# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:26:41 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 4,4'-[(4aR,8aR)-octahydronaphthalen-2(1H)-ylidenemethanediyl]diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)C(=C2CC[C@H]3CCCC[C@@H]3C2)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
 5K5  5K5  4,4'-[(4aR,8aR)-octahydronaphthalen-2(1H)-ylidenemethanediyl]diphenol  ligand  51  25  .  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_5K5
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
 5K5  C01  C  CH2   0  -0.487   1.8174  -0.3462  -0.8764
 5K5  C02  C  CH1   0  -0.207   2.9177   0.2633   0.0032
 5K5  C03  C  CH2   0  -0.414   4.2173  -0.5297  -0.1079
 5K5  C04  C  CH2   0  -0.432   5.3163   0.0607   0.7697
 5K5  C05  C  CH2   0  -0.431   5.5405   1.5372   0.4613
 5K5  C06  C  CH2   0  -0.412   4.2401   2.3272   0.5688
 5K5  C07  C  CH1   0  -0.215   3.1516   1.7390  -0.3253
 5K5  C08  C  CH2   0  -0.412   1.8489   2.5260  -0.2473
 5K5  C09  C  CH2   0  -0.511   0.7687   1.8996  -1.1302
 5K5  C10  C  C     0   0.120   0.5482   0.4543  -0.7797
 5K5  C11  C  C     0  -0.033  -0.6342  -0.0524  -0.3852
 5K5  C12  C  CR6   0   0.016  -1.8289   0.7935  -0.1366
 5K5  C13  C  CR16  0  -0.286  -1.8058   1.8561   0.7639
 5K5  C14  C  CR16  0  -0.374  -2.9315   2.6317   1.0026
 5K5  C15  C  CR6   0   0.339  -4.1220   2.3523   0.3386
 5K5  O01  O  OH1   0  -0.633  -5.2490   3.0695   0.5255
 5K5  C16  C  CR16  0  -0.323  -4.1702   1.2835  -0.5552
 5K5  C17  C  CR16  0  -0.280  -3.0395   0.5165  -0.7752
 5K5  C18  C  CR6   0   0.019  -0.8599  -1.5029  -0.1659
 5K5  C19  C  CR16  0  -0.281  -1.3860  -1.9641   1.0428
 5K5  C20  C  CR16  0  -0.324  -1.6227  -3.3090   1.2670
 5K5  C21  C  CR6   0   0.339  -1.3511  -4.2395   0.2650
 5K5  O02  O  OH1   0  -0.633  -1.6032  -5.5388   0.5254
 5K5  C22  C  CR16  0  -0.375  -0.8455  -3.7986  -0.9540
 5K5  C23  C  CR16  0  -0.286  -0.6086  -2.4469  -1.1590
 5K5  H1   H  HCH2  0   0.223   2.1660  -0.3555  -1.9172
 5K5  H2   H  HCH2  0   0.243   1.6671  -1.3863  -0.5858
 5K5  H3   H  HCH1  0   0.207   2.5759   0.2044   1.0472
 5K5  H4   H  HCH2  0   0.223   4.0390  -1.5745   0.1641
 5K5  H5   H  HCH2  0   0.205   4.5459  -0.5333  -1.1542
 5K5  H6   H  HCH2  0   0.208   5.0336  -0.0506   1.8223
 5K5  H7   H  HCH2  0   0.225   6.2447  -0.5006   0.6376
 5K5  H8   H  HCH2  0   0.225   6.2964   1.9549   1.1310
 5K5  H9   H  HCH2  0   0.207   5.9361   1.6386  -0.5551
 5K5  H10  H  HCH2  0   0.204   3.8923   2.3232   1.6088
 5K5  H11  H  HCH2  0   0.222   4.4105   3.3747   0.3026
 5K5  H12  H  HCH1  0   0.201   3.5067   1.7922  -1.3661
 5K5  H13  H  HCH2  0   0.211   1.5000   2.5604   0.7917
 5K5  H14  H  HCH2  0   0.227   2.0211   3.5620  -0.5533
 5K5  H15  H  HCH2  0   0.247  -0.1496   2.4830  -1.0866
 5K5  H16  H  HCH2  0   0.234   1.1124   1.9428  -2.1719
 5K5  H19  H  HCR6  0   0.255  -0.8913   2.0824   1.2991
 5K5  H20  H  HCR6  0   0.268  -2.8798   3.4489   1.7133
 5K5  H21  H  HOH1  0   0.473  -5.0926   3.7824   1.1545
 5K5  H22  H  HCR6  0   0.260  -5.0941   1.0581  -1.0740
 5K5  H23  H  HCR6  0   0.247  -3.0979  -0.3126  -1.4703
 5K5  H24  H  HCR6  0   0.246  -1.6094  -1.2560   1.8318
 5K5  H25  H  HCR6  0   0.260  -2.0201  -3.6434   2.2173
 5K5  H26  H  HOH1  0   0.473  -1.3634  -6.0851  -0.2313
 5K5  H27  H  HCR6  0   0.268  -0.6446  -4.5053  -1.7512
 5K5  H28  H  HCR6  0   0.255  -0.2293  -2.1216  -2.1200

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
 5K5  O02  C21  single    1.349  0.020  1.349
 5K5  C22  C21  aromatic  1.391  0.020  1.391
 5K5  C22  C23  aromatic  1.388  0.020  1.388
 5K5  C21  C20  aromatic  1.394  0.020  1.394
 5K5  C23  C18  aromatic  1.393  0.020  1.393
 5K5  C20  C19  aromatic  1.384  0.020  1.384
 5K5  C18  C19  aromatic  1.397  0.020  1.397
 5K5  C18  C11  single    1.484  0.020  1.484
 5K5  C13  C14  aromatic  1.388  0.020  1.388
 5K5  C13  C12  aromatic  1.393  0.020  1.393
 5K5  C14  C15  aromatic  1.392  0.020  1.392
 5K5  C11  C12  single    1.485  0.020  1.485
 5K5  C11  C10  double    1.346  0.020  1.346
 5K5  C12  C17  aromatic  1.397  0.020  1.397
 5K5  C15  O01  single    1.349  0.020  1.349
 5K5  C15  C16  aromatic  1.394  0.020  1.394
 5K5  C17  C16  aromatic  1.384  0.020  1.384
 5K5  C01  C10  single    1.504  0.020  1.504
 5K5  C01  C02  single    1.535  0.020  1.535
 5K5  C10  C09  single    1.503  0.020  1.503
 5K5  C03  C02  single    1.526  0.020  1.526
 5K5  C03  C04  single    1.525  0.020  1.525
 5K5  C02  C07  single    1.530  0.020  1.530
 5K5  C04  C05  single    1.525  0.020  1.525
 5K5  C09  C08  single    1.529  0.020  1.529
 5K5  C07  C08  single    1.524  0.020  1.524
 5K5  C07  C06  single    1.527  0.020  1.527
 5K5  C05  C06  single    1.525  0.020  1.525
 5K5  C01  H1   single    0.970  0.020  1.090
 5K5  C01  H2   single    0.970  0.020  1.090
 5K5  C02  H3   single    0.970  0.020  1.090
 5K5  C03  H4   single    0.970  0.020  1.090
 5K5  C03  H5   single    0.970  0.020  1.090
 5K5  C04  H6   single    0.970  0.020  1.090
 5K5  C04  H7   single    0.970  0.020  1.090
 5K5  C05  H8   single    0.970  0.020  1.090
 5K5  C05  H9   single    0.970  0.020  1.090
 5K5  C06  H10  single    0.970  0.020  1.090
 5K5  C06  H11  single    0.970  0.020  1.090
 5K5  C07  H12  single    0.970  0.020  1.090
 5K5  C08  H13  single    0.970  0.020  1.090
 5K5  C08  H14  single    0.970  0.020  1.090
 5K5  C09  H15  single    0.970  0.020  1.090
 5K5  C09  H16  single    0.970  0.020  1.090
 5K5  C13  H19  single    0.930  0.020  1.080
 5K5  C14  H20  single    0.930  0.020  1.080
 5K5  O01  H21  single    0.850  0.020  0.980
 5K5  C16  H22  single    0.930  0.020  1.080
 5K5  C17  H23  single    0.930  0.020  1.080
 5K5  C19  H24  single    0.930  0.020  1.080
 5K5  C20  H25  single    0.930  0.020  1.080
 5K5  O02  H26  single    0.850  0.020  0.980
 5K5  C22  H27  single    0.930  0.020  1.080
 5K5  C23  H28  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
 5K5  H2   C01  H1   106.76  3.000
 5K5  H2   C01  C10  111.98  3.000
 5K5  H1   C01  C10  109.48  3.000
 5K5  H2   C01  C02  108.96  3.000
 5K5  H1   C01  C02  108.61  3.000
 5K5  C10  C01  C02  110.91  3.000
 5K5  H3   C02  C07  107.64  3.000
 5K5  H3   C02  C03  107.81  3.000
 5K5  C07  C02  C03  110.82  3.000
 5K5  H3   C02  C01  107.45  3.000
 5K5  C07  C02  C01  111.69  3.000
 5K5  C03  C02  C01  111.24  3.000
 5K5  H5   C03  H4   106.43  3.000
 5K5  H5   C03  C04  109.53  3.000
 5K5  H4   C03  C04  110.12  3.000
 5K5  H5   C03  C02  109.04  3.000
 5K5  H4   C03  C02  109.83  3.000
 5K5  C04  C03  C02  111.74  3.000
 5K5  H7   C04  H6   106.44  3.000
 5K5  H7   C04  C05  110.36  3.000
 5K5  H6   C04  C05  109.30  3.000
 5K5  H7   C04  C03  110.10  3.000
 5K5  H6   C04  C03  109.12  3.000
 5K5  C05  C04  C03  111.37  3.000
 5K5  H9   C05  H8   106.46  3.000
 5K5  H9   C05  C06  108.99  3.000
 5K5  H8   C05  C06  110.40  3.000
 5K5  H9   C05  C04  109.29  3.000
 5K5  H8   C05  C04  110.36  3.000
 5K5  C06  C05  C04  111.22  3.000
 5K5  H11  C06  H10  106.47  3.000
 5K5  H11  C06  C07  109.72  3.000
 5K5  H10  C06  C07  109.14  3.000
 5K5  H11  C06  C05  110.24  3.000
 5K5  H10  C06  C05  109.59  3.000
 5K5  C07  C06  C05  111.54  3.000
 5K5  H12  C07  C08  107.41  3.000
 5K5  H12  C07  C06  107.76  3.000
 5K5  C08  C07  C06  112.37  3.000
 5K5  H12  C07  C02  107.40  3.000
 5K5  C06  C07  C02  110.79  3.000
 5K5  C08  C07  C02  110.89  3.000
 5K5  H14  C08  H13  106.58  3.000
 5K5  H14  C08  C09  109.73  3.000
 5K5  H13  C08  C09  109.58  3.000
 5K5  H14  C08  C07  109.89  3.000
 5K5  H13  C08  C07  109.67  3.000
 5K5  C09  C08  C07  111.26  3.000
 5K5  H16  C09  H15  106.31  3.000
 5K5  H16  C09  C10  107.76  3.000
 5K5  H15  C09  C10  112.46  3.000
 5K5  H16  C09  C08  108.09  3.000
 5K5  H15  C09  C08  110.68  3.000
 5K5  C10  C09  C08  111.27  3.000
 5K5  C11  C10  C09  124.01  3.000
 5K5  C09  C10  C01  111.90  3.000
 5K5  C11  C10  C01  124.06  3.000
 5K5  C18  C11  C12  114.19  3.000
 5K5  C12  C11  C10  122.79  3.000
 5K5  C18  C11  C10  123.02  3.000
 5K5  C17  C12  C13  117.47  3.000
 5K5  C17  C12  C11  120.53  3.000
 5K5  C13  C12  C11  121.97  3.000
 5K5  H19  C13  C14  118.88  3.000
 5K5  H19  C13  C12  119.51  3.000
 5K5  C14  C13  C12  121.61  3.000
 5K5  H20  C14  C15  120.32  3.000
 5K5  H20  C14  C13  119.69  3.000
 5K5  C15  C14  C13  119.98  3.000
 5K5  C16  C15  O01  117.88  3.000
 5K5  C16  C15  C14  119.30  3.000
 5K5  O01  C15  C14  122.82  3.000
 5K5  H21  O01  C15  110.38  3.000
 5K5  H22  C16  C17  120.35  3.000
 5K5  H22  C16  C15  119.74  3.000
 5K5  C17  C16  C15  119.91  3.000
 5K5  H23  C17  C16  118.82  3.000
 5K5  H23  C17  C12  119.46  3.000
 5K5  C16  C17  C12  121.71  3.000
 5K5  C23  C18  C19  117.46  3.000
 5K5  C19  C18  C11  120.53  3.000
 5K5  C23  C18  C11  121.97  3.000
 5K5  H24  C19  C20  118.81  3.000
 5K5  H24  C19  C18  119.48  3.000
 5K5  C20  C19  C18  121.71  3.000
 5K5  H25  C20  C21  119.74  3.000
 5K5  H25  C20  C19  120.33  3.000
 5K5  C21  C20  C19  119.93  3.000
 5K5  C22  C21  O02  122.83  3.000
 5K5  C22  C21  C20  119.27  3.000
 5K5  O02  C21  C20  117.89  3.000
 5K5  H26  O02  C21  110.37  3.000
 5K5  H27  C22  C23  119.66  3.000
 5K5  H27  C22  C21  120.33  3.000
 5K5  C23  C22  C21  120.01  3.000
 5K5  H28  C23  C22  118.91  3.000
 5K5  H28  C23  C18  119.49  3.000
 5K5  C22  C23  C18  121.60  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
 5K5  CONST_01  C15  C14  C13  C12    0.00   0.0  0
 5K5  CONST_02  C15  C16  C17  C12    0.00   0.0  0
 5K5  CONST_03  C16  C15  C14  C13    0.00   0.0  0
 5K5  CONST_04  C16  C17  C12  C13    0.00   0.0  0
 5K5  CONST_05  C17  C12  C13  C14    0.00   0.0  0
 5K5  CONST_06  C17  C16  C15  C14    0.00   0.0  0
 5K5  CONST_07  C21  C22  C23  C18    0.00   0.0  0
 5K5  CONST_08  C21  C20  C19  C18    0.00   0.0  0
 5K5  CONST_09  C22  C21  C20  C19    0.00   0.0  0
 5K5  CONST_10  C22  C23  C18  C19    0.00   0.0  0
 5K5  CONST_11  C23  C22  C21  C20    0.00   0.0  0
 5K5  CONST_12  C23  C18  C19  C20    0.00   0.0  0
 5K5  CONST_13  C22  C23  C18  C11  180.00   0.0  0
 5K5  CONST_14  C20  C19  C18  C11  180.00   0.0  0
 5K5  CONST_15  C14  C13  C12  C11  180.00   0.0  0
 5K5  CONST_16  C16  C17  C12  C11  180.00   0.0  0
 5K5  CONST_17  O01  C15  C14  C13  180.00   0.0  0
 5K5  CONST_18  C17  C16  C15  O01  180.00   0.0  0
 5K5  CONST_19  O02  C21  C20  C19  180.00   0.0  0
 5K5  CONST_20  C23  C22  C21  O02  180.00   0.0  0
 5K5  CONST_21  H20  C14  C13  C12  180.00   0.0  0
 5K5  CONST_22  H22  C16  C17  C12  180.00   0.0  0
 5K5  CONST_23  H23  C17  C12  C13  180.00   0.0  0
 5K5  CONST_24  H19  C13  C14  C15  180.00   0.0  0
 5K5  CONST_25  H27  C22  C23  C18  180.00   0.0  0
 5K5  CONST_26  H25  C20  C19  C18  180.00   0.0  0
 5K5  CONST_27  H28  C23  C18  C19  180.00   0.0  0
 5K5  CONST_28  H24  C19  C20  C21  180.00   0.0  0
 5K5  Var_01    C08  C09  C10  C01  -56.57  30.0  1
 5K5  Var_02    C09  C10  C01  C02   55.87  30.0  1
 5K5  Var_03    C05  C04  C03  C02  -54.84  30.0  1
 5K5  Var_04    C06  C05  C04  C03   54.42  30.0  1
 5K5  Var_05    C07  C06  C05  C04  -55.41  30.0  1
 5K5  Var_06    C10  C09  C08  C07   55.59  30.0  1
 5K5  Var_07    C18  C11  C10  C01   -8.10  30.0  2
 5K5  Var_08    C23  C18  C11  C10  -55.70  30.0  2
 5K5  Var_09    C13  C12  C11  C10  -55.98  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
 5K5  chir_01  C02  C01  C03  C07  negativ
 5K5  chir_02  C07  C06  C08  C02  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
 5K5  plan-1  C11  0.020
 5K5  plan-1  C12  0.020
 5K5  plan-1  C13  0.020
 5K5  plan-1  C14  0.020
 5K5  plan-1  C15  0.020
 5K5  plan-1  O01  0.020
 5K5  plan-1  C16  0.020
 5K5  plan-1  C17  0.020
 5K5  plan-1  H19  0.020
 5K5  plan-1  H20  0.020
 5K5  plan-1  H22  0.020
 5K5  plan-1  H23  0.020
 5K5  plan-2  C11  0.020
 5K5  plan-2  C18  0.020
 5K5  plan-2  C19  0.020
 5K5  plan-2  C20  0.020
 5K5  plan-2  C21  0.020
 5K5  plan-2  O02  0.020
 5K5  plan-2  C22  0.020
 5K5  plan-2  C23  0.020
 5K5  plan-2  H24  0.020
 5K5  plan-2  H25  0.020
 5K5  plan-2  H27  0.020
 5K5  plan-2  H28  0.020

