# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 23:45:03 2021
#   Inital geometry file: a 157 line input string
#   Ligand name: (3R,5R)-7-[(1S,2S,6R,8S,8aR)-2,6-dimethyl-8-{[(2S)-2-methylbutanoyl]oxy}-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]-3,5-dihydroxyheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](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
 LVA  LVA  '(3R,5R)-7-[(1S,2S,6R,8S,8aR)-2,6-dimethyl-8-{[(2S)-2-methylbutanoyl]oxy}-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]-3,5-dihydroxyheptanoic acid'  ligand  68  30  .  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_LVA
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
 LVA  O1    O  OH1   0  -0.579  84.0627  123.4471  108.7514
 LVA  O2    O  OH1   0  -0.675  86.9212  127.1421  108.8351
 LVA  O3    O  O     0  -0.428  84.5597  124.2022  106.7600
 LVA  O8    O  OH1   0  -0.699  85.3210  129.2372  109.5529
 LVA  O4    O  O2    0  -0.449  80.9572  127.7496  105.8977
 LVA  C5    C  C1    0  -0.256  79.8042  124.8293  108.6238
 LVA  C6    C  C     0   0.162  79.4227  125.8506  107.6585
 LVA  C7    C  CH1   0   0.090  84.2678  128.4454  109.0403
 LVA  C8    C  C1    0  -0.209  80.5450  125.0933  109.7015
 LVA  C9    C  CH1   0  -0.310  79.8512  127.2690  107.9589
 LVA  C10   C  C     0   0.530  84.8203  124.1719  107.9350
 LVA  C11   C  CH1   0  -0.296  81.0811  126.4590  110.0049
 LVA  C12   C  CH1   0  -0.242  81.1944  127.2898  108.7136
 LVA  C13   C  CH1   0   0.060  85.7647  126.4582  108.3851
 LVA  C14   C  C1    0  -0.291  78.6929  125.5324  106.5830
 LVA  C15   C  CH1   0  -0.012  79.8244  128.1274  106.6990
 LVA  C16   C  CH2   0  -0.471  82.9895  128.8755  109.7640
 LVA  C17   C  CH2   0  -0.521  84.5705  126.9526  109.1915
 LVA  C18   C  CH2   0  -0.464  81.6896  128.7146  108.9728
 LVA  C19   C  CH2   0  -0.464  78.5276  127.9427  105.9294
 LVA  C20   C  CH3   0  -0.663  80.2513  127.1199  111.1115
 LVA  C21   C  CH2   0  -0.631  85.9664  124.9440  108.5436
 LVA  C22   C  CH1   0  -0.271  78.2285  126.4931  105.5359
 LVA  C23   C  CH3   0  -0.664  78.7762  126.0956  104.1617
 LVA  C24   C  C     0   0.608  81.5123  128.6458  105.0980
 LVA  C25   C  CH1   0  -0.361  82.7124  128.1131  104.3438
 LVA  O26   O  O     0  -0.468  81.0945  129.7721  104.9608
 LVA  C27   C  CH2   0  -0.427  82.2876  127.8440  102.8886
 LVA  C28   C  CH3   0  -0.659  83.3748  126.9093  104.9990
 LVA  C29   C  CH3   0  -0.670  83.4601  127.5255  101.9717
 LVA  HO1   H  HOH1  0   0.487  84.3720  123.4916  109.6644
 LVA  HO2   H  HOH1  0   0.467  87.6207  127.0411  108.1810
 LVA  HO8   H  HOH1  0   0.447  86.1501  128.7999  109.3119
 LVA  H5    H  H     0   0.232  79.4464  123.8202  108.4451
 LVA  H7    H  HCH1  0   0.177  84.1279  128.6507  107.9639
 LVA  H8    H  H     0   0.237  80.7670  124.3012  110.4088
 LVA  H9    H  HCH1  0   0.252  79.0972  127.7168  108.6200
 LVA  H11   H  HCH1  0   0.242  82.0897  126.3265  110.4107
 LVA  H12   H  HCH1  0   0.239  81.9202  126.7764  108.0727
 LVA  H13   H  HCH1  0   0.231  85.5912  126.6742  107.3234
 LVA  H14   H  H     0   0.233  78.4144  124.4915  106.4349
 LVA  H15   H  HCH1  0   0.262  79.9189  129.1794  106.9738
 LVA  H161  H  HCH2  0   0.224  82.9279  128.3790  110.7381
 LVA  H162  H  HCH2  0   0.244  83.0935  129.9420  109.9799
 LVA  H171  H  HCH2  0   0.245  84.7120  126.7081  110.2508
 LVA  H172  H  HCH2  0   0.245  83.6943  126.3917  108.8630
 LVA  H181  H  HCH2  0   0.237  81.8303  129.2326  108.0203
 LVA  H182  H  HCH2  0   0.232  80.9053  129.2735  109.4924
 LVA  H191  H  HCH2  0   0.249  77.7294  128.3140  106.5784
 LVA  H192  H  HCH2  0   0.247  78.5194  128.5888  105.0486
 LVA  H201  H  HCH3  0   0.232  80.7098  128.0447  111.4622
 LVA  H202  H  HCH3  0   0.225  79.2385  127.3514  110.7787
 LVA  H203  H  HCH3  0   0.237  80.1662  126.4540  111.9712
 LVA  H211  H  HCH2  0   0.268  86.1195  124.7041  109.5985
 LVA  H212  H  HCH2  0   0.297  86.8740  124.6488  108.0102
 LVA  H22   H  HCH1  0   0.244  77.1384  126.3975  105.4666
 LVA  H231  H  HCH3  0   0.227  78.4070  126.7700  103.3873
 LVA  H232  H  HCH3  0   0.229  79.8651  126.1127  104.1381
 LVA  H233  H  HCH3  0   0.229  78.4572  125.0858  103.8985
 LVA  H25   H  HCH1  0   0.260  83.4290  128.9415  104.3223
 LVA  H271  H  HCH2  0   0.230  81.5693  127.0191  102.8661
 LVA  H272  H  HCH2  0   0.237  81.7658  128.7228  102.5032
 LVA  H281  H  HCH3  0   0.236  84.2868  126.6413  104.4670
 LVA  H282  H  HCH3  0   0.230  83.6607  127.1197  106.0300
 LVA  H283  H  HCH3  0   0.230  82.7249  126.0349  105.0091
 LVA  H291  H  HCH3  0   0.237  83.1223  127.4327  100.9394
 LVA  H292  H  HCH3  0   0.222  84.2108  128.3169  102.0064
 LVA  H293  H  HCH3  0   0.227  83.9495  126.5895  102.2400

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
 LVA  O1   C10   single  1.329  0.020  1.329
 LVA  O1   HO1   single  0.850  0.020  0.980
 LVA  O2   C13   single  1.417  0.020  1.417
 LVA  O2   HO2   single  0.850  0.020  0.980
 LVA  O3   C10   double  1.204  0.020  1.204
 LVA  O8   C7    single  1.414  0.020  1.414
 LVA  O8   HO8   single  0.850  0.020  0.980
 LVA  O4   C15   single  1.438  0.020  1.438
 LVA  O4   C24   single  1.323  0.020  1.323
 LVA  C5   C6    single  1.456  0.020  1.456
 LVA  C5   C8    double  1.334  0.020  1.334
 LVA  C5   H5    single  0.930  0.020  1.080
 LVA  C6   C9    single  1.512  0.020  1.512
 LVA  C6   C14   double  1.338  0.020  1.338
 LVA  C7   C16   single  1.531  0.020  1.531
 LVA  C7   C17   single  1.531  0.020  1.531
 LVA  C7   H7    single  0.970  0.020  1.090
 LVA  C8   C11   single  1.498  0.020  1.498
 LVA  C8   H8    single  0.930  0.020  1.080
 LVA  C9   C12   single  1.541  0.020  1.541
 LVA  C9   C15   single  1.525  0.020  1.525
 LVA  C9   H9    single  0.970  0.020  1.090
 LVA  C10  C21   single  1.510  0.020  1.510
 LVA  C11  C12   single  1.540  0.020  1.540
 LVA  C11  C20   single  1.533  0.020  1.533
 LVA  C11  H11   single  0.970  0.020  1.090
 LVA  C12  C18   single  1.530  0.020  1.530
 LVA  C12  H12   single  0.970  0.020  1.090
 LVA  C13  C17   single  1.523  0.020  1.523
 LVA  C13  C21   single  1.536  0.020  1.536
 LVA  C13  H13   single  0.970  0.020  1.090
 LVA  C14  C22   single  1.495  0.020  1.495
 LVA  C14  H14   single  0.930  0.020  1.080
 LVA  C15  C19   single  1.519  0.020  1.519
 LVA  C15  H15   single  0.970  0.020  1.090
 LVA  C16  C18   single  1.530  0.020  1.530
 LVA  C16  H161  single  0.970  0.020  1.090
 LVA  C16  H162  single  0.970  0.020  1.090
 LVA  C17  H171  single  0.970  0.020  1.090
 LVA  C17  H172  single  0.970  0.020  1.090
 LVA  C18  H181  single  0.970  0.020  1.090
 LVA  C18  H182  single  0.970  0.020  1.090
 LVA  C19  C22   single  1.532  0.020  1.532
 LVA  C19  H191  single  0.970  0.020  1.090
 LVA  C19  H192  single  0.970  0.020  1.090
 LVA  C20  H201  single  0.970  0.020  1.090
 LVA  C20  H202  single  0.970  0.020  1.090
 LVA  C20  H203  single  0.970  0.020  1.090
 LVA  C21  H211  single  0.970  0.020  1.090
 LVA  C21  H212  single  0.970  0.020  1.090
 LVA  C22  C23   single  1.532  0.020  1.532
 LVA  C22  H22   single  0.970  0.020  1.090
 LVA  C23  H231  single  0.970  0.020  1.090
 LVA  C23  H232  single  0.970  0.020  1.090
 LVA  C23  H233  single  0.970  0.020  1.090
 LVA  C24  C25   single  1.514  0.020  1.514
 LVA  C24  O26   double  1.209  0.020  1.209
 LVA  C25  C27   single  1.540  0.020  1.540
 LVA  C25  C28   single  1.522  0.020  1.522
 LVA  C25  H25   single  0.970  0.020  1.090
 LVA  C27  C29   single  1.522  0.020  1.522
 LVA  C27  H271  single  0.970  0.020  1.090
 LVA  C27  H272  single  0.970  0.020  1.090
 LVA  C28  H281  single  0.970  0.020  1.090
 LVA  C28  H282  single  0.970  0.020  1.090
 LVA  C28  H283  single  0.970  0.020  1.090
 LVA  C29  H291  single  0.970  0.020  1.090
 LVA  C29  H292  single  0.970  0.020  1.090
 LVA  C29  H293  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
 LVA  HO1   O1   C10   111.92  3.000
 LVA  HO2   O2   C13   109.06  3.000
 LVA  HO8   O8   C7    107.15  3.000
 LVA  C24   O4   C15   119.29  3.000
 LVA  H5    C5   C8    120.00  3.000
 LVA  H5    C5   C6    117.16  3.000
 LVA  C8    C5   C6    122.83  3.000
 LVA  C14   C6   C9    122.51  3.000
 LVA  C14   C6   C5    120.59  3.000
 LVA  C9    C6   C5    116.87  3.000
 LVA  H7    C7   C17   107.61  3.000
 LVA  H7    C7   C16   107.62  3.000
 LVA  C17   C7   C16   113.11  3.000
 LVA  H7    C7   O8    110.09  3.000
 LVA  C17   C7   O8    111.29  3.000
 LVA  C16   C7   O8    107.06  3.000
 LVA  H8    C8   C11   117.41  3.000
 LVA  H8    C8   C5    119.72  3.000
 LVA  C11   C8   C5    122.87  3.000
 LVA  H9    C9   C15   104.82  3.000
 LVA  H9    C9   C12   107.35  3.000
 LVA  C15   C9   C12   114.36  3.000
 LVA  H9    C9   C6    107.91  3.000
 LVA  C15   C9   C6    111.04  3.000
 LVA  C12   C9   C6    110.92  3.000
 LVA  C21   C10  O3    123.01  3.000
 LVA  C21   C10  O1    117.65  3.000
 LVA  O3    C10  O1    119.33  3.000
 LVA  H11   C11  C20   106.45  3.000
 LVA  H11   C11  C12   107.96  3.000
 LVA  C20   C11  C12   114.37  3.000
 LVA  H11   C11  C8    107.11  3.000
 LVA  C20   C11  C8    110.21  3.000
 LVA  C12   C11  C8    110.39  3.000
 LVA  H12   C12  C18   108.72  3.000
 LVA  H12   C12  C11   106.64  3.000
 LVA  C18   C12  C11   112.59  3.000
 LVA  H12   C12  C9    106.53  3.000
 LVA  C18   C12  C9    112.18  3.000
 LVA  C11   C12  C9    109.84  3.000
 LVA  H13   C13  C21   108.35  3.000
 LVA  H13   C13  C17   108.92  3.000
 LVA  C21   C13  C17   111.61  3.000
 LVA  H13   C13  O2    109.96  3.000
 LVA  C21   C13  O2    109.63  3.000
 LVA  C17   C13  O2    108.36  3.000
 LVA  H14   C14  C22   116.10  3.000
 LVA  H14   C14  C6    118.47  3.000
 LVA  C22   C14  C6    125.42  3.000
 LVA  H15   C15  C19   108.58  3.000
 LVA  H15   C15  C9    109.46  3.000
 LVA  C19   C15  C9    111.41  3.000
 LVA  H15   C15  O4    108.98  3.000
 LVA  C19   C15  O4    110.99  3.000
 LVA  C9    C15  O4    107.38  3.000
 LVA  H162  C16  H161  105.78  3.000
 LVA  H162  C16  C18   106.59  3.000
 LVA  H161  C16  C18   111.38  3.000
 LVA  H162  C16  C7    106.75  3.000
 LVA  H161  C16  C7    109.88  3.000
 LVA  C18   C16  C7    115.81  3.000
 LVA  H172  C17  H171  106.25  3.000
 LVA  H172  C17  C13   107.65  3.000
 LVA  H171  C17  C13   109.75  3.000
 LVA  H172  C17  C7    108.23  3.000
 LVA  H171  C17  C7    109.78  3.000
 LVA  C13   C17  C7    114.79  3.000
 LVA  H182  C18  H181  105.30  3.000
 LVA  H182  C18  C16   108.03  3.000
 LVA  H181  C18  C16   106.93  3.000
 LVA  H182  C18  C12   108.91  3.000
 LVA  H181  C18  C12   109.59  3.000
 LVA  C16   C18  C12   117.41  3.000
 LVA  H192  C19  H191  105.79  3.000
 LVA  H192  C19  C22   110.56  3.000
 LVA  H191  C19  C22   109.35  3.000
 LVA  H192  C19  C15   110.05  3.000
 LVA  H191  C19  C15   106.32  3.000
 LVA  C22   C19  C15   114.33  3.000
 LVA  H203  C20  H202  107.31  3.000
 LVA  H203  C20  H201  107.28  3.000
 LVA  H202  C20  H201  107.97  3.000
 LVA  H203  C20  C11   110.36  3.000
 LVA  H202  C20  C11   111.95  3.000
 LVA  H201  C20  C11   111.74  3.000
 LVA  H212  C21  H211  107.18  3.000
 LVA  H212  C21  C13   108.96  3.000
 LVA  H211  C21  C13   109.54  3.000
 LVA  H212  C21  C10   107.18  3.000
 LVA  H211  C21  C10   112.54  3.000
 LVA  C13   C21  C10   111.28  3.000
 LVA  H22   C22  C23   106.03  3.000
 LVA  H22   C22  C19   107.03  3.000
 LVA  C23   C22  C19   113.97  3.000
 LVA  H22   C22  C14   107.28  3.000
 LVA  C23   C22  C14   110.52  3.000
 LVA  C19   C22  C14   111.56  3.000
 LVA  H233  C23  H232  107.56  3.000
 LVA  H233  C23  H231  107.57  3.000
 LVA  H232  C23  H231  108.25  3.000
 LVA  H233  C23  C22   110.61  3.000
 LVA  H232  C23  C22   111.89  3.000
 LVA  H231  C23  C22   110.81  3.000
 LVA  O26   C24  C25   123.02  3.000
 LVA  O26   C24  O4    123.68  3.000
 LVA  C25   C24  O4    113.28  3.000
 LVA  H25   C25  C28   108.77  3.000
 LVA  H25   C25  C27   107.11  3.000
 LVA  C28   C25  C27   112.87  3.000
 LVA  H25   C25  C24   105.20  3.000
 LVA  C28   C25  C24   114.12  3.000
 LVA  C27   C25  C24   108.28  3.000
 LVA  H272  C27  H271  106.61  3.000
 LVA  H272  C27  C29   108.89  3.000
 LVA  H271  C27  C29   109.61  3.000
 LVA  H272  C27  C25   108.94  3.000
 LVA  H271  C27  C25   109.41  3.000
 LVA  C29   C27  C25   113.16  3.000
 LVA  H283  C28  H282  107.61  3.000
 LVA  H283  C28  H281  107.85  3.000
 LVA  H282  C28  H281  106.85  3.000
 LVA  H283  C28  C25   112.28  3.000
 LVA  H282  C28  C25   111.62  3.000
 LVA  H281  C28  C25   110.41  3.000
 LVA  H293  C29  H292  107.83  3.000
 LVA  H293  C29  H291  107.41  3.000
 LVA  H292  C29  H291  107.76  3.000
 LVA  H293  C29  C27   112.17  3.000
 LVA  H292  C29  C27   111.04  3.000
 LVA  H291  C29  C27   110.46  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
 LVA  CONST_01  HO1   O1   C10  O3    180.00   0.0  0
 LVA  Var_01    C22   C14  C6   C5    179.22   0.0  0
 LVA  Var_02    C11   C8   C5   C6     -1.43  30.0  1
 LVA  Var_03    C9    C6   C5   C8     -2.81  30.0  1
 LVA  Var_04    C12   C18  C16  C7     70.11  30.0  3
 LVA  Var_05    C25   C24  O4   C15   178.64  30.0  3
 LVA  Var_06    C13   C21  C10  O1   -115.70  30.0  3
 LVA  Var_07    H291  C29  C27  C25  -174.84  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
 LVA  chir_01  C7   O8   C16  C17  positiv
 LVA  chir_02  C9   C6   C12  C15  negativ
 LVA  chir_03  C11  C20  C12  C8   positiv
 LVA  chir_04  C12  C18  C11  C9   negativ
 LVA  chir_05  C13  O2   C17  C21  positiv
 LVA  chir_06  C15  O4   C9   C19  positiv
 LVA  chir_07  C22  C23  C19  C14  positiv
 LVA  chir_08  C25  C24  C27  C28  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
 LVA  plan-1  O1   0.020
 LVA  plan-1  O3   0.020
 LVA  plan-1  C10  0.020
 LVA  plan-1  C21  0.020
 LVA  plan-1  HO1  0.020
 LVA  plan-2  C5   0.020
 LVA  plan-2  C6   0.020
 LVA  plan-2  C9   0.020
 LVA  plan-2  C14  0.020
 LVA  plan-2  C22  0.020
 LVA  plan-2  H14  0.020
 LVA  plan-3  O4   0.020
 LVA  plan-3  C24  0.020
 LVA  plan-3  C25  0.020
 LVA  plan-3  O26  0.020

