# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:26:12 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-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](CCCO)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3
#
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
 YS2  YS2  (1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol  ligand  65  27  .  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_YS2
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
 YS2  O3   O  OH1   0  -0.676  -8.8448  -2.2077  -0.1367
 YS2  C24  C  CH2   0  -0.136  -7.6773  -1.8942   0.5943
 YS2  C23  C  CH2   0  -0.463  -6.7891  -0.9998  -0.2476
 YS2  C22  C  CH2   0  -0.419  -5.5199  -0.6067   0.5020
 YS2  C20  C  CH1   0  -0.230  -4.4858   0.1590  -0.3354
 YS2  C21  C  CH3   0  -0.674  -5.0783   1.4617  -0.8670
 YS2  C17  C  CR15  0  -0.167  -3.2039   0.3659   0.4871
 YS2  C13  C  CR5   0  -0.059  -2.0100   1.1029  -0.1686
 YS2  C18  C  CH3   0  -0.681  -1.7591   0.5742  -1.5825
 YS2  C12  C  CH2   0  -0.418  -2.0740   2.6324  -0.1614
 YS2  C11  C  CH2   0  -0.434  -0.7351   3.2534  -0.5588
 YS2  C9   C  CH2   0  -0.506   0.4324   2.7421   0.2926
 YS2  C16  C  CH2   0  -0.449  -2.5908  -0.9828   0.9538
 YS2  C15  C  CH2   0  -0.454  -1.0606  -0.8088   0.9794
 YS2  C14  C  CR15  0  -0.245  -0.8669   0.6867   0.7923
 YS2  C8   C  C     0   0.159   0.4599   1.2398   0.3738
 YS2  C7   C  C1    0  -0.370   1.5255   0.4644   0.1161
 YS2  C6   C  C1    0  -0.331   2.8365   0.9149  -0.3150
 YS2  C5   C  C     0   0.119   3.9042   0.1433  -0.5714
 YS2  C4   C  CH2   0  -0.510   5.2028   0.7393  -1.0313
 YS2  C10  C  CH2   0  -0.528   3.9464  -1.3513  -0.4314
 YS2  C1   C  CH1   0   0.048   5.0847  -1.7759   0.5041
 YS2  O1   O  OH1   0  -0.665   5.0937  -3.1793   0.5651
 YS2  C2   C  C     0   0.065   6.3780  -1.1783   0.0088
 YS2  C28  C  C2    0  -0.604   7.4405  -1.8950  -0.3405
 YS2  C3   C  CH1   0   0.000   6.3581   0.3250  -0.1212
 YS2  O2   O  OH1   0  -0.662   6.1577   0.9521   1.1304
 YS2  H1   H  HOH1  0   0.451  -9.3869  -2.7925   0.4000
 YS2  H2   H  HCH2  0   0.186  -7.9209  -1.3791   1.5340
 YS2  H3   H  HCH2  0   0.187  -7.1232  -2.8019   0.8688
 YS2  H4   H  HCH2  0   0.216  -6.5200  -1.5213  -1.1722
 YS2  H5   H  HCH2  0   0.222  -7.3572  -0.1128  -0.5388
 YS2  H6   H  HCH2  0   0.208  -5.7851  -0.0066   1.3815
 YS2  H7   H  HCH2  0   0.231  -5.0623  -1.5214   0.8895
 YS2  H8   H  HCH1  0   0.206  -4.2280  -0.4745  -1.1949
 YS2  H9   H  HCH3  0   0.230  -4.4265   1.9386  -1.5968
 YS2  H10  H  HCH3  0   0.235  -6.0320   1.2924  -1.3672
 YS2  H11  H  HCH3  0   0.211  -5.2522   2.1775  -0.0593
 YS2  H12  H  HCR5  0   0.207  -3.4789   0.9459   1.3797
 YS2  H13  H  HCH3  0   0.230  -2.4840   0.9853  -2.2877
 YS2  H14  H  HCH3  0   0.236  -0.7673   0.8382  -1.9511
 YS2  H15  H  HCH3  0   0.231  -1.8383  -0.5132  -1.6346
 YS2  H16  H  HCH2  0   0.232  -2.8514   3.0079  -0.8280
 YS2  H17  H  HCH2  0   0.211  -2.3433   2.9679   0.8472
 YS2  H18  H  HCH2  0   0.222  -0.5313   3.0524  -1.6141
 YS2  H19  H  HCH2  0   0.233  -0.7936   4.3404  -0.4649
 YS2  H20  H  HCH2  0   0.245   1.3683   3.1551  -0.0834
 YS2  H21  H  HCH2  0   0.231   0.3107   3.1304   1.3112
 YS2  H22  H  HCH2  0   0.233  -2.9767  -1.2668   1.9335
 YS2  H23  H  HCH2  0   0.222  -2.8717  -1.7866   0.2676
 YS2  H24  H  HCH2  0   0.234  -0.6091  -1.1696   1.9049
 YS2  H25  H  HCH2  0   0.221  -0.5995  -1.3721   0.1651
 YS2  H26  H  HCR5  0   0.230  -1.1136   1.1662   1.7532
 YS2  H27  H  H     0   0.231   1.3972  -0.6054   0.2395
 YS2  H28  H  H     0   0.230   2.9683   1.9831  -0.4575
 YS2  H29  H  HCH2  0   0.247   5.4381   0.3811  -2.0400
 YS2  H30  H  HCH2  0   0.252   5.1443   1.8290  -1.0846
 YS2  H31  H  HCH2  0   0.257   3.0070  -1.7588  -0.0585
 YS2  H32  H  HCH2  0   0.244   4.1292  -1.8005  -1.4157
 YS2  H33  H  HCH1  0   0.221   4.8720  -1.3509   1.4955
 YS2  H34  H  HOH1  0   0.454   5.6988  -3.4490   1.2635
 YS2  H35  H  H     0   0.240   8.3394  -1.4140  -0.7061
 YS2  H36  H  H     0   0.238   7.4614  -2.9756  -0.2868
 YS2  H37  H  HCH1  0   0.225   7.3009   0.6554  -0.5768
 YS2  H38  H  HOH1  0   0.450   6.8819   0.6958   1.7103

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
 YS2  C28  C2   double  1.328  0.020  1.328
 YS2  O1   C1   single  1.405  0.020  1.405
 YS2  C2   C3   single  1.509  0.020  1.509
 YS2  C2   C1   single  1.508  0.020  1.508
 YS2  C3   O2   single  1.414  0.020  1.414
 YS2  C3   C4   single  1.528  0.020  1.528
 YS2  C1   C10  single  1.533  0.020  1.533
 YS2  C4   C5   single  1.501  0.020  1.501
 YS2  C10  C5   single  1.502  0.020  1.502
 YS2  C5   C6   double  1.342  0.020  1.342
 YS2  C6   C7   single  1.452  0.020  1.452
 YS2  C7   C8   double  1.343  0.020  1.343
 YS2  C8   C9   single  1.505  0.020  1.505
 YS2  C8   C14  single  1.497  0.020  1.497
 YS2  C15  C14  single  1.520  0.020  1.520
 YS2  C15  C16  single  1.540  0.020  1.540
 YS2  C18  C13  single  1.530  0.020  1.530
 YS2  C9   C11  single  1.533  0.020  1.533
 YS2  C14  C13  single  1.550  0.020  1.550
 YS2  C16  C17  single  1.553  0.020  1.553
 YS2  C13  C17  single  1.549  0.020  1.549
 YS2  C13  C12  single  1.531  0.020  1.531
 YS2  C24  O3   single  1.413  0.020  1.413
 YS2  C24  C23  single  1.516  0.020  1.516
 YS2  C11  C12  single  1.528  0.020  1.528
 YS2  C17  C20  single  1.537  0.020  1.537
 YS2  C20  C21  single  1.527  0.020  1.527
 YS2  C20  C22  single  1.535  0.020  1.535
 YS2  C23  C22  single  1.525  0.020  1.525
 YS2  O3   H1   single  0.850  0.020  0.980
 YS2  C24  H2   single  0.970  0.020  1.090
 YS2  C24  H3   single  0.970  0.020  1.090
 YS2  C23  H4   single  0.970  0.020  1.090
 YS2  C23  H5   single  0.970  0.020  1.090
 YS2  C22  H6   single  0.970  0.020  1.090
 YS2  C22  H7   single  0.970  0.020  1.090
 YS2  C20  H8   single  0.970  0.020  1.090
 YS2  C21  H9   single  0.970  0.020  1.090
 YS2  C21  H10  single  0.970  0.020  1.090
 YS2  C21  H11  single  0.970  0.020  1.090
 YS2  C17  H12  single  0.970  0.020  1.090
 YS2  C18  H13  single  0.970  0.020  1.090
 YS2  C18  H14  single  0.970  0.020  1.090
 YS2  C18  H15  single  0.970  0.020  1.090
 YS2  C12  H16  single  0.970  0.020  1.090
 YS2  C12  H17  single  0.970  0.020  1.090
 YS2  C11  H18  single  0.970  0.020  1.090
 YS2  C11  H19  single  0.970  0.020  1.090
 YS2  C9   H20  single  0.970  0.020  1.090
 YS2  C9   H21  single  0.970  0.020  1.090
 YS2  C16  H22  single  0.970  0.020  1.090
 YS2  C16  H23  single  0.970  0.020  1.090
 YS2  C15  H24  single  0.970  0.020  1.090
 YS2  C15  H25  single  0.970  0.020  1.090
 YS2  C14  H26  single  0.970  0.020  1.090
 YS2  C7   H27  single  0.930  0.020  1.080
 YS2  C6   H28  single  0.930  0.020  1.080
 YS2  C4   H29  single  0.970  0.020  1.090
 YS2  C4   H30  single  0.970  0.020  1.090
 YS2  C10  H31  single  0.970  0.020  1.090
 YS2  C10  H32  single  0.970  0.020  1.090
 YS2  C1   H33  single  0.970  0.020  1.090
 YS2  O1   H34  single  0.850  0.020  0.980
 YS2  C28  H35  single  0.930  0.020  1.080
 YS2  C28  H36  single  0.930  0.020  1.080
 YS2  C3   H37  single  0.970  0.020  1.090
 YS2  O2   H38  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
 YS2  H1   O3   C24  108.19  3.000
 YS2  H3   C24  H2   106.59  3.000
 YS2  H3   C24  C23  109.32  3.000
 YS2  H2   C24  C23  109.16  3.000
 YS2  H3   C24  O3   111.28  3.000
 YS2  H2   C24  O3   111.30  3.000
 YS2  C23  C24  O3   109.14  3.000
 YS2  H5   C23  H4   106.81  3.000
 YS2  H5   C23  C22  110.75  3.000
 YS2  H4   C23  C22  109.46  3.000
 YS2  H5   C23  C24  108.80  3.000
 YS2  H4   C23  C24  109.38  3.000
 YS2  C22  C23  C24  111.51  3.000
 YS2  H7   C22  H6   105.93  3.000
 YS2  H7   C22  C20  109.18  3.000
 YS2  H6   C22  C20  109.10  3.000
 YS2  H7   C22  C23  107.86  3.000
 YS2  H6   C22  C23  109.50  3.000
 YS2  C20  C22  C23  114.89  3.000
 YS2  H8   C20  C17  107.49  3.000
 YS2  H8   C20  C21  108.10  3.000
 YS2  C17  C20  C21  113.28  3.000
 YS2  H8   C20  C22  107.29  3.000
 YS2  C21  C20  C22  110.74  3.000
 YS2  C17  C20  C22  109.70  3.000
 YS2  H11  C21  H10  107.55  3.000
 YS2  H11  C21  H9   107.68  3.000
 YS2  H10  C21  H9   106.51  3.000
 YS2  H11  C21  C20  111.30  3.000
 YS2  H10  C21  C20  111.52  3.000
 YS2  H9   C21  C20  112.02  3.000
 YS2  H12  C17  C16  108.23  3.000
 YS2  H12  C17  C13  106.59  3.000
 YS2  C16  C17  C13  103.66  3.000
 YS2  H12  C17  C20  107.27  3.000
 YS2  C13  C17  C20  118.71  3.000
 YS2  C16  C17  C20  111.90  3.000
 YS2  C14  C13  C12  107.23  3.000
 YS2  C12  C13  C18  110.88  3.000
 YS2  C14  C13  C18  111.04  3.000
 YS2  C12  C13  C17  116.18  3.000
 YS2  C14  C13  C17  100.27  3.000
 YS2  C18  C13  C17  110.68  3.000
 YS2  H15  C18  H14  106.92  3.000
 YS2  H15  C18  H13  107.22  3.000
 YS2  H14  C18  H13  107.12  3.000
 YS2  H15  C18  C13  112.11  3.000
 YS2  H14  C18  C13  112.20  3.000
 YS2  H13  C18  C13  110.97  3.000
 YS2  H17  C12  H16  106.36  3.000
 YS2  H17  C12  C11  109.27  3.000
 YS2  H16  C12  C11  109.00  3.000
 YS2  H17  C12  C13  108.68  3.000
 YS2  H16  C12  C13  111.77  3.000
 YS2  C11  C12  C13  111.60  3.000
 YS2  H19  C11  H18  106.01  3.000
 YS2  H19  C11  C9   108.96  3.000
 YS2  H18  C11  C9   109.44  3.000
 YS2  H19  C11  C12  109.57  3.000
 YS2  H18  C11  C12  109.85  3.000
 YS2  C9   C11  C12  112.79  3.000
 YS2  H21  C9   H20  106.35  3.000
 YS2  H21  C9   C8   107.78  3.000
 YS2  H20  C9   C8   112.41  3.000
 YS2  H21  C9   C11  108.26  3.000
 YS2  H20  C9   C11  109.63  3.000
 YS2  C8   C9   C11  112.14  3.000
 YS2  H23  C16  H22  106.34  3.000
 YS2  H23  C16  C15  110.40  3.000
 YS2  H22  C16  C15  111.47  3.000
 YS2  H23  C16  C17  110.38  3.000
 YS2  H22  C16  C17  110.88  3.000
 YS2  C15  C16  C17  107.40  3.000
 YS2  H25  C15  H24  106.69  3.000
 YS2  H25  C15  C14  111.22  3.000
 YS2  H24  C15  C14  112.15  3.000
 YS2  H25  C15  C16  110.41  3.000
 YS2  H24  C15  C16  112.82  3.000
 YS2  C14  C15  C16  103.64  3.000
 YS2  H26  C14  C8   106.35  3.000
 YS2  H26  C14  C15  107.00  3.000
 YS2  C8   C14  C15  120.73  3.000
 YS2  H26  C14  C13  104.99  3.000
 YS2  C15  C14  C13  104.27  3.000
 YS2  C8   C14  C13  112.40  3.000
 YS2  C7   C8   C14  122.93  3.000
 YS2  C14  C8   C9   111.58  3.000
 YS2  C7   C8   C9   125.49  3.000
 YS2  H27  C7   C6   116.54  3.000
 YS2  H27  C7   C8   116.99  3.000
 YS2  C6   C7   C8   126.47  3.000
 YS2  H28  C6   C5   116.36  3.000
 YS2  H28  C6   C7   117.00  3.000
 YS2  C5   C6   C7   126.64  3.000
 YS2  C10  C5   C4   113.54  3.000
 YS2  C10  C5   C6   125.22  3.000
 YS2  C4   C5   C6   121.24  3.000
 YS2  H30  C4   H29  107.02  3.000
 YS2  H30  C4   C3   109.88  3.000
 YS2  H29  C4   C3   107.29  3.000
 YS2  H30  C4   C5   111.38  3.000
 YS2  H29  C4   C5   109.75  3.000
 YS2  C3   C4   C5   111.34  3.000
 YS2  H32  C10  H31  107.31  3.000
 YS2  H32  C10  C1   108.07  3.000
 YS2  H31  C10  C1   109.13  3.000
 YS2  H32  C10  C5   109.18  3.000
 YS2  H31  C10  C5   112.32  3.000
 YS2  C1   C10  C5   110.69  3.000
 YS2  H33  C1   C2   107.99  3.000
 YS2  H33  C1   O1   110.38  3.000
 YS2  C2   C1   O1   113.86  3.000
 YS2  H33  C1   C10  107.43  3.000
 YS2  C2   C1   C10  109.06  3.000
 YS2  O1   C1   C10  107.93  3.000
 YS2  H34  O1   C1   108.39  3.000
 YS2  C3   C2   C28  121.69  3.000
 YS2  C3   C2   C1   114.31  3.000
 YS2  C28  C2   C1   123.95  3.000
 YS2  H36  C28  H35  116.37  3.000
 YS2  H36  C28  C2   122.77  3.000
 YS2  H35  C28  C2   120.87  3.000
 YS2  H37  C3   O2   110.82  3.000
 YS2  H37  C3   C2   108.92  3.000
 YS2  O2   C3   C2   111.56  3.000
 YS2  H37  C3   C4   108.69  3.000
 YS2  O2   C3   C4   107.44  3.000
 YS2  C2   C3   C4   109.36  3.000
 YS2  H38  O2   C3   107.97  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
 YS2  Var_01  C14  C15  C16  C17   10.53  30.0  1
 YS2  Var_02  C9   C11  C12  C13  -53.90  30.0  1
 YS2  Var_03  C8   C9   C11  C12   49.94  30.0  1
 YS2  Var_04  C14  C8   C9   C11  -51.59  30.0  1
 YS2  Var_05  C1   C10  C5   C4    55.44  30.0  1
 YS2  Var_06  C3   C4   C5   C10  -54.81  30.0  1
 YS2  Var_07  C6   C7   C8   C9    -1.45  30.0  2
 YS2  Var_08  C5   C6   C7   C8   179.89  30.0  1
 YS2  Var_09  C4   C5   C6   C7   179.13  30.0  2
 YS2  Var_10  H35  C28  C2   C1   178.94  30.0  2
 YS2  Var_11  C22  C23  C24  O3   178.98  30.0  3
 YS2  Var_12  C20  C22  C23  C24  172.98  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
 YS2  chir_01  C20  C17  C21  C22  positiv
 YS2  chir_02  C17  C20  C13  C16  positiv
 YS2  chir_03  C13  C14  C17  C12  negativ
 YS2  chir_04  C14  C8   C15  C13  positiv
 YS2  chir_05  C1   O1   C10  C2   positiv
 YS2  chir_06  C3   O2   C4   C2   positiv

