# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  8 07:14:23 2020
#   Inital geometry file: a 177 line input string
#   Ligand name: (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(O)(CC)CS[C@@H](C)C1=CC[C@H]2/C(CCC[C@]12C)=C/C=C3C[C@@H](O)C(=CCO)[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
 YI2  YI2  (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol  ligand  77  33  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YI2
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
 YI2  C12  C  CH2   0  -0.421   -1.3821   2.9662  -0.2767
 YI2  C13  C  CT    0  -0.144   -1.2638   1.4600  -0.0542
 YI2  C14  C  CH1   0  -0.265   -0.0928   1.2163   0.9251
 YI2  C15  C  CH2   0  -0.467   -0.3657  -0.1700   1.5011
 YI2  C16  C  C1    0  -0.283   -1.8737  -0.1639   1.5168
 YI2  C21  C  CH3   0  -0.633   -4.4870   1.6815   1.6601
 YI2  C24  C  CT    0   0.230   -7.2711  -1.1251  -0.5567
 YI2  C29  C  CH3   0  -0.685   -8.2101  -0.5300   1.7682
 YI2  C27  C  CH2   0  -0.444   -7.5564  -1.5773   0.8781
 YI2  C26  C  CH2   0  -0.444   -8.5434  -0.6482  -1.2753
 YI2  C28  C  CH3   0  -0.671   -9.6722  -1.6685  -1.3173
 YI2  O03  O  OH1   0  -0.674   -6.7294  -2.2660  -1.2046
 YI2  S22  S  S2    0   0.001   -4.6132  -0.5399  -0.0429
 YI2  C20  C  CH1   0  -0.462   -3.8307   1.0419   0.4423
 YI2  C17  C  C     0   0.232   -2.3799   0.7582   0.6954
 YI2  C18  C  CH3   0  -0.646   -1.0800   0.7272  -1.3905
 YI2  C11  C  CH2   0  -0.439   -0.0576   3.5337  -0.8028
 YI2  C09  C  CH2   0  -0.505    1.1742   3.1148   0.0199
 YI2  C08  C  C     0   0.160    1.2057   1.6383   0.3259
 YI2  C07  C  C1    0  -0.367    2.2332   0.8031   0.1109
 YI2  C06  C  C1    0  -0.333    3.5239   1.1596  -0.4497
 YI2  C05  C  C     0   0.130    4.5541   0.3320  -0.6829
 YI2  C10  C  CH2   0  -0.546    5.8585   0.8433  -1.2125
 YI2  C01  C  CH1   0  -0.017    7.0002   0.5090  -0.2431
 YI2  O01  O  OH1   0  -0.666    6.8225   1.1405   1.0093
 YI2  C04  C  CH2   0  -0.544    4.5737  -1.1402  -0.4050
 YI2  C03  C  CH1   0   0.057    5.7250  -1.5134   0.5480
 YI2  O02  O  OH1   0  -0.666    5.8091  -2.9047   0.7225
 YI2  C02  C  C     0   0.062    7.0262  -0.9781   0.0033
 YI2  C30  C  C1    0  -0.332    8.0589  -1.7706  -0.2788
 YI2  C31  C  CH2   0  -0.198    9.3784  -1.3854  -0.8672
 YI2  O04  O  OH1   0  -0.675   10.3913  -2.0243  -0.1139
 YI2  H1   H  HCH2  0   0.229   -2.1828   3.2058  -0.9827
 YI2  H2   H  HCH2  0   0.223   -1.6414   3.4510   0.6703
 YI2  H3   H  HCH1  0   0.240   -0.2809   1.9110   1.7577
 YI2  H4   H  HCH2  0   0.232    0.0145  -0.9851   0.8737
 YI2  H5   H  HCH2  0   0.243    0.0732  -0.3089   2.4913
 YI2  H6   H  H     0   0.234   -2.4583  -0.8601   2.1069
 YI2  H8   H  HCH3  0   0.230   -4.4625   1.0038   2.5129
 YI2  H9   H  HCH3  0   0.238   -3.9553   2.5955   1.9327
 YI2  H10  H  HCH3  0   0.234   -5.5252   1.9545   1.4701
 YI2  H11  H  HCH2  0   0.265   -6.1639   0.3952  -1.6293
 YI2  H12  H  HCH2  0   0.261   -6.5832   0.8545   0.0093
 YI2  H13  H  HCH3  0   0.239   -8.3672  -0.9323   2.7691
 YI2  H14  H  HCH3  0   0.222   -7.5930   0.3630   1.8752
 YI2  H15  H  HCH3  0   0.225   -9.1829  -0.2140   1.3890
 YI2  H16  H  HCH2  0   0.234   -8.1968  -2.4623   0.8373
 YI2  H17  H  HCH2  0   0.235   -6.6182  -1.9002   1.3354
 YI2  H18  H  HCH2  0   0.228   -8.8932   0.2741  -0.8037
 YI2  H19  H  HCH2  0   0.230   -8.2707  -0.3696  -2.2990
 YI2  H20  H  HCH3  0   0.223   -9.3449  -2.6066  -1.7657
 YI2  H21  H  HCH3  0   0.223  -10.0625  -1.8930  -0.3240
 YI2  H22  H  HCH3  0   0.233  -10.5040  -1.2921  -1.9132
 YI2  H23  H  HOH1  0   0.444   -6.5517  -2.0397  -2.1242
 YI2  H24  H  HCH1  0   0.272   -3.9183   1.7215  -0.4099
 YI2  H26  H  HCH3  0   0.230   -1.9880   0.8047  -1.9929
 YI2  H27  H  HCH3  0   0.232   -0.2585   1.1318  -1.9813
 YI2  H28  H  HCH3  0   0.233   -0.8769  -0.3333  -1.2366
 YI2  H29  H  HCH2  0   0.226    0.0871   3.2260  -1.8405
 YI2  H30  H  HCH2  0   0.238   -0.1108   4.6243  -0.8202
 YI2  H31  H  HCH2  0   0.247    2.0744   3.4531  -0.4927
 YI2  H32  H  HCH2  0   0.234    1.1472   3.6534   0.9750
 YI2  H33  H  H     0   0.229    2.0920  -0.2343   0.3970
 YI2  H34  H  H     0   0.232    3.6785   2.2052  -0.6982
 YI2  H35  H  HCH2  0   0.250    6.0918   0.3736  -2.1745
 YI2  H36  H  HCH2  0   0.256    5.8206   1.9222  -1.3899
 YI2  H37  H  HCH1  0   0.229    7.9375   0.8353  -0.7060
 YI2  H38  H  HOH1  0   0.451    6.6111   2.0670   0.8538
 YI2  H39  H  HCH2  0   0.251    3.6315  -1.4939   0.0169
 YI2  H40  H  HCH2  0   0.245    4.7292  -1.6840  -1.3448
 YI2  H41  H  HCH1  0   0.224    5.5286  -1.0210   1.5108
 YI2  H42  H  HOH1  0   0.456    4.9890  -3.2038   1.1272
 YI2  H43  H  H     0   0.248    7.9537  -2.8359  -0.1021
 YI2  H44  H  HCH2  0   0.212    9.4032  -1.7160  -1.9145
 YI2  H45  H  HCH2  0   0.208    9.5200  -0.2994  -0.8832
 YI2  H46  H  HOH1  0   0.455   11.2241  -1.9067  -0.5795
 YI2  C23  C  CH2   0  -0.565   -6.2488   0.0186  -0.6058

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
 YI2  O04  C31  single  1.415  0.020  1.415
 YI2  C31  C30  single  1.495  0.020  1.495
 YI2  C30  C02  double  1.332  0.020  1.332
 YI2  O01  C01  single  1.414  0.020  1.414
 YI2  C02  C01  single  1.508  0.020  1.508
 YI2  C02  C03  single  1.509  0.020  1.509
 YI2  C01  C10  single  1.535  0.020  1.535
 YI2  C03  O02  single  1.405  0.020  1.405
 YI2  C03  C04  single  1.540  0.020  1.540
 YI2  C10  C05  single  1.498  0.020  1.498
 YI2  C04  C05  single  1.498  0.020  1.498
 YI2  C05  C06  double  1.342  0.020  1.342
 YI2  C06  C07  single  1.452  0.020  1.452
 YI2  C07  C08  double  1.342  0.020  1.342
 YI2  C15  C14  single  1.526  0.020  1.526
 YI2  C15  C16  single  1.508  0.020  1.508
 YI2  C08  C14  single  1.491  0.020  1.491
 YI2  C08  C09  single  1.508  0.020  1.508
 YI2  C18  C13  single  1.535  0.020  1.535
 YI2  C14  C13  single  1.546  0.020  1.546
 YI2  C09  C11  single  1.539  0.020  1.539
 YI2  C16  C17  double  1.335  0.020  1.335
 YI2  C26  C28  single  1.522  0.020  1.522
 YI2  C26  C24  single  1.537  0.020  1.537
 YI2  C13  C17  single  1.517  0.020  1.517
 YI2  C13  C12  single  1.527  0.020  1.527
 YI2  C11  C12  single  1.534  0.020  1.534
 YI2  C17  C20  single  1.500  0.020  1.500
 YI2  C23  C24  single  1.535  0.020  1.535
 YI2  C23  S22  single  1.818  0.020  1.818
 YI2  C24  O03  single  1.419  0.020  1.419
 YI2  C24  C27  single  1.531  0.020  1.531
 YI2  C29  C27  single  1.522  0.020  1.522
 YI2  C20  S22  single  1.830  0.020  1.830
 YI2  C20  C21  single  1.524  0.020  1.524
 YI2  C12  H1   single  0.970  0.020  1.090
 YI2  C12  H2   single  0.970  0.020  1.090
 YI2  C14  H3   single  0.970  0.020  1.090
 YI2  C15  H4   single  0.970  0.020  1.090
 YI2  C15  H5   single  0.970  0.020  1.090
 YI2  C16  H6   single  0.930  0.020  1.080
 YI2  C21  H8   single  0.970  0.020  1.090
 YI2  C21  H9   single  0.970  0.020  1.090
 YI2  C21  H10  single  0.970  0.020  1.090
 YI2  C23  H11  single  0.970  0.020  1.090
 YI2  C23  H12  single  0.970  0.020  1.090
 YI2  C29  H13  single  0.970  0.020  1.090
 YI2  C29  H14  single  0.970  0.020  1.090
 YI2  C29  H15  single  0.970  0.020  1.090
 YI2  C27  H16  single  0.970  0.020  1.090
 YI2  C27  H17  single  0.970  0.020  1.090
 YI2  C26  H18  single  0.970  0.020  1.090
 YI2  C26  H19  single  0.970  0.020  1.090
 YI2  C28  H20  single  0.970  0.020  1.090
 YI2  C28  H21  single  0.970  0.020  1.090
 YI2  C28  H22  single  0.970  0.020  1.090
 YI2  O03  H23  single  0.850  0.020  0.980
 YI2  C20  H24  single  0.970  0.020  1.090
 YI2  C18  H26  single  0.970  0.020  1.090
 YI2  C18  H27  single  0.970  0.020  1.090
 YI2  C18  H28  single  0.970  0.020  1.090
 YI2  C11  H29  single  0.970  0.020  1.090
 YI2  C11  H30  single  0.970  0.020  1.090
 YI2  C09  H31  single  0.970  0.020  1.090
 YI2  C09  H32  single  0.970  0.020  1.090
 YI2  C07  H33  single  0.930  0.020  1.080
 YI2  C06  H34  single  0.930  0.020  1.080
 YI2  C10  H35  single  0.970  0.020  1.090
 YI2  C10  H36  single  0.970  0.020  1.090
 YI2  C01  H37  single  0.970  0.020  1.090
 YI2  O01  H38  single  0.850  0.020  0.980
 YI2  C04  H39  single  0.970  0.020  1.090
 YI2  C04  H40  single  0.970  0.020  1.090
 YI2  C03  H41  single  0.970  0.020  1.090
 YI2  O02  H42  single  0.850  0.020  0.980
 YI2  C30  H43  single  0.930  0.020  1.080
 YI2  C31  H44  single  0.970  0.020  1.090
 YI2  C31  H45  single  0.970  0.020  1.090
 YI2  O04  H46  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
 YI2  H2   C12  H1   106.72  3.000
 YI2  H2   C12  C11  109.71  3.000
 YI2  H1   C12  C11  109.24  3.000
 YI2  H2   C12  C13  109.21  3.000
 YI2  H1   C12  C13  111.51  3.000
 YI2  C11  C12  C13  110.37  3.000
 YI2  C18  C13  C17  107.30  3.000
 YI2  C17  C13  C14   99.87  3.000
 YI2  C18  C13  C14  112.68  3.000
 YI2  C17  C13  C12  118.13  3.000
 YI2  C14  C13  C12  107.85  3.000
 YI2  C18  C13  C12  110.69  3.000
 YI2  H3   C14  C08  105.92  3.000
 YI2  H3   C14  C15  104.91  3.000
 YI2  C08  C14  C15  124.38  3.000
 YI2  H3   C14  C13  104.49  3.000
 YI2  C08  C14  C13  111.13  3.000
 YI2  C15  C14  C13  104.29  3.000
 YI2  H5   C15  H4   106.55  3.000
 YI2  H5   C15  C16  113.14  3.000
 YI2  H4   C15  C16  110.83  3.000
 YI2  H5   C15  C14  112.71  3.000
 YI2  H4   C15  C14  113.41  3.000
 YI2  C16  C15  C14  100.32  3.000
 YI2  H6   C16  C17  125.05  3.000
 YI2  H6   C16  C15  122.85  3.000
 YI2  C17  C16  C15  112.06  3.000
 YI2  H10  C21  H9   107.31  3.000
 YI2  H10  C21  H8   108.27  3.000
 YI2  H9   C21  H8   108.32  3.000
 YI2  H10  C21  C20  112.08  3.000
 YI2  H9   C21  C20  109.94  3.000
 YI2  H8   C21  C20  110.77  3.000
 YI2  O03  C24  C26  110.60  3.000
 YI2  O03  C24  C27  105.15  3.000
 YI2  C26  C24  C27  112.05  3.000
 YI2  C27  C24  C23  111.97  3.000
 YI2  O03  C24  C23  109.28  3.000
 YI2  C26  C24  C23  107.78  3.000
 YI2  H15  C29  H14  107.55  3.000
 YI2  H15  C29  H13  107.32  3.000
 YI2  H14  C29  H13  107.08  3.000
 YI2  H15  C29  C27  112.27  3.000
 YI2  H14  C29  C27  112.19  3.000
 YI2  H13  C29  C27  110.18  3.000
 YI2  H17  C27  H16  106.22  3.000
 YI2  H17  C27  C29  109.11  3.000
 YI2  H16  C27  C29  109.11  3.000
 YI2  H17  C27  C24  108.64  3.000
 YI2  H16  C27  C24  108.26  3.000
 YI2  C29  C27  C24  115.14  3.000
 YI2  H19  C26  H18  105.55  3.000
 YI2  H19  C26  C28  109.23  3.000
 YI2  H18  C26  C28  109.88  3.000
 YI2  H19  C26  C24  108.05  3.000
 YI2  H18  C26  C24  108.96  3.000
 YI2  C28  C26  C24  114.76  3.000
 YI2  H22  C28  H21  107.21  3.000
 YI2  H22  C28  H20  107.54  3.000
 YI2  H21  C28  H20  107.76  3.000
 YI2  H22  C28  C26  110.45  3.000
 YI2  H21  C28  C26  112.22  3.000
 YI2  H20  C28  C26  111.44  3.000
 YI2  H23  O03  C24  108.49  3.000
 YI2  C20  S22  C23  101.61  3.000
 YI2  H24  C20  C17  109.06  3.000
 YI2  H24  C20  S22  107.23  3.000
 YI2  C17  C20  S22  107.15  3.000
 YI2  H24  C20  C21  109.11  3.000
 YI2  S22  C20  C21  112.98  3.000
 YI2  C17  C20  C21  111.17  3.000
 YI2  C20  C17  C16  126.97  3.000
 YI2  C20  C17  C13  122.75  3.000
 YI2  C16  C17  C13  110.17  3.000
 YI2  H28  C18  H27  107.28  3.000
 YI2  H28  C18  H26  107.56  3.000
 YI2  H27  C18  H26  107.53  3.000
 YI2  H28  C18  C13  111.32  3.000
 YI2  H27  C18  C13  112.64  3.000
 YI2  H26  C18  C13  110.28  3.000
 YI2  H30  C11  H29  105.83  3.000
 YI2  H30  C11  C09  108.62  3.000
 YI2  H29  C11  C09  108.97  3.000
 YI2  H30  C11  C12  109.44  3.000
 YI2  H29  C11  C12  109.64  3.000
 YI2  C09  C11  C12  114.01  3.000
 YI2  H32  C09  H31  106.11  3.000
 YI2  H32  C09  C08  107.73  3.000
 YI2  H31  C09  C08  112.47  3.000
 YI2  H32  C09  C11  108.18  3.000
 YI2  H31  C09  C11  108.97  3.000
 YI2  C08  C09  C11  113.05  3.000
 YI2  C07  C08  C09  126.37  3.000
 YI2  C09  C08  C14  109.90  3.000
 YI2  C07  C08  C14  123.73  3.000
 YI2  H33  C07  C06  116.89  3.000
 YI2  H33  C07  C08  116.95  3.000
 YI2  C06  C07  C08  126.16  3.000
 YI2  H34  C06  C05  116.41  3.000
 YI2  H34  C06  C07  116.84  3.000
 YI2  C05  C06  C07  126.75  3.000
 YI2  C04  C05  C10  112.93  3.000
 YI2  C04  C05  C06  125.72  3.000
 YI2  C10  C05  C06  121.30  3.000
 YI2  H36  C10  H35  106.71  3.000
 YI2  H36  C10  C01  110.06  3.000
 YI2  H35  C10  C01  107.63  3.000
 YI2  H36  C10  C05  111.34  3.000
 YI2  H35  C10  C05  110.46  3.000
 YI2  C01  C10  C05  110.50  3.000
 YI2  H37  C01  C02  110.38  3.000
 YI2  H37  C01  O01  110.42  3.000
 YI2  C02  C01  O01  107.34  3.000
 YI2  H37  C01  C10  107.75  3.000
 YI2  C02  C01  C10  109.32  3.000
 YI2  O01  C01  C10  111.64  3.000
 YI2  H38  O01  C01  108.32  3.000
 YI2  H40  C04  H39  107.04  3.000
 YI2  H40  C04  C03  107.70  3.000
 YI2  H39  C04  C03  109.12  3.000
 YI2  H40  C04  C05  109.27  3.000
 YI2  H39  C04  C05  112.26  3.000
 YI2  C03  C04  C05  111.26  3.000
 YI2  H41  C03  C02  108.15  3.000
 YI2  H41  C03  O02  110.22  3.000
 YI2  C02  C03  O02  110.16  3.000
 YI2  H41  C03  C04  107.45  3.000
 YI2  O02  C03  C04  111.19  3.000
 YI2  C02  C03  C04  109.59  3.000
 YI2  H42  O02  C03  108.01  3.000
 YI2  C30  C02  C03  122.28  3.000
 YI2  C03  C02  C01  113.21  3.000
 YI2  C30  C02  C01  124.45  3.000
 YI2  H43  C30  C31  113.74  3.000
 YI2  H43  C30  C02  118.33  3.000
 YI2  C31  C30  C02  127.90  3.000
 YI2  H45  C31  H44  106.36  3.000
 YI2  H45  C31  O04  111.28  3.000
 YI2  H44  C31  O04  110.83  3.000
 YI2  H45  C31  C30  112.04  3.000
 YI2  H44  C31  C30  108.52  3.000
 YI2  O04  C31  C30  107.81  3.000
 YI2  H46  O04  C31  107.88  3.000
 YI2  H12  C23  H11  106.72  3.000
 YI2  H12  C23  S22  109.69  3.000
 YI2  H11  C23  S22  109.01  3.000
 YI2  H12  C23  C24  110.42  3.000
 YI2  H11  C23  C24  109.76  3.000
 YI2  S22  C23  C24  111.14  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
 YI2  Var_01  C08  C09  C11  C12    47.01  30.0  1
 YI2  Var_02  C15  C16  C17  C13     3.10  30.0  1
 YI2  Var_03  C09  C11  C12  C13   -50.05  30.0  1
 YI2  Var_04  C17  C16  C15  C14    19.49  30.0  1
 YI2  Var_05  C11  C09  C08  C14   -51.52  30.0  1
 YI2  Var_06  C03  C04  C05  C10    55.13  30.0  1
 YI2  Var_07  C04  C05  C10  C01   -56.40  30.0  1
 YI2  Var_08  C06  C07  C08  C14  -179.06  30.0  2
 YI2  Var_09  C05  C06  C07  C08  -179.23  30.0  1
 YI2  Var_10  C10  C05  C06  C07  -177.28  30.0  2
 YI2  Var_11  C31  C30  C02  C01     0.60  30.0  2
 YI2  Var_12  O04  C31  C30  C02   134.13  30.0  1
 YI2  Var_13  C28  C26  C24  C23  -179.88  30.0  1
 YI2  Var_14  C29  C27  C24  C23    64.09  30.0  3
 YI2  Var_15  S22  C23  C24  C27    66.27  30.0  1
 YI2  Var_16  H20  C28  C26  C24   -55.70  30.0  3
 YI2  Var_17  H13  C29  C27  C24  -179.45  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
 YI2  chir_01  C13  C14  C17  C12  negativ
 YI2  chir_02  C14  C13  C08  C15  positiv
 YI2  chir_03  C20  S22  C21  C17  negativ
 YI2  chir_04  C01  O01  C02  C10  negativ
 YI2  chir_05  C03  O02  C04  C02  positiv

