# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  8 18:29:23 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-ethyl-5-oxidanyl-pentan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](CCO)[C@@H](C)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C/3C[C@@H](O)C(=C)[C@H](O)C/3
#
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
 YSE  YSE  (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-ethyl-5-oxidanyl-pentan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol  ligand  71  29  .  2022-07-22  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_YSE
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
 YSE  O2   O  OH1   0  -0.677  -6.9335  -3.0576  -1.7128
 YSE  C23  C  CH2   0  -0.141  -5.8221  -2.3241  -1.2378
 YSE  C22  C  CH2   0  -0.454  -6.3186  -1.2552  -0.2810
 YSE  C21  C  CH1   0  -0.233  -5.2075  -0.5515   0.5067
 YSE  C24  C  CH2   0  -0.426  -5.8134   0.4282   1.5196
 YSE  C25  C  CH3   0  -0.664  -6.5357  -0.2462   2.6801
 YSE  C19  C  CH1   0  -0.234  -4.1518   0.1220  -0.4055
 YSE  C20  C  CH3   0  -0.686  -4.7490   1.3245  -1.1356
 YSE  C17  C  CR15  0  -0.174  -2.8686   0.4484   0.3725
 YSE  C16  C  CH2   0  -0.447  -2.2529  -0.8108   1.0390
 YSE  C15  C  CH2   0  -0.455  -0.7227  -0.6331   1.0268
 YSE  C10  C  CR15  0  -0.242  -0.5383   0.8201   0.6233
 YSE  C11  C  CR5   0  -0.055  -1.6778   1.0717  -0.3976
 YSE  C18  C  CH3   0  -0.681  -1.4157   0.3190  -1.7048
 YSE  C12  C  CH2   0  -0.418  -1.7515   2.5805  -0.6440
 YSE  C13  C  CH2   0  -0.434  -0.4091   3.1460  -1.1083
 YSE  C14  C  CH2   0  -0.506   0.7434   2.7928  -0.1624
 YSE  C8   C  C     0   0.158   0.7873   1.3200   0.1421
 YSE  C7   C  C1    0  -0.371   1.8653   0.5287   0.0163
 YSE  C6   C  C1    0  -0.329   3.1812   0.9354  -0.4424
 YSE  C5   C  C     0   0.118   4.2654   0.1550  -0.5708
 YSE  C    C  CH2   0  -0.511   5.5705   0.7176  -1.0530
 YSE  C4   C  CH2   0  -0.528   4.3271  -1.3095  -0.2471
 YSE  C3   C  CH1   0   0.048   5.4341  -1.5906   0.7768
 YSE  O    O  OH1   0  -0.665   5.4714  -2.9767   1.0025
 YSE  C2   C  C     0   0.066   6.7355  -1.0211   0.2677
 YSE  C9   C  C2    0  -0.604   7.8273  -1.7460   0.0508
 YSE  C1   C  CH1   0  -0.001   6.6881   0.4547  -0.0446
 YSE  O1   O  OH1   0  -0.662   6.4089   1.2225   1.1090
 YSE  H1   H  HOH1  0   0.451  -6.6133  -3.7039  -2.3481
 YSE  H2   H  HCH2  0   0.185  -5.1094  -2.9760  -0.7115
 YSE  H3   H  HCH2  0   0.190  -5.2737  -1.8684  -2.0711
 YSE  H4   H  HCH2  0   0.216  -6.9224  -0.5228  -0.8265
 YSE  H5   H  HCH2  0   0.232  -6.9946  -1.7382   0.4303
 YSE  H6   H  HCH1  0   0.224  -4.6965  -1.3362   1.0774
 YSE  H7   H  HCH2  0   0.226  -5.0269   1.0631   1.9360
 YSE  H8   H  HCH2  0   0.214  -6.5015   1.1068   1.0051
 YSE  H9   H  HCH3  0   0.227  -6.9226   0.4952   3.3805
 YSE  H10  H  HCH3  0   0.220  -7.3825  -0.8502   2.3518
 YSE  H11  H  HCH3  0   0.216  -5.8589  -0.8991   3.2349
 YSE  H12  H  HCH1  0   0.217  -3.8672  -0.6173  -1.1632
 YSE  H13  H  HCH3  0   0.219  -4.8541   2.1886  -0.4777
 YSE  H14  H  HCH3  0   0.233  -4.1385   1.6326  -1.9833
 YSE  H15  H  HCH3  0   0.233  -5.7379   1.0949  -1.5364
 YSE  H16  H  HCR5  0   0.213  -3.1177   1.1644   1.1667
 YSE  H17  H  HCH2  0   0.231  -2.6279  -0.9353   2.0562
 YSE  H18  H  HCH2  0   0.221  -2.5430  -1.7154   0.4975
 YSE  H19  H  HCH2  0   0.234  -0.2642  -0.8610   1.9904
 YSE  H20  H  HCH2  0   0.221  -0.2653  -1.3029   0.2948
 YSE  H21  H  HCR5  0   0.230  -0.8005   1.4344   1.4997
 YSE  H22  H  HCH3  0   0.231  -1.4764  -0.7627  -1.5740
 YSE  H23  H  HCH3  0   0.230  -2.1450   0.5939  -2.4693
 YSE  H24  H  HCH3  0   0.236  -0.4261   0.5367  -2.1076
 YSE  H25  H  HCH2  0   0.231  -2.5155   2.8260  -1.3827
 YSE  H26  H  HCH2  0   0.211  -2.0494   3.0757   0.2878
 YSE  H27  H  HCH2  0   0.222  -0.1782   2.7792  -2.1117
 YSE  H28  H  HCH2  0   0.233  -0.4801   4.2328  -1.1934
 YSE  H29  H  HCH2  0   0.245   1.6826   3.1591  -0.5760
 YSE  H30  H  HCH2  0   0.230   0.5943   3.3317   0.7816
 YSE  H31  H  H     0   0.232   1.7438  -0.5152   0.2851
 YSE  H32  H  H     0   0.230   3.3079   1.9790  -0.7122
 YSE  H33  H  HCH2  0   0.247   5.8596   0.2351  -1.9932
 YSE  H34  H  HCH2  0   0.252   5.4926   1.7889  -1.2529
 YSE  H35  H  HCH2  0   0.257   3.3804  -1.6895   0.1354
 YSE  H36  H  HCH2  0   0.244   4.5585  -1.8710  -1.1608
 YSE  H37  H  HCH1  0   0.221   5.1700  -1.0585   1.7019
 YSE  H38  H  HOH1  0   0.454   6.0536  -3.1467   1.7499
 YSE  H39  H  H     0   0.240   8.7321  -1.2888  -0.3307
 YSE  H40  H  H     0   0.238   7.8684  -2.8122   0.2312
 YSE  H41  H  HCH1  0   0.225   7.6452   0.7556  -0.4909
 YSE  H42  H  HOH1  0   0.450   7.1133   1.0684   1.7467

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
 YSE  C9   C2   double  1.328  0.020  1.328
 YSE  C2   C1   single  1.509  0.020  1.509
 YSE  C2   C3   single  1.509  0.020  1.509
 YSE  O    C3   single  1.405  0.020  1.405
 YSE  C1   O1   single  1.414  0.020  1.414
 YSE  C1   C    single  1.528  0.020  1.528
 YSE  C3   C4   single  1.534  0.020  1.534
 YSE  C    C5   single  1.501  0.020  1.501
 YSE  C4   C5   single  1.501  0.020  1.501
 YSE  C5   C6   double  1.342  0.020  1.342
 YSE  C6   C7   single  1.452  0.020  1.452
 YSE  C7   C8   double  1.343  0.020  1.343
 YSE  C8   C14  single  1.505  0.020  1.505
 YSE  C8   C10  single  1.496  0.020  1.496
 YSE  C15  C10  single  1.519  0.020  1.519
 YSE  C15  C16  single  1.541  0.020  1.541
 YSE  C18  C11  single  1.531  0.020  1.531
 YSE  C14  C13  single  1.532  0.020  1.532
 YSE  C10  C11  single  1.550  0.020  1.550
 YSE  C16  C17  single  1.552  0.020  1.552
 YSE  C11  C17  single  1.549  0.020  1.549
 YSE  C11  C12  single  1.530  0.020  1.530
 YSE  C13  C12  single  1.529  0.020  1.529
 YSE  C17  C19  single  1.536  0.020  1.536
 YSE  C23  O2   single  1.414  0.020  1.414
 YSE  C23  C22  single  1.518  0.020  1.518
 YSE  C19  C21  single  1.549  0.020  1.549
 YSE  C19  C20  single  1.528  0.020  1.528
 YSE  C21  C22  single  1.533  0.020  1.533
 YSE  C21  C24  single  1.534  0.020  1.534
 YSE  C24  C25  single  1.524  0.020  1.524
 YSE  O2   H1   single  0.850  0.020  0.980
 YSE  C23  H2   single  0.970  0.020  1.090
 YSE  C23  H3   single  0.970  0.020  1.090
 YSE  C22  H4   single  0.970  0.020  1.090
 YSE  C22  H5   single  0.970  0.020  1.090
 YSE  C21  H6   single  0.970  0.020  1.090
 YSE  C24  H7   single  0.970  0.020  1.090
 YSE  C24  H8   single  0.970  0.020  1.090
 YSE  C25  H9   single  0.970  0.020  1.090
 YSE  C25  H10  single  0.970  0.020  1.090
 YSE  C25  H11  single  0.970  0.020  1.090
 YSE  C19  H12  single  0.970  0.020  1.090
 YSE  C20  H13  single  0.970  0.020  1.090
 YSE  C20  H14  single  0.970  0.020  1.090
 YSE  C20  H15  single  0.970  0.020  1.090
 YSE  C17  H16  single  0.970  0.020  1.090
 YSE  C16  H17  single  0.970  0.020  1.090
 YSE  C16  H18  single  0.970  0.020  1.090
 YSE  C15  H19  single  0.970  0.020  1.090
 YSE  C15  H20  single  0.970  0.020  1.090
 YSE  C10  H21  single  0.970  0.020  1.090
 YSE  C18  H22  single  0.970  0.020  1.090
 YSE  C18  H23  single  0.970  0.020  1.090
 YSE  C18  H24  single  0.970  0.020  1.090
 YSE  C12  H25  single  0.970  0.020  1.090
 YSE  C12  H26  single  0.970  0.020  1.090
 YSE  C13  H27  single  0.970  0.020  1.090
 YSE  C13  H28  single  0.970  0.020  1.090
 YSE  C14  H29  single  0.970  0.020  1.090
 YSE  C14  H30  single  0.970  0.020  1.090
 YSE  C7   H31  single  0.930  0.020  1.080
 YSE  C6   H32  single  0.930  0.020  1.080
 YSE  C    H33  single  0.970  0.020  1.090
 YSE  C    H34  single  0.970  0.020  1.090
 YSE  C4   H35  single  0.970  0.020  1.090
 YSE  C4   H36  single  0.970  0.020  1.090
 YSE  C3   H37  single  0.970  0.020  1.090
 YSE  O    H38  single  0.850  0.020  0.980
 YSE  C9   H39  single  0.930  0.020  1.080
 YSE  C9   H40  single  0.930  0.020  1.080
 YSE  C1   H41  single  0.970  0.020  1.090
 YSE  O1   H42  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
 YSE  H1   O2   C23  108.00  3.000
 YSE  H3   C23  H2   106.61  3.000
 YSE  H3   C23  C22  110.48  3.000
 YSE  H2   C23  C22  109.13  3.000
 YSE  H3   C23  O2   110.69  3.000
 YSE  H2   C23  O2   111.26  3.000
 YSE  C22  C23  O2   108.66  3.000
 YSE  H5   C22  H4   106.18  3.000
 YSE  H5   C22  C21  108.45  3.000
 YSE  H4   C22  C21  110.41  3.000
 YSE  H5   C22  C23  107.52  3.000
 YSE  H4   C22  C23  109.72  3.000
 YSE  C21  C22  C23  114.21  3.000
 YSE  H6   C21  C19  107.46  3.000
 YSE  H6   C21  C24  107.30  3.000
 YSE  C19  C21  C24  112.36  3.000
 YSE  H6   C21  C22  106.06  3.000
 YSE  C24  C21  C22  110.25  3.000
 YSE  C19  C21  C22  113.01  3.000
 YSE  H8   C24  H7   105.74  3.000
 YSE  H8   C24  C25  109.52  3.000
 YSE  H7   C24  C25  107.93  3.000
 YSE  H8   C24  C21  109.50  3.000
 YSE  H7   C24  C21  109.77  3.000
 YSE  C25  C24  C21  114.04  3.000
 YSE  H11  C25  H10  107.64  3.000
 YSE  H11  C25  H9   107.46  3.000
 YSE  H10  C25  H9   107.10  3.000
 YSE  H11  C25  C24  110.96  3.000
 YSE  H10  C25  C24  112.56  3.000
 YSE  H9   C25  C24  110.87  3.000
 YSE  H12  C19  C17  106.06  3.000
 YSE  H12  C19  C20  107.57  3.000
 YSE  C17  C19  C20  113.66  3.000
 YSE  H12  C19  C21  106.90  3.000
 YSE  C20  C19  C21  110.92  3.000
 YSE  C17  C19  C21  111.31  3.000
 YSE  H15  C20  H14  106.35  3.000
 YSE  H15  C20  H13  107.49  3.000
 YSE  H14  C20  H13  107.41  3.000
 YSE  H15  C20  C19  111.35  3.000
 YSE  H14  C20  C19  112.05  3.000
 YSE  H13  C20  C19  111.89  3.000
 YSE  H16  C17  C11  105.76  3.000
 YSE  H16  C17  C16  107.97  3.000
 YSE  C11  C17  C16  103.59  3.000
 YSE  H16  C17  C19  108.39  3.000
 YSE  C11  C17  C19  118.42  3.000
 YSE  C16  C17  C19  112.12  3.000
 YSE  H18  C16  H17  106.02  3.000
 YSE  H18  C16  C15  110.79  3.000
 YSE  H17  C16  C15  111.22  3.000
 YSE  H18  C16  C17  110.68  3.000
 YSE  H17  C16  C17  110.89  3.000
 YSE  C15  C16  C17  107.28  3.000
 YSE  H20  C15  H19  106.73  3.000
 YSE  H20  C15  C10  110.96  3.000
 YSE  H19  C15  C10  112.54  3.000
 YSE  H20  C15  C16  110.52  3.000
 YSE  H19  C15  C16  112.72  3.000
 YSE  C10  C15  C16  103.47  3.000
 YSE  H21  C10  C8   106.28  3.000
 YSE  H21  C10  C11  104.97  3.000
 YSE  C8   C10  C11  112.65  3.000
 YSE  H21  C10  C15  107.04  3.000
 YSE  C11  C10  C15  103.94  3.000
 YSE  C8   C10  C15  120.83  3.000
 YSE  C12  C11  C18  110.82  3.000
 YSE  C12  C11  C10  107.54  3.000
 YSE  C18  C11  C10  110.89  3.000
 YSE  C12  C11  C17  116.08  3.000
 YSE  C10  C11  C17   99.92  3.000
 YSE  C18  C11  C17  110.99  3.000
 YSE  H24  C18  H23  107.30  3.000
 YSE  H24  C18  H22  107.02  3.000
 YSE  H23  C18  H22  107.24  3.000
 YSE  H24  C18  C11  111.88  3.000
 YSE  H23  C18  C11  111.09  3.000
 YSE  H22  C18  C11  112.05  3.000
 YSE  H26  C12  H25  106.47  3.000
 YSE  H26  C12  C13  109.25  3.000
 YSE  H25  C12  C13  109.03  3.000
 YSE  H26  C12  C11  108.75  3.000
 YSE  H25  C12  C11  111.39  3.000
 YSE  C13  C12  C11  111.79  3.000
 YSE  H28  C13  H27  106.03  3.000
 YSE  H28  C13  C14  109.05  3.000
 YSE  H27  C13  C14  109.30  3.000
 YSE  H28  C13  C12  109.54  3.000
 YSE  H27  C13  C12  109.89  3.000
 YSE  C14  C13  C12  112.81  3.000
 YSE  H30  C14  H29  106.17  3.000
 YSE  H30  C14  C8   108.10  3.000
 YSE  H29  C14  C8   112.38  3.000
 YSE  H30  C14  C13  108.40  3.000
 YSE  H29  C14  C13  109.67  3.000
 YSE  C8   C14  C13  111.87  3.000
 YSE  C7   C8   C14  125.53  3.000
 YSE  C14  C8   C10  111.49  3.000
 YSE  C7   C8   C10  122.98  3.000
 YSE  H31  C7   C6   116.71  3.000
 YSE  H31  C7   C8   116.99  3.000
 YSE  C6   C7   C8   126.31  3.000
 YSE  H32  C6   C5   116.17  3.000
 YSE  H32  C6   C7   116.98  3.000
 YSE  C5   C6   C7   126.85  3.000
 YSE  C4   C5   C    113.53  3.000
 YSE  C4   C5   C6   125.44  3.000
 YSE  C    C5   C6   121.02  3.000
 YSE  H34  C    H33  107.07  3.000
 YSE  H34  C    C1   109.97  3.000
 YSE  H33  C    C1   107.31  3.000
 YSE  H34  C    C5   111.36  3.000
 YSE  H33  C    C5   109.88  3.000
 YSE  C1   C    C5   111.07  3.000
 YSE  H36  C4   H35  107.29  3.000
 YSE  H36  C4   C3   108.05  3.000
 YSE  H35  C4   C3   109.20  3.000
 YSE  H36  C4   C5   109.17  3.000
 YSE  H35  C4   C5   112.35  3.000
 YSE  C3   C4   C5   110.63  3.000
 YSE  H37  C3   C2   107.96  3.000
 YSE  H37  C3   O    110.40  3.000
 YSE  C2   C3   O    113.81  3.000
 YSE  H37  C3   C4   107.43  3.000
 YSE  O    C3   C4   107.89  3.000
 YSE  C2   C3   C4   109.15  3.000
 YSE  H38  O    C3   108.37  3.000
 YSE  C1   C2   C9   121.71  3.000
 YSE  C1   C2   C3   114.32  3.000
 YSE  C9   C2   C3   123.91  3.000
 YSE  H40  C9   H39  116.28  3.000
 YSE  H40  C9   C2   122.80  3.000
 YSE  H39  C9   C2   120.92  3.000
 YSE  H41  C1   O1   110.80  3.000
 YSE  H41  C1   C2   108.95  3.000
 YSE  O1   C1   C2   111.62  3.000
 YSE  H41  C1   C    108.79  3.000
 YSE  O1   C1   C    107.49  3.000
 YSE  C2   C1   C    109.13  3.000
 YSE  H42  O1   C1   108.01  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
 YSE  Var_01  C10  C15  C16  C17    11.15  30.0  1
 YSE  Var_02  C13  C14  C8   C10   -52.36  30.0  1
 YSE  Var_03  C14  C13  C12  C11   -53.69  30.0  1
 YSE  Var_04  C8   C14  C13  C12    50.65  30.0  1
 YSE  Var_05  C3   C4   C5   C      55.57  30.0  1
 YSE  Var_06  C1   C    C5   C4    -55.57  30.0  1
 YSE  Var_07  C6   C7   C8   C10   179.96  30.0  2
 YSE  Var_08  C5   C6   C7   C8    179.92  30.0  1
 YSE  Var_09  C    C5   C6   C7   -179.65  30.0  2
 YSE  Var_10  H39  C9   C2   C3    179.02  30.0  2
 YSE  Var_11  C21  C22  C23  O2    169.38  30.0  3
 YSE  Var_12  H9   C25  C24  C21   178.51  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
 YSE  chir_01  C21  C19  C22  C24  positiv
 YSE  chir_02  C19  C20  C21  C17  positiv
 YSE  chir_03  C17  C19  C11  C16  positiv
 YSE  chir_04  C10  C11  C15  C8   negativ
 YSE  chir_05  C11  C17  C10  C12  positiv
 YSE  chir_06  C3   O    C2   C4   negativ
 YSE  chir_07  C1   O1   C    C2   positiv

