0
 5JX  CONST_20  C13  C12  C10  O11  180.00   0.0  0
 5JX  CONST_21  H22  C22  C23  C02  180.00   0.0  0
 5JX  CONST_22  H3   C04  C03  C02  180.00   0.0  0
 5JX  CONST_23  H23  C23  C02  C03  180.00   0.0  0
 5JX  CONST_24  H2   C03  C04  C05  180.00   0.0  0
 5JX  CONST_25  H6   C09  C08  C07  180.00   0.0  0
 5JX  CONST_26  H8   C12  C13  C07  180.00   0.0  0
 5JX  CONST_27  H9   C13  C07  C08  180.00   0.0  0
 5JX  CONST_28  H5   C08  C09  C10  180.00   0.0  0
 5JX  Var_01    C17  C16  C15  C14   55.95  30.0  1
 5JX  Var_02    C17  C20  C21  C14  -55.60  30.0  1
 5JX  Var_03    C20  C21  C14  C15   57.08  30.0  1
 5JX  Var_04    C21  C14  C15  C16  -57.98  30.0  1
 5JX  Var_05    C07  C06  C05  C04  -53.74  30.0  2
 5JX  Var_06    C08  C07  C06  C05  124.61  30.0  2
 5JX  Var_07    C15  C14  C06  C05   -5.44  30.0  2

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
 5JX  chir_01  C17  C16  C20  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
 5JX  plan-1  C06  0.020
 5JX  plan-1  C07  0.020
 5JX  plan-1  C08  0.020
 5JX  plan-1  C09  0.020
 5JX  plan-1  C10  0.020
 5JX  plan-1  O11  0.020
 5JX  plan-1  C12  0.020
 5JX  plan-1  C13  0.020
 5JX  plan-1  H5   0.020
 5JX  plan-1  H6   0.020
 5JX  plan-1  H8   0.020
 5JX  plan-1  H9   0.020
 5JX  plan-2  O01  0.020
 5JX  plan-2  C02  0.020
 5JX  plan-2  C03  0.020
 5JX  plan-2  C04  0.020
 5JX  plan-2  C05  0.020
 5JX  plan-2  C06  0.020
 5JX  plan-2  C22  0.020
 5JX  plan-2  C23  0.020
 5JX  plan-2  H2   0.020
 5JX  plan-2  H3   0.020
 5JX  plan-2  H22  0.020
 5JX  plan-2  H23  0.020

