# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 12:49:00 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (1S,3aR,5S,7aS)-5-(2,3-difluoro-4-hydroxyphenyl)-7a-methyloctahydro-1H-inden-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@@H](C[C@H]1CC[C@@H]2O)c3ccc(O)c(F)c3F
#
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
 5CK  5CK  (1S,3aR,5S,7aS)-5-(2,3-difluoro-4-hydroxyphenyl)-7a-methyloctahydro-1H-inden-1-ol  ligand  40  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5CK
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
 5CK  C01  C  CH2   0  -0.415  -0.9102   0.2845  -1.1384
 5CK  C02  C  CH1   0  -0.214  -2.4004  -0.0202  -1.0106
 5CK  C03  C  CT    0  -0.097  -3.0471   0.5406   0.2734
 5CK  C04  C  CH2   0  -0.437  -2.1919   0.1848   1.5012
 5CK  C05  C  CH2   0  -0.411  -0.7228   0.5611   1.3513
 5CK  C06  C  CH2   0  -0.443  -2.7554  -1.5198  -1.0110
 5CK  C07  C  CH2   0  -0.496  -3.9615  -1.6755  -0.0631
 5CK  C08  C  CH1   0   0.088  -4.3602  -0.2534   0.3511
 5CK  O01  O  OH1   0  -0.680  -5.2850   0.3126  -0.5570
 5CK  C09  C  CH3   0  -0.652  -3.2634   2.0488   0.2138
 5CK  O02  O  OH1   0  -0.627   5.3962   1.2275  -0.4037
 5CK  F01  F  F     0  -0.304   2.0336  -1.9978   0.3560
 5CK  F02  F  F     0  -0.316   4.6016  -1.3818   0.1160
 5CK  C10  C  CH1   0  -0.341  -0.1138  -0.1001   0.1119
 5CK  C11  C  CR16  0  -0.305   1.7832   1.5366  -0.2956
 5CK  C12  C  CR6   0  -0.024   1.3488   0.2365  -0.0338
 5CK  C13  C  CR6   0   0.365   2.3413  -0.7189   0.0999
 5CK  C14  C  CR6   0   0.307   3.6846  -0.4090  -0.0209
 5CK  C15  C  CR6   0   0.227   4.1023   0.8877  -0.2803
 5CK  C16  C  CR16  0  -0.346   3.1216   1.8660  -0.4173
 5CK  H1   H  HCH2  0   0.236  -0.5022  -0.2351  -2.0105
 5CK  H2   H  HCH2  0   0.225  -0.7800   1.3537  -1.3353
 5CK  H3   H  HCH1  0   0.230  -2.9029   0.4466  -1.8638
 5CK  H4   H  HCH2  0   0.233  -2.6119   0.6752   2.3843
 5CK  H5   H  HCH2  0   0.232  -2.2443  -0.8892   1.7041
 5CK  H6   H  HCH2  0   0.219  -0.6057   1.6471   1.2888
 5CK  H7   H  HCH2  0   0.239  -0.1754   0.2469   2.2436
 5CK  H8   H  HCH2  0   0.234  -2.9815  -1.8606  -2.0220
 5CK  H9   H  HCH2  0   0.226  -1.9171  -2.1279  -0.6641
 5CK  H10  H  HCH2  0   0.239  -4.7995  -2.2023  -0.5257
 5CK  H11  H  HCH2  0   0.232  -3.6894  -2.2602   0.8167
 5CK  H12  H  HCH1  0   0.202  -4.7709  -0.2341   1.3716
 5CK  H13  H  HOH1  0   0.445  -6.0523  -0.2656  -0.5965
 5CK  H14  H  HCH3  0   0.229  -3.8227   2.3434  -0.6733
 5CK  H15  H  HCH3  0   0.220  -3.8105   2.4042   1.0903
 5CK  H16  H  HCH3  0   0.222  -2.3160   2.5899   0.1877
 5CK  H17  H  HOH1  0   0.479   5.9764   0.4688  -0.2706
 5CK  H18  H  HCH1  0   0.242  -0.2058  -1.1807   0.2494
 5CK  H19  H  HCR6  0   0.261   1.0491   2.3242  -0.4079
 5CK  H20  H  HCR6  0   0.277   3.4196   2.8865  -0.6195

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
 5CK  C07  C08  single    1.534  0.020  1.534
 5CK  C07  C06  single    1.542  0.020  1.542
 5CK  O01  C08  single    1.414  0.020  1.414
 5CK  C08  C03  single    1.536  0.020  1.536
 5CK  C06  C02  single    1.541  0.020  1.541
 5CK  C03  C02  single    1.543  0.020  1.543
 5CK  C03  C04  single    1.538  0.020  1.538
 5CK  C03  C09  single    1.525  0.020  1.525
 5CK  C02  C01  single    1.526  0.020  1.526
 5CK  C04  C05  single    1.524  0.020  1.524
 5CK  C01  C10  single    1.531  0.020  1.531
 5CK  C05  C10  single    1.531  0.020  1.531
 5CK  C10  C12  single    1.508  0.020  1.508
 5CK  F01  C13  single    1.340  0.020  1.340
 5CK  C12  C13  aromatic  1.384  0.020  1.384
 5CK  C12  C11  aromatic  1.396  0.020  1.396
 5CK  C13  C14  aromatic  1.384  0.020  1.384
 5CK  C11  C16  aromatic  1.384  0.020  1.384
 5CK  C14  F02  single    1.344  0.020  1.344
 5CK  C14  C15  aromatic  1.387  0.020  1.387
 5CK  C16  C15  aromatic  1.392  0.020  1.392
 5CK  C15  O02  single    1.343  0.020  1.343
 5CK  C01  H1   single    0.970  0.020  1.090
 5CK  C01  H2   single    0.970  0.020  1.090
 5CK  C02  H3   single    0.970  0.020  1.090
 5CK  C04  H4   single    0.970  0.020  1.090
 5CK  C04  H5   single    0.970  0.020  1.090
 5CK  C05  H6   single    0.970  0.020  1.090
 5CK  C05  H7   single    0.970  0.020  1.090
 5CK  C06  H8   single    0.970  0.020  1.090
 5CK  C06  H9   single    0.970  0.020  1.090
 5CK  C07  H10  single    0.970  0.020  1.090
 5CK  C07  H11  single    0.970  0.020  1.090
 5CK  C08  H12  single    0.970  0.020  1.090
 5CK  O01  H13  single    0.850  0.020  0.980
 5CK  C09  H14  single    0.970  0.020  1.090
 5CK  C09  H15  single    0.970  0.020  1.090
 5CK  C09  H16  single    0.970  0.020  1.090
 5CK  O02  H17  single    0.850  0.020  0.980
 5CK  C10  H18  single    0.970  0.020  1.090
 5CK  C11  H19  single    0.930  0.020  1.080
 5CK  C16  H20  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
 5CK  H2   C01  H1   106.02  3.000
 5CK  H2   C01  C10  109.28  3.000
 5CK  H1   C01  C10  109.73  3.000
 5CK  H2   C01  C02  109.03  3.000
 5CK  H1   C01  C02  109.63  3.000
 5CK  C10  C01  C02  112.91  3.000
 5CK  H3   C02  C06  107.99  3.000
 5CK  H3   C02  C03  107.53  3.000
 5CK  C06  C02  C03  104.91  3.000
 5CK  H3   C02  C01  107.33  3.000
 5CK  C03  C02  C01  113.97  3.000
 5CK  C06  C02  C01  114.78  3.000
 5CK  C09  C03  C08  113.07  3.000
 5CK  C09  C03  C04  109.81  3.000
 5CK  C08  C03  C04  108.38  3.000
 5CK  C09  C03  C02  112.73  3.000
 5CK  C04  C03  C02  110.31  3.000
 5CK  C08  C03  C02  102.27  3.000
 5CK  H5   C04  H4   105.78  3.000
 5CK  H5   C04  C05  107.86  3.000
 5CK  H4   C04  C05  109.80  3.000
 5CK  H5   C04  C03  110.40  3.000
 5CK  H4   C04  C03  109.11  3.000
 5CK  C05  C04  C03  113.60  3.000
 5CK  H7   C05  H6   106.17  3.000
 5CK  H7   C05  C10  109.73  3.000
 5CK  H6   C05  C10  109.87  3.000
 5CK  H7   C05  C04  109.37  3.000
 5CK  H6   C05  C04  110.72  3.000
 5CK  C10  C05  C04  110.88  3.000
 5CK  H9   C06  H8   106.23  3.000
 5CK  H9   C06  C07  110.41  3.000
 5CK  H8   C06  C07  112.10  3.000
 5CK  H9   C06  C02  111.40  3.000
 5CK  H8   C06  C02  110.62  3.000
 5CK  C07  C06  C02  106.16  3.000
 5CK  H11  C07  H10  105.92  3.000
 5CK  H11  C07  C08  110.13  3.000
 5CK  H10  C07  C08  111.22  3.000
 5CK  H11  C07  C06  110.79  3.000
 5CK  H10  C07  C06  112.85  3.000
 5CK  C08  C07  C06  106.00  3.000
 5CK  H12  C08  O01  110.15  3.000
 5CK  H12  C08  C07  111.33  3.000
 5CK  O01  C08  C07  111.57  3.000
 5CK  H12  C08  C03  110.91  3.000
 5CK  O01  C08  C03  108.64  3.000
 5CK  C07  C08  C03  104.08  3.000
 5CK  H13  O01  C08  107.91  3.000
 5CK  H16  C09  H15  107.01  3.000
 5CK  H16  C09  H14  106.98  3.000
 5CK  H15  C09  H14  107.95  3.000
 5CK  H16  C09  C03  111.61  3.000
 5CK  H15  C09  C03  111.19  3.000
 5CK  H14  C09  C03  111.85  3.000
 5CK  H17  O02  C15  111.59  3.000
 5CK  H18  C10  C12  108.32  3.000
 5CK  H18  C10  C05  106.96  3.000
 5CK  C12  C10  C05  111.57  3.000
 5CK  H18  C10  C01  107.89  3.000
 5CK  C12  C10  C01  111.68  3.000
 5CK  C05  C10  C01  110.22  3.000
 5CK  H19  C11  C16  118.27  3.000
 5CK  H19  C11  C12  119.09  3.000
 5CK  C16  C11  C12  122.64  3.000
 5CK  C13  C12  C11  115.98  3.000
 5CK  C11  C12  C10  121.87  3.000
 5CK  C13  C12  C10  122.15  3.000
 5CK  C14  C13  C12  122.21  3.000
 5CK  C14  C13  F01  116.95  3.000
 5CK  C12  C13  F01  120.83  3.000
 5CK  C15  C14  C13  121.21  3.000
 5CK  C15  C14  F02  119.36  3.000
 5CK  C13  C14  F02  119.43  3.000
 5CK  C16  C15  C14  117.60  3.000
 5CK  C16  C15  O02  119.46  3.000
 5CK  C14  C15  O02  122.94  3.000
 5CK  H20  C16  C15  119.15  3.000
 5CK  H20  C16  C11  120.48  3.000
 5CK  C15  C16  C11  120.36  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
 5CK  CONST_01  C14  C13  C12  C11    0.00   0.0  0
 5CK  CONST_02  C14  C15  C16  C11    0.00   0.0  0
 5CK  CONST_03  C15  C14  C13  C12    0.00   0.0  0
 5CK  CONST_04  C15  C16  C11  C12    0.00   0.0  0
 5CK  CONST_05  C16  C11  C12  C13    0.00   0.0  0
 5CK  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 5CK  CONST_07  C14  C13  C12  C10  180.00   0.0  0
 5CK  CONST_08  C16  C11  C12  C10  180.00   0.0  0
 5CK  CONST_09  C13  C14  C15  O02  180.00   0.0  0
 5CK  CONST_10  C11  C16  C15  O02  180.00   0.0  0
 5CK  CONST_11  C10  C12  C13  F01    0.00   0.0  0
 5CK  CONST_12  C11  C12  C13  F01  180.00   0.0  0
 5CK  CONST_13  C15  C14  C13  F01  180.00   0.0  0
 5CK  CONST_14  C12  C13  C14  F02  180.00   0.0  0
 5CK  CONST_15  C16  C15  C14  F02  180.00   0.0  0
 5CK  CONST_16  H19  C11  C12  C10    0.00   0.0  0
 5CK  CONST_17  H20  C16  C11  C12  180.00   0.0  0
 5CK  Var_01    C08  C07  C06  C02    5.46  30.0  1
 5CK  Var_02    C10  C05  C04  C03  -56.87  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
 5CK  chir_01  C02  C06  C03  C01  negativ
 5CK  chir_02  C03  C04  C02  C08  negativ
 5CK  chir_03  C08  O01  C03  C07  positiv
 5CK  chir_04  C10  C12  C05  C01  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
 5CK  plan-1  O02  0.020
 5CK  plan-1  F01  0.020
 5CK  plan-1  F02  0.020
 5CK  plan-1  C10  0.020
 5CK  plan-1  C11  0.020
 5CK  plan-1  C12  0.020
 5CK  plan-1  C13  0.020
 5CK  plan-1  C14  0.020
 5CK  plan-1  C15  0.020
 5CK  plan-1  C16  0.020
 5CK  plan-1  H19  0.020
 5CK  plan-1  H20  0.020

