# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 14:15:51 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: 3-{[(14beta,16alpha,17alpha)-3-(2-bromoethyl)-17-hydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@H]3[C@@H](CCc4cc(CCBr)ccc34)[C@@H]1C[C@H](Cc5cccc(c5)C(N)=O)[C@@H]2O
#
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
 F0D  F0D  3-{[(14beta,16alpha,17alpha)-3-(2-bromoethyl)-17-hydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide  ligand  66  32  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_F0D
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
 F0D  C1   C   C1    0  -0.310   3.4286  -1.8531  -0.2914
 F0D  C2   C   C1    0  -0.306   4.7312  -1.4193  -0.1065
 F0D  C31  C   CH2   0  -0.497   6.8926   0.9201  -1.0082
 F0D  C30  C   CH2   0  -0.502   6.4054   0.4166   0.3395
 F0D  C3   C   C     0   0.112   4.9937  -0.0857   0.1889
 F0D  C5   C   C1    0  -0.353   3.9147   0.7823   0.2856
 F0D  C6   C   C     0   0.083   2.5997   0.3604   0.1010
 F0D  C7   C   CH2   0  -0.508   1.4942   1.3753   0.2450
 F0D  C8   C   CH2   0  -0.429   0.1756   0.9111  -0.3501
 F0D  C9   C   CH1   0  -0.236  -0.1286  -0.5065   0.1096
 F0D  C11  C   C     0   0.109   2.3398  -0.9845  -0.1931
 F0D  C10  C   CH1   0  -0.269   0.9266  -1.4683  -0.4628
 F0D  C12  C   CH2   0  -0.448   0.6607  -2.9161  -0.0260
 F0D  C13  C   CH2   0  -0.411  -0.7607  -3.3716  -0.3675
 F0D  C14  C   CT    0  -0.097  -1.8087  -2.4148   0.1939
 F0D  C20  C   CH3   0  -0.675  -1.8267  -2.5072   1.7239
 F0D  C15  C   CH1   0  -0.188  -1.4978  -1.0019  -0.3177
 F0D  C16  C   CH2   0  -0.435  -2.7462  -0.2036   0.0399
 F0D  C18  C   CH1   0   0.106  -3.2195  -2.5939  -0.3764
 F0D  O19  O   OH1   0  -0.671  -3.8946  -3.6615   0.2393
 F0D  C17  C   CH1   0  -0.275  -3.9014  -1.1902  -0.2452
 F0D  C21  C   CH2   0  -0.520  -5.0321  -1.1252   0.7850
 F0D  C22  C   CR6   0   0.174  -5.6906   0.2264   0.7988
 F0D  C23  C   CR16  0  -0.338  -6.5627   0.5888  -0.2233
 F0D  C27  C   CR16  0  -0.317  -5.4329   1.1523   1.8056
 F0D  C26  C   CR16  0  -0.227  -6.0291   2.4062   1.7880
 F0D  C25  C   CR16  0  -0.307  -6.9050   2.7495   0.7706
 F0D  C24  C   CR6   0  -0.015  -7.1838   1.8330  -0.2430
 F0D  C28  C   C     0   0.488  -8.1077   2.1386  -1.3806
 F0D  O29  O   O     0  -0.484  -8.0323   1.5251  -2.4374
 F0D  N30  N   NH2   0  -0.815  -9.0099   3.1085  -1.1715
 F0D  H1   H   H     0   0.241   3.2685  -2.8984  -0.5213
 F0D  H2   H   H     0   0.244   5.5472  -2.1276  -0.1893
 F0D  H3   H   HCH2  0   0.294   6.8965   0.1309  -1.7587
 F0D  H4   H   HCH2  0   0.294   6.2905   1.7527  -1.3697
 F0D  H6   H   HCH2  0   0.262   7.0552  -0.3848   0.6955
 F0D  H7   H   HCH2  0   0.262   6.4463   1.2230   1.0738
 F0D  H8   H   H     0   0.238   4.0958   1.8288   0.5125
 F0D  H9   H   HCH2  0   0.243   1.3476   1.5825   1.3108
 F0D  H10  H   HCH2  0   0.246   1.8083   2.3217  -0.2016
 F0D  H11  H   HCH2  0   0.240  -0.6199   1.5965  -0.0484
 F0D  H12  H   HCH2  0   0.217   0.2184   0.9405  -1.4447
 F0D  H13  H   HCH1  0   0.218  -0.0609  -0.5192   1.2059
 F0D  H14  H   HCH1  0   0.231   0.7953  -1.4438  -1.5561
 F0D  H15  H   HCH2  0   0.238   1.3588  -3.5943  -0.5194
 F0D  H16  H   HCH2  0   0.223   0.8513  -3.0158   1.0469
 F0D  H17  H   HCH2  0   0.215  -0.8657  -3.4114  -1.4584
 F0D  H18  H   HCH2  0   0.227  -0.9199  -4.3901  -0.0012
 F0D  H19  H   HCH3  0   0.233  -0.8584  -2.2557   2.1552
 F0D  H20  H   HCH3  0   0.230  -2.5586  -1.8475   2.1893
 F0D  H21  H   HCH3  0   0.233  -2.0604  -3.5238   2.0418
 F0D  H22  H   HCH1  0   0.211  -1.4705  -1.0674  -1.4177
 F0D  H23  H   HCH2  0   0.218  -2.7263   0.0978   1.0919
 F0D  H24  H   HCH2  0   0.236  -2.8374   0.7123  -0.5448
 F0D  H25  H   HCH1  0   0.211  -3.1090  -2.8029  -1.4504
 F0D  H26  H   HOH1  0   0.450  -4.6848  -3.8592  -0.2717
 F0D  H27  H   HCH1  0   0.240  -4.3379  -0.9405  -1.2174
 F0D  H28  H   HCH2  0   0.242  -5.7867  -1.8822   0.5571
 F0D  H29  H   HCH2  0   0.244  -4.6525  -1.3570   1.7823
 F0D  H30  H   HCR6  0   0.250  -6.7701  -0.1217  -1.0147
 F0D  H31  H   HCR6  0   0.251  -4.7599   0.8913   2.6140
 F0D  H32  H   HCR6  0   0.261  -5.8086   3.1210   2.5699
 F0D  H33  H   HCR6  0   0.255  -7.3445   3.7388   0.7697
 F0D  H34  H   HNH2  0   0.413  -9.1429   3.5471  -0.2777
 F0D  H35  H   HNH2  0   0.405  -9.6541   3.3578  -1.9041
 F0D  BR1  BR  BR    0  -0.157   8.7472   1.5887  -0.8988

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
 F0D  C31  C30  single    1.519  0.020  1.519
 F0D  C30  C3   single    1.506  0.020  1.506
 F0D  C5   C3   aromatic  1.388  0.020  1.388
 F0D  C5   C6   aromatic  1.393  0.020  1.393
 F0D  C3   C2   aromatic  1.391  0.020  1.391
 F0D  C7   C6   single    1.508  0.020  1.508
 F0D  C7   C8   single    1.519  0.020  1.519
 F0D  C6   C11  aromatic  1.401  0.020  1.401
 F0D  C2   C1   aromatic  1.385  0.020  1.385
 F0D  C8   C9   single    1.521  0.020  1.521
 F0D  C11  C1   aromatic  1.396  0.020  1.396
 F0D  C11  C10  single    1.518  0.020  1.518
 F0D  C10  C9   single    1.538  0.020  1.538
 F0D  C10  C12  single    1.536  0.020  1.536
 F0D  C9   C15  single    1.517  0.020  1.517
 F0D  C15  C16  single    1.524  0.020  1.524
 F0D  C15  C14  single    1.534  0.020  1.534
 F0D  C16  C17  single    1.546  0.020  1.546
 F0D  C12  C13  single    1.531  0.020  1.531
 F0D  C26  C25  aromatic  1.386  0.020  1.386
 F0D  C26  C27  aromatic  1.389  0.020  1.389
 F0D  C25  C24  aromatic  1.395  0.020  1.395
 F0D  C13  C14  single    1.526  0.020  1.526
 F0D  C17  C18  single    1.566  0.020  1.566
 F0D  C17  C21  single    1.531  0.020  1.531
 F0D  C14  C18  single    1.532  0.020  1.532
 F0D  C14  C20  single    1.533  0.020  1.533
 F0D  C27  C22  aromatic  1.392  0.020  1.392
 F0D  O29  C28  double    1.224  0.020  1.224
 F0D  C24  C28  single    1.497  0.020  1.497
 F0D  C24  C23  aromatic  1.391  0.020  1.391
 F0D  C28  N30  single    1.341  0.020  1.341
 F0D  C18  O19  single    1.405  0.020  1.405
 F0D  C22  C23  aromatic  1.392  0.020  1.392
 F0D  C22  C21  single    1.503  0.020  1.503
 F0D  C1   H1   single    0.930  0.020  1.080
 F0D  C2   H2   single    0.930  0.020  1.080
 F0D  C31  H3   single    0.970  0.020  1.090
 F0D  C31  H4   single    0.970  0.020  1.090
 F0D  C30  H6   single    0.970  0.020  1.090
 F0D  C30  H7   single    0.970  0.020  1.090
 F0D  C5   H8   single    0.930  0.020  1.080
 F0D  C7   H9   single    0.970  0.020  1.090
 F0D  C7   H10  single    0.970  0.020  1.090
 F0D  C8   H11  single    0.970  0.020  1.090
 F0D  C8   H12  single    0.970  0.020  1.090
 F0D  C9   H13  single    0.970  0.020  1.090
 F0D  C10  H14  single    0.970  0.020  1.090
 F0D  C12  H15  single    0.970  0.020  1.090
 F0D  C12  H16  single    0.970  0.020  1.090
 F0D  C13  H17  single    0.970  0.020  1.090
 F0D  C13  H18  single    0.970  0.020  1.090
 F0D  C20  H19  single    0.970  0.020  1.090
 F0D  C20  H20  single    0.970  0.020  1.090
 F0D  C20  H21  single    0.970  0.020  1.090
 F0D  C15  H22  single    0.970  0.020  1.090
 F0D  C16  H23  single    0.970  0.020  1.090
 F0D  C16  H24  single    0.970  0.020  1.090
 F0D  C18  H25  single    0.970  0.020  1.090
 F0D  O19  H26  single    0.850  0.020  0.980
 F0D  C17  H27  single    0.970  0.020  1.090
 F0D  C21  H28  single    0.970  0.020  1.090
 F0D  C21  H29  single    0.970  0.020  1.090
 F0D  C23  H30  single    0.930  0.020  1.080
 F0D  C27  H31  single    0.930  0.020  1.080
 F0D  C26  H32  single    0.930  0.020  1.080
 F0D  C25  H33  single    0.930  0.020  1.080
 F0D  N30  H34  single    0.860  0.020  1.020
 F0D  N30  H35  single    0.860  0.020  1.020
 F0D  C31  BR1  single    1.974  0.020  1.974

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
 F0D  H1   C1   C11  120.03  3.000
 F0D  H1   C1   C2   118.03  3.000
 F0D  C11  C1   C2   121.94  3.000
 F0D  H2   C2   C3   120.05  3.000
 F0D  H2   C2   C1   119.55  3.000
 F0D  C3   C2   C1   120.40  3.000
 F0D  BR1  C31  H4   106.18  3.000
 F0D  BR1  C31  H3   106.27  3.000
 F0D  H4   C31  H3   109.10  3.000
 F0D  BR1  C31  C30  111.37  3.000
 F0D  H4   C31  C30  111.75  3.000
 F0D  H3   C31  C30  111.86  3.000
 F0D  H7   C30  H6   107.50  3.000
 F0D  H7   C30  C3   110.41  3.000
 F0D  H6   C30  C3   110.23  3.000
 F0D  H7   C30  C31  109.88  3.000
 F0D  H6   C30  C31  109.99  3.000
 F0D  C3   C30  C31  108.81  3.000
 F0D  C5   C3   C30  120.88  3.000
 F0D  C5   C3   C2   117.87  3.000
 F0D  C30  C3   C2   121.20  3.000
 F0D  H8   C5   C6   118.48  3.000
 F0D  H8   C5   C3   119.17  3.000
 F0D  C6   C5   C3   122.35  3.000
 F0D  C11  C6   C7   122.02  3.000
 F0D  C11  C6   C5   119.58  3.000
 F0D  C7   C6   C5   118.39  3.000
 F0D  H10  C7   H9   105.80  3.000
 F0D  H10  C7   C8   110.73  3.000
 F0D  H9   C7   C8   108.83  3.000
 F0D  H10  C7   C6   109.47  3.000
 F0D  H9   C7   C6   108.56  3.000
 F0D  C8   C7   C6   113.16  3.000
 F0D  H12  C8   H11  106.70  3.000
 F0D  H12  C8   C9   109.56  3.000
 F0D  H11  C8   C9   110.84  3.000
 F0D  H12  C8   C7   110.43  3.000
 F0D  H11  C8   C7   109.39  3.000
 F0D  C9   C8   C7   109.87  3.000
 F0D  H13  C9   C15  109.44  3.000
 F0D  H13  C9   C10  108.78  3.000
 F0D  C15  C9   C10  108.07  3.000
 F0D  H13  C9   C8   107.46  3.000
 F0D  C15  C9   C8   113.55  3.000
 F0D  C10  C9   C8   109.46  3.000
 F0D  C10  C11  C6   121.06  3.000
 F0D  C10  C11  C1   121.02  3.000
 F0D  C6   C11  C1   117.86  3.000
 F0D  H14  C10  C12  106.42  3.000
 F0D  H14  C10  C11  106.27  3.000
 F0D  C12  C10  C11  114.28  3.000
 F0D  H14  C10  C9   105.89  3.000
 F0D  C12  C10  C9   111.40  3.000
 F0D  C11  C10  C9   111.92  3.000
 F0D  H16  C12  H15  105.98  3.000
 F0D  H16  C12  C13  110.69  3.000
 F0D  H15  C12  C13  107.95  3.000
 F0D  H16  C12  C10  109.55  3.000
 F0D  H15  C12  C10  110.28  3.000
 F0D  C13  C12  C10  112.20  3.000
 F0D  H18  C13  H17  106.58  3.000
 F0D  H18  C13  C14  111.14  3.000
 F0D  H17  C13  C14  108.84  3.000
 F0D  H18  C13  C12  109.71  3.000
 F0D  H17  C13  C12  108.76  3.000
 F0D  C14  C13  C12  111.65  3.000
 F0D  C18  C14  C15   99.79  3.000
 F0D  C18  C14  C20  110.71  3.000
 F0D  C15  C14  C20  113.00  3.000
 F0D  C20  C14  C13  109.72  3.000
 F0D  C18  C14  C13  114.96  3.000
 F0D  C15  C14  C13  108.39  3.000
 F0D  H21  C20  H20  107.21  3.000
 F0D  H21  C20  H19  106.88  3.000
 F0D  H20  C20  H19  106.75  3.000
 F0D  H21  C20  C14  110.47  3.000
 F0D  H20  C20  C14  113.43  3.000
 F0D  H19  C20  C14  111.76  3.000
 F0D  H22  C15  C16  106.58  3.000
 F0D  H22  C15  C14  106.44  3.000
 F0D  C16  C15  C14  103.77  3.000
 F0D  H22  C15  C9   106.15  3.000
 F0D  C14  C15  C9   112.93  3.000
 F0D  C16  C15  C9   120.13  3.000
 F0D  H24  C16  H23  106.59  3.000
 F0D  H24  C16  C17  112.01  3.000
 F0D  H23  C16  C17  111.50  3.000
 F0D  H24  C16  C15  112.50  3.000
 F0D  H23  C16  C15  110.78  3.000
 F0D  C17  C16  C15  103.56  3.000
 F0D  H25  C18  C17  107.21  3.000
 F0D  H25  C18  O19  109.38  3.000
 F0D  C17  C18  O19  115.79  3.000
 F0D  H25  C18  C14  107.05  3.000
 F0D  O19  C18  C14  111.60  3.000
 F0D  C17  C18  C14  105.36  3.000
 F0D  H26  O19  C18  108.55  3.000
 F0D  H27  C17  C21  107.06  3.000
 F0D  H27  C17  C18  107.68  3.000
 F0D  C21  C17  C18  114.58  3.000
 F0D  H27  C17  C16  108.44  3.000
 F0D  C21  C17  C16  113.62  3.000
 F0D  C18  C17  C16  105.20  3.000
 F0D  H29  C21  H28  106.46  3.000
 F0D  H29  C21  C22  109.55  3.000
 F0D  H28  C21  C22  108.80  3.000
 F0D  H29  C21  C17  110.42  3.000
 F0D  H28  C21  C17  109.89  3.000
 F0D  C22  C21  C17  111.58  3.000
 F0D  C27  C22  C23  118.30  3.000
 F0D  C23  C22  C21  120.12  3.000
 F0D  C27  C22  C21  121.57  3.000
 F0D  H30  C23  C24  119.39  3.000
 F0D  H30  C23  C22  119.06  3.000
 F0D  C24  C23  C22  121.55  3.000
 F0D  H31  C27  C26  119.58  3.000
 F0D  H31  C27  C22  119.62  3.000
 F0D  C26  C27  C22  120.80  3.000
 F0D  H32  C26  C25  119.72  3.000
 F0D  H32  C26  C27  119.99  3.000
 F0D  C25  C26  C27  120.29  3.000
 F0D  H33  C25  C24  121.24  3.000
 F0D  H33  C25  C26  118.93  3.000
 F0D  C24  C25  C26  119.82  3.000
 F0D  C28  C24  C25  122.79  3.000
 F0D  C28  C24  C23  117.97  3.000
 F0D  C25  C24  C23  119.23  3.000
 F0D  N30  C28  O29  122.58  3.000
 F0D  N30  C28  C24  116.38  3.000
 F0D  O29  C28  C24  121.04  3.000
 F0D  H35  N30  H34  117.04  3.000
 F0D  H35  N30  C28  119.74  3.000
 F0D  H34  N30  C28  122.93  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
 F0D  CONST_01  C5   C3   C2   C1      0.00   0.0  0
 F0D  CONST_02  C5   C6   C11  C1      0.00   0.0  0
 F0D  CONST_03  C6   C5   C3   C2      0.00   0.0  0
 F0D  CONST_04  C6   C11  C1   C2      0.00   0.0  0
 F0D  CONST_05  C11  C6   C5   C3      0.00   0.0  0
 F0D  CONST_06  C11  C1   C2   C3      0.00   0.0  0
 F0D  CONST_07  C25  C26  C27  C22     0.00   0.0  0
 F0D  CONST_08  C25  C24  C23  C22     0.00   0.0  0
 F0D  CONST_09  C26  C25  C24  C23     0.00   0.0  0
 F0D  CONST_10  C26  C27  C22  C23     0.00   0.0  0
 F0D  CONST_11  C24  C25  C26  C27     0.00   0.0  0
 F0D  CONST_12  C24  C23  C22  C27     0.00   0.0  0
 F0D  CONST_13  C30  C3   C2   C1    180.00   0.0  0
 F0D  CONST_14  C6   C5   C3   C30   180.00   0.0  0
 F0D  CONST_15  C26  C27  C22  C21   180.00   0.0  0
 F0D  CONST_16  C24  C23  C22  C21   180.00   0.0  0
 F0D  CONST_17  C28  C24  C23  C22   180.00   0.0  0
 F0D  CONST_18  C28  C24  C25  C26   180.00   0.0  0
 F0D  CONST_19  H8   C5   C3   C2    180.00   0.0  0
 F0D  CONST_20  H1   C1   C2   C3    180.00   0.0  0
 F0D  CONST_21  H2   C2   C3   C5    180.00   0.0  0
 F0D  CONST_22  H32  C26  C27  C22   180.00   0.0  0
 F0D  CONST_23  H33  C25  C24  C23   180.00   0.0  0
 F0D  CONST_24  H31  C27  C22  C23   180.00   0.0  0
 F0D  CONST_25  H30  C23  C22  C27   180.00   0.0  0
 F0D  CONST_26  H34  N30  C28  C24     0.00   0.0  0
 F0D  CONST_27  H35  N30  C28  C24   180.00   0.0  0
 F0D  Var_01    C8   C7   C6   C5    163.75  30.0  1
 F0D  Var_02    C9   C8   C7   C6     47.37  30.0  1
 F0D  Var_03    C14  C13  C12  C10   -53.90  30.0  1
 F0D  Var_04    C27  C22  C21  C17  -103.55  30.0  2
 F0D  Var_05    C31  C30  C3   C2     91.62  30.0  3
 F0D  Var_06    O29  C28  C24  C23   -21.22  30.0  2
 F0D  Var_07    BR1  C31  C30  C3   -179.66  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
 F0D  chir_01  C9   C8   C10  C15  positiv
 F0D  chir_02  C10  C12  C9   C11  negativ
 F0D  chir_03  C14  C13  C18  C15  positiv
 F0D  chir_04  C15  C14  C16  C9   negativ
 F0D  chir_05  C18  O19  C14  C17  positiv
 F0D  chir_06  C17  C21  C18  C16  positiv

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
 F0D  plan-1  C21  0.020
 F0D  plan-1  C22  0.020
 F0D  plan-1  C23  0.020
 F0D  plan-1  C27  0.020
 F0D  plan-1  C26  0.020
 F0D  plan-1  C25  0.020
 F0D  plan-1  C24  0.020
 F0D  plan-1  C28  0.020
 F0D  plan-1  H30  0.020
 F0D  plan-1  H31  0.020
 F0D  plan-1  H32  0.020
 F0D  plan-1  H33  0.020
 F0D  plan-2  C1   0.020
 F0D  plan-2  C2   0.020
 F0D  plan-2  C30  0.020
 F0D  plan-2  C3   0.020
 F0D  plan-2  C5   0.020
 F0D  plan-2  C6   0.020
 F0D  plan-2  C7   0.020
 F0D  plan-2  C11  0.020
 F0D  plan-2  C10  0.020
 F0D  plan-2  H1   0.020
 F0D  plan-2  H2   0.020
 F0D  plan-2  H8   0.020
 F0D  plan-3  C24  0.020
 F0D  plan-3  C28  0.020
 F0D  plan-3  O29  0.020
 F0D  plan-3  N30  0.020
 F0D  plan-3  H34  0.020
 F0D  plan-3  H35  0.020

