# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:03:07 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: (1S,2R)-2-{[(1S)-5-methyl-1-[(1-oxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2[C@@H](CN3Cc4ccccc4C3=O)N(CCc12)C(=O)[C@@H]5CCCC[C@@H]5C(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
 1VX  1VX  '(1S,2R)-2-{[(1S)-5-methyl-1-[(1-oxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid'  ligand  63  33  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1VX
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
 1VX  C4   C  CR16  0  -0.247   4.6934  -1.4195  -1.9312
 1VX  C5   C  CR16  0  -0.318   3.3273  -1.3319  -1.7382
 1VX  C6   C  CR6   0   0.138   2.8141  -0.8109  -0.5519
 1VX  C11  C  CH1   0  -0.211   1.3096  -0.7205  -0.3989
 1VX  C7   C  CR6   0   0.019   3.6792  -0.3767   0.4522
 1VX  C8   C  CH2   0  -0.505   3.1364   0.1890   1.7378
 1VX  C9   C  CH2   0  -0.344   1.6628  -0.1265   1.9197
 1VX  C13  C  CH2   0  -0.282   0.7038  -2.1250  -0.2107
 1VX  C3   C  CR16  0  -0.316   5.5563  -0.9745  -0.9379
 1VX  C2   C  CR6   0   0.076   5.0668  -0.4492   0.2512
 1VX  N10  N  NT    0  -0.463   0.9490   0.1615   0.6890
 1VX  N14  N  NR5   0  -0.509  -0.7315  -2.1269  -0.1824
 1VX  C15  C  CH2   0  -0.278  -1.5252  -2.1717  -1.3924
 1VX  C16  C  CR56  0   0.093  -2.9208  -2.2716  -0.8645
 1VX  C17  C  CR16  0  -0.326  -4.1289  -2.3476  -1.5342
 1VX  C18  C  CR16  0  -0.245  -5.2912  -2.4312  -0.7756
 1VX  C19  C  CR16  0  -0.261  -5.2453  -2.4385   0.6187
 1VX  C20  C  CR16  0  -0.306  -4.0297  -2.3606   1.2831
 1VX  C21  C  CR56  0  -0.032  -2.8799  -2.2782   0.5178
 1VX  C22  C  CR5   0   0.562  -1.4730  -2.1827   0.9540
 1VX  O23  O  O     0  -0.483  -1.0478  -2.1872   2.0972
 1VX  C24  C  C     0   0.610   0.1794   1.2739   0.5976
 1VX  O25  O  O     0  -0.495  -0.0650   1.9540   1.5859
 1VX  C26  C  CH1   0  -0.422  -0.3214   1.6916  -0.7768
 1VX  C28  C  CH2   0  -0.436   0.8147   2.3353  -1.5925
 1VX  C29  C  CH2   0  -0.433   1.1950   3.7157  -1.0768
 1VX  C30  C  CH2   0  -0.434  -0.0131   4.6412  -1.0993
 1VX  C31  C  CH2   0  -0.419  -1.1689   4.0851  -0.2747
 1VX  C32  C  CH1   0  -0.386  -1.5169   2.6487  -0.6862
 1VX  C34  C  C     0   0.580  -2.6184   2.0139   0.1298
 1VX  O35  O  OH1   0  -0.595  -3.5331   2.8877   0.5397
 1VX  O36  O  O     0  -0.422  -2.7037   0.8317   0.3534
 1VX  H1   H  HCR6  0   0.253   5.0882  -1.8216  -2.8550
 1VX  H2   H  HCR6  0   0.247   2.6507  -1.6596  -2.5200
 1VX  H3   H  HCH1  0   0.290   0.9149  -0.3259  -1.3339
 1VX  H4   H  HCH2  0   0.253   3.6918  -0.2096   2.5904
 1VX  H5   H  HCH2  0   0.253   3.2916   1.2735   1.7589
 1VX  H6   H  HCH2  0   0.256   1.5305  -1.1781   2.1761
 1VX  H7   H  HCH2  0   0.271   1.2351   0.4490   2.7341
 1VX  H8   H  HCH2  0   0.270   1.0404  -2.7581  -1.0341
 1VX  H9   H  HCH2  0   0.270   1.0759  -2.5833   0.7058
 1VX  H10  H  HCR6  0   0.246   6.6272  -1.0325  -1.0926
 1VX  H11  H  HCH3  0   0.247   5.9461  -0.5677   2.2182
 1VX  H12  H  HCH3  0   0.252   7.0456  -0.0071   0.9628
 1VX  H13  H  HCH3  0   0.244   5.8012   1.0661   1.6003
 1VX  H14  H  HCH2  0   0.264  -1.3887  -1.2771  -2.0069
 1VX  H15  H  HCH2  0   0.274  -1.2527  -3.0336  -2.0089
 1VX  H16  H  HCR6  0   0.257  -4.1768  -2.3431  -2.6158
 1VX  H17  H  HCR6  0   0.261  -6.2494  -2.4943  -1.2753
 1VX  H18  H  HCR6  0   0.260  -6.1661  -2.5064   1.1831
 1VX  H19  H  HCR6  0   0.255  -3.9828  -2.3637   2.3647
 1VX  H20  H  HCH1  0   0.284  -0.6663   0.8092  -1.3180
 1VX  H21  H  HCH2  0   0.248   1.6921   1.6849  -1.6151
 1VX  H22  H  HCH2  0   0.240   0.4736   2.4214  -2.6286
 1VX  H23  H  HCH2  0   0.219   1.5911   3.6446  -0.0588
 1VX  H24  H  HCH2  0   0.236   1.9984   4.1247  -1.6933
 1VX  H25  H  HCH2  0   0.233   0.2548   5.6308  -0.7226
 1VX  H26  H  HCH2  0   0.212  -0.3356   4.7835  -2.1367
 1VX  H27  H  HCH2  0   0.234  -0.9104   4.1237   0.7829
 1VX  H28  H  HCH2  0   0.235  -2.0432   4.7231  -0.4119
 1VX  H29  H  HCH1  0   0.290  -1.9226   2.7066  -1.7075
 1VX  H30  H  HOH1  0   0.477  -4.2311   2.4214   1.0232
 1VX  C1   C  CH3   0  -0.740   6.0141   0.0356   1.3097

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
 1VX  C20  C19  aromatic  1.388  0.020  1.388
 1VX  C20  C21  aromatic  1.384  0.020  1.384
 1VX  C19  C18  aromatic  1.395  0.020  1.395
 1VX  O23  C22  double    1.220  0.020  1.220
 1VX  C21  C22  single    1.476  0.020  1.476
 1VX  C21  C16  aromatic  1.383  0.020  1.383
 1VX  C22  N14  single    1.358  0.020  1.358
 1VX  C18  C17  aromatic  1.390  0.020  1.390
 1VX  C16  C17  aromatic  1.383  0.020  1.383
 1VX  C16  C15  single    1.495  0.020  1.495
 1VX  N14  C15  single    1.448  0.020  1.448
 1VX  N14  C13  single    1.436  0.020  1.436
 1VX  C13  C11  single    1.541  0.020  1.541
 1VX  C5   C4   aromatic  1.383  0.020  1.383
 1VX  C5   C6   aromatic  1.394  0.020  1.394
 1VX  C4   C3   aromatic  1.389  0.020  1.389
 1VX  C11  C6   single    1.515  0.020  1.515
 1VX  C11  N10  single    1.446  0.020  1.446
 1VX  C6   C7   aromatic  1.395  0.020  1.395
 1VX  C9   N10  single    1.452  0.020  1.452
 1VX  C9   C8   single    1.518  0.020  1.518
 1VX  C3   C2   aromatic  1.389  0.020  1.389
 1VX  C7   C2   aromatic  1.404  0.020  1.404
 1VX  C7   C8   single    1.506  0.020  1.506
 1VX  N10  C24  single    1.356  0.020  1.356
 1VX  C2   C1   single    1.501  0.020  1.501
 1VX  C29  C28  single    1.522  0.020  1.522
 1VX  C29  C30  single    1.522  0.020  1.522
 1VX  C28  C26  single    1.540  0.020  1.540
 1VX  C24  O25  double    1.224  0.020  1.224
 1VX  C24  C26  single    1.521  0.020  1.521
 1VX  C26  C32  single    1.534  0.020  1.534
 1VX  C30  C31  single    1.525  0.020  1.525
 1VX  C31  C32  single    1.534  0.020  1.534
 1VX  C32  C34  single    1.511  0.020  1.511
 1VX  C34  O36  double    1.206  0.020  1.206
 1VX  C34  O35  single    1.330  0.020  1.330
 1VX  C4   H1   single    0.930  0.020  1.080
 1VX  C5   H2   single    0.930  0.020  1.080
 1VX  C11  H3   single    0.970  0.020  1.090
 1VX  C8   H4   single    0.970  0.020  1.090
 1VX  C8   H5   single    0.970  0.020  1.090
 1VX  C9   H6   single    0.970  0.020  1.090
 1VX  C9   H7   single    0.970  0.020  1.090
 1VX  C13  H8   single    0.970  0.020  1.090
 1VX  C13  H9   single    0.970  0.020  1.090
 1VX  C3   H10  single    0.930  0.020  1.080
 1VX  C1   H11  single    0.970  0.020  1.090
 1VX  C1   H12  single    0.970  0.020  1.090
 1VX  C1   H13  single    0.970  0.020  1.090
 1VX  C15  H14  single    0.970  0.020  1.090
 1VX  C15  H15  single    0.970  0.020  1.090
 1VX  C17  H16  single    0.930  0.020  1.080
 1VX  C18  H17  single    0.930  0.020  1.080
 1VX  C19  H18  single    0.930  0.020  1.080
 1VX  C20  H19  single    0.930  0.020  1.080
 1VX  C26  H20  single    0.970  0.020  1.090
 1VX  C28  H21  single    0.970  0.020  1.090
 1VX  C28  H22  single    0.970  0.020  1.090
 1VX  C29  H23  single    0.970  0.020  1.090
 1VX  C29  H24  single    0.970  0.020  1.090
 1VX  C30  H25  single    0.970  0.020  1.090
 1VX  C30  H26  single    0.970  0.020  1.090
 1VX  C31  H27  single    0.970  0.020  1.090
 1VX  C31  H28  single    0.970  0.020  1.090
 1VX  C32  H29  single    0.970  0.020  1.090
 1VX  O35  H30  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
 1VX  H1   C4   C3   120.19  3.000
 1VX  H1   C4   C5   120.21  3.000
 1VX  C3   C4   C5   119.59  3.000
 1VX  H2   C5   C6   119.79  3.000
 1VX  H2   C5   C4   119.78  3.000
 1VX  C6   C5   C4   120.42  3.000
 1VX  C7   C6   C11  121.65  3.000
 1VX  C7   C6   C5   120.06  3.000
 1VX  C11  C6   C5   118.29  3.000
 1VX  H3   C11  N10  109.54  3.000
 1VX  H3   C11  C13  107.02  3.000
 1VX  N10  C11  C13  111.46  3.000
 1VX  H3   C11  C6   107.15  3.000
 1VX  N10  C11  C6   111.10  3.000
 1VX  C13  C11  C6   110.39  3.000
 1VX  C2   C7   C8   119.86  3.000
 1VX  C8   C7   C6   120.54  3.000
 1VX  C2   C7   C6   119.59  3.000
 1VX  H5   C8   H4   105.90  3.000
 1VX  H5   C8   C9   109.94  3.000
 1VX  H4   C8   C9   108.91  3.000
 1VX  H5   C8   C7   109.71  3.000
 1VX  H4   C8   C7   110.23  3.000
 1VX  C9   C8   C7   111.97  3.000
 1VX  H7   C9   H6   106.69  3.000
 1VX  H7   C9   N10  109.71  3.000
 1VX  H6   C9   N10  109.33  3.000
 1VX  H7   C9   C8   111.24  3.000
 1VX  H6   C9   C8   110.27  3.000
 1VX  N10  C9   C8   109.55  3.000
 1VX  H9   C13  H8   106.57  3.000
 1VX  H9   C13  N14  108.91  3.000
 1VX  H8   C13  N14  108.80  3.000
 1VX  H9   C13  C11  110.59  3.000
 1VX  H8   C13  C11  108.37  3.000
 1VX  N14  C13  C11  113.36  3.000
 1VX  H10  C3   C2   119.39  3.000
 1VX  H10  C3   C4   119.65  3.000
 1VX  C2   C3   C4   120.96  3.000
 1VX  C1   C2   C3   120.23  3.000
 1VX  C1   C2   C7   120.41  3.000
 1VX  C3   C2   C7   119.37  3.000
 1VX  C24  N10  C9   119.94  3.000
 1VX  C24  N10  C11  126.24  3.000
 1VX  C9   N10  C11  113.21  3.000
 1VX  C22  N14  C15  113.50  3.000
 1VX  C15  N14  C13  122.12  3.000
 1VX  C22  N14  C13  124.22  3.000
 1VX  H15  C15  H14  107.26  3.000
 1VX  H15  C15  C16  112.25  3.000
 1VX  H14  C15  C16  111.68  3.000
 1VX  H15  C15  N14  111.02  3.000
 1VX  H14  C15  N14  112.07  3.000
 1VX  C16  C15  N14  102.63  3.000
 1VX  C21  C16  C17  120.63  3.000
 1VX  C17  C16  C15  130.37  3.000
 1VX  C21  C16  C15  109.00  3.000
 1VX  H16  C17  C18  120.55  3.000
 1VX  H16  C17  C16  121.47  3.000
 1VX  C18  C17  C16  117.98  3.000
 1VX  H17  C18  C19  119.35  3.000
 1VX  H17  C18  C17  119.44  3.000
 1VX  C19  C18  C17  121.20  3.000
 1VX  H18  C19  C20  119.95  3.000
 1VX  H18  C19  C18  119.58  3.000
 1VX  C20  C19  C18  120.47  3.000
 1VX  H19  C20  C21  121.12  3.000
 1VX  H19  C20  C19  121.07  3.000
 1VX  C21  C20  C19  117.81  3.000
 1VX  C22  C21  C20  129.23  3.000
 1VX  C22  C21  C16  108.86  3.000
 1VX  C20  C21  C16  121.91  3.000
 1VX  O23  C22  C21  127.52  3.000
 1VX  C21  C22  N14  106.01  3.000
 1VX  O23  C22  N14  126.45  3.000
 1VX  C26  C24  O25  120.73  3.000
 1VX  C26  C24  N10  118.24  3.000
 1VX  O25  C24  N10  120.97  3.000
 1VX  H20  C26  C32  106.72  3.000
 1VX  H20  C26  C28  107.97  3.000
 1VX  C32  C26  C28  110.21  3.000
 1VX  H20  C26  C24  109.27  3.000
 1VX  C32  C26  C24  111.99  3.000
 1VX  C28  C26  C24  110.52  3.000
 1VX  H22  C28  H21  106.11  3.000
 1VX  H22  C28  C29  109.11  3.000
 1VX  H21  C28  C29  110.27  3.000
 1VX  H22  C28  C26  107.73  3.000
 1VX  H21  C28  C26  110.78  3.000
 1VX  C29  C28  C26  112.59  3.000
 1VX  H24  C29  H23  106.44  3.000
 1VX  H24  C29  C30  110.36  3.000
 1VX  H23  C29  C30  109.91  3.000
 1VX  H24  C29  C28  109.40  3.000
 1VX  H23  C29  C28  110.28  3.000
 1VX  C30  C29  C28  110.38  3.000
 1VX  H26  C30  H25  106.33  3.000
 1VX  H26  C30  C31  109.65  3.000
 1VX  H25  C30  C31  109.25  3.000
 1VX  H26  C30  C29  109.06  3.000
 1VX  H25  C30  C29  110.56  3.000
 1VX  C31  C30  C29  111.83  3.000
 1VX  H28  C31  H27  106.95  3.000
 1VX  H28  C31  C32  109.39  3.000
 1VX  H27  C31  C32  110.33  3.000
 1VX  H28  C31  C30  109.03  3.000
 1VX  H27  C31  C30  109.41  3.000
 1VX  C32  C31  C30  111.61  3.000
 1VX  H29  C32  C34  104.75  3.000
 1VX  H29  C32  C31  106.46  3.000
 1VX  C34  C32  C31  114.45  3.000
 1VX  H29  C32  C26  105.39  3.000
 1VX  C34  C32  C26  109.75  3.000
 1VX  C31  C32  C26  115.04  3.000
 1VX  O36  C34  O35  122.57  3.000
 1VX  O35  C34  C32  113.07  3.000
 1VX  O36  C34  C32  124.31  3.000
 1VX  H30  O35  C34  109.46  3.000
 1VX  H13  C1   H12  107.85  3.000
 1VX  H13  C1   H11  106.72  3.000
 1VX  H12  C1   H11  107.58  3.000
 1VX  H13  C1   C2   111.69  3.000
 1VX  H12  C1   C2   111.13  3.000
 1VX  H11  C1   C2   111.64  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
 1VX  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 1VX  CONST_02  C7   C2   C3   C4     0.00   0.0  0
 1VX  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 1VX  CONST_04  C2   C7   C6   C5     0.00   0.0  0
 1VX  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 1VX  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 1VX  CONST_07  C19  C20  C21  C16    0.00   0.0  0
 1VX  CONST_08  C19  C18  C17  C16    0.00   0.0  0
 1VX  CONST_09  C20  C19  C18  C17    0.00   0.0  0
 1VX  CONST_10  C20  C21  C16  C17    0.00   0.0  0
 1VX  CONST_11  C21  C20  C19  C18    0.00   0.0  0
 1VX  CONST_12  C21  C16  C17  C18    0.00   0.0  0
 1VX  CONST_13  C21  C22  N14  C15    0.00   0.0  0
 1VX  CONST_14  C1   C2   C3   C4   180.00   0.0  0
 1VX  CONST_15  C1   C2   C7   C6   180.00   0.0  0
 1VX  CONST_16  C1   C2   C7   C8     0.00   0.0  0
 1VX  CONST_17  C26  C24  N10  C11    0.00   0.0  0
 1VX  CONST_18  C26  C24  N10  C9   180.00   0.0  0
 1VX  CONST_19  C21  C22  N14  C13  180.00   0.0  0
 1VX  CONST_20  O23  C22  N14  C15  180.00   0.0  0
 1VX  CONST_21  H10  C3   C4   C5   180.00   0.0  0
 1VX  CONST_22  H1   C4   C5   C6   180.00   0.0  0
 1VX  CONST_23  H2   C5   C6   C11    0.00   0.0  0
 1VX  CONST_24  H16  C17  C16  C15    0.00   0.0  0
 1VX  CONST_25  H19  C20  C21  C16  180.00   0.0  0
 1VX  CONST_26  H17  C18  C17  C16  180.00   0.0  0
 1VX  CONST_27  H18  C19  C18  C17  180.00   0.0  0
 1VX  CONST_28  O25  C24  N10  C11  180.00   0.0  0
 1VX  CONST_29  O25  C24  N10  C9     0.00   0.0  0
 1VX  CONST_30  O23  C22  N14  C13    0.00   0.0  0
 1VX  CONST_31  H30  O35  C34  C32  180.00   0.0  0
 1VX  Var_01    C9   C8   C7   C6    15.24  30.0  1
 1VX  Var_02    C8   C9   N10  C11   67.08  30.0  1
 1VX  Var_03    N10  C9   C8   C7   -46.90  30.0  1
 1VX  Var_04    C30  C29  C28  C26  -58.09  30.0  1
 1VX  Var_05    C31  C30  C29  C28   57.59  30.0  1
 1VX  Var_06    C32  C31  C30  C29  -52.76  30.0  1
 1VX  Var_07    C22  N14  C13  C11  -99.96  30.0  2
 1VX  Var_08    H14  C15  C16  C17   59.69  30.0  1
 1VX  Var_09    H11  C1   C2   C7    65.01  30.0  2

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
 1VX  chir_01  C11  C13  C6   N10  positiv
 1VX  chir_02  C26  C32  C24  C28  positiv
 1VX  chir_03  C32  C26  C31  C34  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
 1VX  plan-1  C4   0.020
 1VX  plan-1  C5   0.020
 1VX  plan-1  C6   0.020
 1VX  plan-1  C11  0.020
 1VX  plan-1  C7   0.020
 1VX  plan-1  C8   0.020
 1VX  plan-1  C3   0.020
 1VX  plan-1  C2   0.020
 1VX  plan-1  H1   0.020
 1VX  plan-1  H2   0.020
 1VX  plan-1  H10  0.020
 1VX  plan-1  C1   0.020
 1VX  plan-2  C11  0.020
 1VX  plan-2  C9   0.020
 1VX  plan-2  N10  0.020
 1VX  plan-2  C24  0.020
 1VX  plan-2  O25  0.020
 1VX  plan-2  C26  0.020
 1VX  plan-3  C13  0.020
 1VX  plan-3  N14  0.020
 1VX  plan-3  C15  0.020
 1VX  plan-3  C16  0.020
 1VX  plan-3  C17  0.020
 1VX  plan-3  C18  0.020
 1VX  plan-3  C19  0.020
 1VX  plan-3  C20  0.020
 1VX  plan-3  C21  0.020
 1VX  plan-3  C22  0.020
 1VX  plan-3  O23  0.020
 1VX  plan-3  H16  0.020
 1VX  plan-3  H17  0.020
 1VX  plan-3  H18  0.020
 1VX  plan-3  H19  0.020
 1VX  plan-4  C32  0.020
 1VX  plan-4  C34  0.020
 1VX  plan-4  O35  0.020
 1VX  plan-4  O36  0.020
 1VX  plan-4  H30  0.020

