# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:09:22 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxyestra-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(O)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
 E2B  E2B  3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide  ligand  61  30  .  2022-07-24  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_E2B
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
 E2B  N30   N  NH2   0  -0.818  -7.5248   2.0724  -1.1029
 E2B  C9    C  CH1   0  -0.234   1.8138   0.1098  -0.1107
 E2B  C10   C  CH1   0  -0.264   3.0209  -0.6958  -0.6182
 E2B  C15   C  CR15  0  -0.192   0.5558  -0.6765  -0.4268
 E2B  C8    C  CH2   0  -0.428   1.8402   1.4951  -0.7384
 E2B  C14   C  CR5   0  -0.095   0.5308  -2.0562   0.2464
 E2B  C11   C  CR6   0   0.101   4.3195   0.0676  -0.4331
 E2B  C13   C  CH2   0  -0.419   1.7286  -2.8631  -0.2477
 E2B  C16   C  CH2   0  -0.449  -0.8121  -0.0872  -0.0969
 E2B  C28   C  C     0   0.492  -6.5201   1.1997  -1.2709
 E2B  C25   C  CR16  0  -0.317  -5.3235   2.1596   0.7521
 E2B  C6    C  CR6   0   0.077   4.3303   1.4599  -0.2945
 E2B  C12   C  CH2   0  -0.454   3.0452  -2.1120  -0.0275
 E2B  C17   C  CR15  0  -0.271  -1.7672  -1.2982  -0.2066
 E2B  C18   C  CR15  0   0.099  -0.8284  -2.5473  -0.2587
 E2B  C24   C  CR6   0  -0.017  -5.5003   1.1347  -0.1760
 E2B  C1    C  CR16  0  -0.306   5.5519  -0.5890  -0.4462
 E2B  C26   C  CR16  0  -0.217  -4.3520   2.0393   1.7325
 E2B  C23   C  CR16  0  -0.330  -4.6826   0.0110  -0.1125
 E2B  C27   C  CR16  0  -0.298  -3.5561   0.9042   1.7935
 E2B  C7    C  CH2   0  -0.494   3.0560   2.2641  -0.2475
 E2B  C3    C  CR6   0   0.360   6.7530   1.4660  -0.1830
 E2B  C22   C  CR6   0   0.186  -3.7076  -0.1260   0.8700
 E2B  C5    C  CR16  0  -0.410   5.5413   2.1395  -0.1715
 E2B  C2    C  CR16  0  -0.323   6.7548   0.0826  -0.3231
 E2B  O4    O  OH1   0  -0.624   7.9456   2.0937  -0.0662
 E2B  O29   O  O     0  -0.483  -6.4261   0.4874  -2.2620
 E2B  O19   O  OH1   0  -0.658  -1.2812  -3.6778   0.4462
 E2B  HN30  H  HNH2  0   0.414  -7.6661   2.5902  -0.2535
 E2B  HN3A  H  HNH2  0   0.405  -8.2329   2.1602  -1.8135
 E2B  H9    H  HCH1  0   0.218   1.9008   0.2328   0.9781
 E2B  H10   H  HCH1  0   0.227   2.8679  -0.8117  -1.7024
 E2B  H15   H  HCR5  0   0.212   0.5722  -0.8643  -1.5124
 E2B  H8    H  HCH2  0   0.218   1.8652   1.3998  -1.8292
 E2B  H8A   H  HCH2  0   0.242   0.9356   2.0543  -0.4909
 E2B  H13   H  HCH2  0   0.224   1.7759  -3.8372   0.2475
 E2B  H13A  H  HCH2  0   0.239   1.6088  -3.0617  -1.3188
 E2B  H16   H  HCH2  0   0.222  -0.8119   0.3281   0.9162
 E2B  H16A  H  HCH2  0   0.259  -1.1005   0.7251  -0.7645
 E2B  H25   H  HCR6  0   0.271  -5.9170   3.0635   0.7143
 E2B  H12   H  HCH2  0   0.244   3.8443  -2.6977  -0.4849
 E2B  H12A  H  HCH2  0   0.218   3.2886  -2.0553   1.0378
 E2B  H17   H  HCR5  0   0.237  -2.3050  -1.2403  -1.1582
 E2B  H18   H  HCR5  0   0.219  -0.6959  -2.8086  -1.3182
 E2B  H1    H  HCR6  0   0.239   5.5894  -1.6646  -0.5589
 E2B  H26   H  HCR6  0   0.250  -4.2114   2.8361   2.4507
 E2B  H23   H  HCR6  0   0.239  -4.8183  -0.7781  -0.8425
 E2B  H27   H  HCR6  0   0.225  -2.8052   0.8221   2.5699
 E2B  H7    H  HCH2  0   0.232   3.1831   3.1876  -0.8181
 E2B  H7A   H  HCH2  0   0.234   2.8817   2.5768   0.7879
 E2B  H5    H  HCR6  0   0.221   5.5236   3.2207  -0.0668
 E2B  H2    H  HCR6  0   0.237   7.6901  -0.4622  -0.3385
 E2B  HO4   H  HOH1  0   0.445   7.8171   3.0437  -0.0001
 E2B  HO19  H  HOH1  0   0.427  -1.9813  -4.0894  -0.0653
 E2B  C21   C  CH2   0  -0.509  -2.8242  -1.3423   0.9002
 E2B  C20   C  CH3   0  -0.664   0.5533  -1.9822   1.7772
 E2B  H20   H  HCH3  0   0.218  -0.1942  -1.3042   2.1879
 E2B  H20A  H  HCH3  0   0.232   0.3667  -2.9668   2.2061
 E2B  H20B  H  HCH3  0   0.228   1.5195  -1.6495   2.1552
 E2B  H21   H  HCH2  0   0.224  -3.4441  -2.2356   0.7899
 E2B  H21A  H  HCH2  0   0.237  -2.3458  -1.4207   1.8784

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
 E2B  N30  C28   single    1.341  0.020  1.341
 E2B  C9   C10   single    1.537  0.020  1.537
 E2B  C9   C15   single    1.517  0.020  1.517
 E2B  C9   C8    single    1.521  0.020  1.521
 E2B  C10  C11   single    1.518  0.020  1.518
 E2B  C10  C12   single    1.535  0.020  1.535
 E2B  C15  C14   single    1.535  0.020  1.535
 E2B  C15  C16   single    1.526  0.020  1.526
 E2B  C8   C7    single    1.520  0.020  1.520
 E2B  C14  C13   single    1.526  0.020  1.526
 E2B  C14  C18   single    1.531  0.020  1.531
 E2B  C14  C20   single    1.533  0.020  1.533
 E2B  C11  C6    aromatic  1.399  0.020  1.399
 E2B  C11  C1    aromatic  1.396  0.020  1.396
 E2B  C13  C12   single    1.532  0.020  1.532
 E2B  C16  C17   single    1.546  0.020  1.546
 E2B  C28  C24   single    1.498  0.020  1.498
 E2B  C28  O29   double    1.224  0.020  1.224
 E2B  C25  C24   aromatic  1.394  0.020  1.394
 E2B  C25  C26   aromatic  1.385  0.020  1.385
 E2B  C6   C7    single    1.508  0.020  1.508
 E2B  C6   C5    aromatic  1.394  0.020  1.394
 E2B  C17  C18   single    1.563  0.020  1.563
 E2B  C17  C21   single    1.531  0.020  1.531
 E2B  C18  O19   single    1.407  0.020  1.407
 E2B  C24  C23   aromatic  1.391  0.020  1.391
 E2B  C1   C2    aromatic  1.383  0.020  1.383
 E2B  C26  C27   aromatic  1.388  0.020  1.388
 E2B  C21  C22   single    1.504  0.020  1.504
 E2B  C23  C22   aromatic  1.391  0.020  1.391
 E2B  C27  C22   aromatic  1.392  0.020  1.392
 E2B  C3   C5    aromatic  1.386  0.020  1.386
 E2B  C3   C2    aromatic  1.390  0.020  1.390
 E2B  C3   O4    single    1.353  0.020  1.353
 E2B  N30  HN30  single    0.860  0.020  1.020
 E2B  N30  HN3A  single    0.860  0.020  1.020
 E2B  C9   H9    single    0.970  0.020  1.090
 E2B  C10  H10   single    0.970  0.020  1.090
 E2B  C15  H15   single    0.970  0.020  1.090
 E2B  C8   H8    single    0.970  0.020  1.090
 E2B  C8   H8A   single    0.970  0.020  1.090
 E2B  C13  H13   single    0.970  0.020  1.090
 E2B  C13  H13A  single    0.970  0.020  1.090
 E2B  C16  H16   single    0.970  0.020  1.090
 E2B  C16  H16A  single    0.970  0.020  1.090
 E2B  C25  H25   single    0.930  0.020  1.080
 E2B  C12  H12   single    0.970  0.020  1.090
 E2B  C12  H12A  single    0.970  0.020  1.090
 E2B  C17  H17   single    0.970  0.020  1.090
 E2B  C18  H18   single    0.970  0.020  1.090
 E2B  C20  H20   single    0.970  0.020  1.090
 E2B  C20  H20A  single    0.970  0.020  1.090
 E2B  C20  H20B  single    0.970  0.020  1.090
 E2B  C1   H1    single    0.930  0.020  1.080
 E2B  C26  H26   single    0.930  0.020  1.080
 E2B  C21  H21   single    0.970  0.020  1.090
 E2B  C21  H21A  single    0.970  0.020  1.090
 E2B  C23  H23   single    0.930  0.020  1.080
 E2B  C27  H27   single    0.930  0.020  1.080
 E2B  C7   H7    single    0.970  0.020  1.090
 E2B  C7   H7A   single    0.970  0.020  1.090
 E2B  C5   H5    single    0.930  0.020  1.080
 E2B  C2   H2    single    0.930  0.020  1.080
 E2B  O4   HO4   single    0.850  0.020  0.980
 E2B  O19  HO19  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
 E2B  HN3A  N30  HN30  116.91  3.000
 E2B  HN3A  N30  C28   119.67  3.000
 E2B  HN30  N30  C28   123.13  3.000
 E2B  H9    C9   C8    107.79  3.000
 E2B  H9    C9   C15   109.27  3.000
 E2B  C8    C9   C15   113.61  3.000
 E2B  H9    C9   C10   108.88  3.000
 E2B  C8    C9   C10   109.11  3.000
 E2B  C15   C9   C10   108.10  3.000
 E2B  H10   C10  C12   106.51  3.000
 E2B  H10   C10  C11   106.98  3.000
 E2B  C12   C10  C11   113.81  3.000
 E2B  H10   C10  C9    105.73  3.000
 E2B  C12   C10  C9    111.65  3.000
 E2B  C11   C10  C9    111.59  3.000
 E2B  H15   C15  C16   106.99  3.000
 E2B  H15   C15  C14   106.20  3.000
 E2B  C16   C15  C14   103.76  3.000
 E2B  H15   C15  C9    106.34  3.000
 E2B  C16   C15  C9    119.89  3.000
 E2B  C14   C15  C9    112.83  3.000
 E2B  H8A   C8   H8    106.81  3.000
 E2B  H8A   C8   C7    109.29  3.000
 E2B  H8    C8   C7    110.33  3.000
 E2B  H8A   C8   C9    111.01  3.000
 E2B  H8    C8   C9    109.40  3.000
 E2B  C7    C8   C9    109.96  3.000
 E2B  C20   C14  C18   110.98  3.000
 E2B  C20   C14  C13   109.72  3.000
 E2B  C18   C14  C13   114.85  3.000
 E2B  C20   C14  C15   113.22  3.000
 E2B  C18   C14  C15    99.09  3.000
 E2B  C13   C14  C15   108.68  3.000
 E2B  C1    C11  C6    117.52  3.000
 E2B  C1    C11  C10   121.16  3.000
 E2B  C6    C11  C10   121.28  3.000
 E2B  H13A  C13  H13   106.61  3.000
 E2B  H13A  C13  C12   108.86  3.000
 E2B  H13   C13  C12   109.53  3.000
 E2B  H13A  C13  C14   109.06  3.000
 E2B  H13   C13  C14   110.99  3.000
 E2B  C12   C13  C14   111.64  3.000
 E2B  H16A  C16  H16   106.50  3.000
 E2B  H16A  C16  C17   112.13  3.000
 E2B  H16   C16  C17   111.28  3.000
 E2B  H16A  C16  C15   113.12  3.000
 E2B  H16   C16  C15   110.27  3.000
 E2B  C17   C16  C15   103.65  3.000
 E2B  O29   C28  C24   120.96  3.000
 E2B  O29   C28  N30   122.51  3.000
 E2B  C24   C28  N30   116.53  3.000
 E2B  H25   C25  C26   118.81  3.000
 E2B  H25   C25  C24   121.42  3.000
 E2B  C26   C25  C24   119.75  3.000
 E2B  C5    C6   C7    118.13  3.000
 E2B  C5    C6   C11   120.03  3.000
 E2B  C7    C6   C11   121.83  3.000
 E2B  H12A  C12  H12   105.84  3.000
 E2B  H12A  C12  C13   110.89  3.000
 E2B  H12   C12  C13   107.82  3.000
 E2B  H12A  C12  C10   109.30  3.000
 E2B  H12   C12  C10   110.21  3.000
 E2B  C13   C12  C10   112.56  3.000
 E2B  H17   C17  C21   106.90  3.000
 E2B  H17   C17  C18   107.96  3.000
 E2B  C21   C17  C18   114.56  3.000
 E2B  H17   C17  C16   108.89  3.000
 E2B  C21   C17  C16   113.43  3.000
 E2B  C18   C17  C16   104.91  3.000
 E2B  H18   C18  O19   109.31  3.000
 E2B  H18   C18  C17   107.12  3.000
 E2B  O19   C18  C17   115.59  3.000
 E2B  H18   C18  C14   106.69  3.000
 E2B  O19   C18  C14   112.22  3.000
 E2B  C17   C18  C14   105.41  3.000
 E2B  C23   C24  C25   119.27  3.000
 E2B  C23   C24  C28   117.95  3.000
 E2B  C25   C24  C28   122.77  3.000
 E2B  H1    C1   C2    117.50  3.000
 E2B  H1    C1   C11   119.93  3.000
 E2B  C2    C1   C11   122.57  3.000
 E2B  H26   C26  C27   119.92  3.000
 E2B  H26   C26  C25   119.80  3.000
 E2B  C27   C26  C25   120.29  3.000
 E2B  H23   C23  C22   119.46  3.000
 E2B  H23   C23  C24   118.95  3.000
 E2B  C22   C23  C24   121.59  3.000
 E2B  H27   C27  C22   119.66  3.000
 E2B  H27   C27  C26   119.41  3.000
 E2B  C22   C27  C26   120.92  3.000
 E2B  H7A   C7   H7    105.71  3.000
 E2B  H7A   C7   C6    108.44  3.000
 E2B  H7    C7   C6    109.64  3.000
 E2B  H7A   C7   C8    108.81  3.000
 E2B  H7    C7   C8    110.60  3.000
 E2B  C6    C7   C8    113.34  3.000
 E2B  O4    C3   C2    117.99  3.000
 E2B  O4    C3   C5    122.98  3.000
 E2B  C2    C3   C5    119.04  3.000
 E2B  C27   C22  C23   118.17  3.000
 E2B  C27   C22  C21   121.44  3.000
 E2B  C23   C22  C21   120.38  3.000
 E2B  H5    C5   C3    119.91  3.000
 E2B  H5    C5   C6    118.65  3.000
 E2B  C3    C5   C6    121.44  3.000
 E2B  H2    C2   C3    120.21  3.000
 E2B  H2    C2   C1    120.39  3.000
 E2B  C3    C2   C1    119.40  3.000
 E2B  HO4   O4   C3    110.30  3.000
 E2B  HO19  O19  C18   108.20  3.000
 E2B  H21A  C21  H21   106.28  3.000
 E2B  H21A  C21  C22   109.48  3.000
 E2B  H21   C21  C22   109.02  3.000
 E2B  H21A  C21  C17   110.32  3.000
 E2B  H21   C21  C17   110.01  3.000
 E2B  C22   C21  C17   111.58  3.000
 E2B  H20B  C20  H20A  106.93  3.000
 E2B  H20B  C20  H20   106.72  3.000
 E2B  H20A  C20  H20   107.24  3.000
 E2B  H20B  C20  C14   111.97  3.000
 E2B  H20A  C20  C14   110.29  3.000
 E2B  H20   C20  C14   113.36  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
 E2B  CONST_01  C3    C5   C6   C11    0.00   0.0  0
 E2B  CONST_02  C3    C2   C1   C11    0.00   0.0  0
 E2B  CONST_03  C22   C23  C24  C25    0.00   0.0  0
 E2B  CONST_04  C22   C27  C26  C25    0.00   0.0  0
 E2B  CONST_05  C2    C1   C11  C6     0.00   0.0  0
 E2B  CONST_06  C2    C3   C5   C6     0.00   0.0  0
 E2B  CONST_07  C27   C26  C25  C24    0.00   0.0  0
 E2B  CONST_08  C27   C22  C23  C24    0.00   0.0  0
 E2B  CONST_09  C5    C6   C11  C1     0.00   0.0  0
 E2B  CONST_10  C5    C3   C2   C1     0.00   0.0  0
 E2B  CONST_11  C23   C24  C25  C26    0.00   0.0  0
 E2B  CONST_12  C23   C22  C27  C26    0.00   0.0  0
 E2B  CONST_13  C26   C25  C24  C28  180.00   0.0  0
 E2B  CONST_14  C22   C23  C24  C28  180.00   0.0  0
 E2B  CONST_15  O4    C3   C5   C6   180.00   0.0  0
 E2B  CONST_16  C21   C22  C23  C24  180.00   0.0  0
 E2B  CONST_17  O4    C3   C2   C1   180.00   0.0  0
 E2B  CONST_18  C21   C22  C27  C26  180.00   0.0  0
 E2B  CONST_19  H1    C1   C11  C10    0.00   0.0  0
 E2B  CONST_20  H5    C5   C6   C11  180.00   0.0  0
 E2B  CONST_21  H2    C2   C1   C11  180.00   0.0  0
 E2B  CONST_22  H23   C23  C24  C25  180.00   0.0  0
 E2B  CONST_23  H27   C27  C26  C25  180.00   0.0  0
 E2B  CONST_24  H26   C26  C25  C24  180.00   0.0  0
 E2B  CONST_25  H25   C25  C24  C23  180.00   0.0  0
 E2B  CONST_26  HN30  N30  C28  C24    0.00   0.0  0
 E2B  CONST_27  HN3A  N30  C28  C24  180.00   0.0  0
 E2B  Var_01    C6    C7   C8   C9    46.56  30.0  1
 E2B  Var_02    C14   C13  C12  C10  -52.96  30.0  1
 E2B  Var_03    C11   C6   C7   C8   -15.86  30.0  1
 E2B  Var_04    C23   C22  C21  C17   74.41  30.0  2
 E2B  Var_05    C25   C24  C28  N30  -19.65  30.0  2

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
 E2B  chir_01  C9   C10  C15  C8   positiv
 E2B  chir_02  C10  C12  C11  C9   positiv
 E2B  chir_03  C15  C9   C14  C16  negativ
 E2B  chir_04  C14  C13  C18  C15  positiv
 E2B  chir_05  C17  C16  C18  C21  negativ
 E2B  chir_06  C18  O19  C17  C14  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
 E2B  plan-1  C28   0.020
 E2B  plan-1  C25   0.020
 E2B  plan-1  C24   0.020
 E2B  plan-1  C26   0.020
 E2B  plan-1  C23   0.020
 E2B  plan-1  C27   0.020
 E2B  plan-1  C22   0.020
 E2B  plan-1  H25   0.020
 E2B  plan-1  H26   0.020
 E2B  plan-1  H23   0.020
 E2B  plan-1  H27   0.020
 E2B  plan-1  C21   0.020
 E2B  plan-2  C10   0.020
 E2B  plan-2  C11   0.020
 E2B  plan-2  C6    0.020
 E2B  plan-2  C1    0.020
 E2B  plan-2  C7    0.020
 E2B  plan-2  C3    0.020
 E2B  plan-2  C5    0.020
 E2B  plan-2  C2    0.020
 E2B  plan-2  O4    0.020
 E2B  plan-2  H1    0.020
 E2B  plan-2  H5    0.020
 E2B  plan-2  H2    0.020
 E2B  plan-3  N30   0.020
 E2B  plan-3  C28   0.020
 E2B  plan-3  C24   0.020
 E2B  plan-3  O29   0.020
 E2B  plan-3  HN30  0.020
 E2B  plan-3  HN3A  0.020

