# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 07:51:19 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 4,4'-{[(3R)-3-phenylcyclohexylidene]methanediyl}diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)C(=C2CCC[C@H](C2)c3ccccc3)c4ccc(O)cc4
#
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
 5KB  5KB  4,4'-{[(3R)-3-phenylcyclohexylidene]methanediyl}diphenol  ligand  51  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5KB
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
 5KB  O01  O  OH1   0  -0.633   6.6210   1.4024  -0.0223
 5KB  C02  C  CR6   0   0.340   5.3088   1.0920  -0.0412
 5KB  C03  C  CR16  0  -0.371   4.6965   0.3488   0.9654
 5KB  C04  C  CR16  0  -0.280   3.3441   0.0574   0.8862
 5KB  C05  C  CR6   0   0.027   2.5598   0.5059  -0.1761
 5KB  C06  C  C     0  -0.024   1.1188   0.1601  -0.2487
 5KB  C07  C  CR6   0   0.004   0.8318  -1.2860  -0.0701
 5KB  C08  C  CR16  0  -0.279   1.4436  -2.2392  -0.8866
 5KB  C09  C  CR16  0  -0.323   1.2095  -3.5932  -0.7236
 5KB  C10  C  CR6   0   0.338   0.3597  -4.0361   0.2891
 5KB  O11  O  OH1   0  -0.633   0.1698  -5.3652   0.4163
 5KB  C12  C  CR16  0  -0.372  -0.2459  -3.1037   1.1254
 5KB  C13  C  CR16  0  -0.281  -0.0058  -1.7492   0.9414
 5KB  C14  C  C     0   0.108   0.1539   1.0737  -0.4619
 5KB  C15  C  CH2   0  -0.501   0.3802   2.5605  -0.4562
 5KB  C16  C  CH2   0  -0.431  -0.5207   3.2252   0.5915
 5KB  C17  C  CH2   0  -0.417  -1.9899   2.8837   0.3817
 5KB  C18  C  CH1   0  -0.338  -2.2067   1.3695   0.3666
 5KB  C19  C  CR6   0   0.198  -3.6461   0.9817   0.1434
 5KB  C20  C  CR16  0  -0.323  -4.3588   1.4434  -0.9634
 5KB  C21  C  CR16  0  -0.239  -5.6780   1.0656  -1.1714
 5KB  C22  C  CR16  0  -0.276  -6.3115   0.2136  -0.2748
 5KB  C23  C  CR16  0  -0.238  -5.6133  -0.2559   0.8287
 5KB  C24  C  CR16  0  -0.339  -4.2930   0.1261   1.0319
 5KB  C25  C  CH2   0  -0.484  -1.2909   0.7194  -0.6847
 5KB  C26  C  CR16  0  -0.289   3.1958   1.2364  -1.1809
 5KB  C27  C  CR16  0  -0.328   4.5481   1.5314  -1.1215
 5KB  H1   H  HOH1  0   0.473   7.0401   1.0355   0.7638
 5KB  H2   H  HCR6  0   0.268   5.2741  -0.0080   1.8110
 5KB  H3   H  HCR6  0   0.249   2.8895  -0.5294   1.6754
 5KB  H5   H  HCR6  0   0.247   2.1145  -1.9175  -1.6744
 5KB  H6   H  HCR6  0   0.261   1.6873  -4.3123  -1.3774
 5KB  H7   H  HOH1  0   0.473  -0.4311  -5.5488   1.1467
 5KB  H8   H  HCR6  0   0.268  -0.8977  -3.4284   1.9291
 5KB  H9   H  HCR6  0   0.252  -0.4769  -1.0418   1.6130
 5KB  H11  H  HCH2  0   0.250   1.4191   2.8150  -0.2538
 5KB  H12  H  HCH2  0   0.230   0.1340   2.9726  -1.4420
 5KB  H13  H  HCH2  0   0.220  -0.2082   2.8995   1.5888
 5KB  H14  H  HCH2  0   0.235  -0.3786   4.3078   0.5576
 5KB  H15  H  HCH2  0   0.238  -2.6012   3.3375   1.1657
 5KB  H16  H  HCH2  0   0.218  -2.3279   3.3134  -0.5677
 5KB  H17  H  HCH1  0   0.241  -1.9082   0.9799   1.3474
 5KB  H18  H  HCR6  0   0.246  -3.8818   2.1081  -1.6745
 5KB  H19  H  HCR6  0   0.252  -6.2132   1.4387  -2.0354
 5KB  H20  H  HCR6  0   0.253  -7.3402  -0.0812  -0.4366
 5KB  H21  H  HCR6  0   0.252  -6.0963  -0.9200   1.5343
 5KB  H22  H  HCR6  0   0.243  -3.7560  -0.2475   1.8965
 5KB  H23  H  HCH2  0   0.239  -1.5825   1.0970  -1.6736
 5KB  H24  H  HCH2  0   0.255  -1.4507  -0.3579  -0.7044
 5KB  H25  H  HCR6  0   0.255   2.6250   1.5768  -2.0364
 5KB  H26  H  HCR6  0   0.261   5.0190   2.0947  -1.9177

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
 5KB  O01  C02  single    1.349  0.020  1.349
 5KB  C03  C02  aromatic  1.393  0.020  1.393
 5KB  C03  C04  aromatic  1.386  0.020  1.386
 5KB  C02  C27  aromatic  1.392  0.020  1.392
 5KB  C04  C05  aromatic  1.395  0.020  1.395
 5KB  C27  C26  aromatic  1.385  0.020  1.385
 5KB  C05  C26  aromatic  1.396  0.020  1.396
 5KB  C05  C06  single    1.484  0.020  1.484
 5KB  C06  C07  single    1.485  0.020  1.485
 5KB  C06  C14  double    1.346  0.020  1.346
 5KB  C15  C14  single    1.504  0.020  1.504
 5KB  C15  C16  single    1.533  0.020  1.533
 5KB  C07  C08  aromatic  1.396  0.020  1.396
 5KB  C07  C13  aromatic  1.393  0.020  1.393
 5KB  C08  C09  aromatic  1.384  0.020  1.384
 5KB  C13  C12  aromatic  1.388  0.020  1.388
 5KB  C14  C25  single    1.504  0.020  1.504
 5KB  C09  C10  aromatic  1.394  0.020  1.394
 5KB  C12  C10  aromatic  1.391  0.020  1.391
 5KB  C10  O11  single    1.349  0.020  1.349
 5KB  C16  C17  single    1.523  0.020  1.523
 5KB  C25  C18  single    1.538  0.020  1.538
 5KB  C17  C18  single    1.530  0.020  1.530
 5KB  C18  C19  single    1.507  0.020  1.507
 5KB  C20  C19  aromatic  1.395  0.020  1.395
 5KB  C20  C21  aromatic  1.388  0.020  1.388
 5KB  C19  C24  aromatic  1.393  0.020  1.393
 5KB  C21  C22  aromatic  1.390  0.020  1.390
 5KB  C24  C23  aromatic  1.389  0.020  1.389
 5KB  C22  C23  aromatic  1.388  0.020  1.388
 5KB  O01  H1   single    0.850  0.020  0.980
 5KB  C03  H2   single    0.930  0.020  1.080
 5KB  C04  H3   single    0.930  0.020  1.080
 5KB  C08  H5   single    0.930  0.020  1.080
 5KB  C09  H6   single    0.930  0.020  1.080
 5KB  O11  H7   single    0.850  0.020  0.980
 5KB  C12  H8   single    0.930  0.020  1.080
 5KB  C13  H9   single    0.930  0.020  1.080
 5KB  C15  H11  single    0.970  0.020  1.090
 5KB  C15  H12  single    0.970  0.020  1.090
 5KB  C16  H13  single    0.970  0.020  1.090
 5KB  C16  H14  single    0.970  0.020  1.090
 5KB  C17  H15  single    0.970  0.020  1.090
 5KB  C17  H16  single    0.970  0.020  1.090
 5KB  C18  H17  single    0.970  0.020  1.090
 5KB  C20  H18  single    0.930  0.020  1.080
 5KB  C21  H19  single    0.930  0.020  1.080
 5KB  C22  H20  single    0.930  0.020  1.080
 5KB  C23  H21  single    0.930  0.020  1.080
 5KB  C24  H22  single    0.930  0.020  1.080
 5KB  C25  H23  single    0.970  0.020  1.090
 5KB  C25  H24  single    0.970  0.020  1.090
 5KB  C26  H25  single    0.930  0.020  1.080
 5KB  C27  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
 5KB  H1   O01  C02  110.31  3.000
 5KB  C27  C02  C03  119.27  3.000
 5KB  C27  C02  O01  118.02  3.000
 5KB  C03  C02  O01  122.71  3.000
 5KB  H2   C03  C04  119.68  3.000
 5KB  H2   C03  C02  120.33  3.000
 5KB  C04  C03  C02  119.99  3.000
 5KB  H3   C04  C05  119.55  3.000
 5KB  H3   C04  C03  118.80  3.000
 5KB  C05  C04  C03  121.66  3.000
 5KB  C26  C05  C06  121.97  3.000
 5KB  C06  C05  C04  120.57  3.000
 5KB  C26  C05  C04  117.42  3.000
 5KB  C14  C06  C07  122.79  3.000
 5KB  C14  C06  C05  123.08  3.000
 5KB  C07  C06  C05  114.13  3.000
 5KB  C13  C07  C08  117.47  3.000
 5KB  C13  C07  C06  121.84  3.000
 5KB  C08  C07  C06  120.65  3.000
 5KB  H5   C08  C09  118.74  3.000
 5KB  H5   C08  C07  119.59  3.000
 5KB  C09  C08  C07  121.67  3.000
 5KB  H6   C09  C10  119.76  3.000
 5KB  H6   C09  C08  120.27  3.000
 5KB  C10  C09  C08  119.97  3.000
 5KB  C12  C10  O11  122.85  3.000
 5KB  O11  C10  C09  117.87  3.000
 5KB  C12  C10  C09  119.28  3.000
 5KB  H7   O11  C10  110.31  3.000
 5KB  H8   C12  C13  119.62  3.000
 5KB  H8   C12  C10  120.43  3.000
 5KB  C13  C12  C10  119.94  3.000
 5KB  H9   C13  C12  118.68  3.000
 5KB  H9   C13  C07  119.65  3.000
 5KB  C12  C13  C07  121.67  3.000
 5KB  C25  C14  C15  112.21  3.000
 5KB  C25  C14  C06  123.52  3.000
 5KB  C15  C14  C06  124.24  3.000
 5KB  H12  C15  H11  107.07  3.000
 5KB  H12  C15  C16  108.63  3.000
 5KB  H11  C15  C16  109.41  3.000
 5KB  H12  C15  C14  109.54  3.000
 5KB  H11  C15  C14  112.05  3.000
 5KB  C16  C15  C14  110.04  3.000
 5KB  H14  C16  H13  106.62  3.000
 5KB  H14  C16  C17  110.09  3.000
 5KB  H13  C16  C17  109.52  3.000
 5KB  H14  C16  C15  109.39  3.000
 5KB  H13  C16  C15  109.01  3.000
 5KB  C17  C16  C15  112.05  3.000
 5KB  H16  C17  H15  106.63  3.000
 5KB  H16  C17  C18  109.63  3.000
 5KB  H15  C17  C18  109.81  3.000
 5KB  H16  C17  C16  109.21  3.000
 5KB  H15  C17  C16  110.35  3.000
 5KB  C18  C17  C16  111.10  3.000
 5KB  H17  C18  C25  107.40  3.000
 5KB  H17  C18  C19  107.51  3.000
 5KB  C25  C18  C19  111.02  3.000
 5KB  H17  C18  C17  107.71  3.000
 5KB  C19  C18  C17  113.04  3.000
 5KB  C25  C18  C17  109.92  3.000
 5KB  C24  C19  C20  118.17  3.000
 5KB  C24  C19  C18  120.47  3.000
 5KB  C20  C19  C18  121.34  3.000
 5KB  H18  C20  C21  119.14  3.000
 5KB  H18  C20  C19  119.91  3.000
 5KB  C21  C20  C19  120.96  3.000
 5KB  H19  C21  C22  120.06  3.000
 5KB  H19  C21  C20  119.71  3.000
 5KB  C22  C21  C20  120.23  3.000
 5KB  H20  C22  C23  120.33  3.000
 5KB  H20  C22  C21  120.26  3.000
 5KB  C23  C22  C21  119.42  3.000
 5KB  H21  C23  C24  119.82  3.000
 5KB  H21  C23  C22  120.09  3.000
 5KB  C24  C23  C22  120.09  3.000
 5KB  H22  C24  C23  119.51  3.000
 5KB  H22  C24  C19  119.36  3.000
 5KB  C23  C24  C19  121.13  3.000
 5KB  H24  C25  H23  106.55  3.000
 5KB  H24  C25  C18  110.06  3.000
 5KB  H23  C25  C18  108.19  3.000
 5KB  H24  C25  C14  112.12  3.000
 5KB  H23  C25  C14  107.90  3.000
 5KB  C18  C25  C14  111.78  3.000
 5KB  H25  C26  C27  118.77  3.000
 5KB  H25  C26  C05  119.53  3.000
 5KB  C27  C26  C05  121.70  3.000
 5KB  H26  C27  C26  120.24  3.000
 5KB  H26  C27  C02  119.80  3.000
 5KB  C26  C27  C02  119.95  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
 5KB  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 5KB  CONST_02  C05  C26  C27  C02    0.00   0.0  0
 5KB  CONST_03  C26  C27  C02  C03    0.00   0.0  0
 5KB  CONST_04  C26  C05  C04  C03    0.00   0.0  0
 5KB  CONST_05  C27  C02  C03  C04    0.00   0.0  0
 5KB  CONST_06  C27  C26  C05  C04    0.00   0.0  0
 5KB  CONST_07  C10  C09  C08  C07    0.00   0.0  0
 5KB  CONST_08  C10  C12  C13  C07    0.00   0.0  0
 5KB  CONST_09  C12  C13  C07  C08    0.00   0.0  0
 5KB  CONST_10  C12  C10  C09  C08    0.00   0.0  0
 5KB  CONST_11  C13  C07  C08  C09    0.00   0.0  0
 5KB  CONST_12  C13  C12  C10  C09    0.00   0.0  0
 5KB  CONST_13  C22  C21  C20  C19    0.00   0.0  0
 5KB  CONST_14  C22  C23  C24  C19    0.00   0.0  0
 5KB  CONST_15  C23  C24  C19  C20    0.00   0.0  0
 5KB  CONST_16  C23  C22  C21  C20    0.00   0.0  0
 5KB  CONST_17  C24  C19  C20  C21    0.00   0.0  0
 5KB  CONST_18  C24  C23  C22  C21    0.00   0.0  0
 5KB  CONST_19  C21  C20  C19  C18  180.00   0.0  0
 5KB  CONST_20  C23  C24  C19  C18  180.00   0.0  0
 5KB  CONST_21  C04  C03  C02  O01  180.00   0.0  0
 5KB  CONST_22  C26  C27  C02  O01  180.00   0.0  0
 5KB  CONST_23  C06  C05  C04  C03  180.00   0.0  0
 5KB  CONST_24  C27  C26  C05  C06  180.00   0.0  0
 5KB  CONST_25  C09  C08  C07  C06  180.00   0.0  0
 5KB  CONST_26  C12  C13  C07  C06  180.00   0.0  0
 5KB  CONST_27  O11  C10  C09  C08  180.00   0.0  0
 5KB  CONST_28  C13  C12  C10  O11  180.00   0.0  0
 5KB  CONST_29  H3   C04  C03  C02  180.00   0.0  0
 5KB  CONST_30  H25  C26  C27  C02  180.00   0.0  0
 5KB  CONST_31  H26  C27  C02  C03  180.00   0.0  0
 5KB  CONST_32  H2   C03  C04  C05  180.00   0.0  0
 5KB  CONST_33  H6   C09  C08  C07  180.00   0.0  0
 5KB  CONST_34  H8   C12  C13  C07  180.00   0.0  0
 5KB  CONST_35  H9   C13  C07  C08  180.00   0.0  0
 5KB  CONST_36  H5   C08  C09  C10  180.00   0.0  0
 5KB  CONST_37  H18  C20  C19  C18    0.00   0.0  0
 5KB  CONST_38  H22  C24  C19  C18    0.00   0.0  0
 5KB  CONST_39  H19  C21  C20  C19  180.00   0.0  0
 5KB  CONST_40  H21  C23  C24  C19  180.00   0.0  0
 5KB  CONST_41  H20  C22  C21  C20  180.00   0.0  0
 5KB  Var_01    C17  C16  C15  C14  -55.27  30.0  1
 5KB  Var_02    C18  C25  C14  C15  -56.78  30.0  1
 5KB  Var_03    C18  C17  C16  C15   55.66  30.0  1
 5KB  Var_04    C25  C14  C15  C16   55.66  30.0  1
 5KB  Var_05    C07  C06  C05  C04  -50.11  30.0  2
 5KB  Var_06    C08  C07  C06  C05  -55.36  30.0  2
 5KB  Var_07    C15  C14  C06  C05   -9.14  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
 5KB  chir_01  C18  C25  C17  C19  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
 5KB  plan-1  O01  0.020
 5KB  plan-1  C02  0.020
 5KB  plan-1  C03  0.020
 5KB  plan-1  C04  0.020
 5KB  plan-1  C05  0.020
 5KB  plan-1  C06  0.020
 5KB  plan-1  C26  0.020
 5KB  plan-1  C27  0.020
 5KB  plan-1  H2   0.020
 5KB  plan-1  H3   0.020
 5KB  plan-1  H25  0.020
 5KB  plan-1  H26  0.020
 5KB  plan-2  C06  0.020
 5KB  plan-2  C07  0.020
 5KB  plan-2  C08  0.020
 5KB  plan-2  C09  0.020
 5KB  plan-2  C10  0.020
 5KB  plan-2  O11  0.020
 5KB  plan-2  C12  0.020
 5KB  plan-2  C13  0.020
 5KB  plan-2  H5   0.020
 5KB  plan-2  H6   0.020
 5KB  plan-2  H8   0.020
 5KB  plan-2  H9   0.020
 5KB  plan-3  C18  0.020
 5KB  plan-3  C19  0.020
 5KB  plan-3  C20  0.020
 5KB  plan-3  C21  0.020
 5KB  plan-3  C22  0.020
 5KB  plan-3  C23  0.020
 5KB  plan-3  C24  0.020
 5KB  plan-3  H18  0.020
 5KB  plan-3  H19  0.020
 5KB  plan-3  H20  0.020
 5KB  plan-3  H21  0.020
 5KB  plan-3  H22  0.020

