# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 22:33:05 2020
#   Inital geometry file: a 177 line input string
#   Ligand name: (1R,2Z,3R,5E,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
 5YI  5YI  (1R,2Z,3R,5E,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  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5YI
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
 5YI  C12  C  CH2   0  -0.420   -1.3637   2.9682  -0.2558
 5YI  C13  C  CR5   0  -0.144   -1.2463   1.4622  -0.0315
 5YI  C14  C  CR15  0  -0.265   -0.0765   1.2190   0.9494
 5YI  C15  C  CH2   0  -0.467   -0.3511  -0.1663   1.5269
 5YI  C16  C  CR15  0  -0.282   -1.8593  -0.1588   1.5415
 5YI  C21  C  CH3   0  -0.633   -4.4781   1.6734   1.6792
 5YI  C24  C  CT    0   0.230   -7.2463  -1.1229  -0.5619
 5YI  C29  C  CH3   0  -0.685   -8.1958  -0.5277   1.7587
 5YI  C27  C  CH2   0  -0.444   -7.5367  -1.5745   0.8720
 5YI  C26  C  CH2   0  -0.445   -8.5155  -0.6470  -1.2862
 5YI  C28  C  CH3   0  -0.671   -9.6443  -1.6671  -1.3318
 5YI  O03  O  OH1   0  -0.674   -6.7011  -2.2639  -1.2070
 5YI  S22  S  S2    0   0.000   -4.5899  -0.5366  -0.0399
 5YI  C20  C  CH1   0  -0.462   -3.8143   1.0438   0.4604
 5YI  C17  C  CR5   0   0.232   -2.3637   0.7620   0.7176
 5YI  C18  C  CH3   0  -0.647   -1.0614   0.7274  -1.3665
 5YI  C11  C  CH2   0  -0.439   -0.0387   3.5343  -0.7821
 5YI  C09  C  CH2   0  -0.505    1.1924   3.1149   0.0413
 5YI  C08  C  C     0   0.160    1.2225   1.6388   0.3497
 5YI  C07  C  C1    0  -0.368    2.2494   0.8024   0.1365
 5YI  C06  C  C1    0  -0.333    3.5389   1.1565  -0.4284
 5YI  C05  C  C     0   0.130    4.5691   0.3284  -0.6595
 5YI  C10  C  CH2   0  -0.546    5.8691   0.8370  -1.2026
 5YI  C01  C  CH1   0  -0.017    7.0197   0.5109  -0.2413
 5YI  O01  O  OH1   0  -0.666    6.8539   1.1529   1.0074
 5YI  C04  C  CH2   0  -0.543    4.5923  -1.1413  -0.3691
 5YI  C03  C  CH1   0   0.056    5.7520  -1.5054   0.5774
 5YI  O02  O  OH1   0  -0.666    5.8382  -2.8953   0.7627
 5YI  C02  C  C     0   0.062    7.0483  -0.9740   0.0174
 5YI  C30  C  C1    0  -0.332    8.0789  -1.7685  -0.2665
 5YI  C31  C  CH2   0  -0.198    9.3932  -1.3881  -0.8693
 5YI  O04  O  OH1   0  -0.675   10.4127  -2.0200  -0.1189
 5YI  H1   H  HCH2  0   0.229   -2.1641   3.2076  -0.9622
 5YI  H2   H  HCH2  0   0.223   -1.6232   3.4543   0.6907
 5YI  H3   H  HCR5  0   0.240   -0.2643   1.9151   1.7809
 5YI  H4   H  HCH2  0   0.232    0.0281  -0.9822   0.8998
 5YI  H5   H  HCH2  0   0.243    0.0877  -0.3053   2.5171
 5YI  H6   H  HCR5  0   0.234   -2.4454  -0.8532   2.1321
 5YI  H8   H  HCH3  0   0.231   -4.4560   0.9903   2.5280
 5YI  H9   H  HCH3  0   0.237   -3.9496   2.5867   1.9600
 5YI  H10  H  HCH3  0   0.234   -5.5160   1.9453   1.4861
 5YI  H11  H  HCH2  0   0.266   -6.1365   0.3987  -1.6302
 5YI  H12  H  HCH2  0   0.261   -6.5603   0.8566   0.0078
 5YI  H13  H  HCH3  0   0.239   -8.3593  -0.9307   2.7582
 5YI  H14  H  HCH3  0   0.222   -7.5792   0.3650   1.8698
 5YI  H15  H  HCH3  0   0.225   -9.1661  -0.2112   1.3736
 5YI  H16  H  HCH2  0   0.234   -8.1751  -2.4609   0.8292
 5YI  H17  H  HCH2  0   0.234   -6.5997  -1.8954   1.3332
 5YI  H18  H  HCH2  0   0.228   -8.8671   0.2760  -0.8170
 5YI  H19  H  HCH2  0   0.230   -8.2387  -0.3693  -2.3090
 5YI  H20  H  HCH3  0   0.223   -9.3162  -2.6047  -1.7806
 5YI  H21  H  HCH3  0   0.223  -10.0367  -1.8928  -0.3396
 5YI  H22  H  HCH3  0   0.233  -10.4748  -1.2898  -1.9290
 5YI  H23  H  HOH1  0   0.444   -6.5266  -2.0399  -2.1278
 5YI  H24  H  HCH1  0   0.272   -3.8998   1.7292  -0.3874
 5YI  H26  H  HCH3  0   0.230   -1.9700   0.8008  -1.9682
 5YI  H27  H  HCH3  0   0.232   -0.2418   1.1333  -1.9590
 5YI  H28  H  HCH3  0   0.233   -0.8549  -0.3322  -1.2105
 5YI  H29  H  HCH2  0   0.226    0.1060   3.2256  -1.8195
 5YI  H30  H  HCH2  0   0.238   -0.0910   4.6249  -0.8004
 5YI  H31  H  HCH2  0   0.247    2.0931   3.4516  -0.4715
 5YI  H32  H  HCH2  0   0.234    1.1658   3.6548   0.9957
 5YI  H33  H  H     0   0.230    2.1079  -0.2341   0.4253
 5YI  H34  H  H     0   0.232    3.6911   2.2002  -0.6858
 5YI  H35  H  HCH2  0   0.250    6.0952   0.3611  -2.1634
 5YI  H36  H  HCH2  0   0.256    5.8289   1.9145  -1.3879
 5YI  H37  H  HCH1  0   0.229    7.9525   0.8334  -0.7156
 5YI  H38  H  HOH1  0   0.451    6.6402   2.0780   0.8461
 5YI  H39  H  HCH2  0   0.251    3.6540  -1.4919   0.0638
 5YI  H40  H  HCH2  0   0.245    4.7401  -1.6936  -1.3051
 5YI  H41  H  HCH1  0   0.224    5.5632  -1.0053   1.5378
 5YI  H42  H  HOH1  0   0.456    5.0278  -3.1892   1.1899
 5YI  H43  H  H     0   0.248    7.9753  -2.8323  -0.0801
 5YI  H44  H  HCH2  0   0.212    9.4094  -1.7281  -1.9139
 5YI  H45  H  HCH2  0   0.208    9.5343  -0.3023  -0.8963
 5YI  H46  H  HOH1  0   0.455   11.2415  -1.9062  -0.5926
 5YI  C23  C  CH2   0  -0.565   -6.2242   0.0212  -0.6072

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
 5YI  O04  C31  single  1.415  0.020  1.415
 5YI  C31  C30  single  1.495  0.020  1.495
 5YI  C30  C02  double  1.332  0.020  1.332
 5YI  O01  C01  single  1.414  0.020  1.414
 5YI  C02  C01  single  1.508  0.020  1.508
 5YI  C02  C03  single  1.509  0.020  1.509
 5YI  C01  C10  single  1.534  0.020  1.534
 5YI  C03  O02  single  1.405  0.020  1.405
 5YI  C03  C04  single  1.541  0.020  1.541
 5YI  C10  C05  single  1.498  0.020  1.498
 5YI  C04  C05  single  1.498  0.020  1.498
 5YI  C05  C06  double  1.342  0.020  1.342
 5YI  C06  C07  single  1.452  0.020  1.452
 5YI  C07  C08  double  1.342  0.020  1.342
 5YI  C08  C14  single  1.491  0.020  1.491
 5YI  C08  C09  single  1.508  0.020  1.508
 5YI  C15  C14  single  1.526  0.020  1.526
 5YI  C15  C16  single  1.508  0.020  1.508
 5YI  C28  C26  single  1.522  0.020  1.522
 5YI  C14  C13  single  1.546  0.020  1.546
 5YI  C18  C13  single  1.535  0.020  1.535
 5YI  C09  C11  single  1.539  0.020  1.539
 5YI  C16  C17  double  1.335  0.020  1.335
 5YI  C26  C24  single  1.537  0.020  1.537
 5YI  C13  C17  single  1.517  0.020  1.517
 5YI  C13  C12  single  1.527  0.020  1.527
 5YI  C11  C12  single  1.534  0.020  1.534
 5YI  C17  C20  single  1.500  0.020  1.500
 5YI  C23  C24  single  1.535  0.020  1.535
 5YI  C23  S22  single  1.818  0.020  1.818
 5YI  C24  O03  single  1.419  0.020  1.419
 5YI  C24  C27  single  1.531  0.020  1.531
 5YI  C29  C27  single  1.522  0.020  1.522
 5YI  C20  S22  single  1.830  0.020  1.830
 5YI  C20  C21  single  1.524  0.020  1.524
 5YI  C12  H1   single  0.970  0.020  1.090
 5YI  C12  H2   single  0.970  0.020  1.090
 5YI  C14  H3   single  0.970  0.020  1.090
 5YI  C15  H4   single  0.970  0.020  1.090
 5YI  C15  H5   single  0.970  0.020  1.090
 5YI  C16  H6   single  0.930  0.020  1.080
 5YI  C21  H8   single  0.970  0.020  1.090
 5YI  C21  H9   single  0.970  0.020  1.090
 5YI  C21  H10  single  0.970  0.020  1.090
 5YI  C23  H11  single  0.970  0.020  1.090
 5YI  C23  H12  single  0.970  0.020  1.090
 5YI  C29  H13  single  0.970  0.020  1.090
 5YI  C29  H14  single  0.970  0.020  1.090
 5YI  C29  H15  single  0.970  0.020  1.090
 5YI  C27  H16  single  0.970  0.020  1.090
 5YI  C27  H17  single  0.970  0.020  1.090
 5YI  C26  H18  single  0.970  0.020  1.090
 5YI  C26  H19  single  0.970  0.020  1.090
 5YI  C28  H20  single  0.970  0.020  1.090
 5YI  C28  H21  single  0.970  0.020  1.090
 5YI  C28  H22  single  0.970  0.020  1.090
 5YI  O03  H23  single  0.850  0.020  0.980
 5YI  C20  H24  single  0.970  0.020  1.090
 5YI  C18  H26  single  0.970  0.020  1.090
 5YI  C18  H27  single  0.970  0.020  1.090
 5YI  C18  H28  single  0.970  0.020  1.090
 5YI  C11  H29  single  0.970  0.020  1.090
 5YI  C11  H30  single  0.970  0.020  1.090
 5YI  C09  H31  single  0.970  0.020  1.090
 5YI  C09  H32  single  0.970  0.020  1.090
 5YI  C07  H33  single  0.930  0.020  1.080
 5YI  C06  H34  single  0.930  0.020  1.080
 5YI  C10  H35  single  0.970  0.020  1.090
 5YI  C10  H36  single  0.970  0.020  1.090
 5YI  C01  H37  single  0.970  0.020  1.090
 5YI  O01  H38  single  0.850  0.020  0.980
 5YI  C04  H39  single  0.970  0.020  1.090
 5YI  C04  H40  single  0.970  0.020  1.090
 5YI  C03  H41  single  0.970  0.020  1.090
 5YI  O02  H42  single  0.850  0.020  0.980
 5YI  C30  H43  single  0.930  0.020  1.080
 5YI  C31  H44  single  0.970  0.020  1.090
 5YI  C31  H45  single  0.970  0.020  1.090
 5YI  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
 5YI  H2   C12  H1   106.71  3.000
 5YI  H2   C12  C11  109.72  3.000
 5YI  H1   C12  C11  109.25  3.000
 5YI  H2   C12  C13  109.20  3.000
 5YI  H1   C12  C13  111.52  3.000
 5YI  C11  C12  C13  110.37  3.000
 5YI  C18  C13  C17  107.29  3.000
 5YI  C17  C13  C14   99.88  3.000
 5YI  C18  C13  C14  112.66  3.000
 5YI  C17  C13  C12  118.12  3.000
 5YI  C18  C13  C12  110.71  3.000
 5YI  C14  C13  C12  107.85  3.000
 5YI  H3   C14  C08  105.93  3.000
 5YI  H3   C14  C15  104.93  3.000
 5YI  C08  C14  C15  124.38  3.000
 5YI  H3   C14  C13  104.52  3.000
 5YI  C15  C14  C13  104.29  3.000
 5YI  C08  C14  C13  111.09  3.000
 5YI  H5   C15  H4   106.55  3.000
 5YI  H5   C15  C16  113.18  3.000
 5YI  H4   C15  C16  110.80  3.000
 5YI  H5   C15  C14  112.73  3.000
 5YI  H4   C15  C14  113.38  3.000
 5YI  C16  C15  C14  100.32  3.000
 5YI  H6   C16  C17  125.04  3.000
 5YI  H6   C16  C15  122.88  3.000
 5YI  C17  C16  C15  112.05  3.000
 5YI  H10  C21  H9   107.32  3.000
 5YI  H10  C21  H8   108.28  3.000
 5YI  H9   C21  H8   108.31  3.000
 5YI  H10  C21  C20  112.09  3.000
 5YI  H9   C21  C20  109.90  3.000
 5YI  H8   C21  C20  110.80  3.000
 5YI  O03  C24  C26  110.60  3.000
 5YI  O03  C24  C27  105.15  3.000
 5YI  C26  C24  C27  112.08  3.000
 5YI  C27  C24  C23  111.95  3.000
 5YI  O03  C24  C23  109.27  3.000
 5YI  C26  C24  C23  107.77  3.000
 5YI  H15  C29  H14  107.54  3.000
 5YI  H15  C29  H13  107.31  3.000
 5YI  H14  C29  H13  107.10  3.000
 5YI  H15  C29  C27  112.28  3.000
 5YI  H14  C29  C27  112.18  3.000
 5YI  H13  C29  C27  110.18  3.000
 5YI  H17  C27  H16  106.21  3.000
 5YI  H17  C27  C29  109.12  3.000
 5YI  H16  C27  C29  109.12  3.000
 5YI  H17  C27  C24  108.61  3.000
 5YI  H16  C27  C24  108.26  3.000
 5YI  C29  C27  C24  115.14  3.000
 5YI  H19  C26  H18  105.54  3.000
 5YI  H19  C26  C28  109.23  3.000
 5YI  H18  C26  C28  109.88  3.000
 5YI  H19  C26  C24  108.05  3.000
 5YI  H18  C26  C24  108.95  3.000
 5YI  C28  C26  C24  114.77  3.000
 5YI  H22  C28  H21  107.21  3.000
 5YI  H22  C28  H20  107.54  3.000
 5YI  H21  C28  H20  107.75  3.000
 5YI  H22  C28  C26  110.45  3.000
 5YI  H21  C28  C26  112.22  3.000
 5YI  H20  C28  C26  111.44  3.000
 5YI  H23  O03  C24  108.48  3.000
 5YI  C20  S22  C23  101.62  3.000
 5YI  H24  C20  C17  109.05  3.000
 5YI  H24  C20  S22  107.23  3.000
 5YI  C17  C20  S22  107.13  3.000
 5YI  H24  C20  C21  109.09  3.000
 5YI  S22  C20  C21  113.00  3.000
 5YI  C17  C20  C21  111.20  3.000
 5YI  C20  C17  C16  126.94  3.000
 5YI  C20  C17  C13  122.76  3.000
 5YI  C16  C17  C13  110.18  3.000
 5YI  H28  C18  H27  107.29  3.000
 5YI  H28  C18  H26  107.55  3.000
 5YI  H27  C18  H26  107.52  3.000
 5YI  H28  C18  C13  111.31  3.000
 5YI  H27  C18  C13  112.65  3.000
 5YI  H26  C18  C13  110.29  3.000
 5YI  H30  C11  H29  105.83  3.000
 5YI  H30  C11  C09  108.62  3.000
 5YI  H29  C11  C09  108.98  3.000
 5YI  H30  C11  C12  109.45  3.000
 5YI  H29  C11  C12  109.64  3.000
 5YI  C09  C11  C12  114.00  3.000
 5YI  H32  C09  H31  106.11  3.000
 5YI  H32  C09  C08  107.71  3.000
 5YI  H31  C09  C08  112.46  3.000
 5YI  H32  C09  C11  108.18  3.000
 5YI  H31  C09  C11  108.98  3.000
 5YI  C08  C09  C11  113.07  3.000
 5YI  C07  C08  C09  126.36  3.000
 5YI  C09  C08  C14  109.91  3.000
 5YI  C07  C08  C14  123.73  3.000
 5YI  H33  C07  C06  116.90  3.000
 5YI  H33  C07  C08  116.96  3.000
 5YI  C06  C07  C08  126.14  3.000
 5YI  H34  C06  C05  116.41  3.000
 5YI  H34  C06  C07  116.83  3.000
 5YI  C05  C06  C07  126.76  3.000
 5YI  C04  C05  C10  112.95  3.000
 5YI  C04  C05  C06  125.72  3.000
 5YI  C10  C05  C06  121.28  3.000
 5YI  H36  C10  H35  106.67  3.000
 5YI  H36  C10  C01  110.06  3.000
 5YI  H35  C10  C01  107.59  3.000
 5YI  H36  C10  C05  111.34  3.000
 5YI  H35  C10  C05  110.46  3.000
 5YI  C01  C10  C05  110.58  3.000
 5YI  H37  C01  C02  110.38  3.000
 5YI  H37  C01  O01  110.41  3.000
 5YI  C02  C01  O01  107.34  3.000
 5YI  H37  C01  C10  107.74  3.000
 5YI  C02  C01  C10  109.33  3.000
 5YI  O01  C01  C10  111.65  3.000
 5YI  H38  O01  C01  108.32  3.000
 5YI  H40  C04  H39  107.02  3.000
 5YI  H40  C04  C03  107.69  3.000
 5YI  H39  C04  C03  109.12  3.000
 5YI  H40  C04  C05  109.31  3.000
 5YI  H39  C04  C05  112.26  3.000
 5YI  C03  C04  C05  111.26  3.000
 5YI  H41  C03  C02  108.16  3.000
 5YI  H41  C03  O02  110.21  3.000
 5YI  C02  C03  O02  110.16  3.000
 5YI  H41  C03  C04  107.46  3.000
 5YI  O02  C03  C04  111.17  3.000
 5YI  C02  C03  C04  109.60  3.000
 5YI  H42  O02  C03  108.00  3.000
 5YI  C30  C02  C03  122.27  3.000
 5YI  C03  C02  C01  113.22  3.000
 5YI  C30  C02  C01  124.45  3.000
 5YI  H43  C30  C31  113.74  3.000
 5YI  H43  C30  C02  118.32  3.000
 5YI  C31  C30  C02  127.91  3.000
 5YI  H45  C31  H44  106.35  3.000
 5YI  H45  C31  O04  111.28  3.000
 5YI  H44  C31  O04  110.82  3.000
 5YI  H45  C31  C30  112.04  3.000
 5YI  H44  C31  C30  108.51  3.000
 5YI  O04  C31  C30  107.81  3.000
 5YI  H46  O04  C31  107.88  3.000
 5YI  H12  C23  H11  106.72  3.000
 5YI  H12  C23  S22  109.65  3.000
 5YI  H11  C23  S22  109.01  3.000
 5YI  H12  C23  C24  110.44  3.000
 5YI  H11  C23  C24  109.77  3.000
 5YI  S22  C23  C24  111.15  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
 5YI  Var_01  C08  C09  C11  C12    46.97  30.0  1
 5YI  Var_02  C15  C16  C17  C13     3.02  30.0  1
 5YI  Var_03  C09  C11  C12  C13   -50.02  30.0  1
 5YI  Var_04  C11  C09  C08  C14   -51.51  30.0  1
 5YI  Var_05  C17  C16  C15  C14    19.55  30.0  1
 5YI  Var_06  C03  C04  C05  C10    55.04  30.0  1
 5YI  Var_07  C04  C05  C10  C01   -56.28  30.0  1
 5YI  Var_08  C06  C07  C08  C14  -179.27  30.0  2
 5YI  Var_09  C05  C06  C07  C08  -179.27  30.0  1
 5YI  Var_10  C10  C05  C06  C07  -177.68  30.0  2
 5YI  Var_11  C31  C30  C02  C01     0.59  30.0  2
 5YI  Var_12  O04  C31  C30  C02   134.12  30.0  1
 5YI  Var_13  C28  C26  C24  C23  -179.84  30.0  2
 5YI  Var_14  C29  C27  C24  C23    64.16  30.0  3
 5YI  Var_15  S22  C23  C24  C27    66.35  30.0  2
 5YI  Var_16  H20  C28  C26  C24   -55.88  30.0  3
 5YI  Var_17  H13  C29  C27  C24  -179.64  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
 5YI  chir_01  C13  C14  C17  C12  negativ
 5YI  chir_02  C14  C13  C15  C08  negativ
 5YI  chir_03  C20  S22  C17  C21  positiv
 5YI  chir_04  C01  O01  C02  C10  negativ
 5YI  chir_05  C03  O02  C04  C02  positiv

