# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  8 20:40:29 2020
#   Inital geometry file: a 167 line input string
#   Ligand name: (1R,3R,7E,17beta)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCCC(C)(C)O)[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
 YSV  YSV  (1R,3R,7E,17beta)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol  ligand  74  30  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YSV
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
 YSV  O3   O  OH1   0  -0.678  -8.8486   0.2592   0.2222
 YSV  C25  C  CT    0   0.202  -8.1633   1.4536  -0.1399
 YSV  C27  C  CH3   0  -0.666  -8.9773   2.2243  -1.1795
 YSV  C26  C  CH3   0  -0.666  -8.0500   2.2788   1.1357
 YSV  C24  C  CH2   0  -0.430  -6.7809   1.1279  -0.7235
 YSV  C23  C  CH2   0  -0.429  -5.8520   0.3233   0.1765
 YSV  C22  C  CH2   0  -0.404  -4.5480  -0.0315  -0.5339
 YSV  C20  C  CH1   0  -0.232  -3.4693  -0.6595   0.3614
 YSV  C21  C  CH3   0  -0.674  -3.9731  -1.9666   0.9665
 YSV  C17  C  CR15  0  -0.165  -2.1674  -0.8189  -0.4395
 YSV  C16  C  CH2   0  -0.447  -1.6505   0.5434  -0.9778
 YSV  C13  C  CR5   0  -0.060  -0.9276  -1.4316   0.2561
 YSV  C18  C  CH3   0  -0.679  -0.7218  -0.8113   1.6410
 YSV  C14  C  CR15  0  -0.244   0.1859  -0.9848  -0.7245
 YSV  C15  C  CH2   0  -0.455  -0.1120   0.4821  -0.9858
 YSV  C12  C  CH2   0  -0.419  -0.8801  -2.9596   0.3335
 YSV  C11  C  CH2   0  -0.434   0.5011  -3.4568   0.7606
 YSV  C9   C  CH2   0  -0.506   1.6281  -2.9153  -0.1261
 YSV  C8   C  C     0   0.160   1.5496  -1.4216  -0.2889
 YSV  C7   C  C1    0  -0.370   2.5586  -0.5590  -0.0872
 YSV  C6   C  C1    0  -0.331   3.9096  -0.8883   0.3295
 YSV  C5   C  C     0   0.120   4.9129  -0.0223   0.5412
 YSV  C10  C  CH2   0  -0.511   6.2715  -0.4961   0.9692
 YSV  C4   C  CH2   0  -0.529   4.8206   1.4678   0.3800
 YSV  C3   C  CH1   0   0.048   5.8913   1.9776  -0.5918
 YSV  O2   O  OH1   0  -0.665   5.7764   3.3758  -0.6655
 YSV  C2   C  C     0   0.066   7.2451   1.5009  -0.1278
 YSV  C28  C  C2    0  -0.605   8.2503   2.3120   0.1829
 YSV  C1   C  CH1   0  -0.000   7.3595   0.0037   0.0198
 YSV  O1   O  OH1   0  -0.662   7.1790  -0.6544  -1.2190
 YSV  H1   H  HOH1  0   0.439  -8.9307  -0.2878  -0.5664
 YSV  H2   H  HCH3  0   0.230  -9.9719   2.4632  -0.7988
 YSV  H3   H  HCH3  0   0.222  -8.4862   3.1611  -1.4461
 YSV  H4   H  HCH3  0   0.224  -9.0942   1.6438  -2.0981
 YSV  H5   H  HCH3  0   0.230  -9.0380   2.5485   1.5140
 YSV  H6   H  HCH3  0   0.234  -7.5233   1.7409   1.9245
 YSV  H7   H  HCH3  0   0.222  -7.5060   3.2036   0.9412
 YSV  H8   H  HCH2  0   0.215  -6.9268   0.5813  -1.6644
 YSV  H9   H  HCH2  0   0.216  -6.2931   2.0669  -1.0054
 YSV  H10  H  HCH2  0   0.212  -5.6155   0.8918   1.0819
 YSV  H11  H  HCH2  0   0.216  -6.3667  -0.5807   0.5079
 YSV  H12  H  HCH2  0   0.203  -4.7582  -0.7101  -1.3701
 YSV  H13  H  HCH2  0   0.227  -4.1540   0.8844  -0.9842
 YSV  H14  H  HCH1  0   0.204  -3.2776   0.0488   1.1788
 YSV  H15  H  HCH3  0   0.229  -3.3015  -2.3566   1.7296
 YSV  H16  H  HCH3  0   0.234  -4.9436  -1.8351   1.4457
 YSV  H17  H  HCH3  0   0.210  -4.0886  -2.7371   0.1994
 YSV  H18  H  HCR5  0   0.205  -2.3959  -1.4660  -1.2988
 YSV  H19  H  HCH2  0   0.232  -2.0446   0.7435  -1.9748
 YSV  H20  H  HCH2  0   0.221  -2.0002   1.3619  -0.3425
 YSV  H21  H  HCH3  0   0.229  -1.4199  -1.2349   2.3655
 YSV  H22  H  HCH3  0   0.235   0.2839  -0.9897   2.0224
 YSV  H23  H  HCH3  0   0.231  -0.8761   0.2691   1.6359
 YSV  H24  H  HCR5  0   0.230  -0.0264  -1.5257  -1.6610
 YSV  H25  H  HCH2  0   0.234   0.3201   0.8282  -1.9261
 YSV  H26  H  HCH2  0   0.220   0.3017   1.1160  -0.1984
 YSV  H27  H  HCH2  0   0.231  -1.6279  -3.3513   1.0249
 YSV  H28  H  HCH2  0   0.211  -1.1249  -3.3695  -0.6536
 YSV  H29  H  HCH2  0   0.222   0.6902  -3.1755   1.7997
 YSV  H30  H  HCH2  0   0.233   0.5219  -4.5489   0.7347
 YSV  H31  H  HCH2  0   0.244   2.5917  -3.2403   0.2660
 YSV  H32  H  HCH2  0   0.230   1.5317  -3.3695  -1.1200
 YSV  H33  H  H     0   0.231   2.3512   0.4909  -0.2616
 YSV  H34  H  H     0   0.230   4.1337  -1.9379   0.4925
 YSV  H35  H  HCH2  0   0.248   6.5045  -0.1039   1.9654
 YSV  H36  H  HCH2  0   0.252   6.3090  -1.5860   1.0373
 YSV  H37  H  HCH2  0   0.257   3.8393   1.7881   0.0309
 YSV  H38  H  HCH2  0   0.244   4.9909   1.9443   1.3536
 YSV  H39  H  HCH1  0   0.221   5.6875   1.5244  -1.5722
 YSV  H40  H  HOH1  0   0.454   6.3163   3.6888  -1.3984
 YSV  H41  H  H     0   0.238   8.1744   3.3894   0.1171
 YSV  H42  H  H     0   0.240   9.1977   1.9165   0.5286
 YSV  H43  H  HCH1  0   0.225   8.3403  -0.2380   0.4501
 YSV  H44  H  HOH1  0   0.450   7.8606  -0.3410  -1.8222

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
 YSV  C28  C2   double  1.328  0.020  1.328
 YSV  O2   C3   single  1.405  0.020  1.405
 YSV  C2   C3   single  1.508  0.020  1.508
 YSV  C2   C1   single  1.509  0.020  1.509
 YSV  C3   C4   single  1.533  0.020  1.533
 YSV  C1   O1   single  1.414  0.020  1.414
 YSV  C1   C10  single  1.528  0.020  1.528
 YSV  C4   C5   single  1.502  0.020  1.502
 YSV  C10  C5   single  1.501  0.020  1.501
 YSV  C5   C6   double  1.342  0.020  1.342
 YSV  C6   C7   single  1.452  0.020  1.452
 YSV  C7   C8   double  1.343  0.020  1.343
 YSV  C8   C14  single  1.497  0.020  1.497
 YSV  C8   C9   single  1.505  0.020  1.505
 YSV  C15  C14  single  1.520  0.020  1.520
 YSV  C15  C16  single  1.540  0.020  1.540
 YSV  C18  C13  single  1.531  0.020  1.531
 YSV  C14  C13  single  1.550  0.020  1.550
 YSV  C9   C11  single  1.533  0.020  1.533
 YSV  C16  C17  single  1.553  0.020  1.553
 YSV  C13  C17  single  1.548  0.020  1.548
 YSV  C13  C12  single  1.531  0.020  1.531
 YSV  C26  C25  single  1.523  0.020  1.523
 YSV  C24  C25  single  1.536  0.020  1.536
 YSV  C24  C23  single  1.523  0.020  1.523
 YSV  C11  C12  single  1.529  0.020  1.529
 YSV  C22  C23  single  1.527  0.020  1.527
 YSV  C22  C20  single  1.536  0.020  1.536
 YSV  C17  C20  single  1.537  0.020  1.537
 YSV  C25  C27  single  1.529  0.020  1.529
 YSV  C25  O3   single  1.424  0.020  1.424
 YSV  C20  C21  single  1.526  0.020  1.526
 YSV  O3   H1   single  0.850  0.020  0.980
 YSV  C27  H2   single  0.970  0.020  1.090
 YSV  C27  H3   single  0.970  0.020  1.090
 YSV  C27  H4   single  0.970  0.020  1.090
 YSV  C26  H5   single  0.970  0.020  1.090
 YSV  C26  H6   single  0.970  0.020  1.090
 YSV  C26  H7   single  0.970  0.020  1.090
 YSV  C24  H8   single  0.970  0.020  1.090
 YSV  C24  H9   single  0.970  0.020  1.090
 YSV  C23  H10  single  0.970  0.020  1.090
 YSV  C23  H11  single  0.970  0.020  1.090
 YSV  C22  H12  single  0.970  0.020  1.090
 YSV  C22  H13  single  0.970  0.020  1.090
 YSV  C20  H14  single  0.970  0.020  1.090
 YSV  C21  H15  single  0.970  0.020  1.090
 YSV  C21  H16  single  0.970  0.020  1.090
 YSV  C21  H17  single  0.970  0.020  1.090
 YSV  C17  H18  single  0.970  0.020  1.090
 YSV  C16  H19  single  0.970  0.020  1.090
 YSV  C16  H20  single  0.970  0.020  1.090
 YSV  C18  H21  single  0.970  0.020  1.090
 YSV  C18  H22  single  0.970  0.020  1.090
 YSV  C18  H23  single  0.970  0.020  1.090
 YSV  C14  H24  single  0.970  0.020  1.090
 YSV  C15  H25  single  0.970  0.020  1.090
 YSV  C15  H26  single  0.970  0.020  1.090
 YSV  C12  H27  single  0.970  0.020  1.090
 YSV  C12  H28  single  0.970  0.020  1.090
 YSV  C11  H29  single  0.970  0.020  1.090
 YSV  C11  H30  single  0.970  0.020  1.090
 YSV  C9   H31  single  0.970  0.020  1.090
 YSV  C9   H32  single  0.970  0.020  1.090
 YSV  C7   H33  single  0.930  0.020  1.080
 YSV  C6   H34  single  0.930  0.020  1.080
 YSV  C10  H35  single  0.970  0.020  1.090
 YSV  C10  H36  single  0.970  0.020  1.090
 YSV  C4   H37  single  0.970  0.020  1.090
 YSV  C4   H38  single  0.970  0.020  1.090
 YSV  C3   H39  single  0.970  0.020  1.090
 YSV  O2   H40  single  0.850  0.020  0.980
 YSV  C28  H41  single  0.930  0.020  1.080
 YSV  C28  H42  single  0.930  0.020  1.080
 YSV  C1   H43  single  0.970  0.020  1.090
 YSV  O1   H44  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
 YSV  H1   O3   C25  108.01  3.000
 YSV  C24  C25  C26  111.48  3.000
 YSV  C24  C25  C27  109.13  3.000
 YSV  C26  C25  C27  109.63  3.000
 YSV  C27  C25  O3   109.85  3.000
 YSV  C24  C25  O3   110.61  3.000
 YSV  C26  C25  O3   106.10  3.000
 YSV  H4   C27  H3   107.39  3.000
 YSV  H4   C27  H2   108.17  3.000
 YSV  H3   C27  H2   107.91  3.000
 YSV  H4   C27  C25  111.15  3.000
 YSV  H3   C27  C25  111.07  3.000
 YSV  H2   C27  C25  111.00  3.000
 YSV  H7   C26  H6   107.85  3.000
 YSV  H7   C26  H5   107.68  3.000
 YSV  H6   C26  H5   107.96  3.000
 YSV  H7   C26  C25  110.31  3.000
 YSV  H6   C26  C25  111.99  3.000
 YSV  H5   C26  C25  110.89  3.000
 YSV  H9   C24  H8   105.40  3.000
 YSV  H9   C24  C23  109.47  3.000
 YSV  H8   C24  C23  108.93  3.000
 YSV  H9   C24  C25  108.48  3.000
 YSV  H8   C24  C25  108.16  3.000
 YSV  C23  C24  C25  115.88  3.000
 YSV  H11  C23  H10  106.30  3.000
 YSV  H11  C23  C22  110.58  3.000
 YSV  H10  C23  C22  108.72  3.000
 YSV  H11  C23  C24  109.22  3.000
 YSV  H10  C23  C24  110.25  3.000
 YSV  C22  C23  C24  111.63  3.000
 YSV  H13  C22  H12  105.85  3.000
 YSV  H13  C22  C20  109.22  3.000
 YSV  H12  C22  C20  109.01  3.000
 YSV  H13  C22  C23  107.74  3.000
 YSV  H12  C22  C23  109.56  3.000
 YSV  C20  C22  C23  115.06  3.000
 YSV  H14  C20  C17  107.86  3.000
 YSV  H14  C20  C21  108.36  3.000
 YSV  C17  C20  C21  113.42  3.000
 YSV  H14  C20  C22  107.01  3.000
 YSV  C21  C20  C22  110.46  3.000
 YSV  C17  C20  C22  109.49  3.000
 YSV  H17  C21  H16  107.43  3.000
 YSV  H17  C21  H15  107.73  3.000
 YSV  H16  C21  H15  106.51  3.000
 YSV  H17  C21  C20  111.12  3.000
 YSV  H16  C21  C20  111.39  3.000
 YSV  H15  C21  C20  112.40  3.000
 YSV  H18  C17  C13  106.53  3.000
 YSV  H18  C17  C16  108.32  3.000
 YSV  C13  C17  C16  103.67  3.000
 YSV  H18  C17  C20  106.99  3.000
 YSV  C13  C17  C20  119.04  3.000
 YSV  C16  C17  C20  111.81  3.000
 YSV  H20  C16  H19  106.15  3.000
 YSV  H20  C16  C15  110.63  3.000
 YSV  H19  C16  C15  111.32  3.000
 YSV  H20  C16  C17  110.41  3.000
 YSV  H19  C16  C17  110.94  3.000
 YSV  C15  C16  C17  107.42  3.000
 YSV  C12  C13  C14  107.31  3.000
 YSV  C12  C13  C18  110.76  3.000
 YSV  C14  C13  C18  111.04  3.000
 YSV  C12  C13  C17  116.28  3.000
 YSV  C14  C13  C17  100.20  3.000
 YSV  C18  C13  C17  110.71  3.000
 YSV  H23  C18  H22  107.10  3.000
 YSV  H23  C18  H21  107.26  3.000
 YSV  H22  C18  H21  107.11  3.000
 YSV  H23  C18  C13  112.20  3.000
 YSV  H22  C18  C13  111.96  3.000
 YSV  H21  C18  C13  110.92  3.000
 YSV  H24  C14  C8   106.24  3.000
 YSV  H24  C14  C15  106.85  3.000
 YSV  C8   C14  C15  120.69  3.000
 YSV  H24  C14  C13  104.94  3.000
 YSV  C15  C14  C13  104.26  3.000
 YSV  C8   C14  C13  112.73  3.000
 YSV  H26  C15  H25  106.69  3.000
 YSV  H26  C15  C14  111.22  3.000
 YSV  H25  C15  C14  112.13  3.000
 YSV  H26  C15  C16  110.59  3.000
 YSV  H25  C15  C16  112.81  3.000
 YSV  C14  C15  C16  103.50  3.000
 YSV  H28  C12  H27  106.45  3.000
 YSV  H28  C12  C11  109.36  3.000
 YSV  H27  C12  C11  108.99  3.000
 YSV  H28  C12  C13  108.71  3.000
 YSV  H27  C12  C13  111.66  3.000
 YSV  C11  C12  C13  111.52  3.000
 YSV  H30  C11  H29  106.06  3.000
 YSV  H30  C11  C9   108.98  3.000
 YSV  H29  C11  C9   109.38  3.000
 YSV  H30  C11  C12  109.61  3.000
 YSV  H29  C11  C12  109.76  3.000
 YSV  C9   C11  C12  112.81  3.000
 YSV  H32  C9   H31  106.27  3.000
 YSV  H32  C9   C8   107.96  3.000
 YSV  H31  C9   C8   112.40  3.000
 YSV  H32  C9   C11  108.26  3.000
 YSV  H31  C9   C11  109.67  3.000
 YSV  C8   C9   C11  112.02  3.000
 YSV  C7   C8   C9   125.61  3.000
 YSV  C9   C8   C14  111.64  3.000
 YSV  C7   C8   C14  122.75  3.000
 YSV  H33  C7   C6   116.35  3.000
 YSV  H33  C7   C8   117.01  3.000
 YSV  C6   C7   C8   126.64  3.000
 YSV  H34  C6   C5   116.48  3.000
 YSV  H34  C6   C7   117.04  3.000
 YSV  C5   C6   C7   126.49  3.000
 YSV  C4   C5   C10  113.54  3.000
 YSV  C10  C5   C6   121.19  3.000
 YSV  C4   C5   C6   125.27  3.000
 YSV  H36  C10  H35  107.04  3.000
 YSV  H36  C10  C1   109.91  3.000
 YSV  H35  C10  C1   107.24  3.000
 YSV  H36  C10  C5   111.33  3.000
 YSV  H35  C10  C5   109.80  3.000
 YSV  C1   C10  C5   111.35  3.000
 YSV  H38  C4   H37  107.24  3.000
 YSV  H38  C4   C3   108.04  3.000
 YSV  H37  C4   C3   109.15  3.000
 YSV  H38  C4   C5   109.04  3.000
 YSV  H37  C4   C5   112.42  3.000
 YSV  C3   C4   C5   110.80  3.000
 YSV  H39  C3   C2   108.09  3.000
 YSV  H39  C3   O2   110.39  3.000
 YSV  C2   C3   O2   113.83  3.000
 YSV  H39  C3   C4   107.38  3.000
 YSV  C2   C3   C4   109.07  3.000
 YSV  O2   C3   C4   107.88  3.000
 YSV  H40  O2   C3   108.52  3.000
 YSV  C1   C2   C28  121.71  3.000
 YSV  C1   C2   C3   114.31  3.000
 YSV  C28  C2   C3   123.93  3.000
 YSV  H42  C28  H41  116.38  3.000
 YSV  H42  C28  C2   120.90  3.000
 YSV  H41  C28  C2   122.72  3.000
 YSV  H43  C1   O1   110.79  3.000
 YSV  H43  C1   C2   108.94  3.000
 YSV  O1   C1   C2   111.49  3.000
 YSV  H43  C1   C10  108.69  3.000
 YSV  O1   C1   C10  107.52  3.000
 YSV  C2   C1   C10  109.35  3.000
 YSV  H44  O1   C1   107.88  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
 YSV  Var_01  C14  C15  C16  C17    10.94  30.0  1
 YSV  Var_02  C9   C11  C12  C13   -54.22  30.0  1
 YSV  Var_03  C8   C9   C11  C12    50.32  30.0  1
 YSV  Var_04  C3   C4   C5   C10    55.28  30.0  1
 YSV  Var_05  C1   C10  C5   C4    -54.74  30.0  1
 YSV  Var_06  C6   C7   C8   C14  -179.79  30.0  2
 YSV  Var_07  C5   C6   C7   C8   -179.39  30.0  1
 YSV  Var_08  C4   C5   C6   C7     -0.16  30.0  2
 YSV  Var_09  H41  C28  C2   C3     -0.55  30.0  2
 YSV  Var_10  C23  C24  C25  O3    -57.42  30.0  2
 YSV  Var_11  C22  C23  C24  C25   175.88  30.0  3
 YSV  Var_12  C20  C22  C23  C24   171.33  30.0  1
 YSV  Var_13  H5   C26  C25  O3    -62.44  30.0  3
 YSV  Var_14  H2   C27  C25  O3     58.00  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
 YSV  chir_01  C20  C22  C17  C21  positiv
 YSV  chir_02  C17  C20  C13  C16  positiv
 YSV  chir_03  C13  C14  C17  C12  negativ
 YSV  chir_04  C14  C13  C15  C8   negativ
 YSV  chir_05  C3   O2   C2   C4   negativ
 YSV  chir_06  C1   O1   C10  C2   positiv

