# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:02:30 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (1R,3R,7E,17beta)-2-methylidene-17-[(1S)-1-methylpropyl]-9,10-secoestra-5,7-diene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3
#
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
 VD1  VD1  (1R,3R,7E,17beta)-2-methylidene-17-[(1S)-1-methylpropyl]-9,10-secoestra-5,7-diene-1,3-diol  ligand  61  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VD1
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
 VD1  O2    O  OH1   0  -0.664   5.2764  -1.2653  -1.4373
 VD1  C3    C  CH1   0   0.000   5.5690  -0.9790  -0.0832
 VD1  C2    C  C     0   0.064   5.8341   0.4911   0.1273
 VD1  C28   C  C2    0  -0.604   6.9931   0.9299   0.6053
 VD1  C1    C  CH1   0   0.049   4.6621   1.3837  -0.1954
 VD1  O1    O  OH1   0  -0.665   4.8982   2.7449   0.0587
 VD1  C4    C  CH2   0  -0.512   4.3543  -1.3939   0.7451
 VD1  C5    C  C     0   0.117   3.1722  -0.5124   0.4628
 VD1  C10   C  CH2   0  -0.528   3.4524   0.9521   0.6416
 VD1  C6    C  C1    0  -0.330   1.9952  -1.0347   0.0841
 VD1  C7    C  C1    0  -0.369   0.7754  -0.3046  -0.2108
 VD1  C8    C  C     0   0.159  -0.4061  -0.8391  -0.5598
 VD1  C9    C  CH2   0  -0.505  -0.6916  -2.3086  -0.7092
 VD1  C11   C  CH2   0  -0.433  -1.9133  -2.7340   0.1123
 VD1  C12   C  CH2   0  -0.420  -3.1338  -1.8478  -0.1352
 VD1  C13   C  CT    0  -0.064  -2.8164  -0.3643   0.0752
 VD1  C18   C  CH3   0  -0.676  -2.4740  -0.0813   1.5392
 VD1  C14   C  CH1   0  -0.245  -1.6211  -0.0146  -0.8499
 VD1  C15   C  CH2   0  -0.456  -1.5562   1.5038  -0.8204
 VD1  C17   C  CH1   0  -0.160  -3.8655   0.6423  -0.4591
 VD1  C16   C  CH2   0  -0.446  -3.0353   1.9258  -0.7330
 VD1  C20   C  CH1   0  -0.229  -5.1278   0.9431   0.3644
 VD1  C21   C  CH3   0  -0.672  -5.9891   1.9588  -0.3891
 VD1  C22   C  CH2   0  -0.413  -5.9461  -0.3044   0.7071
 VD1  C23   C  CH3   0  -0.669  -7.2065  -0.0292   1.5203
 VD1  HO2   H  HOH1  0   0.451   6.0333  -0.9979  -1.9685
 VD1  H3    H  HCH1  0   0.226   6.4425  -1.5508   0.2575
 VD1  H281  H  H     0   0.240   7.7982   0.2410   0.8301
 VD1  H282  H  H     0   0.238   7.1902   1.9767   0.7962
 VD1  H1    H  HCH1  0   0.220   4.4013   1.2302  -1.2525
 VD1  HO1   H  HOH1  0   0.454   5.5650   3.0581  -0.5607
 VD1  H41   H  HCH2  0   0.252   4.1177  -2.4441   0.5575
 VD1  H42   H  HCH2  0   0.248   4.6355  -1.3125   1.8011
 VD1  H101  H  HCH2  0   0.244   3.6821   1.1483   1.6964
 VD1  H102  H  HCH2  0   0.256   2.5959   1.5722   0.3764
 VD1  H6    H  H     0   0.230   1.9526  -2.1156  -0.0035
 VD1  H7    H  H     0   0.230   0.8316   0.7763  -0.1467
 VD1  H91   H  HCH2  0   0.231  -0.9002  -2.5068  -1.7678
 VD1  H92   H  HCH2  0   0.244   0.1638  -2.9290  -0.4417
 VD1  H111  H  HCH2  0   0.233  -2.1613  -3.7706  -0.1277
 VD1  H112  H  HCH2  0   0.221  -1.6548  -2.7217   1.1742
 VD1  H121  H  HCH2  0   0.212  -3.4780  -1.9895  -1.1667
 VD1  H122  H  HCH2  0   0.231  -3.9486  -2.1841   0.5074
 VD1  H181  H  HCH3  0   0.234  -1.6036  -0.6495   1.8688
 VD1  H182  H  HCH3  0   0.232  -2.2491   0.9714   1.7155
 VD1  H183  H  HCH3  0   0.229  -3.3013  -0.3484   2.1983
 VD1  H14   H  HCH1  0   0.231  -1.9515  -0.2992  -1.8625
 VD1  H151  H  HCH2  0   0.221  -0.9994   1.8602   0.0491
 VD1  H152  H  HCH2  0   0.234  -1.0549   1.9097  -1.7006
 VD1  H17   H  HCH1  0   0.205  -4.2028   0.2439  -1.4276
 VD1  H161  H  HCH2  0   0.222  -3.1869   2.6562   0.0660
 VD1  H162  H  HCH2  0   0.232  -3.3628   2.4112  -1.6532
 VD1  H20   H  HCH1  0   0.202  -4.8183   1.4062   1.3108
 VD1  H211  H  HCH3  0   0.231  -6.8774   2.2416   0.1754
 VD1  H212  H  HCH3  0   0.236  -5.4437   2.8778  -0.6010
 VD1  H213  H  HCH3  0   0.210  -6.3230   1.5454  -1.3449
 VD1  H221  H  HCH2  0   0.204  -6.2114  -0.8310  -0.2166
 VD1  H222  H  HCH2  0   0.222  -5.3273  -0.9936   1.2818
 VD1  H231  H  HCH3  0   0.214  -6.9757   0.5530   2.4150
 VD1  H232  H  HCH3  0   0.220  -7.9601   0.5193   0.9558
 VD1  H233  H  HCH3  0   0.228  -7.6648  -0.9635   1.8473

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
 VD1  O2   C3    single  1.415  0.020  1.415
 VD1  O2   HO2   single  0.850  0.020  0.980
 VD1  C3   C2    single  1.509  0.020  1.509
 VD1  C3   C4    single  1.528  0.020  1.528
 VD1  C3   H3    single  0.970  0.020  1.090
 VD1  C2   C28   double  1.328  0.020  1.328
 VD1  C2   C1    single  1.508  0.020  1.508
 VD1  C28  H281  single  0.930  0.020  1.080
 VD1  C28  H282  single  0.930  0.020  1.080
 VD1  C1   O1    single  1.405  0.020  1.405
 VD1  C1   C10   single  1.533  0.020  1.533
 VD1  C1   H1    single  0.970  0.020  1.090
 VD1  O1   HO1   single  0.850  0.020  0.980
 VD1  C4   C5    single  1.501  0.020  1.501
 VD1  C4   H41   single  0.970  0.020  1.090
 VD1  C4   H42   single  0.970  0.020  1.090
 VD1  C5   C10   single  1.502  0.020  1.502
 VD1  C5   C6    double  1.342  0.020  1.342
 VD1  C10  H101  single  0.970  0.020  1.090
 VD1  C10  H102  single  0.970  0.020  1.090
 VD1  C6   C7    single  1.452  0.020  1.452
 VD1  C6   H6    single  0.930  0.020  1.080
 VD1  C7   C8    double  1.343  0.020  1.343
 VD1  C7   H7    single  0.930  0.020  1.080
 VD1  C8   C9    single  1.504  0.020  1.504
 VD1  C8   C14   single  1.497  0.020  1.497
 VD1  C9   C11   single  1.533  0.020  1.533
 VD1  C9   H91   single  0.970  0.020  1.090
 VD1  C9   H92   single  0.970  0.020  1.090
 VD1  C11  C12   single  1.528  0.020  1.528
 VD1  C11  H111  single  0.970  0.020  1.090
 VD1  C11  H112  single  0.970  0.020  1.090
 VD1  C12  C13   single  1.532  0.020  1.532
 VD1  C12  H121  single  0.970  0.020  1.090
 VD1  C12  H122  single  0.970  0.020  1.090
 VD1  C13  C18   single  1.530  0.020  1.530
 VD1  C13  C14   single  1.551  0.020  1.551
 VD1  C13  C17   single  1.549  0.020  1.549
 VD1  C18  H181  single  0.970  0.020  1.090
 VD1  C18  H182  single  0.970  0.020  1.090
 VD1  C18  H183  single  0.970  0.020  1.090
 VD1  C14  C15   single  1.520  0.020  1.520
 VD1  C14  H14   single  0.970  0.020  1.090
 VD1  C15  C16   single  1.541  0.020  1.541
 VD1  C15  H151  single  0.970  0.020  1.090
 VD1  C15  H152  single  0.970  0.020  1.090
 VD1  C17  C16   single  1.553  0.020  1.553
 VD1  C17  C20   single  1.537  0.020  1.537
 VD1  C17  H17   single  0.970  0.020  1.090
 VD1  C16  H161  single  0.970  0.020  1.090
 VD1  C16  H162  single  0.970  0.020  1.090
 VD1  C20  C21   single  1.530  0.020  1.530
 VD1  C20  C22   single  1.531  0.020  1.531
 VD1  C20  H20   single  0.970  0.020  1.090
 VD1  C21  H211  single  0.970  0.020  1.090
 VD1  C21  H212  single  0.970  0.020  1.090
 VD1  C21  H213  single  0.970  0.020  1.090
 VD1  C22  C23   single  1.525  0.020  1.525
 VD1  C22  H221  single  0.970  0.020  1.090
 VD1  C22  H222  single  0.970  0.020  1.090
 VD1  C23  H231  single  0.970  0.020  1.090
 VD1  C23  H232  single  0.970  0.020  1.090
 VD1  C23  H233  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
 VD1  HO2   O2   C3    108.02  3.000
 VD1  H3    C3   C4    108.83  3.000
 VD1  H3    C3   C2    108.92  3.000
 VD1  C4    C3   C2    109.19  3.000
 VD1  H3    C3   O2    110.86  3.000
 VD1  C4    C3   O2    107.43  3.000
 VD1  C2    C3   O2    111.54  3.000
 VD1  C1    C2   C28   124.02  3.000
 VD1  C1    C2   C3    114.22  3.000
 VD1  C28   C2   C3    121.71  3.000
 VD1  H282  C28  H281  116.31  3.000
 VD1  H282  C28  C2    122.82  3.000
 VD1  H281  C28  C2    120.87  3.000
 VD1  H1    C1   C10   107.36  3.000
 VD1  H1    C1   O1    110.43  3.000
 VD1  C10   C1   O1    107.86  3.000
 VD1  H1    C1   C2    107.90  3.000
 VD1  C10   C1   C2    109.25  3.000
 VD1  O1    C1   C2    113.84  3.000
 VD1  HO1   O1   C1    108.38  3.000
 VD1  H42   C4   H41   107.00  3.000
 VD1  H42   C4   C5    109.86  3.000
 VD1  H41   C4   C5    111.19  3.000
 VD1  H42   C4   C3    107.35  3.000
 VD1  H41   C4   C3    109.88  3.000
 VD1  C5    C4   C3    111.38  3.000
 VD1  C6    C5   C10   125.22  3.000
 VD1  C6    C5   C4    120.99  3.000
 VD1  C10   C5   C4    113.78  3.000
 VD1  H102  C10  H101  107.25  3.000
 VD1  H102  C10  C5    112.29  3.000
 VD1  H101  C10  C5    109.14  3.000
 VD1  H102  C10  C1    109.08  3.000
 VD1  H101  C10  C1    108.02  3.000
 VD1  C5    C10  C1    110.91  3.000
 VD1  H6    C6   C7    116.84  3.000
 VD1  H6    C6   C5    116.41  3.000
 VD1  C7    C6   C5    126.75  3.000
 VD1  H7    C7   C8    117.25  3.000
 VD1  H7    C7   C6    116.47  3.000
 VD1  C8    C7   C6    126.28  3.000
 VD1  C14   C8   C9    111.39  3.000
 VD1  C14   C8   C7    123.05  3.000
 VD1  C9    C8   C7    125.56  3.000
 VD1  H92   C9   H91   106.45  3.000
 VD1  H92   C9   C11   109.63  3.000
 VD1  H91   C9   C11   108.39  3.000
 VD1  H92   C9   C8    112.50  3.000
 VD1  H91   C9   C8    107.97  3.000
 VD1  C11   C9   C8    111.66  3.000
 VD1  H112  C11  H111  106.13  3.000
 VD1  H112  C11  C12   109.86  3.000
 VD1  H111  C11  C12   109.47  3.000
 VD1  H112  C11  C9    109.22  3.000
 VD1  H111  C11  C9    109.06  3.000
 VD1  C12   C11  C9    112.88  3.000
 VD1  H122  C12  H121  106.25  3.000
 VD1  H122  C12  C13   111.87  3.000
 VD1  H121  C12  C13   108.63  3.000
 VD1  H122  C12  C11   108.80  3.000
 VD1  H121  C12  C11   109.15  3.000
 VD1  C13   C12  C11   111.95  3.000
 VD1  C17   C13  C14    99.77  3.000
 VD1  C17   C13  C18   111.19  3.000
 VD1  C14   C13  C18   110.88  3.000
 VD1  C17   C13  C12   116.21  3.000
 VD1  C14   C13  C12   107.22  3.000
 VD1  C18   C13  C12   110.92  3.000
 VD1  H183  C18  H182  107.15  3.000
 VD1  H183  C18  H181  107.16  3.000
 VD1  H182  C18  H181  106.82  3.000
 VD1  H183  C18  C13   111.29  3.000
 VD1  H182  C18  C13   112.29  3.000
 VD1  H181  C18  C13   111.81  3.000
 VD1  H14   C14  C15   106.77  3.000
 VD1  H14   C14  C13   104.98  3.000
 VD1  C15   C14  C13   104.27  3.000
 VD1  H14   C14  C8    106.21  3.000
 VD1  C15   C14  C8    120.79  3.000
 VD1  C13   C14  C8    112.69  3.000
 VD1  H152  C15  H151  106.65  3.000
 VD1  H152  C15  C16   112.64  3.000
 VD1  H151  C15  C16   110.78  3.000
 VD1  H152  C15  C14   112.06  3.000
 VD1  H151  C15  C14   111.29  3.000
 VD1  C16   C15  C14   103.52  3.000
 VD1  H17   C17  C20   106.91  3.000
 VD1  H17   C17  C16   107.93  3.000
 VD1  C20   C17  C16   111.83  3.000
 VD1  H17   C17  C13   106.02  3.000
 VD1  C20   C17  C13   119.91  3.000
 VD1  C16   C17  C13   103.64  3.000
 VD1  H162  C16  H161  106.12  3.000
 VD1  H162  C16  C17   110.86  3.000
 VD1  H161  C16  C17   110.44  3.000
 VD1  H162  C16  C15   111.24  3.000
 VD1  H161  C16  C15   110.96  3.000
 VD1  C17   C16  C15   107.27  3.000
 VD1  H20   C20  C22   107.54  3.000
 VD1  H20   C20  C21   107.64  3.000
 VD1  C22   C20  C21   110.51  3.000
 VD1  H20   C20  C17   108.23  3.000
 VD1  C22   C20  C17   113.55  3.000
 VD1  C21   C20  C17   109.17  3.000
 VD1  H213  C21  H212  107.57  3.000
 VD1  H213  C21  H211  107.57  3.000
 VD1  H212  C21  H211  106.85  3.000
 VD1  H213  C21  C20   110.57  3.000
 VD1  H212  C21  C20   111.96  3.000
 VD1  H211  C21  C20   112.08  3.000
 VD1  H222  C22  H221  106.14  3.000
 VD1  H222  C22  C23   107.59  3.000
 VD1  H221  C22  C23   109.63  3.000
 VD1  H222  C22  C20   109.26  3.000
 VD1  H221  C22  C20   109.41  3.000
 VD1  C23   C22  C20   114.47  3.000
 VD1  H233  C23  H232  107.21  3.000
 VD1  H233  C23  H231  107.44  3.000
 VD1  H232  C23  H231  107.59  3.000
 VD1  H233  C23  C22   110.65  3.000
 VD1  H232  C23  C22   112.72  3.000
 VD1  H231  C23  C22   111.00  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
 VD1  Var_01  C10   C5   C4   C3    -54.42  30.0  1
 VD1  Var_02  C4    C5   C10  C1     54.43  30.0  1
 VD1  Var_03  C12   C11  C9   C8     50.71  30.0  1
 VD1  Var_04  C13   C12  C11  C9    -53.71  30.0  1
 VD1  Var_05  C14   C8   C9   C11   -52.65  30.0  1
 VD1  Var_06  C17   C16  C15  C14     9.99  30.0  1
 VD1  Var_07  C7    C6   C5   C4    179.58  30.0  2
 VD1  Var_08  C8    C7   C6   C5   -178.38  30.0  2
 VD1  Var_09  C9    C8   C7   C6      0.15  30.0  2
 VD1  Var_10  H281  C28  C2   C3      1.94  30.0  2
 VD1  Var_11  H231  C23  C22  C20   -52.92  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
 VD1  chir_01  C3   O2   C2   C4   negativ
 VD1  chir_02  C1   O1   C2   C10  negativ
 VD1  chir_03  C13  C12  C14  C17  negativ
 VD1  chir_04  C14  C15  C13  C8   positiv
 VD1  chir_05  C17  C13  C16  C20  positiv
 VD1  chir_06  C20  C17  C21  C22  negativ

