# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:04:24 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (1R,2R)-2-{[(1S)-1-[(1,3-dioxo-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: OC(=O)[C@@H]1CCCC[C@H]1C(=O)N2CCc3ccccc3[C@H]2CN4C(=O)c5ccccc5C4=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
 12O  12O  '(1R,2R)-2-{[(1S)-1-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid'  ligand  59  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_12O
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
 12O  O33  O  OH1   0  -0.595  -4.8353  -2.3349  -2.3370
 12O  C31  C  C     0   0.568  -4.2821  -1.2287  -1.8536
 12O  O32  O  O     0  -0.439  -3.6169  -0.4786  -2.5259
 12O  C26  C  CH1   0  -0.359  -4.6099  -1.0179  -0.3970
 12O  C27  C  CH2   0  -0.431  -6.0916  -0.6484  -0.2281
 12O  C28  C  CH2   0  -0.434  -6.4315  -0.4227   1.2401
 12O  C29  C  CH2   0  -0.434  -5.5192   0.6166   1.8785
 12O  C30  C  CH2   0  -0.426  -4.0512   0.2548   1.6913
 12O  C25  C  CH1   0  -0.397  -3.7161   0.0640   0.2044
 12O  C23  C  C     0   0.614  -2.2536  -0.3175   0.0581
 12O  O24  O  O     0  -0.501  -1.9231  -1.4972   0.0752
 12O  N14  N  NT    0  -0.483  -1.3356   0.6736  -0.0364
 12O  C15  C  CH2   0  -0.291  -1.7073   2.0850  -0.1217
 12O  C16  C  CH2   0  -0.550  -0.5272   3.0020   0.1602
 12O  C17  C  CR6   0   0.112   0.6235   2.6555  -0.7303
 12O  C22  C  CR16  0  -0.325   1.4233   3.6055  -1.3517
 12O  C21  C  CR16  0  -0.252   2.4738   3.2121  -2.1699
 12O  C20  C  CR16  0  -0.252   2.7123   1.8625  -2.3924
 12O  C19  C  CR16  0  -0.315   1.9011   0.9110  -1.7900
 12O  C18  C  CR6   0   0.120   0.8661   1.3030  -0.9495
 12O  C13  C  CH1   0  -0.182   0.0623   0.2794  -0.1984
 12O  C12  C  CH2   0  -0.302   0.6771   0.0097   1.1931
 12O  N8   N  NR5   0  -0.597   2.0859  -0.2905   1.1151
 12O  C7   C  CR5   0   0.584   3.0920   0.6516   1.3003
 12O  O11  O  O     0  -0.388   2.9255   1.7953   1.6352
 12O  C2   C  CR56  0  -0.023   4.3649  -0.0551   1.0251
 12O  C9   C  CR5   0   0.569   2.5937  -1.5267   0.7492
 12O  O10  O  O     0  -0.399   1.9352  -2.5102   0.5207
 12O  C3   C  CR56  0  -0.025   4.0655  -1.3675   0.6994
 12O  C4   C  CR16  0  -0.296   5.0505  -2.2820   0.3941
 12O  C5   C  CR16  0  -0.241   6.3687  -1.8304   0.4255
 12O  C6   C  CR16  0  -0.241   6.6700  -0.5114   0.7535
 12O  C1   C  CR16  0  -0.297   5.6642   0.4031   1.0617
 12O  H1   H  HOH1  0   0.480  -4.6341  -2.4221  -3.2809
 12O  H2   H  HCH1  0   0.274  -4.4365  -1.9646   0.1237
 12O  H3   H  HCH2  0   0.229  -6.3102   0.2597  -0.7998
 12O  H4   H  HCH2  0   0.251  -6.7226  -1.4389  -0.6376
 12O  H5   H  HCH2  0   0.239  -7.4758  -0.1154   1.3293
 12O  H6   H  HCH2  0   0.220  -6.3402  -1.3692   1.7832
 12O  H7   H  HCH2  0   0.220  -5.7104   1.5972   1.4307
 12O  H8   H  HCH2  0   0.238  -5.7419   0.7123   2.9433
 12O  H9   H  HCH2  0   0.246  -3.4164   1.0308   2.1260
 12O  H10  H  HCH2  0   0.234  -3.8235  -0.6697   2.2310
 12O  H11  H  HCH1  0   0.267  -3.9298   1.0005  -0.3160
 12O  H12  H  HCH2  0   0.250  -2.1015   2.3108  -1.1168
 12O  H13  H  HCH2  0   0.263  -2.4910   2.3042   0.6006
 12O  H14  H  HCH2  0   0.276  -0.8489   4.0320   0.0028
 12O  H15  H  HCH2  0   0.259  -0.2359   2.9261   1.2121
 12O  H16  H  HCR6  0   0.250   1.2257   4.6591  -1.1921
 12O  H17  H  HCR6  0   0.255   3.0994   3.9582  -2.6425
 12O  H18  H  HCR6  0   0.255   3.5226   1.5516  -3.0387
 12O  H19  H  HCR6  0   0.253   2.0735  -0.1423  -1.9804
 12O  H20  H  HCH1  0   0.285   0.0819  -0.6573  -0.7579
 12O  H21  H  HCH2  0   0.273   0.5584   0.8777   1.8389
 12O  H22  H  HCH2  0   0.285   0.1611  -0.8256   1.6648
 12O  H23  H  HCR6  0   0.276   4.8159  -3.3072   0.1404
 12O  H24  H  HCR6  0   0.279   7.1730  -2.5151   0.1921
 12O  H25  H  HCR6  0   0.279   7.7037  -0.1932   0.7702
 12O  H26  H  HCR6  0   0.276   5.8995   1.4272   1.3188

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
 12O  C5   C6   aromatic  1.392  0.020  1.392
 12O  C5   C4   aromatic  1.394  0.020  1.394
 12O  C6   C1   aromatic  1.394  0.020  1.394
 12O  C4   C3   aromatic  1.378  0.020  1.378
 12O  C1   C2   aromatic  1.378  0.020  1.378
 12O  C3   C2   aromatic  1.385  0.020  1.385
 12O  C3   C9   single    1.481  0.020  1.481
 12O  C2   C7   single    1.482  0.020  1.482
 12O  O10  C9   double    1.205  0.020  1.205
 12O  C9   N8   single    1.386  0.020  1.386
 12O  C7   N8   single    1.391  0.020  1.391
 12O  C7   O11  double    1.203  0.020  1.203
 12O  N8   C12  single    1.443  0.020  1.443
 12O  C12  C13  single    1.545  0.020  1.545
 12O  C13  C18  single    1.503  0.020  1.503
 12O  C13  N14  single    1.461  0.020  1.461
 12O  C19  C18  aromatic  1.390  0.020  1.390
 12O  C19  C20  aromatic  1.388  0.020  1.388
 12O  C29  C30  single    1.523  0.020  1.523
 12O  C29  C28  single    1.523  0.020  1.523
 12O  C18  C17  aromatic  1.391  0.020  1.391
 12O  C20  C21  aromatic  1.388  0.020  1.388
 12O  N14  C15  single    1.462  0.020  1.462
 12O  N14  C23  single    1.354  0.020  1.354
 12O  C15  C16  single    1.521  0.020  1.521
 12O  O24  C23  double    1.225  0.020  1.225
 12O  C23  C25  single    1.518  0.020  1.518
 12O  C30  C25  single    1.536  0.020  1.536
 12O  C17  C16  single    1.496  0.020  1.496
 12O  C17  C22  aromatic  1.389  0.020  1.389
 12O  C28  C27  single    1.524  0.020  1.524
 12O  C21  C22  aromatic  1.388  0.020  1.388
 12O  C25  C26  single    1.527  0.020  1.527
 12O  C26  C27  single    1.536  0.020  1.536
 12O  C26  C31  single    1.508  0.020  1.508
 12O  C31  O32  double    1.207  0.020  1.207
 12O  C31  O33  single    1.328  0.020  1.328
 12O  O33  H1   single    0.850  0.020  0.980
 12O  C26  H2   single    0.970  0.020  1.090
 12O  C27  H3   single    0.970  0.020  1.090
 12O  C27  H4   single    0.970  0.020  1.090
 12O  C28  H5   single    0.970  0.020  1.090
 12O  C28  H6   single    0.970  0.020  1.090
 12O  C29  H7   single    0.970  0.020  1.090
 12O  C29  H8   single    0.970  0.020  1.090
 12O  C30  H9   single    0.970  0.020  1.090
 12O  C30  H10  single    0.970  0.020  1.090
 12O  C25  H11  single    0.970  0.020  1.090
 12O  C15  H12  single    0.970  0.020  1.090
 12O  C15  H13  single    0.970  0.020  1.090
 12O  C16  H14  single    0.970  0.020  1.090
 12O  C16  H15  single    0.970  0.020  1.090
 12O  C22  H16  single    0.930  0.020  1.080
 12O  C21  H17  single    0.930  0.020  1.080
 12O  C20  H18  single    0.930  0.020  1.080
 12O  C19  H19  single    0.930  0.020  1.080
 12O  C13  H20  single    0.970  0.020  1.090
 12O  C12  H21  single    0.970  0.020  1.090
 12O  C12  H22  single    0.970  0.020  1.090
 12O  C4   H23  single    0.930  0.020  1.080
 12O  C5   H24  single    0.930  0.020  1.080
 12O  C6   H25  single    0.930  0.020  1.080
 12O  C1   H26  single    0.930  0.020  1.080

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
 12O  H1   O33  C31  110.06  3.000
 12O  C26  C31  O32  124.82  3.000
 12O  O32  C31  O33  122.99  3.000
 12O  C26  C31  O33  112.18  3.000
 12O  H2   C26  C25  109.44  3.000
 12O  H2   C26  C27  107.97  3.000
 12O  C25  C26  C27  110.54  3.000
 12O  H2   C26  C31  107.72  3.000
 12O  C27  C26  C31  110.45  3.000
 12O  C25  C26  C31  110.63  3.000
 12O  H4   C27  H3   106.82  3.000
 12O  H4   C27  C28  109.87  3.000
 12O  H3   C27  C28  109.61  3.000
 12O  H4   C27  C26  110.01  3.000
 12O  H3   C27  C26  109.55  3.000
 12O  C28  C27  C26  110.89  3.000
 12O  H6   C28  H5   106.41  3.000
 12O  H6   C28  C29  109.39  3.000
 12O  H5   C28  C29  110.27  3.000
 12O  H6   C28  C27  109.34  3.000
 12O  H5   C28  C27  109.49  3.000
 12O  C29  C28  C27  111.79  3.000
 12O  H8   C29  H7   106.54  3.000
 12O  H8   C29  C30  109.70  3.000
 12O  H7   C29  C30  109.31  3.000
 12O  H8   C29  C28  110.26  3.000
 12O  H7   C29  C28  109.58  3.000
 12O  C30  C29  C28  111.32  3.000
 12O  H10  C30  H9   106.43  3.000
 12O  H10  C30  C25  109.09  3.000
 12O  H9   C30  C25  110.27  3.000
 12O  H10  C30  C29  109.91  3.000
 12O  H9   C30  C29  110.01  3.000
 12O  C25  C30  C29  111.02  3.000
 12O  H11  C25  C23  110.97  3.000
 12O  H11  C25  C30  108.17  3.000
 12O  C23  C25  C30  109.55  3.000
 12O  H11  C25  C26  107.77  3.000
 12O  C30  C25  C26  109.97  3.000
 12O  C23  C25  C26  110.36  3.000
 12O  N14  C23  O24  121.52  3.000
 12O  O24  C23  C25  120.02  3.000
 12O  N14  C23  C25  118.41  3.000
 12O  C13  N14  C15  119.81  3.000
 12O  C15  N14  C23  122.57  3.000
 12O  C13  N14  C23  117.30  3.000
 12O  H13  C15  H12  107.62  3.000
 12O  H13  C15  C16  108.32  3.000
 12O  H12  C15  C16  108.89  3.000
 12O  H13  C15  N14  109.81  3.000
 12O  H12  C15  N14  110.12  3.000
 12O  C16  C15  N14  111.96  3.000
 12O  H15  C16  H14  106.43  3.000
 12O  H15  C16  C17  110.58  3.000
 12O  H14  C16  C17  111.09  3.000
 12O  H15  C16  C15  110.06  3.000
 12O  H14  C16  C15  108.29  3.000
 12O  C17  C16  C15  110.30  3.000
 12O  C18  C17  C22  119.61  3.000
 12O  C22  C17  C16  123.44  3.000
 12O  C18  C17  C16  116.94  3.000
 12O  H16  C22  C21  120.01  3.000
 12O  H16  C22  C17  119.62  3.000
 12O  C21  C22  C17  120.37  3.000
 12O  H17  C21  C20  120.05  3.000
 12O  H17  C21  C22  119.95  3.000
 12O  C20  C21  C22  119.99  3.000
 12O  H18  C20  C19  119.99  3.000
 12O  H18  C20  C21  120.24  3.000
 12O  C19  C20  C21  119.76  3.000
 12O  H19  C19  C18  119.91  3.000
 12O  H19  C19  C20  119.79  3.000
 12O  C18  C19  C20  120.29  3.000
 12O  C13  C18  C19  120.57  3.000
 12O  C19  C18  C17  119.95  3.000
 12O  C13  C18  C17  119.35  3.000
 12O  H20  C13  C12  107.75  3.000
 12O  H20  C13  C18  108.59  3.000
 12O  C12  C13  C18  110.87  3.000
 12O  H20  C13  N14  107.79  3.000
 12O  C18  C13  N14  112.54  3.000
 12O  C12  C13  N14  109.14  3.000
 12O  H22  C12  H21  107.64  3.000
 12O  H22  C12  N8   109.06  3.000
 12O  H21  C12  N8   107.73  3.000
 12O  H22  C12  C13  109.59  3.000
 12O  H21  C12  C13  110.59  3.000
 12O  N8   C12  C13  112.10  3.000
 12O  C9   N8   C7   111.99  3.000
 12O  C7   N8   C12  123.94  3.000
 12O  C9   N8   C12  123.91  3.000
 12O  C2   C7   O11  128.61  3.000
 12O  O11  C7   N8   125.51  3.000
 12O  C2   C7   N8   105.88  3.000
 12O  C1   C2   C3   121.68  3.000
 12O  C3   C2   C7   108.06  3.000
 12O  C1   C2   C7   130.26  3.000
 12O  C3   C9   O10  128.62  3.000
 12O  O10  C9   N8   125.29  3.000
 12O  C3   C9   N8   106.09  3.000
 12O  C4   C3   C9   130.26  3.000
 12O  C9   C3   C2   107.98  3.000
 12O  C4   C3   C2   121.75  3.000
 12O  H23  C4   C5   121.16  3.000
 12O  H23  C4   C3   121.71  3.000
 12O  C5   C4   C3   117.13  3.000
 12O  H24  C5   C6   119.31  3.000
 12O  H24  C5   C4   119.56  3.000
 12O  C6   C5   C4   121.13  3.000
 12O  H25  C6   C1   119.55  3.000
 12O  H25  C6   C5   119.29  3.000
 12O  C1   C6   C5   121.17  3.000
 12O  H26  C1   C6   121.11  3.000
 12O  H26  C1   C2   121.75  3.000
 12O  C6   C1   C2   117.14  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
 12O  CONST_01  C20  C19  C18  C17    0.00   0.0  0
 12O  CONST_02  C20  C21  C22  C17    0.00   0.0  0
 12O  CONST_03  C19  C18  C17  C22    0.00   0.0  0
 12O  CONST_04  C19  C20  C21  C22    0.00   0.0  0
 12O  CONST_05  C18  C19  C20  C21    0.00   0.0  0
 12O  CONST_06  C18  C17  C22  C21    0.00   0.0  0
 12O  CONST_07  C5   C6   C1   C2     0.00   0.0  0
 12O  CONST_08  C5   C4   C3   C2     0.00   0.0  0
 12O  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 12O  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 12O  CONST_11  C1   C6   C5   C4     0.00   0.0  0
 12O  CONST_12  C1   C2   C3   C4     0.00   0.0  0
 12O  CONST_13  C9   N8   C7   C2     0.00   0.0  0
 12O  CONST_14  C13  N14  C23  C25  180.00   0.0  0
 12O  CONST_15  C15  N14  C23  C25    0.00   0.0  0
 12O  CONST_16  C2   C7   N8   C12  180.00   0.0  0
 12O  CONST_17  C9   N8   C7   O11  180.00   0.0  0
 12O  CONST_18  H16  C22  C17  C16    0.00   0.0  0
 12O  CONST_19  H19  C19  C18  C17  180.00   0.0  0
 12O  CONST_20  H17  C21  C22  C17  180.00   0.0  0
 12O  CONST_21  H18  C20  C21  C22  180.00   0.0  0
 12O  CONST_22  H26  C1   C2   C7     0.00   0.0  0
 12O  CONST_23  H25  C6   C1   C2   180.00   0.0  0
 12O  CONST_24  H23  C4   C3   C2   180.00   0.0  0
 12O  CONST_25  H24  C5   C4   C3   180.00   0.0  0
 12O  CONST_26  C13  N14  C23  O24    0.00   0.0  0
 12O  CONST_27  C15  N14  C23  O24  180.00   0.0  0
 12O  CONST_28  O11  C7   N8   C12    0.00   0.0  0
 12O  CONST_29  H1   O33  C31  C26  180.00   0.0  0
 12O  Var_01    C29  C28  C27  C26   54.82  30.0  1
 12O  Var_02    C30  C29  C28  C27  -54.40  30.0  1
 12O  Var_03    C25  C30  C29  C28   55.69  30.0  1
 12O  Var_04    C17  C16  C15  N14   53.76  30.0  1
 12O  Var_05    C18  C17  C16  C15  -40.35  30.0  1
 12O  Var_06    C13  N14  C15  C16  -22.22  30.0  1
 12O  Var_07    C9   N8   C12  C13  -79.04  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
 12O  chir_01  C26  C25  C27  C31  negativ
 12O  chir_02  C25  C26  C30  C23  negativ
 12O  chir_03  C13  N14  C12  C18  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
 12O  plan-1  C12  0.020
 12O  plan-1  N8   0.020
 12O  plan-1  C7   0.020
 12O  plan-1  O11  0.020
 12O  plan-1  C2   0.020
 12O  plan-1  C9   0.020
 12O  plan-1  O10  0.020
 12O  plan-1  C3   0.020
 12O  plan-1  C4   0.020
 12O  plan-1  C5   0.020
 12O  plan-1  C6   0.020
 12O  plan-1  C1   0.020
 12O  plan-1  H23  0.020
 12O  plan-1  H24  0.020
 12O  plan-1  H25  0.020
 12O  plan-1  H26  0.020
 12O  plan-2  C16  0.020
 12O  plan-2  C17  0.020
 12O  plan-2  C22  0.020
 12O  plan-2  C21  0.020
 12O  plan-2  C20  0.020
 12O  plan-2  C19  0.020
 12O  plan-2  C18  0.020
 12O  plan-2  C13  0.020
 12O  plan-2  H16  0.020
 12O  plan-2  H17  0.020
 12O  plan-2  H18  0.020
 12O  plan-2  H19  0.020
 12O  plan-3  C25  0.020
 12O  plan-3  C23  0.020
 12O  plan-3  O24  0.020
 12O  plan-3  N14  0.020
 12O  plan-3  C15  0.020
 12O  plan-3  C13  0.020
 12O  plan-4  O33  0.020
 12O  plan-4  C31  0.020
 12O  plan-4  O32  0.020
 12O  plan-4  C26  0.020
 12O  plan-4  H1   0.020

