# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:59:09 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: 3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxy-2-methoxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2[C@H]3CC[C@]4(C)[C@@H](O)[C@H](C[C@H]4[C@@H]3CCc2cc1O)Cc5cccc(c5)C(N)=O
#
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
 F0A  F0A  3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxy-2-methoxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide  ligand  65  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_F0A
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
 F0A  O29  O  O     0  -0.484   4.6489   3.0130  -1.7931
 F0A  C28  C  C     0   0.488   5.5882   2.6828  -1.0807
 F0A  N30  N  NH2   0  -0.815   6.7064   3.4157  -0.9748
 F0A  C24  C  CR6   0  -0.019   5.5414   1.4209  -0.2773
 F0A  C25  C  CR16  0  -0.306   6.3325   1.2130   0.8494
 F0A  C26  C  CR16  0  -0.225   6.2310   0.0207   1.5527
 F0A  C27  C  CR16  0  -0.308   5.3482  -0.9639   1.1376
 F0A  C22  C  CR6   0   0.176   4.5396  -0.7716   0.0180
 F0A  C23  C  CR16  0  -0.346   4.6452   0.4298  -0.6716
 F0A  C21  C  CH2   0  -0.521   3.5615  -1.8285  -0.4145
 F0A  C17  C  CR15  0  -0.276   2.3559  -1.8985   0.5283
 F0A  C18  C  CR15  0   0.105   1.2953  -2.9898   0.1597
 F0A  O19  O  OH1   0  -0.671   1.7098  -3.9488  -0.7800
 F0A  C14  C  CR5   0  -0.096   0.0684  -2.2112  -0.3271
 F0A  C20  C  CH3   0  -0.674   0.2478  -1.7907  -1.7901
 F0A  C15  C  CR15  0  -0.191   0.1099  -1.0274   0.6497
 F0A  C16  C  CH2   0  -0.433   1.5636  -0.5745   0.6048
 F0A  C13  C  CH2   0  -0.409  -1.2689  -2.9277  -0.1572
 F0A  C12  C  CH2   0  -0.452  -2.4499  -1.9680  -0.3352
 F0A  C10  C  CH1   0  -0.262  -2.3490  -0.7334   0.5718
 F0A  C11  C  CR6   0   0.119  -3.5073   0.2372   0.4197
 F0A  C6   C  CR6   0   0.040  -3.3270   1.6098   0.5821
 F0A  C7   C  CH2   0  -0.503  -1.9770   2.2160   0.8736
 F0A  C8   C  CH2   0  -0.429  -0.9490   1.1894   1.3205
 F0A  C9   C  CH1   0  -0.235  -0.9981  -0.0210   0.4003
 F0A  C5   C  CR16  0  -0.388  -4.4240   2.4665   0.4593
 F0A  C3   C  CR6   0   0.272  -5.6914   1.9945   0.1867
 F0A  O4   O  OH1   0  -0.638  -6.7186   2.8656   0.0751
 F0A  C2   C  CR6   0   0.310  -5.8803   0.6128   0.0360
 F0A  C1   C  CR16  0  -0.465  -4.7981  -0.2392   0.1557
 F0A  O31  O  O2    0  -0.493  -7.1546   0.2355  -0.2221
 F0A  C32  C  CH3   0  -0.432  -7.4176  -1.1309  -0.4629
 F0A  H1   H  HNH2  0   0.405   6.7942   4.2685  -1.5030
 F0A  H2   H  HNH2  0   0.413   7.5242   3.0957  -0.4867
 F0A  H3   H  HCR6  0   0.255   7.0171   1.9730   1.2042
 F0A  H4   H  HCR6  0   0.261   6.8450  -0.1371   2.4297
 F0A  H5   H  HCR6  0   0.252   5.2890  -1.8943   1.6911
 F0A  H6   H  HCR6  0   0.248   4.0257   0.5909  -1.5453
 F0A  H7   H  HCH2  0   0.245   3.2342  -1.6179  -1.4346
 F0A  H8   H  HCH2  0   0.243   4.0725  -2.7945  -0.4411
 F0A  H9   H  HCR5  0   0.239   2.7424  -2.1313   1.5254
 F0A  H10  H  HCR5  0   0.210   1.0086  -3.4929   1.0951
 F0A  H11  H  HOH1  0   0.450   2.3763  -4.5081  -0.3705
 F0A  H12  H  HCH3  0   0.233  -0.5200  -1.0883  -2.1116
 F0A  H13  H  HCH3  0   0.230   1.2101  -1.3189  -1.9845
 F0A  H14  H  HCH3  0   0.232   0.1787  -2.6615  -2.4429
 F0A  H15  H  HCR5  0   0.212  -0.0662  -1.4456   1.6541
 F0A  H16  H  HCH2  0   0.236   1.8512   0.0241   1.4698
 F0A  H17  H  HCH2  0   0.219   1.7394   0.0500  -0.2774
 F0A  H18  H  HCH2  0   0.226  -1.3612  -3.7572  -0.8645
 F0A  H19  H  HCH2  0   0.215  -1.3165  -3.3647   0.8469
 F0A  H20  H  HCH2  0   0.222  -2.5302  -1.6466  -1.3779
 F0A  H21  H  HCH2  0   0.236  -3.3661  -2.5219  -0.1229
 F0A  H22  H  HCH1  0   0.226  -2.3684  -1.1033   1.6088
 F0A  H23  H  HCH2  0   0.238  -1.6094   2.7134  -0.0308
 F0A  H24  H  HCH2  0   0.243  -2.0857   3.0038   1.6232
 F0A  H25  H  HCH2  0   0.238   0.0447   1.6435   1.3167
 F0A  H26  H  HCH2  0   0.215  -1.1470   0.8724   2.3505
 F0A  H27  H  HCH1  0   0.216  -0.9209   0.3476  -0.6321
 F0A  H28  H  HCR6  0   0.250  -4.2828   3.5354   0.5815
 F0A  H29  H  HOH1  0   0.469  -7.5371   2.3872  -0.1027
 F0A  H30  H  HCR6  0   0.265  -4.9519  -1.3039   0.0450
 F0A  H31  H  HCH3  0   0.228  -6.8490  -1.5072  -1.3173
 F0A  H32  H  HCH3  0   0.228  -7.1931  -1.7498   0.4096
 F0A  H33  H  HCH3  0   0.262  -8.4789  -1.2095  -0.6846

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
 F0A  O4   C3   single    1.352  0.020  1.352
 F0A  C5   C3   aromatic  1.380  0.020  1.380
 F0A  C5   C6   aromatic  1.397  0.020  1.397
 F0A  C7   C8   single    1.520  0.020  1.520
 F0A  C7   C6   single    1.508  0.020  1.508
 F0A  C3   C2   aromatic  1.403  0.020  1.403
 F0A  C8   C9   single    1.521  0.020  1.521
 F0A  C6   C11  aromatic  1.394  0.020  1.394
 F0A  C2   O31  single    1.354  0.020  1.354
 F0A  C2   C1   aromatic  1.383  0.020  1.383
 F0A  C11  C1   aromatic  1.401  0.020  1.401
 F0A  C11  C10  single    1.519  0.020  1.519
 F0A  O31  C32  single    1.412  0.020  1.412
 F0A  C26  C25  aromatic  1.388  0.020  1.388
 F0A  C26  C27  aromatic  1.386  0.020  1.386
 F0A  C9   C10  single    1.537  0.020  1.537
 F0A  C9   C15  single    1.517  0.020  1.517
 F0A  C25  C24  aromatic  1.392  0.020  1.392
 F0A  C10  C12  single    1.535  0.020  1.535
 F0A  C16  C15  single    1.523  0.020  1.523
 F0A  C16  C17  single    1.545  0.020  1.545
 F0A  C15  C14  single    1.535  0.020  1.535
 F0A  C27  C22  aromatic  1.394  0.020  1.394
 F0A  C24  C28  single    1.497  0.020  1.497
 F0A  C24  C23  aromatic  1.393  0.020  1.393
 F0A  O29  C28  double    1.224  0.020  1.224
 F0A  C28  N30  single    1.341  0.020  1.341
 F0A  C22  C23  aromatic  1.389  0.020  1.389
 F0A  C22  C21  single    1.503  0.020  1.503
 F0A  C17  C21  single    1.532  0.020  1.532
 F0A  C17  C18  single    1.566  0.020  1.566
 F0A  C12  C13  single    1.532  0.020  1.532
 F0A  C14  C13  single    1.527  0.020  1.527
 F0A  C14  C18  single    1.532  0.020  1.532
 F0A  C14  C20  single    1.533  0.020  1.533
 F0A  C18  O19  single    1.405  0.020  1.405
 F0A  N30  H1   single    0.860  0.020  1.020
 F0A  N30  H2   single    0.860  0.020  1.020
 F0A  C25  H3   single    0.930  0.020  1.080
 F0A  C26  H4   single    0.930  0.020  1.080
 F0A  C27  H5   single    0.930  0.020  1.080
 F0A  C23  H6   single    0.930  0.020  1.080
 F0A  C21  H7   single    0.970  0.020  1.090
 F0A  C21  H8   single    0.970  0.020  1.090
 F0A  C17  H9   single    0.970  0.020  1.090
 F0A  C18  H10  single    0.970  0.020  1.090
 F0A  O19  H11  single    0.850  0.020  0.980
 F0A  C20  H12  single    0.970  0.020  1.090
 F0A  C20  H13  single    0.970  0.020  1.090
 F0A  C20  H14  single    0.970  0.020  1.090
 F0A  C15  H15  single    0.970  0.020  1.090
 F0A  C16  H16  single    0.970  0.020  1.090
 F0A  C16  H17  single    0.970  0.020  1.090
 F0A  C13  H18  single    0.970  0.020  1.090
 F0A  C13  H19  single    0.970  0.020  1.090
 F0A  C12  H20  single    0.970  0.020  1.090
 F0A  C12  H21  single    0.970  0.020  1.090
 F0A  C10  H22  single    0.970  0.020  1.090
 F0A  C7   H23  single    0.970  0.020  1.090
 F0A  C7   H24  single    0.970  0.020  1.090
 F0A  C8   H25  single    0.970  0.020  1.090
 F0A  C8   H26  single    0.970  0.020  1.090
 F0A  C9   H27  single    0.970  0.020  1.090
 F0A  C5   H28  single    0.930  0.020  1.080
 F0A  O4   H29  single    0.850  0.020  0.980
 F0A  C1   H30  single    0.930  0.020  1.080
 F0A  C32  H31  single    0.970  0.020  1.090
 F0A  C32  H32  single    0.970  0.020  1.090
 F0A  C32  H33  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
 F0A  C24  C28  N30  116.39  3.000
 F0A  N30  C28  O29  122.56  3.000
 F0A  C24  C28  O29  121.05  3.000
 F0A  H2   N30  H1   116.97  3.000
 F0A  H2   N30  C28  122.88  3.000
 F0A  H1   N30  C28  119.62  3.000
 F0A  C23  C24  C25  119.23  3.000
 F0A  C23  C24  C28  117.90  3.000
 F0A  C25  C24  C28  122.86  3.000
 F0A  H3   C25  C26  118.89  3.000
 F0A  H3   C25  C24  121.31  3.000
 F0A  C26  C25  C24  119.79  3.000
 F0A  H4   C26  C27  120.03  3.000
 F0A  H4   C26  C25  119.63  3.000
 F0A  C27  C26  C25  120.33  3.000
 F0A  H5   C27  C22  119.78  3.000
 F0A  H5   C27  C26  119.44  3.000
 F0A  C22  C27  C26  120.79  3.000
 F0A  C21  C22  C23  120.96  3.000
 F0A  C21  C22  C27  120.75  3.000
 F0A  C23  C22  C27  118.28  3.000
 F0A  H6   C23  C22  119.05  3.000
 F0A  H6   C23  C24  119.37  3.000
 F0A  C22  C23  C24  121.57  3.000
 F0A  H8   C21  H7   106.72  3.000
 F0A  H8   C21  C17  110.02  3.000
 F0A  H7   C21  C17  110.36  3.000
 F0A  H8   C21  C22  108.91  3.000
 F0A  H7   C21  C22  109.16  3.000
 F0A  C17  C21  C22  111.53  3.000
 F0A  H9   C17  C16  108.56  3.000
 F0A  H9   C17  C18  107.78  3.000
 F0A  C16  C17  C18  105.16  3.000
 F0A  H9   C17  C21  107.01  3.000
 F0A  C18  C17  C21  114.84  3.000
 F0A  C16  C17  C21  113.26  3.000
 F0A  H10  C18  C14  107.09  3.000
 F0A  H10  C18  O19  109.47  3.000
 F0A  C14  C18  O19  111.74  3.000
 F0A  H10  C18  C17  107.16  3.000
 F0A  O19  C18  C17  115.68  3.000
 F0A  C14  C18  C17  105.25  3.000
 F0A  H11  O19  C18  108.46  3.000
 F0A  C13  C14  C15  108.34  3.000
 F0A  C13  C14  C20  109.72  3.000
 F0A  C15  C14  C20  113.12  3.000
 F0A  C20  C14  C18  110.42  3.000
 F0A  C13  C14  C18  115.31  3.000
 F0A  C15  C14  C18   99.67  3.000
 F0A  H14  C20  H13  107.16  3.000
 F0A  H14  C20  H12  107.08  3.000
 F0A  H13  C20  H12  106.90  3.000
 F0A  H14  C20  C14  110.17  3.000
 F0A  H13  C20  C14  113.11  3.000
 F0A  H12  C20  C14  112.10  3.000
 F0A  H15  C15  C9   106.55  3.000
 F0A  H15  C15  C16  106.98  3.000
 F0A  C9   C15  C16  119.65  3.000
 F0A  H15  C15  C14  106.44  3.000
 F0A  C16  C15  C14  103.66  3.000
 F0A  C9   C15  C14  112.78  3.000
 F0A  H17  C16  H16  106.48  3.000
 F0A  H17  C16  C15  110.28  3.000
 F0A  H16  C16  C15  113.05  3.000
 F0A  H17  C16  C17  111.51  3.000
 F0A  H16  C16  C17  111.99  3.000
 F0A  C15  C16  C17  103.66  3.000
 F0A  H19  C13  H18  106.63  3.000
 F0A  H19  C13  C12  108.82  3.000
 F0A  H18  C13  C12  109.56  3.000
 F0A  H19  C13  C14  109.09  3.000
 F0A  H18  C13  C14  110.97  3.000
 F0A  C12  C13  C14  111.61  3.000
 F0A  H21  C12  H20  105.83  3.000
 F0A  H21  C12  C10  110.39  3.000
 F0A  H20  C12  C10  109.37  3.000
 F0A  H21  C12  C13  107.86  3.000
 F0A  H20  C12  C13  110.57  3.000
 F0A  C10  C12  C13  112.60  3.000
 F0A  H22  C10  C9   106.04  3.000
 F0A  H22  C10  C11  107.18  3.000
 F0A  C9   C10  C11  111.28  3.000
 F0A  H22  C10  C12  106.57  3.000
 F0A  C9   C10  C12  111.39  3.000
 F0A  C11  C10  C12  113.87  3.000
 F0A  C1   C11  C6   118.43  3.000
 F0A  C1   C11  C10  120.27  3.000
 F0A  C6   C11  C10  121.26  3.000
 F0A  C5   C6   C7   118.24  3.000
 F0A  C7   C6   C11  122.28  3.000
 F0A  C5   C6   C11  119.47  3.000
 F0A  H24  C7   H23  105.80  3.000
 F0A  H24  C7   C8   110.63  3.000
 F0A  H23  C7   C8   108.81  3.000
 F0A  H24  C7   C6   109.47  3.000
 F0A  H23  C7   C6   108.86  3.000
 F0A  C8   C7   C6   113.00  3.000
 F0A  H26  C8   H25  106.73  3.000
 F0A  H26  C8   C9   109.43  3.000
 F0A  H25  C8   C9   110.98  3.000
 F0A  H26  C8   C7   110.46  3.000
 F0A  H25  C8   C7   109.47  3.000
 F0A  C9   C8   C7   109.73  3.000
 F0A  H27  C9   C8   107.41  3.000
 F0A  H27  C9   C10  108.79  3.000
 F0A  C8   C9   C10  109.25  3.000
 F0A  H27  C9   C15  109.00  3.000
 F0A  C10  C9   C15  108.42  3.000
 F0A  C8   C9   C15  113.87  3.000
 F0A  H28  C5   C3   118.61  3.000
 F0A  H28  C5   C6   119.47  3.000
 F0A  C3   C5   C6   121.92  3.000
 F0A  C2   C3   O4   121.58  3.000
 F0A  C2   C3   C5   118.82  3.000
 F0A  O4   C3   C5   119.61  3.000
 F0A  H29  O4   C3   109.91  3.000
 F0A  O31  C2   C1   125.55  3.000
 F0A  C1   C2   C3   119.50  3.000
 F0A  O31  C2   C3   114.95  3.000
 F0A  H30  C1   C2   119.11  3.000
 F0A  H30  C1   C11  119.03  3.000
 F0A  C2   C1   C11  121.86  3.000
 F0A  C32  O31  C2   118.52  3.000
 F0A  H33  C32  H32  108.80  3.000
 F0A  H33  C32  H31  108.88  3.000
 F0A  H32  C32  H31  108.79  3.000
 F0A  H33  C32  O31  106.65  3.000
 F0A  H32  C32  O31  111.93  3.000
 F0A  H31  C32  O31  111.69  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
 F0A  CONST_01  C27  C26  C25  C24     0.00   0.0  0
 F0A  CONST_02  C27  C22  C23  C24     0.00   0.0  0
 F0A  CONST_03  C22  C27  C26  C25     0.00   0.0  0
 F0A  CONST_04  C22  C23  C24  C25     0.00   0.0  0
 F0A  CONST_05  C23  C24  C25  C26     0.00   0.0  0
 F0A  CONST_06  C23  C22  C27  C26     0.00   0.0  0
 F0A  CONST_07  C3   C5   C6   C11     0.00   0.0  0
 F0A  CONST_08  C3   C2   C1   C11     0.00   0.0  0
 F0A  CONST_09  C2   C3   C5   C6      0.00   0.0  0
 F0A  CONST_10  C2   C1   C11  C6      0.00   0.0  0
 F0A  CONST_11  C1   C2   C3   C5      0.00   0.0  0
 F0A  CONST_12  C1   C11  C6   C5      0.00   0.0  0
 F0A  CONST_13  C26  C25  C24  C28   180.00   0.0  0
 F0A  CONST_14  C22  C23  C24  C28   180.00   0.0  0
 F0A  CONST_15  C21  C22  C23  C24   180.00   0.0  0
 F0A  CONST_16  C21  C22  C27  C26   180.00   0.0  0
 F0A  CONST_17  O31  C2   C1   C11   180.00   0.0  0
 F0A  CONST_18  O4   C3   C5   C6    180.00   0.0  0
 F0A  CONST_19  O31  C2   C3   C5    180.00   0.0  0
 F0A  CONST_20  C1   C2   C3   O4    180.00   0.0  0
 F0A  CONST_21  H4   C26  C25  C24   180.00   0.0  0
 F0A  CONST_22  H5   C27  C26  C25   180.00   0.0  0
 F0A  CONST_23  H6   C23  C24  C25   180.00   0.0  0
 F0A  CONST_24  H3   C25  C26  C27   180.00   0.0  0
 F0A  CONST_25  H30  C1   C11  C10     0.00   0.0  0
 F0A  CONST_26  H28  C5   C6   C11   180.00   0.0  0
 F0A  CONST_27  H1   N30  C28  C24   180.00   0.0  0
 F0A  CONST_28  H2   N30  C28  C24     0.00   0.0  0
 F0A  Var_01    C10  C12  C13  C14   -53.47  30.0  1
 F0A  Var_02    C8   C7   C6   C11   -14.92  30.0  1
 F0A  Var_03    C9   C8   C7   C6     46.40  30.0  1
 F0A  Var_04    C17  C21  C22  C27    73.15  30.0  2
 F0A  Var_05    C25  C24  C28  O29  -158.00  30.0  1
 F0A  Var_06    H31  C32  O31  C2    -58.95  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
 F0A  chir_01  C17  C16  C21  C18  positiv
 F0A  chir_02  C18  O19  C17  C14  negativ
 F0A  chir_03  C14  C13  C18  C15  positiv
 F0A  chir_04  C15  C14  C16  C9   negativ
 F0A  chir_05  C10  C12  C9   C11  negativ
 F0A  chir_06  C9   C8   C10  C15  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
 F0A  plan-1  C28  0.020
 F0A  plan-1  C24  0.020
 F0A  plan-1  C25  0.020
 F0A  plan-1  C26  0.020
 F0A  plan-1  C27  0.020
 F0A  plan-1  C22  0.020
 F0A  plan-1  C23  0.020
 F0A  plan-1  C21  0.020
 F0A  plan-1  H3   0.020
 F0A  plan-1  H4   0.020
 F0A  plan-1  H5   0.020
 F0A  plan-1  H6   0.020
 F0A  plan-2  C10  0.020
 F0A  plan-2  C11  0.020
 F0A  plan-2  C6   0.020
 F0A  plan-2  C7   0.020
 F0A  plan-2  C5   0.020
 F0A  plan-2  C3   0.020
 F0A  plan-2  O4   0.020
 F0A  plan-2  C2   0.020
 F0A  plan-2  C1   0.020
 F0A  plan-2  O31  0.020
 F0A  plan-2  H28  0.020
 F0A  plan-2  H30  0.020
 F0A  plan-3  O29  0.020
 F0A  plan-3  C28  0.020
 F0A  plan-3  N30  0.020
 F0A  plan-3  C24  0.020
 F0A  plan-3  H1   0.020
 F0A  plan-3  H2   0.020

