# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:10:45 2020
#   Inital geometry file: a 173 line input string
#   Ligand name: (1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,2S)-2-(2-hydroxyethyl)-1-methylhexyl]-7a-methyloctahydro-4H-inden-4-ylidene}ethylidene]-4-methylidenecyclohexane-1,3-diol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@@H](CCO)[C@@H](C)[C@H]1CC[C@H]2\C(CCC[C@]12C)=C\C=C3\C[C@@H](O)C[C@H](O)C3=C
#
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
 JB1  JB1  '(1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,2S)-2-(2-hydroxyethyl)-1-methylhexyl]-7a-methyloctahydro-4H-inden-4-ylidene}ethylidene]-4-methylidenecyclohexane-1,3-diol (non-preferred name)'  ligand  77  31  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JB1
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
 JB1  C31   C  CH3   0  -0.662   8.2843  -1.1128   2.6508
 JB1  C30   C  CH2   0  -0.418   7.1050  -1.3891   1.7289
 JB1  C29   C  CH2   0  -0.413   6.4588  -0.1178   1.1901
 JB1  C28   C  CH2   0  -0.416   5.2872  -0.4138   0.2591
 JB1  C22   C  CH1   0  -0.232   4.4732   0.8088  -0.1761
 JB1  C23   C  CH2   0  -0.460   5.3649   1.8391  -0.8809
 JB1  C24   C  CH2   0  -0.141   4.6329   3.0873  -1.3365
 JB1  O03   O  OH1   0  -0.677   5.5889   4.0450  -1.7464
 JB1  C20   C  CH1   0  -0.239   3.2268   0.4189  -1.0125
 JB1  C21   C  CH3   0  -0.685   3.6285  -0.2530  -2.3259
 JB1  C17   C  CH1   0  -0.177   2.2269  -0.4086  -0.1915
 JB1  C16   C  CH2   0  -0.444   1.7967   0.3159   1.1118
 JB1  C15   C  CH2   0  -0.453   0.3357  -0.0832   1.3962
 JB1  C14   C  CH1   0  -0.244   0.0769  -1.2135   0.4133
 JB1  C13   C  CT    0  -0.057   0.8831  -0.8114  -0.8491
 JB1  C18   C  CH3   0  -0.679   0.2317   0.3806  -1.5511
 JB1  C12   C  CH2   0  -0.415   0.9321  -2.0300  -1.7752
 JB1  C11   C  CH2   0  -0.434  -0.4650  -2.5560  -2.1052
 JB1  C09   C  CH2   0  -0.505  -1.3109  -2.8231  -0.8549
 JB1  C08   C  C     0   0.152  -1.3162  -1.6385   0.0726
 JB1  C07   C  C1    0  -0.357  -2.4100  -1.0076   0.5294
 JB1  C06   C  C1    0  -0.302  -3.7829  -1.3233   0.1861
 JB1  C05   C  C     0   0.098  -4.8836  -0.7112   0.6561
 JB1  C04   C  CH2   0  -0.533  -6.2593  -1.0562   0.1527
 JB1  C03   C  CH1   0   0.071  -6.9859   0.1888  -0.3645
 JB1  O02   O  OH1   0  -0.674  -8.3214  -0.0977  -0.7243
 JB1  C02   C  CH2   0  -0.488  -7.0220   1.2582   0.7172
 JB1  C01   C  CH1   0  -0.029  -5.6298   1.6181   1.2175
 JB1  O01   O  OH1   0  -0.663  -4.9458   2.2563   0.1552
 JB1  C10   C  C     0   0.069  -4.8814   0.3776   1.6515
 JB1  C19   C  C2    0  -0.587  -4.3082   0.2966   2.8508
 JB1  H31   H  HCH3  0   0.215   9.0645  -0.5501   2.1350
 JB1  H31A  H  HCH3  0   0.215   7.9778  -0.5263   3.5190
 JB1  H31B  H  HCH3  0   0.225   8.7314  -2.0373   3.0183
 JB1  H30   H  HCH2  0   0.210   7.4358  -2.0083   0.8887
 JB1  H30A  H  HCH2  0   0.210   6.3524  -1.9796   2.2608
 JB1  H29   H  HCH2  0   0.205   6.1142   0.4972   2.0300
 JB1  H29A  H  HCH2  0   0.213   7.2214   0.4722   0.6740
 JB1  H28   H  HCH2  0   0.212   5.6610  -0.9427  -0.6242
 JB1  H28A  H  HCH2  0   0.221   4.6251  -1.1176   0.7724
 JB1  H22   H  HCH1  0   0.222   4.1129   1.2987   0.7374
 JB1  H23   H  HCH2  0   0.235   6.1470   2.1529  -0.1839
 JB1  H23A  H  HCH2  0   0.215   5.8865   1.3880  -1.7315
 JB1  H24   H  HCH2  0   0.192   3.9438   2.8519  -2.1566
 JB1  H24A  H  HCH2  0   0.185   4.0177   3.4671  -0.5074
 JB1  HO03  H  HOH1  0   0.451   5.1197   4.7931  -2.1259
 JB1  H20   H  HCH1  0   0.219   2.7129   1.3541  -1.2654
 JB1  H21   H  HCH3  0   0.219   3.9416  -1.2883  -2.1792
 JB1  H21A  H  HCH3  0   0.232   2.8090  -0.2582  -3.0426
 JB1  H21B  H  HCH3  0   0.234   4.4557   0.2701  -2.8065
 JB1  H17   H  HCH1  0   0.215   2.7098  -1.3541   0.0853
 JB1  H16   H  HCH2  0   0.231   2.4553   0.0466   1.9396
 JB1  H16A  H  HCH2  0   0.221   1.8838   1.3997   0.9971
 JB1  H15   H  HCH2  0   0.234   0.1732  -0.3918   2.4301
 JB1  H15A  H  HCH2  0   0.221  -0.3327   0.7608   1.2124
 JB1  H14   H  HCH1  0   0.229   0.5867  -2.1063   0.8091
 JB1  H18   H  HCH3  0   0.230   0.7716   0.6456  -2.4612
 JB1  H18A  H  HCH3  0   0.237  -0.7990   0.1696  -1.8363
 JB1  H18B  H  HCH3  0   0.231   0.2079   1.2671  -0.9149
 JB1  H12   H  HCH2  0   0.231   1.4513  -1.8005  -2.7066
 JB1  H12A  H  HCH2  0   0.211   1.5113  -2.8206  -1.2832
 JB1  H11   H  HCH2  0   0.221  -0.9893  -1.8445  -2.7485
 JB1  H11A  H  HCH2  0   0.233  -0.3807  -3.4798  -2.6825
 JB1  H09   H  HCH2  0   0.244  -2.3150  -3.1300  -1.1473
 JB1  H09A  H  HCH2  0   0.231  -0.8733  -3.6734  -0.3175
 JB1  H07   H  H     0   0.229  -2.2700  -0.1729   1.2066
 JB1  H06   H  H     0   0.233  -3.9408  -2.1028  -0.5530
 JB1  H04   H  HCH2  0   0.245  -6.1983  -1.8131  -0.6338
 JB1  H04A  H  HCH2  0   0.236  -6.8551  -1.4801   0.9706
 JB1  H03   H  HCH1  0   0.206  -6.4309   0.5718  -1.2309
 JB1  HO02  H  HOH1  0   0.449  -8.3081  -0.6962  -1.4778
 JB1  H02   H  HCH2  0   0.250  -7.5242   2.1581   0.3505
 JB1  H02A  H  HCH2  0   0.237  -7.6060   0.8907   1.5675
 JB1  H01   H  HCH1  0   0.226  -5.7281   2.2944   2.0771
 JB1  HO01  H  HOH1  0   0.449  -4.0519   2.4566   0.4506
 JB1  H19   H  H     0   0.246  -3.7868  -0.5938   3.1781
 JB1  H19A  H  H     0   0.244  -4.3553   1.1214   3.5519

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
 JB1  C31  C30   single  1.522  0.020  1.522
 JB1  C30  C29   single  1.525  0.020  1.525
 JB1  C29  C28   single  1.525  0.020  1.525
 JB1  C28  C22   single  1.532  0.020  1.532
 JB1  C22  C23   single  1.534  0.020  1.534
 JB1  C22  C20   single  1.551  0.020  1.551
 JB1  C23  C24   single  1.517  0.020  1.517
 JB1  C24  O03   single  1.414  0.020  1.414
 JB1  C20  C21   single  1.529  0.020  1.529
 JB1  C20  C17   single  1.536  0.020  1.536
 JB1  C17  C16   single  1.552  0.020  1.552
 JB1  C17  C13   single  1.549  0.020  1.549
 JB1  C16  C15   single  1.541  0.020  1.541
 JB1  C15  C14   single  1.520  0.020  1.520
 JB1  C14  C13   single  1.551  0.020  1.551
 JB1  C14  C08   single  1.496  0.020  1.496
 JB1  C13  C18   single  1.529  0.020  1.529
 JB1  C13  C12   single  1.531  0.020  1.531
 JB1  C12  C11   single  1.529  0.020  1.529
 JB1  C11  C09   single  1.533  0.020  1.533
 JB1  C09  C08   single  1.504  0.020  1.504
 JB1  C08  C07   double  1.343  0.020  1.343
 JB1  C07  C06   single  1.450  0.020  1.450
 JB1  C06  C05   double  1.344  0.020  1.344
 JB1  C05  C04   single  1.505  0.020  1.505
 JB1  C05  C10   single  1.475  0.020  1.475
 JB1  C04  C03   single  1.531  0.020  1.531
 JB1  C03  O02   single  1.413  0.020  1.413
 JB1  C03  C02   single  1.522  0.020  1.522
 JB1  C02  C01   single  1.523  0.020  1.523
 JB1  C01  O01   single  1.415  0.020  1.415
 JB1  C01  C10   single  1.512  0.020  1.512
 JB1  C10  C19   double  1.332  0.020  1.332
 JB1  C31  H31   single  0.970  0.020  1.090
 JB1  C31  H31A  single  0.970  0.020  1.090
 JB1  C31  H31B  single  0.970  0.020  1.090
 JB1  C30  H30   single  0.970  0.020  1.090
 JB1  C30  H30A  single  0.970  0.020  1.090
 JB1  C29  H29   single  0.970  0.020  1.090
 JB1  C29  H29A  single  0.970  0.020  1.090
 JB1  C28  H28   single  0.970  0.020  1.090
 JB1  C28  H28A  single  0.970  0.020  1.090
 JB1  C22  H22   single  0.970  0.020  1.090
 JB1  C23  H23   single  0.970  0.020  1.090
 JB1  C23  H23A  single  0.970  0.020  1.090
 JB1  C24  H24   single  0.970  0.020  1.090
 JB1  C24  H24A  single  0.970  0.020  1.090
 JB1  O03  HO03  single  0.850  0.020  0.980
 JB1  C20  H20   single  0.970  0.020  1.090
 JB1  C21  H21   single  0.970  0.020  1.090
 JB1  C21  H21A  single  0.970  0.020  1.090
 JB1  C21  H21B  single  0.970  0.020  1.090
 JB1  C17  H17   single  0.970  0.020  1.090
 JB1  C16  H16   single  0.970  0.020  1.090
 JB1  C16  H16A  single  0.970  0.020  1.090
 JB1  C15  H15   single  0.970  0.020  1.090
 JB1  C15  H15A  single  0.970  0.020  1.090
 JB1  C14  H14   single  0.970  0.020  1.090
 JB1  C18  H18   single  0.970  0.020  1.090
 JB1  C18  H18A  single  0.970  0.020  1.090
 JB1  C18  H18B  single  0.970  0.020  1.090
 JB1  C12  H12   single  0.970  0.020  1.090
 JB1  C12  H12A  single  0.970  0.020  1.090
 JB1  C11  H11   single  0.970  0.020  1.090
 JB1  C11  H11A  single  0.970  0.020  1.090
 JB1  C09  H09   single  0.970  0.020  1.090
 JB1  C09  H09A  single  0.970  0.020  1.090
 JB1  C07  H07   single  0.930  0.020  1.080
 JB1  C06  H06   single  0.930  0.020  1.080
 JB1  C04  H04   single  0.970  0.020  1.090
 JB1  C04  H04A  single  0.970  0.020  1.090
 JB1  C03  H03   single  0.970  0.020  1.090
 JB1  O02  HO02  single  0.850  0.020  0.980
 JB1  C02  H02   single  0.970  0.020  1.090
 JB1  C02  H02A  single  0.970  0.020  1.090
 JB1  C01  H01   single  0.970  0.020  1.090
 JB1  O01  HO01  single  0.850  0.020  0.980
 JB1  C19  H19   single  0.930  0.020  1.080
 JB1  C19  H19A  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
 JB1  H31B  C31  H31A  107.61  3.000
 JB1  H31B  C31  H31   107.65  3.000
 JB1  H31A  C31  H31   107.43  3.000
 JB1  H31B  C31  C30   111.58  3.000
 JB1  H31A  C31  C30   111.20  3.000
 JB1  H31   C31  C30   111.17  3.000
 JB1  H30A  C30  H30   106.00  3.000
 JB1  H30A  C30  C29   109.28  3.000
 JB1  H30   C30  C29   109.18  3.000
 JB1  H30A  C30  C31   109.65  3.000
 JB1  H30   C30  C31   109.47  3.000
 JB1  C29   C30  C31   113.02  3.000
 JB1  H29A  C29  H29   106.14  3.000
 JB1  H29A  C29  C28   110.62  3.000
 JB1  H29   C29  C28   109.57  3.000
 JB1  H29A  C29  C30   108.73  3.000
 JB1  H29   C29  C30   109.28  3.000
 JB1  C28   C29  C30   112.30  3.000
 JB1  H28A  C28  H28   105.92  3.000
 JB1  H28A  C28  C22   108.97  3.000
 JB1  H28   C28  C22   109.74  3.000
 JB1  H28A  C28  C29   107.65  3.000
 JB1  H28   C28  C29   108.90  3.000
 JB1  C22   C28  C29   115.25  3.000
 JB1  H22   C22  C20   107.29  3.000
 JB1  H22   C22  C23   105.87  3.000
 JB1  C20   C22  C23   112.84  3.000
 JB1  H22   C22  C28   107.12  3.000
 JB1  C20   C22  C28   112.31  3.000
 JB1  C23   C22  C28   110.96  3.000
 JB1  H23A  C23  H23   105.82  3.000
 JB1  H23A  C23  C24   109.60  3.000
 JB1  H23   C23  C24   107.48  3.000
 JB1  H23A  C23  C22   110.92  3.000
 JB1  H23   C23  C22   108.39  3.000
 JB1  C24   C23  C22   114.22  3.000
 JB1  H24A  C24  H24   106.63  3.000
 JB1  H24A  C24  O03   111.27  3.000
 JB1  H24   C24  O03   110.70  3.000
 JB1  H24A  C24  C23   109.12  3.000
 JB1  H24   C24  C23   110.55  3.000
 JB1  O03   C24  C23   108.55  3.000
 JB1  HO03  O03  C24   108.16  3.000
 JB1  H20   C20  C17   106.12  3.000
 JB1  H20   C20  C21   107.44  3.000
 JB1  C17   C20  C21   113.16  3.000
 JB1  H20   C20  C22   106.66  3.000
 JB1  C17   C20  C22   111.74  3.000
 JB1  C21   C20  C22   111.26  3.000
 JB1  H21B  C21  H21A  106.45  3.000
 JB1  H21B  C21  H21   107.26  3.000
 JB1  H21A  C21  H21   107.45  3.000
 JB1  H21B  C21  C20   111.53  3.000
 JB1  H21A  C21  C20   111.71  3.000
 JB1  H21   C21  C20   112.13  3.000
 JB1  H17   C17  C13   105.36  3.000
 JB1  H17   C17  C16   108.21  3.000
 JB1  C13   C17  C16   103.73  3.000
 JB1  H17   C17  C20   108.21  3.000
 JB1  C13   C17  C20   118.55  3.000
 JB1  C16   C17  C20   112.20  3.000
 JB1  H16A  C16  H16   106.03  3.000
 JB1  H16A  C16  C15   110.59  3.000
 JB1  H16   C16  C15   111.61  3.000
 JB1  H16A  C16  C17   110.64  3.000
 JB1  H16   C16  C17   110.76  3.000
 JB1  C15   C16  C17   107.27  3.000
 JB1  H15A  C15  H15   106.67  3.000
 JB1  H15A  C15  C14   111.20  3.000
 JB1  H15   C15  C14   112.15  3.000
 JB1  H15A  C15  C16   110.43  3.000
 JB1  H15   C15  C16   112.91  3.000
 JB1  C14   C15  C16   103.57  3.000
 JB1  H14   C14  C08   106.41  3.000
 JB1  H14   C14  C13   105.19  3.000
 JB1  C08   C14  C13   111.86  3.000
 JB1  H14   C14  C15   106.95  3.000
 JB1  C08   C14  C15   121.14  3.000
 JB1  C13   C14  C15   104.18  3.000
 JB1  C12   C13  C18   110.88  3.000
 JB1  C12   C13  C14   107.62  3.000
 JB1  C18   C13  C14   110.75  3.000
 JB1  C12   C13  C17   115.83  3.000
 JB1  C18   C13  C17   111.20  3.000
 JB1  C14   C13  C17    99.95  3.000
 JB1  H18B  C18  H18A  106.81  3.000
 JB1  H18B  C18  H18   107.44  3.000
 JB1  H18A  C18  H18   107.26  3.000
 JB1  H18B  C18  C13   112.02  3.000
 JB1  H18A  C18  C13   111.84  3.000
 JB1  H18   C18  C13   111.19  3.000
 JB1  H12A  C12  H12   106.46  3.000
 JB1  H12A  C12  C11   109.36  3.000
 JB1  H12   C12  C11   108.84  3.000
 JB1  H12A  C12  C13   108.62  3.000
 JB1  H12   C12  C13   111.37  3.000
 JB1  C11   C12  C13   112.02  3.000
 JB1  H11A  C11  H11   106.04  3.000
 JB1  H11A  C11  C09   109.04  3.000
 JB1  H11   C11  C09   109.19  3.000
 JB1  H11A  C11  C12   109.54  3.000
 JB1  H11   C11  C12   109.96  3.000
 JB1  C09   C11  C12   112.84  3.000
 JB1  H09A  C09  H09   106.30  3.000
 JB1  H09A  C09  C08   108.04  3.000
 JB1  H09   C09  C08   112.57  3.000
 JB1  H09A  C09  C11   108.33  3.000
 JB1  H09   C09  C11   109.79  3.000
 JB1  C08   C09  C11   111.56  3.000
 JB1  C07   C08  C09   125.63  3.000
 JB1  C07   C08  C14   123.21  3.000
 JB1  C09   C08  C14   111.15  3.000
 JB1  H07   C07  C06   115.97  3.000
 JB1  H07   C07  C08   117.98  3.000
 JB1  C06   C07  C08   126.05  3.000
 JB1  H06   C06  C05   116.47  3.000
 JB1  H06   C06  C07   117.08  3.000
 JB1  C05   C06  C07   126.40  3.000
 JB1  C10   C05  C04   113.34  3.000
 JB1  C10   C05  C06   124.80  3.000
 JB1  C04   C05  C06   121.81  3.000
 JB1  H04A  C04  H04   107.40  3.000
 JB1  H04A  C04  C03   107.95  3.000
 JB1  H04   C04  C03   110.26  3.000
 JB1  H04A  C04  C05   109.62  3.000
 JB1  H04   C04  C05   110.39  3.000
 JB1  C03   C04  C05   111.12  3.000
 JB1  H03   C03  C02   109.14  3.000
 JB1  H03   C03  O02   110.34  3.000
 JB1  C02   C03  O02   107.53  3.000
 JB1  H03   C03  C04   108.07  3.000
 JB1  C02   C03  C04   110.03  3.000
 JB1  O02   C03  C04   111.70  3.000
 JB1  HO02  O02  C03   108.21  3.000
 JB1  H02A  C02  H02   106.95  3.000
 JB1  H02A  C02  C01   108.18  3.000
 JB1  H02   C02  C01   109.61  3.000
 JB1  H02A  C02  C03   109.19  3.000
 JB1  H02   C02  C03   110.53  3.000
 JB1  C01   C02  C03   112.21  3.000
 JB1  H01   C01  C10   108.96  3.000
 JB1  H01   C01  O01   110.67  3.000
 JB1  C10   C01  O01   110.24  3.000
 JB1  H01   C01  C02   108.72  3.000
 JB1  C10   C01  C02   110.67  3.000
 JB1  O01   C01  C02   107.57  3.000
 JB1  HO01  O01  C01   108.20  3.000
 JB1  C19   C10  C01   121.42  3.000
 JB1  C19   C10  C05   124.29  3.000
 JB1  C01   C10  C05   114.27  3.000
 JB1  H19A  C19  H19   116.84  3.000
 JB1  H19A  C19  C10   121.18  3.000
 JB1  H19   C19  C10   121.98  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
 JB1  Var_01  C14  C15  C16  C17   10.53  30.0  1
 JB1  Var_02  C11  C09  C08  C14  -53.96  30.0  1
 JB1  Var_03  C08  C09  C11  C12   50.66  30.0  1
 JB1  Var_04  C01  C10  C05  C04  -51.32  30.0  1
 JB1  Var_05  C10  C05  C04  C03   53.11  30.0  1
 JB1  Var_06  C06  C07  C08  C14  176.67  30.0  2
 JB1  Var_07  C05  C06  C07  C08  178.81  30.0  2
 JB1  Var_08  C04  C05  C06  C07  175.43  30.0  2
 JB1  Var_09  H19  C19  C10  C05    0.50  30.0  2
 JB1  Var_10  C28  C29  C30  C31  179.50  30.0  3
 JB1  Var_11  C22  C28  C29  C30  172.33  30.0  3
 JB1  Var_12  O03  C24  C23  C22  169.67  30.0  3
 JB1  Var_13  H31  C31  C30  C29  -59.53  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
 JB1  chir_01  C22  C28  C23  C20  negativ
 JB1  chir_02  C20  C22  C21  C17  negativ
 JB1  chir_03  C17  C13  C16  C20  positiv
 JB1  chir_04  C14  C15  C13  C08  positiv
 JB1  chir_05  C13  C12  C14  C17  negativ
 JB1  chir_06  C03  C04  O02  C02  negativ
 JB1  chir_07  C01  O01  C02  C10  negativ

