# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 15:19:03 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  62  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   4.7032  -1.3986  -1.9044
 1VX  C5   C  CR16   0  -0.321   3.3320  -1.3297  -1.7395
 1VX  C6   C  CR6    0   0.137   2.7864  -0.8265  -0.5602
 1VX  C11  C  CH1    0  -0.208   1.2778  -0.7446  -0.4385
 1VX  C7   C  CR6    0   0.020   3.6255  -0.3924   0.4668
 1VX  C8   C  CH2    0  -0.505   3.0498   0.1533   1.7473
 1VX  C9   C  CH2    0  -0.346   1.5730  -0.1711   1.8870
 1VX  C13  C  CH2    0  -0.281   0.6797  -2.1568  -0.2749
 1VX  C3   C  CR16   0  -0.318   5.5394  -0.9516  -0.8896
 1VX  C2   C  CR6    0   0.076   5.0177  -0.4445   0.2940
 1VX  N10  N  NT     0  -0.465   0.8891   0.1289   0.6436
 1VX  N14  N  NR5    0  -0.502  -0.7515  -2.1680  -0.1835
 1VX  C15  C  CH2    0  -0.282  -1.6028  -1.9976  -1.3424
 1VX  C16  C  CR56   0   0.125  -2.9703  -2.1946  -0.7750
 1VX  C17  C  CR16   0  -0.330  -4.2060  -2.1996  -1.3952
 1VX  C18  C  CR16   0  -0.245  -5.3322  -2.4063  -0.6061
 1VX  C19  C  CR16   0  -0.263  -5.2240  -2.6016   0.7710
 1VX  C20  C  CR16   0  -0.312  -3.9799  -2.5951   1.3865
 1VX  C21  C  CR56   0  -0.040  -2.8671  -2.3901   0.5898
 1VX  C22  C  CR5    0   0.557  -1.4411  -2.3551   0.9688
 1VX  O23  O  O      0  -0.490  -0.9666  -2.5052   2.0840
 1VX  C24  C  C      0   0.614   0.1952   1.2945   0.5192
 1VX  O25  O  O      0  -0.503  -0.0015   1.9994   1.5010
 1VX  C26  C  CH1    0  -0.415  -0.2465   1.7278  -0.8664
 1VX  C28  C  CH2    0  -0.428   0.9303   2.3782  -1.6160
 1VX  C29  C  CH2    0  -0.427   1.2667   3.7676  -1.0918
 1VX  C30  C  CH2    0  -0.429   0.0446   4.6742  -1.1691
 1VX  C31  C  CH2    0  -0.408  -1.1393   4.0928  -0.4027
 1VX  C32  C  CH1    0  -0.376  -1.4608   2.6600  -0.8277
 1VX  C34  C  C      0   0.440  -2.6320   2.0289  -0.0458
 1VX  O35  O  OC    -1  -0.621  -3.5379   2.8015   0.3356
 1VX  O36  O  O      0  -0.566  -2.6074   0.7921   0.1118
 1VX  H1   H  HCR6   0   0.251   5.1223  -1.7867  -2.8235
 1VX  H2   H  HCR6   0   0.246   2.6770  -1.6571  -2.5395
 1VX  H3   H  HCH1   0   0.289   0.9025  -0.3445  -1.3786
 1VX  H4   H  HCH2   0   0.250   3.5892  -0.2532   2.6067
 1VX  H5   H  HCH2   0   0.250   3.1986   1.2383   1.7857
 1VX  H6   H  HCH2   0   0.255   1.4394  -1.2269   2.1247
 1VX  H7   H  HCH2   0   0.265   1.1225   0.3902   2.6993
 1VX  H8   H  HCH2   0   0.264   0.9870  -2.7592  -1.1330
 1VX  H9   H  HCH2   0   0.267   1.0852  -2.6453   0.6110
 1VX  H10  H  HCR6   0   0.244   6.6141  -0.9934  -1.0225
 1VX  H11  H  HCH3   0   0.246   5.8540  -0.5602   2.2807
 1VX  H12  H  HCH3   0   0.251   6.9759   0.0147   1.0517
 1VX  H13  H  HCH3   0   0.244   5.7067   1.0736   1.6637
 1VX  H14  H  HCH2   0   0.273  -1.5011  -0.9968  -1.7686
 1VX  H15  H  HCH2   0   0.263  -1.3581  -2.7258  -2.1208
 1VX  H16  H  HCR6   0   0.253  -4.3028  -2.0506  -2.4634
 1VX  H17  H  HCR6   0   0.259  -6.3112  -2.4183  -1.0679
 1VX  H18  H  HCR6   0   0.257  -6.1178  -2.7634   1.3593
 1VX  H19  H  HCR6   0   0.253  -3.8842  -2.7462   2.4544
 1VX  H20  H  HCH1   0   0.269  -0.5566   0.8491  -1.4310
 1VX  H21  H  HCH2   0   0.234   1.8151   1.7350  -1.5915
 1VX  H22  H  HCH2   0   0.226   0.6455   2.4588  -2.6702
 1VX  H23  H  HCH2   0   0.212   1.6197   3.7064  -0.0578
 1VX  H24  H  HCH2   0   0.224   2.0904   4.1877  -1.6746
 1VX  H25  H  HCH2   0   0.218   0.2846   5.6698  -0.7858
 1VX  H26  H  HCH2   0   0.198  -0.2288   4.8094  -2.2223
 1VX  H27  H  HCH2   0   0.210  -0.9267   4.1285   0.6662
 1VX  H28  H  HCH2   0   0.207  -2.0212   4.7149  -0.5634
 1VX  H29  H  HCH1   0   0.222  -1.8009   2.7211  -1.8741
 1VX  C1   C  CH3    0  -0.740   5.9364   0.0459   1.3753

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    1.221  0.020  1.221
 1VX  C21  C22  single    1.476  0.020  1.476
 1VX  C21  C16  aromatic  1.383  0.020  1.383
 1VX  C22  N14  single    1.356  0.020  1.356
 1VX  C18  C17  aromatic  1.391  0.020  1.391
 1VX  C16  C17  aromatic  1.383  0.020  1.383
 1VX  C16  C15  single    1.494  0.020  1.494
 1VX  N14  C15  single    1.448  0.020  1.448
 1VX  N14  C13  single    1.434  0.020  1.434
 1VX  C13  C11  single    1.542  0.020  1.542
 1VX  C5   C4   aromatic  1.383  0.020  1.383
 1VX  C5   C6   aromatic  1.393  0.020  1.393
 1VX  C4   C3   aromatic  1.389  0.020  1.389
 1VX  C11  C6   single    1.516  0.020  1.516
 1VX  C11  N10  single    1.444  0.020  1.444
 1VX  C6   C7   aromatic  1.395  0.020  1.395
 1VX  C9   N10  single    1.450  0.020  1.450
 1VX  C9   C8   single    1.519  0.020  1.519
 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    1.362  0.020  1.362
 1VX  C2   C1   single    1.501  0.020  1.501
 1VX  C29  C28  single    1.523  0.020  1.523
 1VX  C29  C30  single    1.524  0.020  1.524
 1VX  C28  C26  single    1.539  0.020  1.539
 1VX  C24  O25  double    1.224  0.020  1.224
 1VX  C24  C26  single    1.518  0.020  1.518
 1VX  C26  C32  single    1.531  0.020  1.531
 1VX  C30  C31  single    1.525  0.020  1.525
 1VX  C31  C32  single    1.529  0.020  1.529
 1VX  C32  C34  single    1.543  0.020  1.543
 1VX  C34  O36  deloc     1.247  0.020  1.247
 1VX  C34  O35  deloc     1.250  0.020  1.250
 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

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   119.60  3.000
 1VX  H2   C5   C6   119.80  3.000
 1VX  H2   C5   C4   119.72  3.000
 1VX  C6   C5   C4   120.48  3.000
 1VX  C7   C6   C11  121.51  3.000
 1VX  C7   C6   C5   119.98  3.000
 1VX  C11  C6   C5   118.50  3.000
 1VX  H3   C11  N10  109.39  3.000
 1VX  H3   C11  C13  107.13  3.000
 1VX  N10  C11  C13  111.71  3.000
 1VX  H3   C11  C6   107.08  3.000
 1VX  N10  C11  C6   111.15  3.000
 1VX  C13  C11  C6   110.18  3.000
 1VX  C2   C7   C8   119.81  3.000
 1VX  C8   C7   C6   120.57  3.000
 1VX  C2   C7   C6   119.62  3.000
 1VX  H5   C8   H4   105.88  3.000
 1VX  H5   C8   C9   109.90  3.000
 1VX  H4   C8   C9   109.15  3.000
 1VX  H5   C8   C7   109.67  3.000
 1VX  H4   C8   C7   110.19  3.000
 1VX  C9   C8   C7   111.87  3.000
 1VX  H7   C9   H6   106.67  3.000
 1VX  H7   C9   N10  109.81  3.000
 1VX  H6   C9   N10  109.23  3.000
 1VX  H7   C9   C8   111.23  3.000
 1VX  H6   C9   C8   110.25  3.000
 1VX  N10  C9   C8   109.60  3.000
 1VX  H9   C13  H8   106.66  3.000
 1VX  H9   C13  N14  108.42  3.000
 1VX  H8   C13  N14  109.05  3.000
 1VX  H9   C13  C11  110.63  3.000
 1VX  H8   C13  C11  108.20  3.000
 1VX  N14  C13  C11  113.64  3.000
 1VX  H10  C3   C2   119.40  3.000
 1VX  H10  C3   C4   119.68  3.000
 1VX  C2   C3   C4   120.92  3.000
 1VX  C1   C2   C3   120.20  3.000
 1VX  C1   C2   C7   120.41  3.000
 1VX  C3   C2   C7   119.39  3.000
 1VX  C24  N10  C9   119.70  3.000
 1VX  C24  N10  C11  125.90  3.000
 1VX  C9   N10  C11  112.98  3.000
 1VX  C22  N14  C15  113.42  3.000
 1VX  C15  N14  C13  122.33  3.000
 1VX  C22  N14  C13  124.25  3.000
 1VX  H15  C15  H14  108.15  3.000
 1VX  H15  C15  C16  112.79  3.000
 1VX  H14  C15  C16  110.75  3.000
 1VX  H15  C15  N14  111.09  3.000
 1VX  H14  C15  N14  111.42  3.000
 1VX  C16  C15  N14  102.64  3.000
 1VX  C21  C16  C17  120.60  3.000
 1VX  C17  C16  C15  130.42  3.000
 1VX  C21  C16  C15  108.98  3.000
 1VX  H16  C17  C18  120.52  3.000
 1VX  H16  C17  C16  121.46  3.000
 1VX  C18  C17  C16  118.02  3.000
 1VX  H17  C18  C19  119.32  3.000
 1VX  H17  C18  C17  119.47  3.000
 1VX  C19  C18  C17  121.21  3.000
 1VX  H18  C19  C20  119.99  3.000
 1VX  H18  C19  C18  119.58  3.000
 1VX  C20  C19  C18  120.43  3.000
 1VX  H19  C20  C21  121.16  3.000
 1VX  H19  C20  C19  121.06  3.000
 1VX  C21  C20  C19  117.78  3.000
 1VX  C22  C21  C20  129.24  3.000
 1VX  C22  C21  C16  108.80  3.000
 1VX  C20  C21  C16  121.95  3.000
 1VX  O23  C22  C21  127.37  3.000
 1VX  C21  C22  N14  106.05  3.000
 1VX  O23  C22  N14  126.54  3.000
 1VX  C26  C24  O25  121.40  3.000
 1VX  C26  C24  N10  118.42  3.000
 1VX  O25  C24  N10  120.08  3.000
 1VX  H20  C26  C32  106.16  3.000
 1VX  H20  C26  C28  107.82  3.000
 1VX  C32  C26  C28  111.18  3.000
 1VX  H20  C26  C24  109.01  3.000
 1VX  C32  C26  C24  112.43  3.000
 1VX  C28  C26  C24  110.04  3.000
 1VX  H22  C28  H21  105.97  3.000
 1VX  H22  C28  C29  108.77  3.000
 1VX  H21  C28  C29  110.49  3.000
 1VX  H22  C28  C26  107.52  3.000
 1VX  H21  C28  C26  111.04  3.000
 1VX  C29  C28  C26  112.76  3.000
 1VX  H24  C29  H23  106.39  3.000
 1VX  H24  C29  C30  110.41  3.000
 1VX  H23  C29  C30  109.87  3.000
 1VX  H24  C29  C28  109.49  3.000
 1VX  H23  C29  C28  110.21  3.000
 1VX  C30  C29  C28  110.38  3.000
 1VX  H26  C30  H25  106.21  3.000
 1VX  H26  C30  C31  109.64  3.000
 1VX  H25  C30  C31  109.95  3.000
 1VX  H26  C30  C29  108.79  3.000
 1VX  H25  C30  C29  110.36  3.000
 1VX  C31  C30  C29  111.73  3.000
 1VX  H28  C31  H27  106.46  3.000
 1VX  H28  C31  C32  108.87  3.000
 1VX  H27  C31  C32  110.14  3.000
 1VX  H28  C31  C30  109.63  3.000
 1VX  H27  C31  C30  109.19  3.000
 1VX  C32  C31  C30  112.38  3.000
 1VX  H29  C32  C34  105.64  3.000
 1VX  H29  C32  C31  106.07  3.000
 1VX  C34  C32  C31  113.71  3.000
 1VX  H29  C32  C26  104.74  3.000
 1VX  C34  C32  C26  111.45  3.000
 1VX  C31  C32  C26  114.25  3.000
 1VX  O36  C34  O35  126.06  3.000
 1VX  O35  C34  C32  116.86  3.000
 1VX  O36  C34  C32  117.04  3.000
 1VX  H13  C1   H12  107.83  3.000
 1VX  H13  C1   H11  106.70  3.000
 1VX  H12  C1   H11  107.60  3.000
 1VX  H13  C1   C2   111.65  3.000
 1VX  H12  C1   C2   111.14  3.000
 1VX  H11  C1   C2   111.69  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  Var_01    C9   C8   C7   C6     14.68  30.0  1
 1VX  Var_02    C8   C9   N10  C11    67.46  30.0  1
 1VX  Var_03    N10  C9   C8   C7    -46.79  30.0  1
 1VX  Var_04    C30  C29  C28  C26   -56.92  30.0  1
 1VX  Var_05    C31  C30  C29  C28    56.92  30.0  1
 1VX  Var_06    C32  C31  C30  C29   -53.09  30.0  1
 1VX  Var_07    C22  N14  C13  C11  -104.39  30.0  2
 1VX  Var_08    H14  C15  C16  C17    63.46  30.0  1
 1VX  Var_09    H11  C1   C2   C7     64.64  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

