# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 05:52:38 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 4,4'-{[(3S)-3-ethylcyclohexylidene]methanediyl}diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[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
 5K4  5K4  4,4'-{[(3S)-3-ethylcyclohexylidene]methanediyl}diphenol  ligand  47  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_5K4
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
 5K4  O01  O  OH1   0  -0.633   5.7191  -0.6777   0.8535
 5K4  C02  C  CR6   0   0.339   4.4182  -0.5078   0.5402
 5K4  C03  C  CR16  0  -0.370   3.9876   0.4133  -0.4121
 5K4  C04  C  CR16  0  -0.280   2.6359   0.5480  -0.6856
 5K4  C05  C  CR6   0   0.017   1.6774  -0.2339  -0.0416
 5K4  C06  C  C     0  -0.022   0.2323  -0.0509  -0.3273
 5K4  C07  C  CR6   0   0.014  -0.2330   1.3552  -0.2232
 5K4  C08  C  CR16  0  -0.280   0.0333   2.1137   0.9162
 5K4  C09  C  CR16  0  -0.371  -0.3637   3.4377   1.0168
 5K4  C10  C  CR6   0   0.340  -1.0309   4.0470  -0.0437
 5K4  O11  O  OH1   0  -0.633  -1.4336   5.3338  -0.0082
 5K4  C12  C  CR16  0  -0.329  -1.2922   3.3119  -1.1969
 5K4  C13  C  CR16  0  -0.283  -0.8930   1.9877  -1.2774
 5K4  C14  C  C     0   0.111  -0.5846  -1.0667  -0.6639
 5K4  C15  C  CH2   0  -0.505  -0.1144  -2.4657  -0.9537
 5K4  C16  C  CH2   0  -0.428  -0.8039  -3.4889  -0.0519
 5K4  C17  C  CH2   0  -0.427  -2.3200  -3.3644  -0.1342
 5K4  C18  C  CH1   0  -0.215  -2.7880  -1.9426   0.1658
 5K4  C19  C  CH2   0  -0.410  -4.3031  -1.7816   0.0488
 5K4  C20  C  CH3   0  -0.672  -5.1050  -2.6108   1.0434
 5K4  C21  C  CH2   0  -0.487  -2.0803  -0.9399  -0.7617
 5K4  C22  C  CR16  0  -0.287   2.1292  -1.1407   0.9178
 5K4  C23  C  CR16  0  -0.327   3.4764  -1.2853   1.2086
 5K4  H1   H  HOH1  0   0.473   6.2663  -0.0588   0.3572
 5K4  H2   H  HCR6  0   0.268   4.7066   1.0305  -0.9390
 5K4  H3   H  HCR6  0   0.249   2.3248   1.2787  -1.4226
 5K4  H5   H  HCR6  0   0.248   0.5589   1.6608   1.7483
 5K4  H6   H  HCR6  0   0.268  -0.1478   3.9976   1.9203
 5K4  H7   H  HOH1  0   0.473  -1.1750   5.7415   0.8256
 5K4  H8   H  HCR6  0   0.260  -1.7970   3.7814  -2.0321
 5K4  H9   H  HCR6  0   0.252  -1.0905   1.4373  -2.1894
 5K4  H11  H  HCH2  0   0.234  -0.3818  -2.6926  -1.9941
 5K4  H12  H  HCH2  0   0.247   0.9684  -2.5612  -0.8863
 5K4  H13  H  HCH2  0   0.231  -0.4905  -4.4975  -0.3309
 5K4  H14  H  HCH2  0   0.216  -0.4801  -3.3369   0.9833
 5K4  H15  H  HCH2  0   0.206  -2.6545  -3.6420  -1.1418
 5K4  H16  H  HCH2  0   0.233  -2.7840  -4.0760   0.5528
 5K4  H17  H  HCH1  0   0.210  -2.4972  -1.6978   1.1971
 5K4  H18  H  HCH2  0   0.218  -4.5533  -0.7251   0.1882
 5K4  H19  H  HCH2  0   0.208  -4.6111  -2.0319  -0.9726
 5K4  H20  H  HCH3  0   0.222  -4.9617  -3.6820   0.8974
 5K4  H21  H  HCH3  0   0.216  -4.8190  -2.3771   2.0707
 5K4  H22  H  HCH3  0   0.229  -6.1729  -2.4113   0.9464
 5K4  H23  H  HCH2  0   0.244  -2.4176   0.0667  -0.5150
 5K4  H24  H  HCH2  0   0.223  -2.4024  -1.1378  -1.7927
 5K4  H25  H  HCR6  0   0.252   1.4124  -1.7398   1.4659
 5K4  H26  H  HCR6  0   0.260   3.7981  -1.9922   1.9636

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
 5K4  O01  C02  single    1.349  0.020  1.349
 5K4  C23  C02  aromatic  1.392  0.020  1.392
 5K4  C23  C22  aromatic  1.386  0.020  1.386
 5K4  C02  C03  aromatic  1.393  0.020  1.393
 5K4  C22  C05  aromatic  1.395  0.020  1.395
 5K4  C03  C04  aromatic  1.386  0.020  1.386
 5K4  C05  C04  aromatic  1.395  0.020  1.395
 5K4  C05  C06  single    1.484  0.020  1.484
 5K4  C06  C07  single    1.485  0.020  1.485
 5K4  C06  C14  double    1.346  0.020  1.346
 5K4  C13  C07  aromatic  1.395  0.020  1.395
 5K4  C13  C12  aromatic  1.385  0.020  1.385
 5K4  C07  C08  aromatic  1.394  0.020  1.394
 5K4  C12  C10  aromatic  1.392  0.020  1.392
 5K4  C08  C09  aromatic  1.386  0.020  1.386
 5K4  C10  C09  aromatic  1.393  0.020  1.393
 5K4  C10  O11  single    1.349  0.020  1.349
 5K4  C21  C14  single    1.504  0.020  1.504
 5K4  C21  C18  single    1.538  0.020  1.538
 5K4  C14  C15  single    1.504  0.020  1.504
 5K4  C19  C18  single    1.528  0.020  1.528
 5K4  C19  C20  single    1.523  0.020  1.523
 5K4  C18  C17  single    1.527  0.020  1.527
 5K4  C15  C16  single    1.528  0.020  1.528
 5K4  C17  C16  single    1.523  0.020  1.523
 5K4  O01  H1   single    0.850  0.020  0.980
 5K4  C03  H2   single    0.930  0.020  1.080
 5K4  C04  H3   single    0.930  0.020  1.080
 5K4  C08  H5   single    0.930  0.020  1.080
 5K4  C09  H6   single    0.930  0.020  1.080
 5K4  O11  H7   single    0.850  0.020  0.980
 5K4  C12  H8   single    0.930  0.020  1.080
 5K4  C13  H9   single    0.930  0.020  1.080
 5K4  C15  H11  single    0.970  0.020  1.090
 5K4  C15  H12  single    0.970  0.020  1.090
 5K4  C16  H13  single    0.970  0.020  1.090
 5K4  C16  H14  single    0.970  0.020  1.090
 5K4  C17  H15  single    0.970  0.020  1.090
 5K4  C17  H16  single    0.970  0.020  1.090
 5K4  C18  H17  single    0.970  0.020  1.090
 5K4  C19  H18  single    0.970  0.020  1.090
 5K4  C19  H19  single    0.970  0.020  1.090
 5K4  C20  H20  single    0.970  0.020  1.090
 5K4  C20  H21  single    0.970  0.020  1.090
 5K4  C20  H22  single    0.970  0.020  1.090
 5K4  C21  H23  single    0.970  0.020  1.090
 5K4  C21  H24  single    0.970  0.020  1.090
 5K4  C22  H25  single    0.930  0.020  1.080
 5K4  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
 5K4  H1   O01  C02  110.31  3.000
 5K4  C23  C02  C03  119.23  3.000
 5K4  C03  C02  O01  122.70  3.000
 5K4  C23  C02  O01  118.08  3.000
 5K4  H2   C03  C04  119.71  3.000
 5K4  H2   C03  C02  120.24  3.000
 5K4  C04  C03  C02  120.05  3.000
 5K4  H3   C04  C05  119.66  3.000
 5K4  H3   C04  C03  118.68  3.000
 5K4  C05  C04  C03  121.65  3.000
 5K4  C22  C05  C06  121.85  3.000
 5K4  C06  C05  C04  120.74  3.000
 5K4  C22  C05  C04  117.34  3.000
 5K4  C14  C06  C07  122.82  3.000
 5K4  C14  C06  C05  123.08  3.000
 5K4  C07  C06  C05  114.10  3.000
 5K4  C13  C07  C08  117.46  3.000
 5K4  C08  C07  C06  120.84  3.000
 5K4  C13  C07  C06  121.63  3.000
 5K4  H5   C08  C09  118.85  3.000
 5K4  H5   C08  C07  119.53  3.000
 5K4  C09  C08  C07  121.62  3.000
 5K4  H6   C09  C10  120.24  3.000
 5K4  H6   C09  C08  119.78  3.000
 5K4  C10  C09  C08  119.98  3.000
 5K4  C12  C10  O11  118.00  3.000
 5K4  O11  C10  C09  122.70  3.000
 5K4  C12  C10  C09  119.31  3.000
 5K4  H7   O11  C10  110.26  3.000
 5K4  H8   C12  C13  120.25  3.000
 5K4  H8   C12  C10  119.83  3.000
 5K4  C13  C12  C10  119.91  3.000
 5K4  H9   C13  C12  118.81  3.000
 5K4  H9   C13  C07  119.47  3.000
 5K4  C12  C13  C07  121.71  3.000
 5K4  C21  C14  C15  112.13  3.000
 5K4  C15  C14  C06  124.07  3.000
 5K4  C21  C14  C06  123.78  3.000
 5K4  H12  C15  H11  106.42  3.000
 5K4  H12  C15  C16  110.69  3.000
 5K4  H11  C15  C16  108.11  3.000
 5K4  H12  C15  C14  112.36  3.000
 5K4  H11  C15  C14  107.38  3.000
 5K4  C16  C15  C14  111.59  3.000
 5K4  H14  C16  H13  106.54  3.000
 5K4  H14  C16  C17  109.51  3.000
 5K4  H13  C16  C17  110.32  3.000
 5K4  H14  C16  C15  109.36  3.000
 5K4  H13  C16  C15  109.75  3.000
 5K4  C17  C16  C15  111.25  3.000
 5K4  H16  C17  H15  106.45  3.000
 5K4  H16  C17  C18  110.66  3.000
 5K4  H15  C17  C18  108.82  3.000
 5K4  H16  C17  C16  109.60  3.000
 5K4  H15  C17  C16  109.41  3.000
 5K4  C18  C17  C16  111.75  3.000
 5K4  H17  C18  C21  107.39  3.000
 5K4  H17  C18  C19  108.10  3.000
 5K4  C21  C18  C19  109.96  3.000
 5K4  H17  C18  C17  108.10  3.000
 5K4  C19  C18  C17  112.77  3.000
 5K4  C21  C18  C17  110.33  3.000
 5K4  H19  C19  H18  105.96  3.000
 5K4  H19  C19  C20  109.65  3.000
 5K4  H18  C19  C20  108.78  3.000
 5K4  H19  C19  C18  109.02  3.000
 5K4  H18  C19  C18  108.57  3.000
 5K4  C20  C19  C18  114.50  3.000
 5K4  H22  C20  H21  107.52  3.000
 5K4  H22  C20  H20  107.24  3.000
 5K4  H21  C20  H20  107.57  3.000
 5K4  H22  C20  C19  110.97  3.000
 5K4  H21  C20  C19  111.10  3.000
 5K4  H20  C20  C19  112.22  3.000
 5K4  H24  C21  H23  106.75  3.000
 5K4  H24  C21  C18  108.28  3.000
 5K4  H23  C21  C18  108.85  3.000
 5K4  H24  C21  C14  109.73  3.000
 5K4  H23  C21  C14  111.77  3.000
 5K4  C18  C21  C14  111.31  3.000
 5K4  H25  C22  C23  118.65  3.000
 5K4  H25  C22  C05  119.55  3.000
 5K4  C23  C22  C05  121.80  3.000
 5K4  H26  C23  C22  120.21  3.000
 5K4  H26  C23  C02  119.87  3.000
 5K4  C22  C23  C02  119.91  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
 5K4  CONST_01  C05  C22  C23  C02    0.00   0.0  0
 5K4  CONST_02  C05  C04  C03  C02    0.00   0.0  0
 5K4  CONST_03  C22  C23  C02  C03    0.00   0.0  0
 5K4  CONST_04  C22  C05  C04  C03    0.00   0.0  0
 5K4  CONST_05  C23  C02  C03  C04    0.00   0.0  0
 5K4  CONST_06  C23  C22  C05  C04    0.00   0.0  0
 5K4  CONST_07  C10  C12  C13  C07    0.00   0.0  0
 5K4  CONST_08  C10  C09  C08  C07    0.00   0.0  0
 5K4  CONST_09  C12  C13  C07  C08    0.00   0.0  0
 5K4  CONST_10  C12  C10  C09  C08    0.00   0.0  0
 5K4  CONST_11  C13  C07  C08  C09    0.00   0.0  0
 5K4  CONST_12  C13  C12  C10  C09    0.00   0.0  0
 5K4  CONST_13  C22  C23  C02  O01  180.00   0.0  0
 5K4  CONST_14  C04  C03  C02  O01  180.00   0.0  0
 5K4  CONST_15  C06  C05  C04  C03  180.00   0.0  0
 5K4  CONST_16  C23  C22  C05  C06  180.00   0.0  0
 5K4  CONST_17  C12  C13  C07  C06  180.00   0.0  0
 5K4  CONST_18  C09  C08  C07  C06  180.00   0.0  0
 5K4  CONST_19  O11  C10  C09  C08  180.00   0.0  0
 5K4  CONST_20  C13  C12  C10  O11  180.00   0.0  0
 5K4  CONST_21  H25  C22  C23  C02  180.00   0.0  0
 5K4  CONST_22  H3   C04  C03  C02  180.00   0.0  0
 5K4  CONST_23  H26  C23  C02  C03  180.00   0.0  0
 5K4  CONST_24  H2   C03  C04  C05  180.00   0.0  0
 5K4  CONST_25  H8   C12  C13  C07  180.00   0.0  0
 5K4  CONST_26  H6   C09  C08  C07  180.00   0.0  0
 5K4  CONST_27  H9   C13  C07  C08  180.00   0.0  0
 5K4  CONST_28  H5   C08  C09  C10  180.00   0.0  0
 5K4  Var_01    C17  C16  C15  C14   53.94  30.0  1
 5K4  Var_02    C18  C21  C14  C15   55.96  30.0  1
 5K4  Var_03    C18  C17  C16  C15  -54.43  30.0  1
 5K4  Var_04    C21  C14  C15  C16  -55.13  30.0  1
 5K4  Var_05    C07  C06  C05  C04  -51.17  30.0  2
 5K4  Var_06    C13  C07  C06  C05  125.17  30.0  2
 5K4  Var_07    H20  C20  C19  C18  -63.17  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
 5K4  chir_01  C18  C21  C19  C17  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
 5K4  plan-1  C06  0.020
 5K4  plan-1  C07  0.020
 5K4  plan-1  C08  0.020
 5K4  plan-1  C09  0.020
 5K4  plan-1  C10  0.020
 5K4  plan-1  O11  0.020
 5K4  plan-1  C12  0.020
 5K4  plan-1  C13  0.020
 5K4  plan-1  H5   0.020
 5K4  plan-1  H6   0.020
 5K4  plan-1  H8   0.020
 5K4  plan-1  H9   0.020
 5K4  plan-2  O01  0.020
 5K4  plan-2  C02  0.020
 5K4  plan-2  C03  0.020
 5K4  plan-2  C04  0.020
 5K4  plan-2  C05  0.020
 5K4  plan-2  C06  0.020
 5K4  plan-2  C22  0.020
 5K4  plan-2  C23  0.020
 5K4  plan-2  H2   0.020
 5K4  plan-2  H3   0.020
 5K4  plan-2  H25  0.020
 5K4  plan-2  H26  0.020

