# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 05:51:41 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (3beta,9beta,25R)-3-hydroxy-26-iodocholest-5-ene-16,22-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CI)CCC(=O)[C@@H](C)[C@H]1C(=O)C[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
#
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
 L39  L39  (3beta,9beta,25R)-3-hydroxy-26-iodocholest-5-ene-16,22-dione  ligand  72  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L39
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
 L39  I1   I  I     0  -0.079    8.5497  -0.7384   0.5172
 L39  C18  C  CH3   0  -0.681   -1.9594  -0.4550  -1.6378
 L39  C13  C  CR5   0  -0.077   -2.1806  -0.4726  -0.1222
 L39  C12  C  CH2   0  -0.407   -2.9730  -1.7062   0.2994
 L39  C11  C  CH2   0  -0.449   -4.4013  -1.6578  -0.2455
 L39  C9   C  CH1   0  -0.185   -5.1691  -0.3787   0.1119
 L39  C10  C  CT    0  -0.127   -6.5899  -0.3379  -0.5069
 L39  C19  C  CH3   0  -0.679   -6.5526  -0.5876  -2.0243
 L39  C1   C  CH2   0  -0.432   -7.4550  -1.4177   0.1772
 L39  C2   C  CH2   0  -0.468   -8.9400  -1.3390  -0.1542
 L39  C3   C  CH1   0   0.089   -9.4955   0.0197   0.2238
 L39  O1   O  OH1   0  -0.677  -10.8715   0.0488  -0.0970
 L39  C4   C  CH2   0  -0.548   -8.7176   1.1144  -0.5026
 L39  C5   C  C     0   0.206   -7.2347   1.0162  -0.2572
 L39  C6   C  C1    0  -0.328   -6.5460   2.0798   0.1546
 L39  C7   C  CH2   0  -0.453   -5.0707   2.1080   0.3801
 L39  C8   C  CH1   0  -0.243   -4.3638   0.8901  -0.2020
 L39  C14  C  CR15  0  -0.201   -2.9690   0.7536   0.3835
 L39  C15  C  CH2   0  -0.569   -1.9976   1.9182   0.2466
 L39  C16  C  CR5   0   0.433   -0.6494   1.2616   0.4517
 L39  O16  O  O     0  -0.397    0.4178   1.8282   0.4529
 L39  C17  C  CR15  0  -0.328   -0.8336  -0.2421   0.6003
 L39  C20  C  CH1   0  -0.371    0.4157  -1.0027   0.1712
 L39  C21  C  CH3   0  -0.663    0.2839  -2.5254   0.2998
 L39  C22  C  C     0   0.452    1.6144  -0.6087   1.0223
 L39  O22  O  O     0  -0.415    1.5338  -0.5161   2.2267
 L39  C24  C  CH2   0  -0.407    4.1410  -0.2998   1.1575
 L39  C25  C  CH1   0  -0.238    5.4556  -0.3554   0.3625
 L39  C27  C  CH3   0  -0.661    5.5554   0.7768  -0.6512
 L39  C26  C  CH2   0  -0.594    6.5815  -0.3290   1.3810
 L39  H1   H  HCH3  0   0.240   -1.4330  -1.3569  -1.9564
 L39  H2   H  HCH3  0   0.243   -2.8907  -0.4208  -2.2020
 L39  H3   H  HCH3  0   0.233   -1.3604   0.3962  -1.9697
 L39  H4   H  HCH2  0   0.233   -2.5010  -2.6260  -0.0507
 L39  H5   H  HCH2  0   0.218   -2.9908  -1.7589   1.3939
 L39  H6   H  HCH2  0   0.226   -4.3656  -1.7819  -1.3298
 L39  H7   H  HCH2  0   0.239   -4.9420  -2.5277   0.1336
 L39  H8   H  HCH1  0   0.210   -5.3074  -0.3826   1.2036
 L39  H9   H  HCH3  0   0.230   -6.3188  -1.6277  -2.2555
 L39  H10  H  HCH3  0   0.237   -7.5101  -0.3645  -2.4938
 L39  H11  H  HCH3  0   0.232   -5.8065   0.0431  -2.5112
 L39  H12  H  HCH2  0   0.237   -7.0847  -2.4091  -0.0924
 L39  H13  H  HCH2  0   0.222   -7.3309  -1.3269   1.2619
 L39  H14  H  HCH2  0   0.221   -9.1052  -1.5197  -1.2216
 L39  H15  H  HCH2  0   0.238   -9.4737  -2.1264   0.3847
 L39  H16  H  HCH1  0   0.190   -9.3526   0.1590   1.3069
 L39  H17  H  HOH1  0   0.446  -11.2316   0.8903   0.2003
 L39  H18  H  HCH2  0   0.230   -8.9344   1.0280  -1.5742
 L39  H19  H  HCH2  0   0.241   -9.0752   2.1005  -0.1911
 L39  H20  H  H     0   0.222   -7.0831   3.0071   0.3378
 L39  H21  H  HCH2  0   0.241   -4.6559   3.0259  -0.0478
 L39  H22  H  HCH2  0   0.226   -4.8687   2.1757   1.4577
 L39  H23  H  HCH1  0   0.222   -4.2946   1.0209  -1.2889
 L39  H24  H  HCR5  0   0.230   -3.1099   0.5869   1.4622
 L39  H25  H  HCH2  0   0.274   -2.0206   2.3746  -0.7487
 L39  H26  H  HCH2  0   0.284   -2.1525   2.7231   0.9673
 L39  H27  H  HCR5  0   0.285   -1.0089  -0.4260   1.6717
 L39  H28  H  HCH1  0   0.261    0.6432  -0.7675  -0.8728
 L39  H29  H  HCH3  0   0.234   -0.0658  -2.8066   1.2932
 L39  H30  H  HCH3  0   0.248   -0.4152  -2.9250  -0.4319
 L39  H31  H  HCH3  0   0.245    1.2413  -3.0194   0.1242
 L39  H34  H  HCH2  0   0.262    3.0191  -1.3105  -0.3969
 L39  H35  H  HCH2  0   0.277    2.7813   0.4076  -0.3885
 L39  H36  H  HCH2  0   0.231    4.0899   0.6423   1.7122
 L39  H37  H  HCH2  0   0.239    4.1461  -1.0987   1.9036
 L39  H38  H  HCH1  0   0.243    5.4834  -1.3141  -0.1664
 L39  H39  H  HCH3  0   0.242    4.7393   0.7353  -1.3715
 L39  H40  H  HCH3  0   0.222    5.5138   1.7480  -0.1527
 L39  H41  H  HCH3  0   0.238    6.4842   0.7335  -1.2205
 L39  H42  H  HCH2  0   0.297    6.4610  -1.0986   2.1403
 L39  H43  H  HCH2  0   0.288    6.6766   0.6428   1.8641
 L39  C23  C  CH2   0  -0.583    2.9119  -0.4516   0.2767

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
 L39  C19  C10  single  1.538  0.020  1.538
 L39  C21  C20  single  1.534  0.020  1.534
 L39  C18  C13  single  1.532  0.020  1.532
 L39  C11  C12  single  1.529  0.020  1.529
 L39  C11  C9   single  1.534  0.020  1.534
 L39  C2   C1   single  1.524  0.020  1.524
 L39  C2   C3   single  1.516  0.020  1.516
 L39  C12  C13  single  1.526  0.020  1.526
 L39  C1   C10  single  1.543  0.020  1.543
 L39  C20  C22  single  1.522  0.020  1.522
 L39  C20  C17  single  1.524  0.020  1.524
 L39  C10  C9   single  1.550  0.020  1.550
 L39  C10  C5   single  1.520  0.020  1.520
 L39  C13  C17  single  1.546  0.020  1.546
 L39  C13  C14  single  1.543  0.020  1.543
 L39  C9   C8   single  1.535  0.020  1.535
 L39  C23  C22  single  1.505  0.020  1.505
 L39  C23  C24  single  1.520  0.020  1.520
 L39  O1   C3   single  1.413  0.020  1.413
 L39  C22  O22  double  1.211  0.020  1.211
 L39  C3   C4   single  1.527  0.020  1.527
 L39  C17  C16  single  1.522  0.020  1.522
 L39  I1   C26  single  2.188  0.020  2.188
 L39  C8   C14  single  1.519  0.020  1.519
 L39  C8   C7   single  1.524  0.020  1.524
 L39  C5   C4   single  1.506  0.020  1.506
 L39  C5   C6   double  1.332  0.020  1.332
 L39  C14  C15  single  1.523  0.020  1.523
 L39  C24  C25  single  1.537  0.020  1.537
 L39  C16  O16  double  1.208  0.020  1.208
 L39  C16  C15  single  1.513  0.020  1.513
 L39  C6   C7   single  1.493  0.020  1.493
 L39  C25  C26  single  1.518  0.020  1.518
 L39  C25  C27  single  1.523  0.020  1.523
 L39  C18  H1   single  0.970  0.020  1.090
 L39  C18  H2   single  0.970  0.020  1.090
 L39  C18  H3   single  0.970  0.020  1.090
 L39  C12  H4   single  0.970  0.020  1.090
 L39  C12  H5   single  0.970  0.020  1.090
 L39  C11  H6   single  0.970  0.020  1.090
 L39  C11  H7   single  0.970  0.020  1.090
 L39  C9   H8   single  0.970  0.020  1.090
 L39  C19  H9   single  0.970  0.020  1.090
 L39  C19  H10  single  0.970  0.020  1.090
 L39  C19  H11  single  0.970  0.020  1.090
 L39  C1   H12  single  0.970  0.020  1.090
 L39  C1   H13  single  0.970  0.020  1.090
 L39  C2   H14  single  0.970  0.020  1.090
 L39  C2   H15  single  0.970  0.020  1.090
 L39  C3   H16  single  0.970  0.020  1.090
 L39  O1   H17  single  0.850  0.020  0.980
 L39  C4   H18  single  0.970  0.020  1.090
 L39  C4   H19  single  0.970  0.020  1.090
 L39  C6   H20  single  0.930  0.020  1.080
 L39  C7   H21  single  0.970  0.020  1.090
 L39  C7   H22  single  0.970  0.020  1.090
 L39  C8   H23  single  0.970  0.020  1.090
 L39  C14  H24  single  0.970  0.020  1.090
 L39  C15  H25  single  0.970  0.020  1.090
 L39  C15  H26  single  0.970  0.020  1.090
 L39  C17  H27  single  0.970  0.020  1.090
 L39  C20  H28  single  0.970  0.020  1.090
 L39  C21  H29  single  0.970  0.020  1.090
 L39  C21  H30  single  0.970  0.020  1.090
 L39  C21  H31  single  0.970  0.020  1.090
 L39  C23  H34  single  0.970  0.020  1.090
 L39  C23  H35  single  0.970  0.020  1.090
 L39  C24  H36  single  0.970  0.020  1.090
 L39  C24  H37  single  0.970  0.020  1.090
 L39  C25  H38  single  0.970  0.020  1.090
 L39  C27  H39  single  0.970  0.020  1.090
 L39  C27  H40  single  0.970  0.020  1.090
 L39  C27  H41  single  0.970  0.020  1.090
 L39  C26  H42  single  0.970  0.020  1.090
 L39  C26  H43  single  0.970  0.020  1.090

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
 L39  H3   C18  H2   106.67  3.000
 L39  H3   C18  H1   106.90  3.000
 L39  H2   C18  H1   106.67  3.000
 L39  H3   C18  C13  112.88  3.000
 L39  H2   C18  C13  112.91  3.000
 L39  H1   C18  C13  110.42  3.000
 L39  C17  C13  C14  100.00  3.000
 L39  C14  C13  C12  106.66  3.000
 L39  C17  C13  C12  116.36  3.000
 L39  C14  C13  C18  112.89  3.000
 L39  C17  C13  C18  109.57  3.000
 L39  C12  C13  C18  110.96  3.000
 L39  H5   C12  H4   106.67  3.000
 L39  H5   C12  C11  110.01  3.000
 L39  H4   C12  C11  108.44  3.000
 L39  H5   C12  C13  108.86  3.000
 L39  H4   C12  C13  111.60  3.000
 L39  C11  C12  C13  111.16  3.000
 L39  H7   C11  H6   105.68  3.000
 L39  H7   C11  C9   109.60  3.000
 L39  H6   C11  C9   110.03  3.000
 L39  H7   C11  C12  108.27  3.000
 L39  H6   C11  C12  108.64  3.000
 L39  C9   C11  C12  114.26  3.000
 L39  H8   C9   C8   105.76  3.000
 L39  H8   C9   C10  106.31  3.000
 L39  C8   C9   C10  112.17  3.000
 L39  H8   C9   C11  106.92  3.000
 L39  C8   C9   C11  112.27  3.000
 L39  C10  C9   C11  112.81  3.000
 L39  C5   C10  C1   108.22  3.000
 L39  C5   C10  C19  108.48  3.000
 L39  C1   C10  C19  109.71  3.000
 L39  C5   C10  C9   110.28  3.000
 L39  C1   C10  C9   108.56  3.000
 L39  C19  C10  C9   111.54  3.000
 L39  H11  C19  H10  106.87  3.000
 L39  H11  C19  H9   108.06  3.000
 L39  H10  C19  H9   106.99  3.000
 L39  H11  C19  C10  111.27  3.000
 L39  H10  C19  C10  111.74  3.000
 L39  H9   C19  C10  111.65  3.000
 L39  H13  C1   H12  106.34  3.000
 L39  H13  C1   C2   108.75  3.000
 L39  H12  C1   C2   108.89  3.000
 L39  H13  C1   C10  108.50  3.000
 L39  H12  C1   C10  109.61  3.000
 L39  C2   C1   C10  114.44  3.000
 L39  H15  C2   H14  106.74  3.000
 L39  H15  C2   C3   110.11  3.000
 L39  H14  C2   C3   109.62  3.000
 L39  H15  C2   C1   109.35  3.000
 L39  H14  C2   C1   110.51  3.000
 L39  C3   C2   C1   110.45  3.000
 L39  H16  C3   C4   108.12  3.000
 L39  H16  C3   O1   110.31  3.000
 L39  C4   C3   O1   111.92  3.000
 L39  H16  C3   C2   108.12  3.000
 L39  C4   C3   C2   109.71  3.000
 L39  O1   C3   C2   108.58  3.000
 L39  H17  O1   C3   108.19  3.000
 L39  H19  C4   H18  106.54  3.000
 L39  H19  C4   C5   109.52  3.000
 L39  H18  C4   C5   110.41  3.000
 L39  H19  C4   C3   110.13  3.000
 L39  H18  C4   C3   107.92  3.000
 L39  C5   C4   C3   112.17  3.000
 L39  C6   C5   C4   120.47  3.000
 L39  C6   C5   C10  122.86  3.000
 L39  C4   C5   C10  116.67  3.000
 L39  H20  C6   C7   116.53  3.000
 L39  H20  C6   C5   118.53  3.000
 L39  C7   C6   C5   124.93  3.000
 L39  H22  C7   H21  105.20  3.000
 L39  H22  C7   C8   109.80  3.000
 L39  H21  C7   C8   110.19  3.000
 L39  H22  C7   C6   109.34  3.000
 L39  H21  C7   C6   109.35  3.000
 L39  C8   C7   C6   112.68  3.000
 L39  H23  C8   C14  109.56  3.000
 L39  H23  C8   C7   108.21  3.000
 L39  C14  C8   C7   110.52  3.000
 L39  H23  C8   C9   109.53  3.000
 L39  C7   C8   C9   109.82  3.000
 L39  C14  C8   C9   109.18  3.000
 L39  H24  C14  C15  106.60  3.000
 L39  H24  C14  C8   105.90  3.000
 L39  C15  C14  C8   118.85  3.000
 L39  H24  C14  C13  105.44  3.000
 L39  C15  C14  C13  104.62  3.000
 L39  C8   C14  C13  114.48  3.000
 L39  H26  C15  H25  106.84  3.000
 L39  H26  C15  C16  110.91  3.000
 L39  H25  C15  C16  108.82  3.000
 L39  H26  C15  C14  114.46  3.000
 L39  H25  C15  C14  112.77  3.000
 L39  C16  C15  C14  102.96  3.000
 L39  C17  C16  O16  124.75  3.000
 L39  O16  C16  C15  125.69  3.000
 L39  C17  C16  C15  109.51  3.000
 L39  H27  C17  C20  108.73  3.000
 L39  H27  C17  C16  106.21  3.000
 L39  C20  C17  C16  111.49  3.000
 L39  H27  C17  C13  106.93  3.000
 L39  C16  C17  C13  101.95  3.000
 L39  C20  C17  C13  120.55  3.000
 L39  H28  C20  C22  108.31  3.000
 L39  H28  C20  C21  108.13  3.000
 L39  C22  C20  C21  106.13  3.000
 L39  H28  C20  C17  109.38  3.000
 L39  C22  C20  C17  111.04  3.000
 L39  C21  C20  C17  113.66  3.000
 L39  H31  C21  H30  106.81  3.000
 L39  H31  C21  H29  108.13  3.000
 L39  H30  C21  H29  108.18  3.000
 L39  H31  C21  C20  111.13  3.000
 L39  H30  C21  C20  111.32  3.000
 L39  H29  C21  C20  111.10  3.000
 L39  C23  C22  O22  122.85  3.000
 L39  O22  C22  C20  121.58  3.000
 L39  C23  C22  C20  115.41  3.000
 L39  H37  C24  H36  106.47  3.000
 L39  H37  C24  C25  108.82  3.000
 L39  H36  C24  C25  109.46  3.000
 L39  H37  C24  C23  109.05  3.000
 L39  H36  C24  C23  110.00  3.000
 L39  C25  C24  C23  112.84  3.000
 L39  H38  C25  C26  108.69  3.000
 L39  H38  C25  C27  109.12  3.000
 L39  C26  C25  C27  112.64  3.000
 L39  H38  C25  C24  107.64  3.000
 L39  C27  C25  C24  111.92  3.000
 L39  C26  C25  C24  106.65  3.000
 L39  H41  C27  H40  107.82  3.000
 L39  H41  C27  H39  106.95  3.000
 L39  H40  C27  H39  107.88  3.000
 L39  H41  C27  C25  111.95  3.000
 L39  H40  C27  C25  110.77  3.000
 L39  H39  C27  C25  111.27  3.000
 L39  H43  C26  H42  109.34  3.000
 L39  H43  C26  C25  112.19  3.000
 L39  H42  C26  C25  111.94  3.000
 L39  H43  C26  I1   105.28  3.000
 L39  H42  C26  I1   104.06  3.000
 L39  C25  C26  I1   113.51  3.000
 L39  H35  C23  H34  104.67  3.000
 L39  H35  C23  C24  111.74  3.000
 L39  H34  C23  C24  110.80  3.000
 L39  H35  C23  C22  106.27  3.000
 L39  H34  C23  C22  107.86  3.000
 L39  C24  C23  C22  114.87  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
 L39  Var_01  C9   C11  C12  C13   -54.13  30.0  1
 L39  Var_02  C3   C2   C1   C10   -57.71  30.0  1
 L39  Var_03  C3   C4   C5   C10    51.63  30.0  1
 L39  Var_04  C7   C6   C5   C10     2.16  30.0  1
 L39  Var_05  C8   C7   C6   C5     12.92  30.0  1
 L39  Var_06  C17  C16  C15  C14     3.94  30.0  1
 L39  Var_07  C24  C23  C22  C20  -169.77  30.0  1
 L39  Var_08  C25  C24  C23  C22   171.35  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
 L39  chir_01  C13  C12  C17  C14  positiv
 L39  chir_02  C9   C8   C10  C11  negativ
 L39  chir_03  C10  C9   C1   C5   negativ
 L39  chir_04  C3   O1   C4   C2   positiv
 L39  chir_05  C8   C7   C14  C9   negativ
 L39  chir_06  C14  C15  C8   C13  negativ
 L39  chir_07  C17  C16  C13  C20  negativ
 L39  chir_08  C20  C17  C22  C21  negativ
 L39  chir_09  C25  C27  C26  C24  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 L39  plan-1  C15  0.020
 L39  plan-1  C16  0.020
 L39  plan-1  O16  0.020
 L39  plan-1  C17  0.020
 L39  plan-2  C20  0.020
 L39  plan-2  C22  0.020
 L39  plan-2  O22  0.020
 L39  plan-2  C23  0.020

