# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 10:43:20 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4,4'-[(9s)-bicyclo[3.3.1]non-9-ylmethanediyl]diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)C(C2C3CCCC2CCC3)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
 5J1  5J1  4,4'-[(9s)-bicyclo[3.3.1]non-9-ylmethanediyl]diphenol  ligand  50  24  .  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_5J1
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
 5J1  C01  C  CH2   0  -0.435   1.6650  -2.5322   1.1836
 5J1  C02  C  CH2   0  -0.449   0.4971  -3.3943   1.6737
 5J1  C03  C  CH2   0  -0.440  -0.8763  -2.8647   1.2490
 5J1  C04  C  CH1   0  -0.220  -0.9403  -2.3312  -0.1864
 5J1  C05  C  CH2   0  -0.420  -0.8610  -3.4173  -1.2639
 5J1  C06  C  CH2   0  -0.450   0.5037  -4.0969  -1.3750
 5J1  C07  C  CH2   0  -0.422   1.6541  -3.0910  -1.3344
 5J1  C08  C  CH1   0  -0.226   1.5173  -2.0144  -0.2510
 5J1  C09  C  CH1   0  -0.205   0.1714  -1.3009  -0.4326
 5J1  C10  C  CH1   0  -0.438   0.0211  -0.0415   0.4422
 5J1  C11  C  CR6   0   0.182   1.1595   0.9451   0.2792
 5J1  C12  C  CR6   0   0.197  -1.3109   0.6470   0.2250
 5J1  C13  C  CR16  0  -0.321  -2.1617   0.8884   1.2964
 5J1  C14  C  CR16  0  -0.369  -3.3815   1.5329   1.1331
 5J1  C15  C  CR6   0   0.333  -3.7786   1.9525  -0.1310
 5J1  C16  C  CR16  0  -0.322  -2.9409   1.7157  -1.2200
 5J1  C17  C  CR16  0  -0.303  -1.7287   1.0726  -1.0354
 5J1  C18  C  CR16  0  -0.308   1.6930   1.5784   1.3989
 5J1  C19  C  CR16  0  -0.323   2.7164   2.5083   1.2995
 5J1  C20  C  CR6   0   0.334   3.2416   2.8282   0.0511
 5J1  C21  C  CR16  0  -0.371   2.7238   2.2058  -1.0815
 5J1  C22  C  CR16  0  -0.312   1.6983   1.2794  -0.9600
 5J1  O01  O  OH1   0  -0.636   4.2425   3.7329  -0.0046
 5J1  O02  O  OH1   0  -0.636  -4.9492   2.5863  -0.3596
 5J1  H1   H  HCH2  0   0.220   1.7832  -1.6711   1.8492
 5J1  H2   H  HCH2  0   0.225   2.5969  -3.0990   1.2695
 5J1  H3   H  HCH2  0   0.220   0.6238  -4.4179   1.3218
 5J1  H4   H  HCH2  0   0.227   0.5330  -3.4612   2.7643
 5J1  H5   H  HCH2  0   0.226  -1.6277  -3.6492   1.3792
 5J1  H6   H  HCH2  0   0.219  -1.1769  -2.0602   1.9274
 5J1  H7   H  HCH1  0   0.229  -1.9124  -1.8416  -0.3040
 5J1  H8   H  HCH2  0   0.220  -1.6385  -4.1674  -1.0919
 5J1  H9   H  HCH2  0   0.213  -1.1004  -2.9496  -2.2254
 5J1  H10  H  HCH2  0   0.219   0.6232  -4.8410  -0.5868
 5J1  H11  H  HCH2  0   0.227   0.5501  -4.6604  -2.3112
 5J1  H12  H  HCH2  0   0.220   2.6067  -3.6167  -1.2209
 5J1  H13  H  HCH2  0   0.213   1.7025  -2.5770  -2.3010
 5J1  H14  H  HCH1  0   0.231   2.3279  -1.2977  -0.4152
 5J1  H15  H  HCH1  0   0.217   0.1003  -0.9866  -1.4829
 5J1  H16  H  HCH1  0   0.254   0.0375  -0.3520   1.4909
 5J1  H17  H  HCR6  0   0.246  -1.8673   0.5704   2.2901
 5J1  H18  H  HCR6  0   0.266  -4.0191   1.7029   1.9936
 5J1  H19  H  HCR6  0   0.259  -3.2433   2.0361  -2.2095
 5J1  H20  H  HCR6  0   0.242  -1.1018   0.9053  -1.9030
 5J1  H21  H  HCR6  0   0.244   1.3015   1.3376   2.3809
 5J1  H22  H  HCR6  0   0.259   3.1133   2.9816   2.1893
 5J1  H23  H  HCR6  0   0.267   3.1236   2.4374  -2.0624
 5J1  H24  H  HCR6  0   0.250   1.3295   0.8077  -1.8626
 5J1  H25  H  HOH1  0   0.472   4.5423   3.8433  -0.9136
 5J1  H26  H  HOH1  0   0.472  -5.4297   2.7073   0.4666

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
 5J1  O02  C15  single    1.351  0.020  1.351
 5J1  C14  C15  aromatic  1.390  0.020  1.390
 5J1  C14  C13  aromatic  1.389  0.020  1.389
 5J1  C15  C16  aromatic  1.394  0.020  1.394
 5J1  C13  C12  aromatic  1.389  0.020  1.389
 5J1  C16  C17  aromatic  1.385  0.020  1.385
 5J1  C12  C17  aromatic  1.394  0.020  1.394
 5J1  C12  C10  single    1.515  0.020  1.515
 5J1  C22  C21  aromatic  1.387  0.020  1.387
 5J1  C22  C11  aromatic  1.392  0.020  1.392
 5J1  C21  C20  aromatic  1.392  0.020  1.392
 5J1  C10  C11  single    1.515  0.020  1.515
 5J1  C10  C09  single    1.541  0.020  1.541
 5J1  C11  C18  aromatic  1.393  0.020  1.393
 5J1  C20  O01  single    1.350  0.020  1.350
 5J1  C20  C19  aromatic  1.392  0.020  1.392
 5J1  C18  C19  aromatic  1.386  0.020  1.386
 5J1  C09  C04  single    1.536  0.020  1.536
 5J1  C09  C08  single    1.534  0.020  1.534
 5J1  C04  C05  single    1.532  0.020  1.532
 5J1  C04  C03  single    1.533  0.020  1.533
 5J1  C05  C06  single    1.529  0.020  1.529
 5J1  C08  C07  single    1.533  0.020  1.533
 5J1  C08  C01  single    1.532  0.020  1.532
 5J1  C06  C07  single    1.529  0.020  1.529
 5J1  C03  C02  single    1.532  0.020  1.532
 5J1  C01  C02  single    1.532  0.020  1.532
 5J1  C01  H1   single    0.970  0.020  1.090
 5J1  C01  H2   single    0.970  0.020  1.090
 5J1  C02  H3   single    0.970  0.020  1.090
 5J1  C02  H4   single    0.970  0.020  1.090
 5J1  C03  H5   single    0.970  0.020  1.090
 5J1  C03  H6   single    0.970  0.020  1.090
 5J1  C04  H7   single    0.970  0.020  1.090
 5J1  C05  H8   single    0.970  0.020  1.090
 5J1  C05  H9   single    0.970  0.020  1.090
 5J1  C06  H10  single    0.970  0.020  1.090
 5J1  C06  H11  single    0.970  0.020  1.090
 5J1  C07  H12  single    0.970  0.020  1.090
 5J1  C07  H13  single    0.970  0.020  1.090
 5J1  C08  H14  single    0.970  0.020  1.090
 5J1  C09  H15  single    0.970  0.020  1.090
 5J1  C10  H16  single    0.970  0.020  1.090
 5J1  C13  H17  single    0.930  0.020  1.080
 5J1  C14  H18  single    0.930  0.020  1.080
 5J1  C16  H19  single    0.930  0.020  1.080
 5J1  C17  H20  single    0.930  0.020  1.080
 5J1  C18  H21  single    0.930  0.020  1.080
 5J1  C19  H22  single    0.930  0.020  1.080
 5J1  C21  H23  single    0.930  0.020  1.080
 5J1  C22  H24  single    0.930  0.020  1.080
 5J1  O01  H25  single    0.850  0.020  0.980
 5J1  O02  H26  single    0.850  0.020  0.980

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
 5J1  H2   C01  H1   105.54  3.000
 5J1  H2   C01  C08  109.31  3.000
 5J1  H1   C01  C08  108.29  3.000
 5J1  H2   C01  C02  109.43  3.000
 5J1  H1   C01  C02  109.30  3.000
 5J1  C08  C01  C02  114.59  3.000
 5J1  H4   C02  H3   105.12  3.000
 5J1  H4   C02  C03  109.10  3.000
 5J1  H3   C02  C03  109.84  3.000
 5J1  H4   C02  C01  109.17  3.000
 5J1  H3   C02  C01  109.67  3.000
 5J1  C03  C02  C01  113.59  3.000
 5J1  H6   C03  H5   105.34  3.000
 5J1  H6   C03  C04  108.26  3.000
 5J1  H5   C03  C04  109.41  3.000
 5J1  H6   C03  C02  109.17  3.000
 5J1  H5   C03  C02  109.56  3.000
 5J1  C04  C03  C02  114.67  3.000
 5J1  H7   C04  C09  109.00  3.000
 5J1  H7   C04  C05  106.70  3.000
 5J1  C09  C04  C05  108.99  3.000
 5J1  H7   C04  C03  107.06  3.000
 5J1  C05  C04  C03  114.19  3.000
 5J1  C09  C04  C03  110.70  3.000
 5J1  H9   C05  H8   105.99  3.000
 5J1  H9   C05  C06  108.73  3.000
 5J1  H8   C05  C06  109.94  3.000
 5J1  H9   C05  C04  107.66  3.000
 5J1  H8   C05  C04  109.80  3.000
 5J1  C06  C05  C04  114.36  3.000
 5J1  H11  C06  H10  105.22  3.000
 5J1  H11  C06  C07  109.26  3.000
 5J1  H10  C06  C07  110.32  3.000
 5J1  H11  C06  C05  109.21  3.000
 5J1  H10  C06  C05  110.40  3.000
 5J1  C07  C06  C05  112.17  3.000
 5J1  H13  C07  H12  106.16  3.000
 5J1  H13  C07  C08  107.33  3.000
 5J1  H12  C07  C08  109.98  3.000
 5J1  H13  C07  C06  108.57  3.000
 5J1  H12  C07  C06  109.99  3.000
 5J1  C08  C07  C06  114.43  3.000
 5J1  H14  C08  C09  109.12  3.000
 5J1  H14  C08  C07  106.72  3.000
 5J1  C09  C08  C07  108.73  3.000
 5J1  H14  C08  C01  106.88  3.000
 5J1  C07  C08  C01  114.56  3.000
 5J1  C09  C08  C01  110.64  3.000
 5J1  H15  C09  C10  107.62  3.000
 5J1  H15  C09  C08  107.64  3.000
 5J1  C10  C09  C08  113.49  3.000
 5J1  H15  C09  C04  107.36  3.000
 5J1  C08  C09  C04  107.70  3.000
 5J1  C10  C09  C04  112.75  3.000
 5J1  H16  C10  C12  106.23  3.000
 5J1  H16  C10  C11  106.06  3.000
 5J1  C12  C10  C11  110.44  3.000
 5J1  H16  C10  C09  108.11  3.000
 5J1  C11  C10  C09  113.45  3.000
 5J1  C12  C10  C09  112.07  3.000
 5J1  C22  C11  C18  117.28  3.000
 5J1  C18  C11  C10  119.83  3.000
 5J1  C22  C11  C10  122.88  3.000
 5J1  C17  C12  C13  117.42  3.000
 5J1  C17  C12  C10  122.12  3.000
 5J1  C13  C12  C10  120.45  3.000
 5J1  H17  C13  C14  118.83  3.000
 5J1  H17  C13  C12  119.32  3.000
 5J1  C14  C13  C12  121.85  3.000
 5J1  H18  C14  C15  120.43  3.000
 5J1  H18  C14  C13  119.72  3.000
 5J1  C15  C14  C13  119.86  3.000
 5J1  O02  C15  C16  117.92  3.000
 5J1  C16  C15  C14  119.17  3.000
 5J1  O02  C15  C14  122.90  3.000
 5J1  H19  C16  C17  120.24  3.000
 5J1  H19  C16  C15  119.71  3.000
 5J1  C17  C16  C15  120.05  3.000
 5J1  H20  C17  C16  118.14  3.000
 5J1  H20  C17  C12  120.22  3.000
 5J1  C16  C17  C12  121.64  3.000
 5J1  H21  C18  C19  118.71  3.000
 5J1  H21  C18  C11  119.28  3.000
 5J1  C19  C18  C11  122.02  3.000
 5J1  H22  C19  C20  119.88  3.000
 5J1  H22  C19  C18  120.31  3.000
 5J1  C20  C19  C18  119.81  3.000
 5J1  O01  C20  C21  122.80  3.000
 5J1  O01  C20  C19  118.08  3.000
 5J1  C21  C20  C19  119.12  3.000
 5J1  H23  C21  C22  119.63  3.000
 5J1  H23  C21  C20  120.22  3.000
 5J1  C22  C21  C20  120.15  3.000
 5J1  H24  C22  C21  118.01  3.000
 5J1  H24  C22  C11  120.36  3.000
 5J1  C21  C22  C11  121.63  3.000
 5J1  H25  O01  C20  110.26  3.000
 5J1  H26  O02  C15  110.25  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
 5J1  CONST_01  C20  C21  C22  C11    0.00   0.0  0
 5J1  CONST_02  C20  C19  C18  C11    0.00   0.0  0
 5J1  CONST_03  C15  C14  C13  C12    0.00   0.0  0
 5J1  CONST_04  C15  C16  C17  C12    0.00   0.0  0
 5J1  CONST_05  C16  C15  C14  C13    0.00   0.0  0
 5J1  CONST_06  C16  C17  C12  C13    0.00   0.0  0
 5J1  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 5J1  CONST_08  C17  C12  C13  C14    0.00   0.0  0
 5J1  CONST_09  C21  C22  C11  C18    0.00   0.0  0
 5J1  CONST_10  C21  C20  C19  C18    0.00   0.0  0
 5J1  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 5J1  CONST_12  C22  C11  C18  C19    0.00   0.0  0
 5J1  CONST_13  C14  C13  C12  C10  180.00   0.0  0
 5J1  CONST_14  C16  C17  C12  C10  180.00   0.0  0
 5J1  CONST_15  C21  C22  C11  C10  180.00   0.0  0
 5J1  CONST_16  C19  C18  C11  C10  180.00   0.0  0
 5J1  CONST_17  O02  C15  C14  C13  180.00   0.0  0
 5J1  CONST_18  O02  C15  C16  C17  180.00   0.0  0
 5J1  CONST_19  O01  C20  C19  C18  180.00   0.0  0
 5J1  CONST_20  O01  C20  C21  C22  180.00   0.0  0
 5J1  CONST_21  H23  C21  C22  C11  180.00   0.0  0
 5J1  CONST_22  H22  C19  C18  C11  180.00   0.0  0
 5J1  CONST_23  H18  C14  C13  C12  180.00   0.0  0
 5J1  CONST_24  H19  C16  C17  C12  180.00   0.0  0
 5J1  CONST_25  H20  C17  C12  C13  180.00   0.0  0
 5J1  CONST_26  H17  C13  C14  C15  180.00   0.0  0
 5J1  CONST_27  H24  C22  C11  C18  180.00   0.0  0
 5J1  CONST_28  H21  C18  C19  C20  180.00   0.0  0
 5J1  Var_01    C04  C03  C02  C01   40.78  30.0  1
 5J1  Var_02    C08  C01  C02  C03  -40.96  30.0  1
 5J1  Var_03    C07  C06  C05  C04  -44.48  30.0  3
 5J1  Var_04    C08  C07  C06  C05   44.71  30.0  3
 5J1  Var_05    C13  C12  C10  C09  124.21  30.0  2
 5J1  Var_06    C22  C11  C10  C09   43.06  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
 5J1  chir_01  C04  C09  C05  C03  negativ
 5J1  chir_02  C08  C09  C07  C01  positiv
 5J1  chir_03  C09  C10  C04  C08  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
 5J1  plan-1  C10  0.020
 5J1  plan-1  C12  0.020
 5J1  plan-1  C13  0.020
 5J1  plan-1  C14  0.020
 5J1  plan-1  C15  0.020
 5J1  plan-1  C16  0.020
 5J1  plan-1  C17  0.020
 5J1  plan-1  O02  0.020
 5J1  plan-1  H17  0.020
 5J1  plan-1  H18  0.020
 5J1  plan-1  H19  0.020
 5J1  plan-1  H20  0.020
 5J1  plan-2  C10  0.020
 5J1  plan-2  C11  0.020
 5J1  plan-2  C18  0.020
 5J1  plan-2  C19  0.020
 5J1  plan-2  C20  0.020
 5J1  plan-2  C21  0.020
 5J1  plan-2  C22  0.020
 5J1  plan-2  O01  0.020
 5J1  plan-2  H21  0.020
 5J1  plan-2  H22  0.020
 5J1  plan-2  H23  0.020
 5J1  plan-2  H24  0.020

