# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:48:27 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-dimethyl-3-oxo-2,3,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]propanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C)C(O)=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
 3G6  3G6  '(2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-dimethyl-3-oxo-2,3,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]propanoic acid (non-preferred name)'  ligand  56  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3G6
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
 3G6  CAY  C  CR5    0  -0.048  -1.6434  -0.2773   0.2383
 3G6  CAX  C  CT     0  -0.147   2.8210  -0.4488   0.3824
 3G6  CAW  C  CR15   0  -0.172  -0.7860   0.9593  -0.0835
 3G6  CAV  C  CR15   0  -0.176  -2.9643   0.1288  -0.4581
 3G6  CAU  C  CH1    0  -0.179   1.3406  -0.3122  -0.0808
 3G6  CAT  C  CH1    0  -0.238   0.6220   0.9202   0.4908
 3G6  CAS  C  CH1    0  -0.336  -4.2466  -0.6388  -0.1270
 3G6  CAR  C  C      0   0.260   3.5312   0.8709   0.1586
 3G6  CAQ  C  C      0   0.417  -5.4411   0.0201  -0.8478
 3G6  CAP  C  C      0   0.404   5.5647  -0.1905  -0.7689
 3G6  CAO  C  CH2    0  -0.407  -0.9171  -1.4942  -0.3341
 3G6  OAD  O  O      0  -0.442   6.6507  -0.0625  -1.3094
 3G6  CAM  C  CH2    0  -0.447   0.5266  -1.5855   0.1673
 3G6  CAL  C  CH2    0  -0.450  -1.6890   2.1393   0.2597
 3G6  CAH  C  CH2    0  -0.573   5.0155  -1.5295  -0.3643
 3G6  CAG  C  C1     0  -0.465   4.7450   0.9645  -0.4121
 3G6  CAA  C  CH3    0  -0.665  -4.1878  -2.1184  -0.5032
 3G6  CAC  C  CH3    0  -0.684  -1.8743  -0.4469   1.7428
 3G6  OAE  O  OC    -1  -0.621  -6.3475   0.5089  -0.1406
 3G6  OAF  O  O      0  -0.621  -5.4159   0.0043  -2.0971
 3G6  CAK  C  CH2    0  -0.442  -3.0966   1.6366  -0.1199
 3G6  CAJ  C  CH2    0  -0.417   1.3968   2.1874   0.1595
 3G6  CAI  C  CH2    0  -0.510   2.8379   2.1035   0.6478
 3G6  CAN  C  CH2    0  -0.447   3.4977  -1.5482  -0.4494
 3G6  CAB  C  CH3    0  -0.670   2.9193  -0.7875   1.8811
 3G6  H1   H  HCR5   0   0.205  -0.6660   0.9642  -1.1786
 3G6  H2   H  HCR5   0   0.200  -2.7966   0.0311  -1.5382
 3G6  H3   H  HCH1   0   0.213   1.3824  -0.1611  -1.1705
 3G6  H4   H  HCH1   0   0.212   0.5613   0.8333   1.5836
 3G6  H5   H  HCH1   0   0.191  -4.4216  -0.5595   0.9514
 3G6  H6   H  HCH2   0   0.224  -1.4268  -2.4238  -0.0740
 3G6  H7   H  HCH2   0   0.208  -0.9259  -1.4296  -1.4283
 3G6  H8   H  HCH2   0   0.238   1.0066  -2.4403  -0.3136
 3G6  H9   H  HCH2   0   0.221   0.5199  -1.8107   1.2370
 3G6  H10  H  HCH2   0   0.214  -1.6281   2.3806   1.3248
 3G6  H11  H  HCH2   0   0.227  -1.4082   3.0455  -0.2798
 3G6  H12  H  HCH2   0   0.265   5.4535  -2.3133  -0.9844
 3G6  H13  H  HCH2   0   0.264   5.3471  -1.7233   0.6625
 3G6  H14  H  H      0   0.247   5.1891   1.9423  -0.5719
 3G6  H15  H  HCH3   0   0.220  -5.1600  -2.5975  -0.3665
 3G6  H16  H  HCH3   0   0.210  -3.8963  -2.2494  -1.5462
 3G6  H17  H  HCH3   0   0.217  -3.4763  -2.6697   0.1111
 3G6  H18  H  HCH3   0   0.229  -0.9462  -0.5251   2.3094
 3G6  H19  H  HCH3   0   0.231  -2.4369   0.3862   2.1680
 3G6  H20  H  HCH3   0   0.228  -2.4468  -1.3547   1.9438
 3G6  H22  H  HCH2   0   0.225  -3.5066   2.1862  -0.9686
 3G6  H23  H  HCH2   0   0.216  -3.8025   1.7801   0.7017
 3G6  H24  H  HCH2   0   0.217   1.3861   2.3480  -0.9245
 3G6  H25  H  HCH2   0   0.243   0.9162   3.0591   0.6089
 3G6  H26  H  HCH2   0   0.251   2.8415   2.0832   1.7442
 3G6  H27  H  HCH2   0   0.253   3.4000   2.9922   0.3557
 3G6  H28  H  HCH2   0   0.248   3.1362  -2.5286  -0.1376
 3G6  H29  H  HCH2   0   0.238   3.2029  -1.4283  -1.4972
 3G6  H30  H  HCH3   0   0.240   3.9529  -0.7484   2.2279
 3G6  H31  H  HCH3   0   0.240   2.3414  -0.0997   2.4981
 3G6  H32  H  HCH3   0   0.242   2.5484  -1.7936   2.0751

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
 3G6  OAF  CAQ  deloc   1.250  0.020  1.250
 3G6  CAL  CAK  single  1.542  0.020  1.542
 3G6  CAL  CAW  single  1.525  0.020  1.525
 3G6  CAK  CAV  single  1.551  0.020  1.551
 3G6  CAQ  OAE  deloc   1.249  0.020  1.249
 3G6  CAQ  CAS  single  1.543  0.020  1.543
 3G6  CAJ  CAI  single  1.524  0.020  1.524
 3G6  CAJ  CAT  single  1.522  0.020  1.522
 3G6  CAI  CAR  single  1.496  0.020  1.496
 3G6  CAW  CAT  single  1.521  0.020  1.521
 3G6  CAW  CAY  single  1.539  0.020  1.539
 3G6  CAV  CAS  single  1.531  0.020  1.531
 3G6  CAV  CAY  single  1.547  0.020  1.547
 3G6  CAC  CAY  single  1.532  0.020  1.532
 3G6  CAS  CAA  single  1.528  0.020  1.528
 3G6  CAT  CAU  single  1.537  0.020  1.537
 3G6  CAY  CAO  single  1.528  0.020  1.528
 3G6  CAR  CAG  double  1.344  0.020  1.344
 3G6  CAR  CAX  single  1.515  0.020  1.515
 3G6  CAU  CAX  single  1.557  0.020  1.557
 3G6  CAU  CAM  single  1.532  0.020  1.532
 3G6  CAG  CAP  single  1.461  0.020  1.461
 3G6  CAO  CAM  single  1.531  0.020  1.531
 3G6  CAB  CAX  single  1.540  0.020  1.540
 3G6  CAX  CAN  single  1.536  0.020  1.536
 3G6  CAP  OAD  double  1.220  0.020  1.220
 3G6  CAP  CAH  single  1.503  0.020  1.503
 3G6  CAN  CAH  single  1.520  0.020  1.520
 3G6  CAW  H1   single  0.970  0.020  1.090
 3G6  CAV  H2   single  0.970  0.020  1.090
 3G6  CAU  H3   single  0.970  0.020  1.090
 3G6  CAT  H4   single  0.970  0.020  1.090
 3G6  CAS  H5   single  0.970  0.020  1.090
 3G6  CAO  H6   single  0.970  0.020  1.090
 3G6  CAO  H7   single  0.970  0.020  1.090
 3G6  CAM  H8   single  0.970  0.020  1.090
 3G6  CAM  H9   single  0.970  0.020  1.090
 3G6  CAL  H10  single  0.970  0.020  1.090
 3G6  CAL  H11  single  0.970  0.020  1.090
 3G6  CAH  H12  single  0.970  0.020  1.090
 3G6  CAH  H13  single  0.970  0.020  1.090
 3G6  CAG  H14  single  0.930  0.020  1.080
 3G6  CAA  H15  single  0.970  0.020  1.090
 3G6  CAA  H16  single  0.970  0.020  1.090
 3G6  CAA  H17  single  0.970  0.020  1.090
 3G6  CAC  H18  single  0.970  0.020  1.090
 3G6  CAC  H19  single  0.970  0.020  1.090
 3G6  CAC  H20  single  0.970  0.020  1.090
 3G6  CAK  H22  single  0.970  0.020  1.090
 3G6  CAK  H23  single  0.970  0.020  1.090
 3G6  CAJ  H24  single  0.970  0.020  1.090
 3G6  CAJ  H25  single  0.970  0.020  1.090
 3G6  CAI  H26  single  0.970  0.020  1.090
 3G6  CAI  H27  single  0.970  0.020  1.090
 3G6  CAN  H28  single  0.970  0.020  1.090
 3G6  CAN  H29  single  0.970  0.020  1.090
 3G6  CAB  H30  single  0.970  0.020  1.090
 3G6  CAB  H31  single  0.970  0.020  1.090
 3G6  CAB  H32  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
 3G6  CAC  CAY  CAO  110.57  3.000
 3G6  CAO  CAY  CAV  116.49  3.000
 3G6  CAC  CAY  CAV  110.03  3.000
 3G6  CAO  CAY  CAW  107.26  3.000
 3G6  CAC  CAY  CAW  112.24  3.000
 3G6  CAV  CAY  CAW   99.82  3.000
 3G6  CAB  CAX  CAN  109.97  3.000
 3G6  CAN  CAX  CAR  109.70  3.000
 3G6  CAB  CAX  CAR  107.79  3.000
 3G6  CAN  CAX  CAU  108.70  3.000
 3G6  CAB  CAX  CAU  111.69  3.000
 3G6  CAR  CAX  CAU  108.98  3.000
 3G6  H1   CAW  CAL  106.54  3.000
 3G6  H1   CAW  CAT  105.94  3.000
 3G6  CAL  CAW  CAT  118.88  3.000
 3G6  H1   CAW  CAY  105.80  3.000
 3G6  CAT  CAW  CAY  114.59  3.000
 3G6  CAL  CAW  CAY  104.17  3.000
 3G6  H2   CAV  CAK  108.31  3.000
 3G6  H2   CAV  CAS  107.23  3.000
 3G6  CAK  CAV  CAS  111.65  3.000
 3G6  H2   CAV  CAY  106.81  3.000
 3G6  CAS  CAV  CAY  119.09  3.000
 3G6  CAK  CAV  CAY  103.28  3.000
 3G6  H3   CAU  CAM  107.14  3.000
 3G6  H3   CAU  CAT  106.01  3.000
 3G6  CAM  CAU  CAT  110.97  3.000
 3G6  H3   CAU  CAX  105.69  3.000
 3G6  CAM  CAU  CAX  112.60  3.000
 3G6  CAT  CAU  CAX  113.84  3.000
 3G6  H4   CAT  CAJ  108.10  3.000
 3G6  H4   CAT  CAU  109.43  3.000
 3G6  CAJ  CAT  CAU  110.41  3.000
 3G6  H4   CAT  CAW  109.07  3.000
 3G6  CAU  CAT  CAW  108.24  3.000
 3G6  CAJ  CAT  CAW  111.57  3.000
 3G6  H5   CAS  CAA  108.59  3.000
 3G6  H5   CAS  CAQ  107.77  3.000
 3G6  CAA  CAS  CAQ  109.17  3.000
 3G6  H5   CAS  CAV  108.09  3.000
 3G6  CAA  CAS  CAV  113.58  3.000
 3G6  CAQ  CAS  CAV  109.47  3.000
 3G6  CAI  CAR  CAG  119.98  3.000
 3G6  CAG  CAR  CAX  123.12  3.000
 3G6  CAI  CAR  CAX  116.87  3.000
 3G6  OAF  CAQ  OAE  125.84  3.000
 3G6  OAE  CAQ  CAS  117.67  3.000
 3G6  OAF  CAQ  CAS  116.49  3.000
 3G6  CAG  CAP  CAH  115.71  3.000
 3G6  CAH  CAP  OAD  122.56  3.000
 3G6  CAG  CAP  OAD  121.66  3.000
 3G6  H7   CAO  H6   106.52  3.000
 3G6  H7   CAO  CAM  109.76  3.000
 3G6  H6   CAO  CAM  108.15  3.000
 3G6  H7   CAO  CAY  108.85  3.000
 3G6  H6   CAO  CAY  111.52  3.000
 3G6  CAM  CAO  CAY  111.90  3.000
 3G6  H9   CAM  H8   105.80  3.000
 3G6  H9   CAM  CAO  109.09  3.000
 3G6  H8   CAM  CAO  108.48  3.000
 3G6  H9   CAM  CAU  109.45  3.000
 3G6  H8   CAM  CAU  110.23  3.000
 3G6  CAO  CAM  CAU  113.49  3.000
 3G6  H11  CAL  H10  106.49  3.000
 3G6  H11  CAL  CAK  112.57  3.000
 3G6  H10  CAL  CAK  111.25  3.000
 3G6  H11  CAL  CAW  112.26  3.000
 3G6  H10  CAL  CAW  110.91  3.000
 3G6  CAK  CAL  CAW  103.47  3.000
 3G6  H13  CAH  H12  106.49  3.000
 3G6  H13  CAH  CAN  110.62  3.000
 3G6  H12  CAH  CAN  111.11  3.000
 3G6  H13  CAH  CAP  107.41  3.000
 3G6  H12  CAH  CAP  109.90  3.000
 3G6  CAN  CAH  CAP  111.15  3.000
 3G6  H14  CAG  CAP  116.53  3.000
 3G6  H14  CAG  CAR  119.63  3.000
 3G6  CAP  CAG  CAR  123.73  3.000
 3G6  H17  CAA  H16  107.68  3.000
 3G6  H17  CAA  H15  106.78  3.000
 3G6  H16  CAA  H15  107.75  3.000
 3G6  H17  CAA  CAS  112.10  3.000
 3G6  H16  CAA  CAS  111.22  3.000
 3G6  H15  CAA  CAS  111.08  3.000
 3G6  H20  CAC  H19  107.02  3.000
 3G6  H20  CAC  H18  106.92  3.000
 3G6  H19  CAC  H18  106.93  3.000
 3G6  H20  CAC  CAY  110.61  3.000
 3G6  H19  CAC  CAY  112.07  3.000
 3G6  H18  CAC  CAY  112.96  3.000
 3G6  H23  CAK  H22  106.02  3.000
 3G6  H23  CAK  CAL  111.22  3.000
 3G6  H22  CAK  CAL  111.73  3.000
 3G6  H23  CAK  CAV  110.29  3.000
 3G6  H22  CAK  CAV  110.62  3.000
 3G6  CAL  CAK  CAV  107.02  3.000
 3G6  H25  CAJ  H24  106.60  3.000
 3G6  H25  CAJ  CAI  109.16  3.000
 3G6  H24  CAJ  CAI  109.52  3.000
 3G6  H25  CAJ  CAT  110.55  3.000
 3G6  H24  CAJ  CAT  109.42  3.000
 3G6  CAI  CAJ  CAT  111.46  3.000
 3G6  H27  CAI  H26  106.32  3.000
 3G6  H27  CAI  CAJ  110.89  3.000
 3G6  H26  CAI  CAJ  108.93  3.000
 3G6  H27  CAI  CAR  110.16  3.000
 3G6  H26  CAI  CAR  108.06  3.000
 3G6  CAJ  CAI  CAR  112.25  3.000
 3G6  H29  CAN  H28  106.43  3.000
 3G6  H29  CAN  CAH  108.72  3.000
 3G6  H28  CAN  CAH  109.03  3.000
 3G6  H29  CAN  CAX  108.73  3.000
 3G6  H28  CAN  CAX  110.05  3.000
 3G6  CAH  CAN  CAX  113.63  3.000
 3G6  H32  CAB  H31  107.54  3.000
 3G6  H32  CAB  H30  107.40  3.000
 3G6  H31  CAB  H30  107.45  3.000
 3G6  H32  CAB  CAX  110.78  3.000
 3G6  H31  CAB  CAX  112.23  3.000
 3G6  H30  CAB  CAX  111.23  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
 3G6  Var_01  CAU  CAM  CAO  CAY  -54.24  30.0  1
 3G6  Var_02  CAJ  CAI  CAR  CAX  -51.04  30.0  1
 3G6  Var_03  CAP  CAG  CAR  CAX   -5.73  30.0  1
 3G6  Var_04  CAP  CAH  CAN  CAX  -56.17  30.0  1
 3G6  Var_05  CAV  CAK  CAL  CAW    8.37  30.0  1
 3G6  Var_06  CAR  CAI  CAJ  CAT   53.08  30.0  1
 3G6  Var_07  CAH  CAP  CAG  CAR   -4.44  30.0  1
 3G6  Var_08  CAN  CAH  CAP  CAG   34.40  30.0  1

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
 3G6  chir_01  CAY  CAV  CAW  CAO  positiv
 3G6  chir_02  CAX  CAN  CAU  CAR  positiv
 3G6  chir_03  CAW  CAY  CAT  CAL  positiv
 3G6  chir_04  CAV  CAK  CAS  CAY  positiv
 3G6  chir_05  CAU  CAT  CAX  CAM  negativ
 3G6  chir_06  CAT  CAU  CAW  CAJ  positiv
 3G6  chir_07  CAS  CAQ  CAV  CAA  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
 3G6  plan-1  CAP  0.020
 3G6  plan-1  OAD  0.020
 3G6  plan-1  CAH  0.020
 3G6  plan-1  CAG  0.020
 3G6  plan-2  CAS  0.020
 3G6  plan-2  CAQ  0.020
 3G6  plan-2  OAE  0.020
 3G6  plan-2  OAF  0.020

