# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 04:34:31 2021
#   Inital geometry file: a 163 line input string
#   Ligand name: (3R,5R)-7-{(1S,2S,6R,8S,8aR)-8-[(2,2-dimethylbutanoyl)oxy]-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl}-3,5-dihydroxyheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(C)(C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H](O)C[C@@H](O)CC(O)=O)[C@@H]12
#
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
 SIM  SIM  '(3R,5R)-7-{(1S,2S,6R,8S,8aR)-8-[(2,2-dimethylbutanoyl)oxy]-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl}-3,5-dihydroxyheptanoic acid'  ligand  71  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SIM
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
 SIM  O1A   O  O     0  -0.444  3.9928  -12.9147   -6.9891
 SIM  O1B   O  OH1   0  -0.591  5.0796  -12.9352   -5.0433
 SIM  O3    O  OH1   0  -0.672  6.4854  -11.1326   -7.8831
 SIM  O5    O  OH1   0  -0.676  6.4676   -7.0776   -8.7865
 SIM  O14   O  O2    0  -0.447  3.8925   -9.7061  -13.7948
 SIM  O18   O  O     0  -0.464  5.8589  -10.7256  -14.0540
 SIM  C1    C  C     0   0.545  4.6147  -12.3356   -6.1337
 SIM  C2    C  CH2   0  -0.577  4.9227  -10.8615   -6.1551
 SIM  C3    C  CH1   0   0.027  5.3263  -10.3943   -7.5428
 SIM  C4    C  CH2   0  -0.469  5.5806   -8.8898   -7.5560
 SIM  C5    C  CH1   0   0.061  5.8052   -8.3175   -8.9529
 SIM  C6    C  CH2   0  -0.463  4.4923   -8.1532   -9.7125
 SIM  C7    C  CH2   0  -0.465  4.6698   -7.7826  -11.1828
 SIM  C8    C  CH1   0  -0.224  3.3442   -7.6232  -11.9274
 SIM  C9    C  CH1   0  -0.293  2.4633   -6.5175  -11.3144
 SIM  C10   C  C1    0  -0.216  1.2079   -6.3371  -12.1111
 SIM  C11   C  C1    0  -0.260  1.0929   -6.7105  -13.3869
 SIM  C12   C  C     0   0.162  2.1938   -7.2923  -14.1409
 SIM  C17   C  C1    0  -0.288  2.0149   -7.6840  -15.4082
 SIM  C16   C  CH1   0  -0.271  3.0687   -8.2692  -16.2924
 SIM  C15   C  CH2   0  -0.465  4.4485   -8.2020  -15.6309
 SIM  C14   C  CH1   0  -0.015  4.4243   -8.4127  -14.1264
 SIM  C13   C  CH1   0  -0.317  3.5304   -7.3856  -13.4389
 SIM  C9A   C  CH3   0  -0.668  3.1752   -5.1714  -11.1411
 SIM  C19   C  CT    0  -0.237  3.9643  -12.0470  -13.3752
 SIM  C20   C  CH2   0  -0.390  4.7281  -12.6733  -12.1934
 SIM  C21   C  CH3   0  -0.699  4.7979  -11.8227  -10.9338
 SIM  C22   C  CH3   0  -0.643  4.0450  -13.0121  -14.5660
 SIM  C23   C  CH3   0  -0.646  2.4966  -11.8251  -13.0132
 SIM  C24   C  CH3   0  -0.666  2.6646   -9.6695  -16.7644
 SIM  H1B   H  HOH1  0   0.478  4.8378  -13.8737   -5.0540
 SIM  HO3   H  HOH1  0   0.452  6.6845  -11.0028   -8.8148
 SIM  HO5   H  HOH1  0   0.448  6.6330   -6.6970   -9.6541
 SIM  H21   H  HCH2  0   0.292  4.0199  -10.3296   -5.8414
 SIM  H22   H  HCH2  0   0.266  5.7015  -10.6192   -5.4295
 SIM  H3    H  HCH1  0   0.220  4.5047  -10.6305   -8.2310
 SIM  H41   H  HCH2  0   0.231  4.7318   -8.3747   -7.0940
 SIM  H42   H  HCH2  0   0.242  6.4556   -8.6830   -6.9324
 SIM  H5    H  HCH1  0   0.178  6.4532   -9.0031   -9.5252
 SIM  H61   H  HCH2  0   0.225  3.9235   -9.0872   -9.6634
 SIM  H62   H  HCH2  0   0.238  3.8898   -7.4090   -9.1831
 SIM  H71   H  HCH2  0   0.217  5.2628   -6.8670  -11.2891
 SIM  H72   H  HCH2  0   0.240  5.2671   -8.5713  -11.6483
 SIM  H8    H  HCH1  0   0.240  2.7859   -8.5593  -11.8076
 SIM  H9    H  HCH1  0   0.247  2.1609   -6.8510  -10.3162
 SIM  H10   H  H     0   0.241  0.3651   -5.8726  -11.6102
 SIM  H11   H  H     0   0.234  0.1532   -6.5680  -13.9113
 SIM  H17   H  H     0   0.233  1.0245   -7.5801  -15.8452
 SIM  H16   H  HCH1  0   0.245  3.1149   -7.6480  -17.1947
 SIM  H151  H  HCH2  0   0.248  5.1383   -8.9058  -16.1023
 SIM  H152  H  HCH2  0   0.250  4.8741   -7.2080  -15.7938
 SIM  H14   H  HCH1  0   0.261  5.4448   -8.3343  -13.7464
 SIM  H13   H  HCH1  0   0.254  4.0425   -6.4214  -13.5596
 SIM  H9A1  H  HCH3  0   0.238  2.4822   -4.4191  -10.7621
 SIM  H9A2  H  HCH3  0   0.229  4.0019   -5.2370  -10.4322
 SIM  H9A3  H  HCH3  0   0.226  3.5745   -4.8026  -12.0874
 SIM  H201  H  HCH2  0   0.234  4.2390  -13.6230  -11.9594
 SIM  H202  H  HCH2  0   0.234  5.7402  -12.9235  -12.5190
 SIM  H211  H  HCH3  0   0.240  5.3381  -12.3566  -10.1521
 SIM  H212  H  HCH3  0   0.219  5.3193  -10.8776  -11.1071
 SIM  H213  H  HCH3  0   0.229  3.8099  -11.5867  -10.5376
 SIM  H221  H  HCH3  0   0.238  3.5683  -13.9565  -14.2985
 SIM  H222  H  HCH3  0   0.235  3.5284  -12.6192  -15.4435
 SIM  H223  H  HCH3  0   0.238  5.0768  -13.2249  -14.8442
 SIM  H231  H  HCH3  0   0.228  2.0576  -12.7737  -12.6992
 SIM  H232  H  HCH3  0   0.239  2.3610  -11.1120  -12.2009
 SIM  H233  H  HCH3  0   0.238  1.9199  -11.4632  -13.8649
 SIM  H241  H  HCH3  0   0.228  3.4205  -10.0872  -17.4315
 SIM  H242  H  HCH3  0   0.230  2.5257  -10.3601  -15.9332
 SIM  H243  H  HCH3  0   0.229  1.7244   -9.6308  -17.3173
 SIM  C18   C  C     0   0.638  4.6827  -10.7642  -13.7776

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
 SIM  O1A  C1    double  1.206  0.020  1.206
 SIM  O1B  C1    single  1.328  0.020  1.328
 SIM  O1B  H1B   single  0.850  0.020  0.980
 SIM  O3   C3    single  1.416  0.020  1.416
 SIM  O3   HO3   single  0.850  0.020  0.980
 SIM  O5   C5    single  1.416  0.020  1.416
 SIM  O5   HO5   single  0.850  0.020  0.980
 SIM  O14  C14   single  1.437  0.020  1.437
 SIM  O14  C18   single  1.321  0.020  1.321
 SIM  O18  C18   double  1.209  0.020  1.209
 SIM  C1   C2    single  1.506  0.020  1.506
 SIM  C2   C3    single  1.519  0.020  1.519
 SIM  C2   H21   single  0.970  0.020  1.090
 SIM  C2   H22   single  0.970  0.020  1.090
 SIM  C3   C4    single  1.526  0.020  1.526
 SIM  C3   H3    single  0.970  0.020  1.090
 SIM  C4   C5    single  1.526  0.020  1.526
 SIM  C4   H41   single  0.970  0.020  1.090
 SIM  C4   H42   single  0.970  0.020  1.090
 SIM  C5   C6    single  1.526  0.020  1.526
 SIM  C5   H5    single  0.970  0.020  1.090
 SIM  C6   C7    single  1.527  0.020  1.527
 SIM  C6   H61   single  0.970  0.020  1.090
 SIM  C6   H62   single  0.970  0.020  1.090
 SIM  C7   C8    single  1.529  0.020  1.529
 SIM  C7   H71   single  0.970  0.020  1.090
 SIM  C7   H72   single  0.970  0.020  1.090
 SIM  C8   C9    single  1.541  0.020  1.541
 SIM  C8   C13   single  1.541  0.020  1.541
 SIM  C8   H8    single  0.970  0.020  1.090
 SIM  C9   C10   single  1.498  0.020  1.498
 SIM  C9   C9A   single  1.533  0.020  1.533
 SIM  C9   H9    single  0.970  0.020  1.090
 SIM  C10  C11   double  1.334  0.020  1.334
 SIM  C10  H10   single  0.930  0.020  1.080
 SIM  C11  C12   single  1.456  0.020  1.456
 SIM  C11  H11   single  0.930  0.020  1.080
 SIM  C12  C17   double  1.338  0.020  1.338
 SIM  C12  C13   single  1.513  0.020  1.513
 SIM  C17  C16   single  1.495  0.020  1.495
 SIM  C17  H17   single  0.930  0.020  1.080
 SIM  C16  C15   single  1.532  0.020  1.532
 SIM  C16  C24   single  1.532  0.020  1.532
 SIM  C16  H16   single  0.970  0.020  1.090
 SIM  C15  C14   single  1.519  0.020  1.519
 SIM  C15  H151  single  0.970  0.020  1.090
 SIM  C15  H152  single  0.970  0.020  1.090
 SIM  C14  C13   single  1.525  0.020  1.525
 SIM  C14  H14   single  0.970  0.020  1.090
 SIM  C13  H13   single  0.970  0.020  1.090
 SIM  C9A  H9A1  single  0.970  0.020  1.090
 SIM  C9A  H9A2  single  0.970  0.020  1.090
 SIM  C9A  H9A3  single  0.970  0.020  1.090
 SIM  C18  C19   single  1.524  0.020  1.524
 SIM  C19  C20   single  1.540  0.020  1.540
 SIM  C19  C22   single  1.535  0.020  1.535
 SIM  C19  C23   single  1.528  0.020  1.528
 SIM  C20  C21   single  1.521  0.020  1.521
 SIM  C20  H201  single  0.970  0.020  1.090
 SIM  C20  H202  single  0.970  0.020  1.090
 SIM  C21  H211  single  0.970  0.020  1.090
 SIM  C21  H212  single  0.970  0.020  1.090
 SIM  C21  H213  single  0.970  0.020  1.090
 SIM  C22  H221  single  0.970  0.020  1.090
 SIM  C22  H222  single  0.970  0.020  1.090
 SIM  C22  H223  single  0.970  0.020  1.090
 SIM  C23  H231  single  0.970  0.020  1.090
 SIM  C23  H232  single  0.970  0.020  1.090
 SIM  C23  H233  single  0.970  0.020  1.090
 SIM  C24  H241  single  0.970  0.020  1.090
 SIM  C24  H242  single  0.970  0.020  1.090
 SIM  C24  H243  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
 SIM  H1B   O1B  C1    109.92  3.000
 SIM  HO3   O3   C3    109.40  3.000
 SIM  HO5   O5   C5    108.73  3.000
 SIM  C18   O14  C14   120.17  3.000
 SIM  C2    C1   O1B   112.45  3.000
 SIM  C2    C1   O1A   124.43  3.000
 SIM  O1B   C1   O1A   123.10  3.000
 SIM  H22   C2   H21   106.87  3.000
 SIM  H22   C2   C3    110.46  3.000
 SIM  H21   C2   C3    109.38  3.000
 SIM  H22   C2   C1    110.71  3.000
 SIM  H21   C2   C1    107.64  3.000
 SIM  C3    C2   C1    111.62  3.000
 SIM  H3    C3   C4    109.36  3.000
 SIM  H3    C3   C2    107.93  3.000
 SIM  C4    C3   C2    110.82  3.000
 SIM  H3    C3   O3    110.48  3.000
 SIM  C4    C3   O3    112.06  3.000
 SIM  C2    C3   O3    106.07  3.000
 SIM  H42   C4   H41   106.89  3.000
 SIM  H42   C4   C5    109.45  3.000
 SIM  H41   C4   C5    108.90  3.000
 SIM  H42   C4   C3    108.34  3.000
 SIM  H41   C4   C3    109.33  3.000
 SIM  C5    C4   C3    113.72  3.000
 SIM  H5    C5   C6    108.30  3.000
 SIM  H5    C5   C4    109.16  3.000
 SIM  C6    C5   C4    111.68  3.000
 SIM  H5    C5   O5    109.30  3.000
 SIM  C6    C5   O5    111.52  3.000
 SIM  C4    C5   O5    106.84  3.000
 SIM  H62   C6   H61   105.82  3.000
 SIM  H62   C6   C7    111.40  3.000
 SIM  H61   C6   C7    108.11  3.000
 SIM  H62   C6   C5    107.83  3.000
 SIM  H61   C6   C5    109.45  3.000
 SIM  C7    C6   C5    113.93  3.000
 SIM  H72   C7   H71   105.41  3.000
 SIM  H72   C7   C8    109.97  3.000
 SIM  H71   C7   C8    109.56  3.000
 SIM  H72   C7   C6    107.36  3.000
 SIM  H71   C7   C6    111.05  3.000
 SIM  C8    C7   C6    113.18  3.000
 SIM  H8    C8   C13   107.48  3.000
 SIM  H8    C8   C9    106.15  3.000
 SIM  C13   C8   C9    110.40  3.000
 SIM  H8    C8   C7    107.41  3.000
 SIM  C13   C8   C7    112.89  3.000
 SIM  C9    C8   C7    112.13  3.000
 SIM  H9    C9   C9A   107.02  3.000
 SIM  H9    C9   C10   106.86  3.000
 SIM  C9A   C9   C10   110.10  3.000
 SIM  H9    C9   C8    107.58  3.000
 SIM  C9A   C9   C8    114.19  3.000
 SIM  C10   C9   C8    110.73  3.000
 SIM  H10   C10  C11   119.62  3.000
 SIM  H10   C10  C9    117.20  3.000
 SIM  C11   C10  C9    123.17  3.000
 SIM  H11   C11  C12   117.19  3.000
 SIM  H11   C11  C10   119.98  3.000
 SIM  C12   C11  C10   122.82  3.000
 SIM  C13   C12  C17   122.65  3.000
 SIM  C13   C12  C11   116.90  3.000
 SIM  C17   C12  C11   120.42  3.000
 SIM  H17   C17  C16   116.21  3.000
 SIM  H17   C17  C12   118.31  3.000
 SIM  C16   C17  C12   125.48  3.000
 SIM  H16   C16  C24   105.99  3.000
 SIM  H16   C16  C15   107.01  3.000
 SIM  C24   C16  C15   114.26  3.000
 SIM  H16   C16  C17   107.14  3.000
 SIM  C24   C16  C17   110.74  3.000
 SIM  C15   C16  C17   111.25  3.000
 SIM  H152  C15  H151  106.00  3.000
 SIM  H152  C15  C14   106.25  3.000
 SIM  H151  C15  C14   110.37  3.000
 SIM  H152  C15  C16   109.04  3.000
 SIM  H151  C15  C16   110.74  3.000
 SIM  C14   C15  C16   114.03  3.000
 SIM  H14   C14  C13   110.03  3.000
 SIM  H14   C14  C15   108.65  3.000
 SIM  C13   C14  C15   111.24  3.000
 SIM  H14   C14  O14   109.28  3.000
 SIM  C13   C14  O14   106.57  3.000
 SIM  C15   C14  O14   111.05  3.000
 SIM  H13   C13  C14   105.57  3.000
 SIM  H13   C13  C12   107.86  3.000
 SIM  C14   C13  C12   110.50  3.000
 SIM  H13   C13  C8    107.42  3.000
 SIM  C14   C13  C8    114.14  3.000
 SIM  C12   C13  C8    110.97  3.000
 SIM  H9A3  C9A  H9A2  107.85  3.000
 SIM  H9A3  C9A  H9A1  107.50  3.000
 SIM  H9A2  C9A  H9A1  107.29  3.000
 SIM  H9A3  C9A  C9    111.64  3.000
 SIM  H9A2  C9A  C9    111.88  3.000
 SIM  H9A1  C9A  C9    110.48  3.000
 SIM  C23   C19  C22   109.01  3.000
 SIM  C23   C19  C20   110.71  3.000
 SIM  C22   C19  C20   108.27  3.000
 SIM  C23   C19  C18   113.14  3.000
 SIM  C22   C19  C18   107.43  3.000
 SIM  C20   C19  C18   108.12  3.000
 SIM  H202  C20  H201  106.21  3.000
 SIM  H202  C20  C21   109.41  3.000
 SIM  H201  C20  C21   109.20  3.000
 SIM  H202  C20  C19   108.90  3.000
 SIM  H201  C20  C19   107.19  3.000
 SIM  C21   C20  C19   115.51  3.000
 SIM  H213  C21  H212  107.61  3.000
 SIM  H213  C21  H211  107.13  3.000
 SIM  H212  C21  H211  107.51  3.000
 SIM  H213  C21  C20   112.35  3.000
 SIM  H212  C21  C20   111.96  3.000
 SIM  H211  C21  C20   110.04  3.000
 SIM  H223  C22  H222  108.26  3.000
 SIM  H223  C22  H221  107.89  3.000
 SIM  H222  C22  H221  107.57  3.000
 SIM  H223  C22  C19   111.76  3.000
 SIM  H222  C22  C19   111.87  3.000
 SIM  H221  C22  C19   109.33  3.000
 SIM  H233  C23  H232  107.42  3.000
 SIM  H233  C23  H231  107.49  3.000
 SIM  H232  C23  H231  107.72  3.000
 SIM  H233  C23  C19   111.79  3.000
 SIM  H232  C23  C19   113.04  3.000
 SIM  H231  C23  C19   109.16  3.000
 SIM  H243  C24  H242  107.41  3.000
 SIM  H243  C24  H241  107.49  3.000
 SIM  H242  C24  H241  108.18  3.000
 SIM  H243  C24  C16   110.54  3.000
 SIM  H242  C24  C16   112.21  3.000
 SIM  H241  C24  C16   110.83  3.000
 SIM  C19   C18  O18   123.08  3.000
 SIM  C19   C18  O14   113.30  3.000
 SIM  O18   C18  O14   123.62  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
 SIM  CONST_01  H1B   O1B  C1   O1A     0.00   0.0  0
 SIM  Var_01    C16   C17  C12  C11   178.78   0.0  0
 SIM  Var_02    C12   C11  C10  C9     -2.01  30.0  1
 SIM  Var_03    C17   C12  C11  C10   178.15  30.0  1
 SIM  Var_04    C8    C7   C6   C5    179.96  30.0  3
 SIM  Var_05    C19   C18  O14  C14   178.66  30.0  3
 SIM  Var_06    C3    C2   C1   O1A   -41.78  30.0  3
 SIM  Var_07    C20   C19  C18  O14  -125.71  30.0  3
 SIM  Var_08    C21   C20  C19  C18    61.64  30.0  3
 SIM  Var_09    H221  C22  C19  C18   178.07  30.0  3
 SIM  Var_10    H231  C23  C19  C18  -177.80  30.0  3
 SIM  Var_11    H211  C21  C20  C19   178.87  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
 SIM  chir_01  C3   O3   C2   C4   negativ
 SIM  chir_02  C5   O5   C4   C6   negativ
 SIM  chir_03  C8   C7   C9   C13  negativ
 SIM  chir_04  C9   C8   C10  C9A  positiv
 SIM  chir_05  C16  C24  C15  C17  positiv
 SIM  chir_06  C14  O14  C15  C13  negativ
 SIM  chir_07  C13  C14  C12  C8   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
 SIM  plan-1  O1A  0.020
 SIM  plan-1  O1B  0.020
 SIM  plan-1  C1   0.020
 SIM  plan-1  C2   0.020
 SIM  plan-1  H1B  0.020
 SIM  plan-2  O14  0.020
 SIM  plan-2  O18  0.020
 SIM  plan-2  C19  0.020
 SIM  plan-2  C18  0.020
 SIM  plan-3  C11  0.020
 SIM  plan-3  C12  0.020
 SIM  plan-3  C17  0.020
 SIM  plan-3  C16  0.020
 SIM  plan-3  C13  0.020
 SIM  plan-3  H17  0.020

