# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  8 13:53:24 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCC(C)(C)O)[C@H]1CC[C@H]2\C(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
 YS3  YS3  (1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol  ligand  71  29  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YS3
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
 YS3  OAH  O  OH1   0  -0.681   7.6671  -0.7393  -1.2952
 YS3  CBA  C  CT    0   0.203   7.2551  -1.4594  -0.1386
 YS3  CAC  C  CH3   0  -0.683   6.6926  -2.8231  -0.5406
 YS3  CAD  C  CH3   0  -0.665   8.4466  -1.6593   0.7988
 YS3  CAP  C  CH2   0  -0.419   6.2074  -0.5881   0.5626
 YS3  CAM  C  CH2   0  -0.419   4.9680  -0.2553  -0.2620
 YS3  CAW  C  CH1   0  -0.229   3.8734   0.4931   0.5152
 YS3  CAB  C  CH3   0  -0.673   4.3920   1.8329   1.0304
 YS3  CAZ  C  CH1   0  -0.166   2.6190   0.6272  -0.3636
 YS3  CAN  C  CH2   0  -0.451   2.0779  -0.7575  -0.8120
 YS3  CAQ  C  CH2   0  -0.453   0.5466  -0.6381  -0.9271
 YS3  CBB  C  CH1   0  -0.245   0.2881   0.8522  -0.7804
 YS3  CBC  C  CT    0  -0.060   1.3708   1.3333   0.2208
 YS3  CAE  C  CH3   0  -0.680   1.0798   0.8264   1.6346
 YS3  CAO  C  CH2   0  -0.418   1.3782   2.8636   0.1786
 YS3  CAK  C  CH2   0  -0.433  -0.0000   3.4420   0.4998
 YS3  CAL  C  CH2   0  -0.506  -1.1095   2.8649  -0.3868
 YS3  CAV  C  C     0   0.158  -1.0754   1.3612  -0.4278
 YS3  CAJ  C  C1    0  -0.368  -2.1151   0.5493  -0.1777
 YS3  CAI  C  C1    0  -0.332  -3.4560   0.9513   0.2080
 YS3  CAU  C  C     0   0.120  -4.4849   0.1340   0.4813
 YS3  CAS  C  CH2   0  -0.510  -5.8206   0.6748   0.9023
 YS3  CAR  C  CH2   0  -0.528  -4.4400  -1.3655   0.4152
 YS3  CAX  C  CH1   0   0.049  -5.5449  -1.9025  -0.5017
 YS3  OAF  O  OH1   0  -0.665  -5.4686  -3.3053  -0.4941
 YS3  CAT  C  C     0   0.065  -6.8749  -1.3614  -0.0406
 YS3  CAA  C  C2    0  -0.604  -7.8943  -2.1239   0.3388
 YS3  CAY  C  CH1   0   0.000  -6.9466   0.1448   0.0161
 YS3  OAG  O  OH1   0  -0.663  -6.7860   0.7192  -1.2662
 YS3  H1   H  HOH1  0   0.440   8.3218  -1.2701  -1.7608
 YS3  H2   H  HCH3  0   0.227   7.4793  -3.4529  -0.9637
 YS3  H3   H  HCH3  0   0.223   6.2819  -3.3502   0.3219
 YS3  H4   H  HCH3  0   0.234   5.9038  -2.7346  -1.2877
 YS3  H5   H  HCH3  0   0.228   8.8699  -0.7009   1.1054
 YS3  H6   H  HCH3  0   0.221   8.1530  -2.1993   1.7004
 YS3  H7   H  HCH3  0   0.225   9.2341  -2.2401   0.3124
 YS3  H8   H  HCH2  0   0.214   5.9037  -1.1035   1.4799
 YS3  H9   H  HCH2  0   0.223   6.7067   0.3304   0.8851
 YS3  H10  H  HCH2  0   0.209   5.2499   0.3362  -1.1392
 YS3  H11  H  HCH2  0   0.234   4.5473  -1.1863  -0.6470
 YS3  H12  H  HCH1  0   0.204   3.6054  -0.1263   1.3822
 YS3  H13  H  HCH3  0   0.211   4.5763   2.5294   0.2082
 YS3  H14  H  HCH3  0   0.229   3.6908   2.3082   1.7145
 YS3  H15  H  HCH3  0   0.234   5.3269   1.7179   1.5794
 YS3  H16  H  HCH1  0   0.206   2.9074   1.1919  -1.2618
 YS3  H17  H  HCH2  0   0.233   2.5288  -1.0646  -1.7561
 YS3  H18  H  HCH2  0   0.221   2.3443  -1.5235  -0.0784
 YS3  H19  H  HCH2  0   0.234   0.1625  -1.0297  -1.8704
 YS3  H20  H  HCH2  0   0.221   0.0595  -1.2050  -0.1311
 YS3  H21  H  HCH1  0   0.230   0.5585   1.3228  -1.7390
 YS3  H22  H  HCH3  0   0.229   1.7708   1.2674   2.3557
 YS3  H23  H  HCH3  0   0.236   0.0698   1.0727   1.9632
 YS3  H24  H  HCH3  0   0.231   1.1835  -0.2576   1.7090
 YS3  H25  H  HCH2  0   0.232   2.1089   3.2849   0.8703
 YS3  H26  H  HCH2  0   0.211   1.6810   3.1828  -0.8261
 YS3  H27  H  HCH2  0   0.222  -0.2439   3.2578   1.5497
 YS3  H28  H  HCH2  0   0.232   0.0214   4.5279   0.3811
 YS3  H29  H  HCH2  0   0.244  -2.0761   3.2495  -0.0615
 YS3  H30  H  HCH2  0   0.231  -0.9586   3.2320  -1.4095
 YS3  H32  H  H     0   0.229  -1.9401  -0.5170  -0.2669
 YS3  H33  H  H     0   0.230  -3.6437   2.0164   0.3035
 YS3  H35  H  HCH2  0   0.248  -6.0384   0.3566   1.9282
 YS3  H36  H  HCH2  0   0.252  -5.8276   1.7673   0.8977
 YS3  H37  H  HCH2  0   0.257  -3.4769  -1.7372   0.0665
 YS3  H38  H  HCH2  0   0.244  -4.6028  -1.7738   1.4206
 YS3  H39  H  HCH1  0   0.221  -5.3514  -1.5138  -1.5114
 YS3  H40  H  HOH1  0   0.454  -6.0346  -3.6453  -1.1946
 YS3  H41  H  H     0   0.238  -7.8488  -3.2050   0.3357
 YS3  H42  H  H     0   0.240  -8.8231  -1.6824   0.6787
 YS3  H43  H  HCH1  0   0.225  -7.9081   0.4382   0.4578
 YS3  H44  H  HOH1  0   0.450  -7.4918   0.3865  -1.8301

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
 YS3  CAB  CAW  single  1.526  0.020  1.526
 YS3  OAH  CBA  single  1.423  0.020  1.423
 YS3  CAC  CBA  single  1.529  0.020  1.529
 YS3  CAP  CBA  single  1.532  0.020  1.532
 YS3  CAP  CAM  single  1.525  0.020  1.525
 YS3  CAW  CAM  single  1.537  0.020  1.537
 YS3  CAW  CAZ  single  1.537  0.020  1.537
 YS3  CBA  CAD  single  1.529  0.020  1.529
 YS3  CAO  CAK  single  1.529  0.020  1.529
 YS3  CAO  CBC  single  1.531  0.020  1.531
 YS3  CAZ  CBC  single  1.549  0.020  1.549
 YS3  CAZ  CAN  single  1.553  0.020  1.553
 YS3  CAK  CAL  single  1.533  0.020  1.533
 YS3  CBC  CBB  single  1.551  0.020  1.551
 YS3  CBC  CAE  single  1.530  0.020  1.530
 YS3  CAL  CAV  single  1.505  0.020  1.505
 YS3  CAN  CAQ  single  1.540  0.020  1.540
 YS3  CBB  CAQ  single  1.520  0.020  1.520
 YS3  CBB  CAV  single  1.497  0.020  1.497
 YS3  CAV  CAJ  double  1.343  0.020  1.343
 YS3  CAJ  CAI  single  1.452  0.020  1.452
 YS3  CAI  CAU  double  1.342  0.020  1.342
 YS3  CAU  CAS  single  1.501  0.020  1.501
 YS3  CAU  CAR  single  1.502  0.020  1.502
 YS3  CAS  CAY  single  1.528  0.020  1.528
 YS3  CAR  CAX  single  1.533  0.020  1.533
 YS3  OAG  CAY  single  1.414  0.020  1.414
 YS3  CAY  CAT  single  1.509  0.020  1.509
 YS3  CAX  CAT  single  1.508  0.020  1.508
 YS3  CAX  OAF  single  1.405  0.020  1.405
 YS3  CAT  CAA  double  1.328  0.020  1.328
 YS3  OAH  H1   single  0.850  0.020  0.980
 YS3  CAC  H2   single  0.970  0.020  1.090
 YS3  CAC  H3   single  0.970  0.020  1.090
 YS3  CAC  H4   single  0.970  0.020  1.090
 YS3  CAD  H5   single  0.970  0.020  1.090
 YS3  CAD  H6   single  0.970  0.020  1.090
 YS3  CAD  H7   single  0.970  0.020  1.090
 YS3  CAP  H8   single  0.970  0.020  1.090
 YS3  CAP  H9   single  0.970  0.020  1.090
 YS3  CAM  H10  single  0.970  0.020  1.090
 YS3  CAM  H11  single  0.970  0.020  1.090
 YS3  CAW  H12  single  0.970  0.020  1.090
 YS3  CAB  H13  single  0.970  0.020  1.090
 YS3  CAB  H14  single  0.970  0.020  1.090
 YS3  CAB  H15  single  0.970  0.020  1.090
 YS3  CAZ  H16  single  0.970  0.020  1.090
 YS3  CAN  H17  single  0.970  0.020  1.090
 YS3  CAN  H18  single  0.970  0.020  1.090
 YS3  CAQ  H19  single  0.970  0.020  1.090
 YS3  CAQ  H20  single  0.970  0.020  1.090
 YS3  CBB  H21  single  0.970  0.020  1.090
 YS3  CAE  H22  single  0.970  0.020  1.090
 YS3  CAE  H23  single  0.970  0.020  1.090
 YS3  CAE  H24  single  0.970  0.020  1.090
 YS3  CAO  H25  single  0.970  0.020  1.090
 YS3  CAO  H26  single  0.970  0.020  1.090
 YS3  CAK  H27  single  0.970  0.020  1.090
 YS3  CAK  H28  single  0.970  0.020  1.090
 YS3  CAL  H29  single  0.970  0.020  1.090
 YS3  CAL  H30  single  0.970  0.020  1.090
 YS3  CAJ  H32  single  0.930  0.020  1.080
 YS3  CAI  H33  single  0.930  0.020  1.080
 YS3  CAS  H35  single  0.970  0.020  1.090
 YS3  CAS  H36  single  0.970  0.020  1.090
 YS3  CAR  H37  single  0.970  0.020  1.090
 YS3  CAR  H38  single  0.970  0.020  1.090
 YS3  CAX  H39  single  0.970  0.020  1.090
 YS3  OAF  H40  single  0.850  0.020  0.980
 YS3  CAA  H41  single  0.930  0.020  1.080
 YS3  CAA  H42  single  0.930  0.020  1.080
 YS3  CAY  H43  single  0.970  0.020  1.090
 YS3  OAG  H44  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
 YS3  H1   OAH  CBA  108.11  3.000
 YS3  CAP  CBA  CAD  109.06  3.000
 YS3  CAD  CBA  CAC  109.34  3.000
 YS3  CAP  CBA  CAC  112.08  3.000
 YS3  CAD  CBA  OAH  109.80  3.000
 YS3  CAP  CBA  OAH  106.38  3.000
 YS3  CAC  CBA  OAH  110.12  3.000
 YS3  H4   CAC  H3   107.97  3.000
 YS3  H4   CAC  H2   107.60  3.000
 YS3  H3   CAC  H2   107.37  3.000
 YS3  H4   CAC  CBA  111.96  3.000
 YS3  H3   CAC  CBA  111.19  3.000
 YS3  H2   CAC  CBA  110.55  3.000
 YS3  H7   CAD  H6   107.38  3.000
 YS3  H7   CAD  H5   108.18  3.000
 YS3  H6   CAD  H5   107.87  3.000
 YS3  H7   CAD  CBA  110.99  3.000
 YS3  H6   CAD  CBA  111.20  3.000
 YS3  H5   CAD  CBA  111.07  3.000
 YS3  H9   CAP  H8   105.95  3.000
 YS3  H9   CAP  CAM  110.30  3.000
 YS3  H8   CAP  CAM  109.27  3.000
 YS3  H9   CAP  CBA  107.47  3.000
 YS3  H8   CAP  CBA  107.77  3.000
 YS3  CAM  CAP  CBA  115.60  3.000
 YS3  H11  CAM  H10  106.10  3.000
 YS3  H11  CAM  CAW  108.61  3.000
 YS3  H10  CAM  CAW  108.99  3.000
 YS3  H11  CAM  CAP  108.53  3.000
 YS3  H10  CAM  CAP  109.98  3.000
 YS3  CAW  CAM  CAP  114.30  3.000
 YS3  H12  CAW  CAZ  107.53  3.000
 YS3  H12  CAW  CAB  108.14  3.000
 YS3  CAZ  CAW  CAB  113.18  3.000
 YS3  H12  CAW  CAM  107.35  3.000
 YS3  CAZ  CAW  CAM  109.54  3.000
 YS3  CAB  CAW  CAM  110.87  3.000
 YS3  H15  CAB  H14  106.37  3.000
 YS3  H15  CAB  H13  107.54  3.000
 YS3  H14  CAB  H13  107.64  3.000
 YS3  H15  CAB  CAW  111.64  3.000
 YS3  H14  CAB  CAW  112.12  3.000
 YS3  H13  CAB  CAW  111.27  3.000
 YS3  H16  CAZ  CBC  106.59  3.000
 YS3  H16  CAZ  CAN  108.27  3.000
 YS3  CBC  CAZ  CAN  103.58  3.000
 YS3  H16  CAZ  CAW  107.32  3.000
 YS3  CAN  CAZ  CAW  111.81  3.000
 YS3  CBC  CAZ  CAW  118.79  3.000
 YS3  H18  CAN  H17  106.43  3.000
 YS3  H18  CAN  CAQ  110.28  3.000
 YS3  H17  CAN  CAQ  111.60  3.000
 YS3  H18  CAN  CAZ  110.24  3.000
 YS3  H17  CAN  CAZ  110.92  3.000
 YS3  CAQ  CAN  CAZ  107.39  3.000
 YS3  H20  CAQ  H19  106.67  3.000
 YS3  H20  CAQ  CBB  111.27  3.000
 YS3  H19  CAQ  CBB  112.06  3.000
 YS3  H20  CAQ  CAN  110.41  3.000
 YS3  H19  CAQ  CAN  112.76  3.000
 YS3  CBB  CAQ  CAN  103.76  3.000
 YS3  H21  CBB  CAV  106.45  3.000
 YS3  H21  CBB  CBC  104.94  3.000
 YS3  CAV  CBB  CBC  112.22  3.000
 YS3  H21  CBB  CAQ  107.05  3.000
 YS3  CAV  CBB  CAQ  120.73  3.000
 YS3  CBC  CBB  CAQ  104.35  3.000
 YS3  CAO  CBC  CAE  110.95  3.000
 YS3  CAE  CBC  CBB  111.15  3.000
 YS3  CAO  CBC  CBB  107.20  3.000
 YS3  CAE  CBC  CAZ  110.55  3.000
 YS3  CBB  CBC  CAZ  100.23  3.000
 YS3  CAO  CBC  CAZ  116.20  3.000
 YS3  H24  CAE  H23  106.97  3.000
 YS3  H24  CAE  H22  107.22  3.000
 YS3  H23  CAE  H22  107.21  3.000
 YS3  H24  CAE  CBC  111.97  3.000
 YS3  H23  CAE  CBC  112.33  3.000
 YS3  H22  CAE  CBC  110.86  3.000
 YS3  H26  CAO  H25  106.47  3.000
 YS3  H26  CAO  CAK  109.34  3.000
 YS3  H25  CAO  CAK  108.94  3.000
 YS3  H26  CAO  CBC  108.51  3.000
 YS3  H25  CAO  CBC  111.83  3.000
 YS3  CAK  CAO  CBC  111.59  3.000
 YS3  H28  CAK  H27  106.03  3.000
 YS3  H28  CAK  CAL  108.99  3.000
 YS3  H27  CAK  CAL  109.30  3.000
 YS3  H28  CAK  CAO  109.60  3.000
 YS3  H27  CAK  CAO  109.82  3.000
 YS3  CAL  CAK  CAO  112.87  3.000
 YS3  H30  CAL  H29  106.39  3.000
 YS3  H30  CAL  CAV  107.81  3.000
 YS3  H29  CAL  CAV  112.39  3.000
 YS3  H30  CAL  CAK  108.28  3.000
 YS3  H29  CAL  CAK  109.66  3.000
 YS3  CAV  CAL  CAK  112.06  3.000
 YS3  CAJ  CAV  CAL  125.57  3.000
 YS3  CAJ  CAV  CBB  122.91  3.000
 YS3  CAL  CAV  CBB  111.52  3.000
 YS3  H32  CAJ  CAI  116.31  3.000
 YS3  H32  CAJ  CAV  117.03  3.000
 YS3  CAI  CAJ  CAV  126.66  3.000
 YS3  H33  CAI  CAU  116.55  3.000
 YS3  H33  CAI  CAJ  117.05  3.000
 YS3  CAU  CAI  CAJ  126.40  3.000
 YS3  CAR  CAU  CAS  113.50  3.000
 YS3  CAR  CAU  CAI  125.19  3.000
 YS3  CAS  CAU  CAI  121.32  3.000
 YS3  H36  CAS  H35  107.04  3.000
 YS3  H36  CAS  CAY  109.86  3.000
 YS3  H35  CAS  CAY  107.21  3.000
 YS3  H36  CAS  CAU  111.39  3.000
 YS3  H35  CAS  CAU  109.56  3.000
 YS3  CAY  CAS  CAU  111.60  3.000
 YS3  H38  CAR  H37  107.30  3.000
 YS3  H38  CAR  CAX  108.10  3.000
 YS3  H37  CAR  CAX  109.04  3.000
 YS3  H38  CAR  CAU  109.08  3.000
 YS3  H37  CAR  CAU  112.40  3.000
 YS3  CAX  CAR  CAU  110.77  3.000
 YS3  H39  CAX  CAT  108.01  3.000
 YS3  H39  CAX  OAF  110.40  3.000
 YS3  CAT  CAX  OAF  113.86  3.000
 YS3  H39  CAX  CAR  107.38  3.000
 YS3  OAF  CAX  CAR  107.90  3.000
 YS3  CAT  CAX  CAR  109.09  3.000
 YS3  H40  OAF  CAX  108.47  3.000
 YS3  CAY  CAT  CAA  121.72  3.000
 YS3  CAA  CAT  CAX  123.92  3.000
 YS3  CAY  CAT  CAX  114.31  3.000
 YS3  H42  CAA  H41  116.37  3.000
 YS3  H42  CAA  CAT  120.91  3.000
 YS3  H41  CAA  CAT  122.72  3.000
 YS3  H43  CAY  OAG  110.83  3.000
 YS3  H43  CAY  CAT  108.87  3.000
 YS3  OAG  CAY  CAT  111.46  3.000
 YS3  H43  CAY  CAS  108.63  3.000
 YS3  CAT  CAY  CAS  109.45  3.000
 YS3  OAG  CAY  CAS  107.54  3.000
 YS3  H44  OAG  CAY  107.91  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
 YS3  Var_01  CBB  CAQ  CAN  CAZ     9.48  30.0  1
 YS3  Var_02  CAK  CAL  CAV  CBB   -51.85  30.0  1
 YS3  Var_03  CAL  CAK  CAO  CBC   -53.73  30.0  1
 YS3  Var_04  CAV  CAL  CAK  CAO    49.89  30.0  1
 YS3  Var_05  CAX  CAR  CAU  CAS    55.26  30.0  1
 YS3  Var_06  CAY  CAS  CAU  CAR   -54.38  30.0  1
 YS3  Var_07  CAI  CAJ  CAV  CBB   178.07  30.0  2
 YS3  Var_08  CAU  CAI  CAJ  CAV  -178.65  30.0  2
 YS3  Var_09  CAS  CAU  CAI  CAJ   178.53  30.0  2
 YS3  Var_10  H41  CAA  CAT  CAX    -0.64  30.0  2
 YS3  Var_11  CAM  CAP  CBA  OAH    59.72  30.0  2
 YS3  Var_12  CAW  CAM  CAP  CBA   173.91  30.0  3
 YS3  Var_13  H2   CAC  CBA  OAH    66.39  30.0  3
 YS3  Var_14  H5   CAD  CBA  OAH    59.16  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
 YS3  chir_01  CAW  CAB  CAM  CAZ  positiv
 YS3  chir_02  CAZ  CAN  CBC  CAW  negativ
 YS3  chir_03  CBB  CBC  CAQ  CAV  negativ
 YS3  chir_04  CBC  CAZ  CBB  CAO  positiv
 YS3  chir_05  CAX  CAR  CAT  OAF  positiv
 YS3  chir_06  CAY  OAG  CAT  CAS  negativ

