# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 19:53:30 2020
#   Inital geometry file: a 171 line input string
#   Ligand name: (1S,3R,5Z,7E,14beta,17alpha)-17-[(2S,4S)-4-(2-hydroxy-2-methylpropyl)-2-methyltetrahydrofuran-2-yl]-9,10-secoandrosta-5,7,10-triene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)C[C@@H]1CO[C@@](C)(C1)[C@H]2CC[C@H]3C(/CCC[C@]23C)=C/C=C4/C[C@@H](O)C[C@H](O)C4=C
#
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
 COV  COV  (1S,3R,5Z,7E,14beta,17alpha)-17-[(2S,4S)-4-(2-hydroxy-2-methylpropyl)-2-methyltetrahydrofuran-2-yl]-9,10-secoandrosta-5,7,10-triene-1,3-diol  ligand  76  32  .  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_COV
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
 COV  C1    C  CH1   0  -0.030  -5.8068  -2.3345  -0.8167
 COV  C20   C  CT    0   0.250   3.1831   1.0491   0.4208
 COV  C2    C  CH2   0  -0.488  -7.2222  -2.0590  -0.3291
 COV  C25   C  CT    0   0.204   7.2998  -1.7468   0.0125
 COV  C26   C  CH3   0  -0.667   8.2029  -2.3645  -1.0561
 COV  C27   C  CH3   0  -0.684   8.1514  -0.9530   1.0022
 COV  C3    C  CH1   0   0.070  -7.2653  -0.9245   0.6834
 COV  C4    C  CH2   0  -0.533  -6.6552   0.3416   0.0786
 COV  C5    C  C     0   0.104  -5.2666   0.0959  -0.4498
 COV  C6    C  C1    0  -0.304  -4.2367   0.8922  -0.1147
 COV  C7    C  C1    0  -0.366  -2.8485   0.7163  -0.4982
 COV  C8    C  C     0   0.154  -1.8693   1.6249  -0.3640
 COV  C9    C  CH2   0  -0.504  -2.0473   3.0335   0.1336
 COV  C10   C  C     0   0.066  -5.1690  -1.0705  -1.3468
 COV  C11   C  CH2   0  -0.436  -1.0238   3.4049   1.2111
 COV  C12   C  CH2   0  -0.418   0.4131   3.0623   0.8157
 COV  C13   C  CT    0  -0.073   0.5554   1.5991   0.3856
 COV  C14   C  CH1   0  -0.243  -0.4539   1.3565  -0.7658
 COV  C15   C  CH2   0  -0.454  -0.0494   0.0058  -1.3333
 COV  C16   C  CH2   0  -0.444   1.4884   0.0196  -1.2340
 COV  C17   C  CH1   0  -0.188   1.8693   1.2396  -0.3543
 COV  C18   C  CH3   0  -0.654   0.2720   0.6634   1.5631
 COV  C19   C  C2    0  -0.584  -4.6024  -1.0383  -2.5523
 COV  O3    O  OH1   0  -0.674  -8.6168  -0.7281   1.0456
 COV  C21   C  CH3   0  -0.685   3.4982   2.2315   1.3365
 COV  C22   C  CH2   0  -0.466   4.3568   0.8193  -0.5448
 COV  C23   C  CH1   0  -0.314   5.2910  -0.1026   0.2342
 COV  C24   C  CH2   0  -0.415   6.2546  -0.8604  -0.6694
 COV  C28   C  CH2   0  -0.120   4.2737  -0.9584   0.9833
 COV  O1    O  OH1   0  -0.665  -5.0652  -2.8361   0.2800
 COV  O21   O  O2    0  -0.515   3.1445  -0.1344   1.2210
 COV  O25   O  OH1   0  -0.670   6.5875  -2.7739   0.6896
 COV  H1    H  HCH1  0   0.225  -5.8508  -3.0756  -1.6257
 COV  H2    H  HCH2  0   0.237  -7.8365  -1.7916  -1.1948
 COV  H2A   H  HCH2  0   0.250  -7.6476  -2.9712   0.0982
 COV  H26   H  HCH3  0   0.227   8.9357  -3.0381  -0.6043
 COV  H26A  H  HCH3  0   0.229   7.6198  -2.9368  -1.7801
 COV  H26B  H  HCH3  0   0.222   8.7554  -1.5976  -1.6004
 COV  H27   H  HCH3  0   0.224   8.6320  -0.1030   0.5148
 COV  H27A  H  HCH3  0   0.236   7.5578  -0.5735   1.8349
 COV  H27B  H  HCH3  0   0.229   8.9437  -1.5799   1.4185
 COV  H3    H  HCH1  0   0.206  -6.6731  -1.2077   1.5635
 COV  H4    H  HCH2  0   0.237  -7.3042   0.6662  -0.7448
 COV  H4A   H  HCH2  0   0.245  -6.6420   1.1460   0.8189
 COV  H6    H  H     0   0.234  -4.4678   1.7297   0.5365
 COV  H7    H  H     0   0.234  -2.5894  -0.2456  -0.9277
 COV  H9    H  HCH2  0   0.232  -1.9116   3.7077  -0.7216
 COV  H9A   H  HCH2  0   0.243  -3.0565   3.2176   0.5028
 COV  H11   H  HCH2  0   0.233  -1.0981   4.4748   1.4197
 COV  H11A  H  HCH2  0   0.222  -1.2856   2.8989   2.1437
 COV  H12   H  HCH2  0   0.211   0.7234   3.7045  -0.0173
 COV  H12A  H  HCH2  0   0.231   1.0750   3.3033   1.6487
 COV  H14   H  HCH1  0   0.230  -0.2092   2.1142  -1.5278
 COV  H15   H  HCH2  0   0.221  -0.4684  -0.8106  -0.7408
 COV  H15A  H  HCH2  0   0.233  -0.4010  -0.1373  -2.3565
 COV  H16   H  HCH2  0   0.232   1.8553  -0.9118  -0.8010
 COV  H16A  H  HCH2  0   0.229   1.9389   0.1022  -2.2235
 COV  H17   H  HCH1  0   0.220   2.0620   2.0834  -1.0309
 COV  H18   H  HCH3  0   0.224  -0.7557   0.7680   1.9128
 COV  H18A  H  HCH3  0   0.230   0.4208  -0.3855   1.3094
 COV  H18B  H  HCH3  0   0.225   0.9285   0.8840   2.4054
 COV  H19   H  H     0   0.244  -4.5757  -1.9197  -3.1820
 COV  H19A  H  H     0   0.245  -4.1633  -0.1354  -2.9564
 COV  HO3   H  HOH1  0   0.449  -8.6458  -0.0844   1.7603
 COV  H21   H  HCH3  0   0.232   2.8214   2.2722   2.1893
 COV  H21A  H  HCH3  0   0.236   4.5137   2.1538   1.7311
 COV  H21B  H  HCH3  0   0.219   3.4245   3.1795   0.8017
 COV  H22   H  HCH2  0   0.240   4.0274   0.3119  -1.4563
 COV  H22A  H  HCH2  0   0.246   4.8297   1.7551  -0.8472
 COV  H23   H  HCH1  0   0.240   5.8603   0.4975   0.9517
 COV  H24   H  HCH2  0   0.231   6.7923  -0.1327  -1.2853
 COV  H24A  H  HCH2  0   0.222   5.6744  -1.4769  -1.3672
 COV  H28   H  HCH2  0   0.186   3.9852  -1.8258   0.3746
 COV  H28A  H  HCH2  0   0.213   4.6471  -1.3341   1.9375
 COV  HO1   H  HOH1  0   0.449  -4.1548  -2.9617  -0.0062
 COV  HO25  H  HOH1  0   0.442   7.2244  -3.3203   1.1624

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
 COV  C1   C2    single  1.522  0.020  1.522
 COV  C1   C10   single  1.512  0.020  1.512
 COV  C1   O1    single  1.416  0.020  1.416
 COV  C20  C17   single  1.537  0.020  1.537
 COV  C20  C21   single  1.528  0.020  1.528
 COV  C20  C22   single  1.537  0.020  1.537
 COV  C20  O21   single  1.429  0.020  1.429
 COV  C2   C3    single  1.521  0.020  1.521
 COV  C25  C26   single  1.529  0.020  1.529
 COV  C25  C27   single  1.528  0.020  1.528
 COV  C25  C24   single  1.531  0.020  1.531
 COV  C25  O25   single  1.422  0.020  1.422
 COV  C3   C4    single  1.530  0.020  1.530
 COV  C3   O3    single  1.413  0.020  1.413
 COV  C4   C5    single  1.506  0.020  1.506
 COV  C5   C6    double  1.344  0.020  1.344
 COV  C5   C10   single  1.475  0.020  1.475
 COV  C6   C7    single  1.451  0.020  1.451
 COV  C7   C8    double  1.343  0.020  1.343
 COV  C8   C9    single  1.504  0.020  1.504
 COV  C8   C14   single  1.496  0.020  1.496
 COV  C9   C11   single  1.532  0.020  1.532
 COV  C10  C19   double  1.332  0.020  1.332
 COV  C11  C12   single  1.529  0.020  1.529
 COV  C12  C13   single  1.532  0.020  1.532
 COV  C13  C14   single  1.550  0.020  1.550
 COV  C13  C17   single  1.550  0.020  1.550
 COV  C13  C18   single  1.530  0.020  1.530
 COV  C14  C15   single  1.520  0.020  1.520
 COV  C15  C16   single  1.541  0.020  1.541
 COV  C16  C17   single  1.552  0.020  1.552
 COV  C22  C23   single  1.526  0.020  1.526
 COV  C23  C24   single  1.523  0.020  1.523
 COV  C23  C28   single  1.526  0.020  1.526
 COV  C28  O21   single  1.418  0.020  1.418
 COV  C1   H1    single  0.970  0.020  1.090
 COV  C2   H2    single  0.970  0.020  1.090
 COV  C2   H2A   single  0.970  0.020  1.090
 COV  C26  H26   single  0.970  0.020  1.090
 COV  C26  H26A  single  0.970  0.020  1.090
 COV  C26  H26B  single  0.970  0.020  1.090
 COV  C27  H27   single  0.970  0.020  1.090
 COV  C27  H27A  single  0.970  0.020  1.090
 COV  C27  H27B  single  0.970  0.020  1.090
 COV  C3   H3    single  0.970  0.020  1.090
 COV  C4   H4    single  0.970  0.020  1.090
 COV  C4   H4A   single  0.970  0.020  1.090
 COV  C6   H6    single  0.930  0.020  1.080
 COV  C7   H7    single  0.930  0.020  1.080
 COV  C9   H9    single  0.970  0.020  1.090
 COV  C9   H9A   single  0.970  0.020  1.090
 COV  C11  H11   single  0.970  0.020  1.090
 COV  C11  H11A  single  0.970  0.020  1.090
 COV  C12  H12   single  0.970  0.020  1.090
 COV  C12  H12A  single  0.970  0.020  1.090
 COV  C14  H14   single  0.970  0.020  1.090
 COV  C15  H15   single  0.970  0.020  1.090
 COV  C15  H15A  single  0.970  0.020  1.090
 COV  C16  H16   single  0.970  0.020  1.090
 COV  C16  H16A  single  0.970  0.020  1.090
 COV  C17  H17   single  0.970  0.020  1.090
 COV  C18  H18   single  0.970  0.020  1.090
 COV  C18  H18A  single  0.970  0.020  1.090
 COV  C18  H18B  single  0.970  0.020  1.090
 COV  C19  H19   single  0.930  0.020  1.080
 COV  C19  H19A  single  0.930  0.020  1.080
 COV  O3   HO3   single  0.850  0.020  0.980
 COV  C21  H21   single  0.970  0.020  1.090
 COV  C21  H21A  single  0.970  0.020  1.090
 COV  C21  H21B  single  0.970  0.020  1.090
 COV  C22  H22   single  0.970  0.020  1.090
 COV  C22  H22A  single  0.970  0.020  1.090
 COV  C23  H23   single  0.970  0.020  1.090
 COV  C24  H24   single  0.970  0.020  1.090
 COV  C24  H24A  single  0.970  0.020  1.090
 COV  C28  H28   single  0.970  0.020  1.090
 COV  C28  H28A  single  0.970  0.020  1.090
 COV  O1   HO1   single  0.850  0.020  0.980
 COV  O25  HO25  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
 COV  H1    C1   O1    110.65  3.000
 COV  H1    C1   C10   108.83  3.000
 COV  O1    C1   C10   110.30  3.000
 COV  H1    C1   C2    108.72  3.000
 COV  O1    C1   C2    107.64  3.000
 COV  C10   C1   C2    110.69  3.000
 COV  O21   C20  C22   104.39  3.000
 COV  O21   C20  C21   108.10  3.000
 COV  C22   C20  C21   109.55  3.000
 COV  O21   C20  C17   111.21  3.000
 COV  C22   C20  C17   110.76  3.000
 COV  C21   C20  C17   112.48  3.000
 COV  H2A   C2   H2    107.12  3.000
 COV  H2A   C2   C3    110.55  3.000
 COV  H2    C2   C3    109.16  3.000
 COV  H2A   C2   C1    109.63  3.000
 COV  H2    C2   C1    108.23  3.000
 COV  C3    C2   C1    112.00  3.000
 COV  O25   C25  C24   106.76  3.000
 COV  O25   C25  C27   110.25  3.000
 COV  C24   C25  C27   111.61  3.000
 COV  O25   C25  C26   109.68  3.000
 COV  C24   C25  C26   109.01  3.000
 COV  C27   C25  C26   109.47  3.000
 COV  H26B  C26  H26A  107.95  3.000
 COV  H26B  C26  H26   107.45  3.000
 COV  H26A  C26  H26   108.01  3.000
 COV  H26B  C26  C25   111.33  3.000
 COV  H26A  C26  C25   111.09  3.000
 COV  H26   C26  C25   110.85  3.000
 COV  H27B  C27  H27A  107.66  3.000
 COV  H27B  C27  H27   107.32  3.000
 COV  H27A  C27  H27   108.04  3.000
 COV  H27B  C27  C25   110.66  3.000
 COV  H27A  C27  C25   111.84  3.000
 COV  H27   C27  C25   111.15  3.000
 COV  H3    C3   O3    110.26  3.000
 COV  H3    C3   C4    108.38  3.000
 COV  O3    C3   C4    111.58  3.000
 COV  H3    C3   C2    109.01  3.000
 COV  O3    C3   C2    107.54  3.000
 COV  C4    C3   C2    110.04  3.000
 COV  H4A   C4   H4    107.31  3.000
 COV  H4A   C4   C5    110.27  3.000
 COV  H4    C4   C5    109.29  3.000
 COV  H4A   C4   C3    110.24  3.000
 COV  H4    C4   C3    107.79  3.000
 COV  C5    C4   C3    111.80  3.000
 COV  C10   C5   C6    124.71  3.000
 COV  C10   C5   C4    113.80  3.000
 COV  C6    C5   C4    121.49  3.000
 COV  H6    C6   C7    117.11  3.000
 COV  H6    C6   C5    116.32  3.000
 COV  C7    C6   C5    126.54  3.000
 COV  H7    C7   C8    117.74  3.000
 COV  H7    C7   C6    116.14  3.000
 COV  C8    C7   C6    126.12  3.000
 COV  C14   C8   C9    111.64  3.000
 COV  C14   C8   C7    122.82  3.000
 COV  C9    C8   C7    125.48  3.000
 COV  H9A   C9   H9    105.94  3.000
 COV  H9A   C9   C11   109.84  3.000
 COV  H9    C9   C11   108.45  3.000
 COV  H9A   C9   C8    112.31  3.000
 COV  H9    C9   C8    107.63  3.000
 COV  C11   C9   C8    112.37  3.000
 COV  C19   C10  C5    124.01  3.000
 COV  C19   C10  C1    121.12  3.000
 COV  C5    C10  C1    114.84  3.000
 COV  H11A  C11  H11   105.91  3.000
 COV  H11A  C11  C12   110.00  3.000
 COV  H11   C11  C12   109.43  3.000
 COV  H11A  C11  C9    109.15  3.000
 COV  H11   C11  C9    109.05  3.000
 COV  C12   C11  C9    113.05  3.000
 COV  H12A  C12  H12   106.19  3.000
 COV  H12A  C12  C13   111.66  3.000
 COV  H12   C12  C13   108.65  3.000
 COV  H12A  C12  C11   108.86  3.000
 COV  H12   C12  C11   109.34  3.000
 COV  C13   C12  C11   111.96  3.000
 COV  C18   C13  C17   112.48  3.000
 COV  C18   C13  C14   110.81  3.000
 COV  C17   C13  C14    99.27  3.000
 COV  C18   C13  C12   110.53  3.000
 COV  C17   C13  C12   115.74  3.000
 COV  C14   C13  C12   107.31  3.000
 COV  H14   C14  C15   107.08  3.000
 COV  H14   C14  C13   105.16  3.000
 COV  C15   C14  C13   104.07  3.000
 COV  H14   C14  C8    105.81  3.000
 COV  C15   C14  C8    120.77  3.000
 COV  C13   C14  C8    112.87  3.000
 COV  H15A  C15  H15   106.68  3.000
 COV  H15A  C15  C16   112.52  3.000
 COV  H15   C15  C16   110.76  3.000
 COV  H15A  C15  C14   112.39  3.000
 COV  H15   C15  C14   111.07  3.000
 COV  C16   C15  C14   103.51  3.000
 COV  H16A  C16  H16   106.62  3.000
 COV  H16A  C16  C17   110.70  3.000
 COV  H16   C16  C17   111.33  3.000
 COV  H16A  C16  C15   110.76  3.000
 COV  H16   C16  C15   110.71  3.000
 COV  C17   C16  C15   106.77  3.000
 COV  H17   C17  C16   107.32  3.000
 COV  H17   C17  C13   105.34  3.000
 COV  C16   C17  C13   104.18  3.000
 COV  H17   C17  C20   104.82  3.000
 COV  C16   C17  C20   113.47  3.000
 COV  C13   C17  C20   120.83  3.000
 COV  H18B  C18  H18A  107.00  3.000
 COV  H18B  C18  H18   107.48  3.000
 COV  H18A  C18  H18   107.20  3.000
 COV  H18B  C18  C13   111.05  3.000
 COV  H18A  C18  C13   112.59  3.000
 COV  H18   C18  C13   111.26  3.000
 COV  H19A  C19  H19   116.85  3.000
 COV  H19A  C19  C10   122.04  3.000
 COV  H19   C19  C10   121.11  3.000
 COV  HO3   O3   C3    108.20  3.000
 COV  H21B  C21  H21A  107.57  3.000
 COV  H21B  C21  H21   108.02  3.000
 COV  H21A  C21  H21   107.30  3.000
 COV  H21B  C21  C20   111.38  3.000
 COV  H21A  C21  C20   110.67  3.000
 COV  H21   C21  C20   111.70  3.000
 COV  H22A  C22  H22   107.30  3.000
 COV  H22A  C22  C23   113.21  3.000
 COV  H22   C22  C23   109.24  3.000
 COV  H22A  C22  C20   112.13  3.000
 COV  H22   C22  C20   111.27  3.000
 COV  C23   C22  C20   103.71  3.000
 COV  H23   C23  C28   109.41  3.000
 COV  H23   C23  C24   109.43  3.000
 COV  C28   C23  C24   115.72  3.000
 COV  H23   C23  C22   108.76  3.000
 COV  C28   C23  C22   100.44  3.000
 COV  C24   C23  C22   112.64  3.000
 COV  H24A  C24  H24   105.99  3.000
 COV  H24A  C24  C23   108.81  3.000
 COV  H24   C24  C23   108.29  3.000
 COV  H24A  C24  C25   108.61  3.000
 COV  H24   C24  C25   107.47  3.000
 COV  C23   C24  C25   117.12  3.000
 COV  H28A  C28  H28   107.61  3.000
 COV  H28A  C28  O21   109.03  3.000
 COV  H28   C28  O21   110.04  3.000
 COV  H28A  C28  C23   113.21  3.000
 COV  H28   C28  C23   110.24  3.000
 COV  O21   C28  C23   106.70  3.000
 COV  HO1   O1   C1    108.14  3.000
 COV  C28   O21  C20   111.46  3.000
 COV  HO25  O25  C25   108.20  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
 COV  Var_01  C4   C5   C10  C1    -48.96  30.0  1
 COV  Var_02  C23  C28  O21  C20    14.66  30.0  1
 COV  Var_03  C10  C5   C4   C3     50.75  30.0  1
 COV  Var_04  C12  C11  C9   C8     49.24  30.0  1
 COV  Var_05  C13  C12  C11  C9    -53.01  30.0  1
 COV  Var_06  C14  C8   C9   C11   -51.06  30.0  1
 COV  Var_07  C17  C16  C15  C14    11.42  30.0  1
 COV  Var_08  C7   C6   C5   C4    176.40  30.0  2
 COV  Var_09  C8   C7   C6   C5    167.51  30.0  2
 COV  Var_10  C9   C8   C7   C6     -4.04  30.0  2
 COV  Var_11  H19  C19  C10  C1     -0.54  30.0  2
 COV  Var_12  C23  C24  C25  C26  -177.43  30.0  3
 COV  Var_13  H27  C27  C25  C26    64.56  30.0  3
 COV  Var_14  H26  C26  C25  C27    60.05  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
 COV  chir_01  C1   C2   C10  O1   negativ
 COV  chir_02  C20  C17  C22  O21  positiv
 COV  chir_03  C3   C2   C4   O3   negativ
 COV  chir_04  C13  C14  C17  C12  negativ
 COV  chir_05  C14  C8   C13  C15  negativ
 COV  chir_06  C17  C16  C13  C20  negativ
 COV  chir_07  C23  C28  C24  C22  negativ

