# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 03:08:03 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (5R)-5-[(6-methoxy-1-oxo-isoindol-2-ium-2-yl)methyl]-5-(4-pyridin-3-ylphenyl)imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2C=[N+](C[C@]3(NC(=O)NC3=O)c4ccc(cc4)c5cccnc5)C(=O)c2c1
#
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
 Z93  Z93  (5R)-5-[(6-methoxy-1-oxo-isoindol-2-ium-2-yl)methyl]-5-(4-pyridin-3-ylphenyl)imidazolidine-2,4-dione  ligand  51  32  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Z93
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
 Z93  N1    N  NH1   0  -0.686  -0.8437   2.1419   0.4250
 Z93  C2    C  C     0   0.577  -0.2137   1.0767   0.9824
 Z93  C3    C  CT    0  -0.078   0.2548   0.1959  -0.1909
 Z93  N4    N  NH1   0  -0.688  -0.2437   0.9388  -1.3139
 Z93  C5    C  C     0   0.669  -0.8323   2.1143  -0.9664
 Z93  O6    O  O     0  -0.441  -1.2772   2.9662  -1.6927
 Z93  O7    O  O     0  -0.393  -0.0491   0.8426   2.1497
 Z93  C8    C  CR6   0   0.175   1.7664   0.0606  -0.1493
 Z93  C9    C  CR16  0  -0.291   2.5732   0.7552  -1.0426
 Z93  C10   C  CR16  0  -0.289   3.9528   0.6315  -0.9923
 Z93  C11   C  CR6   0   0.084   4.5656  -0.1832  -0.0431
 Z93  C12   C  CR16  0  -0.295   3.7515  -0.8679   0.8594
 Z93  C13   C  CR16  0  -0.280   2.3738  -0.7473   0.8101
 Z93  C14   C  CR6   0  -0.006   6.0310  -0.3211   0.0078
 Z93  C15   C  CR16  0  -0.194   6.6458  -1.5368   0.2994
 Z93  C16   C  CR16  0  -0.315   8.0278  -1.6076   0.3316
 Z93  C17   C  CR16  0  -0.069   8.7575  -0.4581   0.0684
 Z93  N18   N  N     0  -0.398   8.1901   0.7108  -0.2060
 Z93  C19   C  CR16  0  -0.099   6.8668   0.7705  -0.2319
 Z93  N20   N  NR5   1  -0.518  -1.8529  -1.0887  -0.1995
 Z93  C21   C  CR15  0   0.174  -2.5574  -0.9067  -1.2985
 Z93  C22   C  CR5   0   0.603  -2.7321  -1.1078   0.9499
 Z93  C23   C  CH2   0  -0.310  -0.4116  -1.1956  -0.1274
 Z93  C24   C  CR56  0   0.023  -4.0791  -0.8763   0.3836
 Z93  C25   C  CR56  0  -0.006  -3.9308  -0.7608  -1.0066
 Z93  C26   C  CR16  0  -0.258  -5.0334  -0.5442  -1.8196
 Z93  C27   C  CR16  0  -0.369  -6.2779  -0.4385  -1.2206
 Z93  C28   C  CR6   0   0.454  -6.4160  -0.5546   0.1705
 Z93  C29   C  CR16  0  -0.356  -5.2840  -0.7845   1.0007
 Z93  O30   O  O     0  -0.298  -2.3608  -1.2885   2.0637
 Z93  O31   O  O2    0  -0.429  -7.5611  -0.4645   0.8103
 Z93  C32   C  CH3   0  -0.452  -8.7659  -0.2268   0.0864
 Z93  HN1   H  HNH1  0   0.441  -1.2413   2.9081   0.9521
 Z93  HN4   H  HNH1  0   0.431   0.0211   0.7493  -2.2695
 Z93  H9    H  HCR6  0   0.259   2.1405   1.3973  -1.7972
 Z93  H10   H  HCR6  0   0.265   4.5511   1.1626  -1.7215
 Z93  H12   H  HCR6  0   0.265   4.1952  -1.4904   1.6261
 Z93  H13   H  HCR6  0   0.264   1.7866  -1.2846   1.5418
 Z93  H15   H  HCR6  0   0.273   6.0524  -2.4240   0.4813
 Z93  H16   H  HCR6  0   0.275   8.5334  -2.5381   0.5495
 Z93  H17   H  HCR6  0   0.268   9.8413  -0.4821   0.0804
 Z93  H19   H  HCR6  0   0.263   6.4367   1.7456  -0.4376
 Z93  H21   H  HCR5  0   0.376  -2.0965  -0.9080  -2.2765
 Z93  H23   H  HCH2  0   0.342  -0.0630  -1.7995  -0.9638
 Z93  H23A  H  HCH2  0   0.315  -0.1557  -1.7160   0.7914
 Z93  H26   H  HCR6  0   0.305  -4.9351  -0.4565  -2.8930
 Z93  H27   H  HCR6  0   0.319  -7.1409  -0.2657  -1.8472
 Z93  H29   H  HCR6  0   0.309  -5.4031  -0.8759   2.0726
 Z93  H32   H  HCH3  0   0.280  -9.5583  -0.1949   0.8269
 Z93  H32A  H  HCH3  0   0.254  -8.7251   0.7268  -0.4413
 Z93  H32B  H  HCH3  0   0.254  -8.9651  -1.0315  -0.6221

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
 Z93  N1   C2    single    1.357  0.020  1.357
 Z93  N1   C5    single    1.392  0.020  1.392
 Z93  C2   C3    single    1.540  0.020  1.540
 Z93  C2   O7    double    1.202  0.020  1.202
 Z93  C3   N4    single    1.436  0.020  1.436
 Z93  C3   C8    single    1.518  0.020  1.518
 Z93  C3   C23   single    1.544  0.020  1.544
 Z93  N4   C5    single    1.360  0.020  1.360
 Z93  C5   O6    double    1.205  0.020  1.205
 Z93  C8   C9    aromatic  1.390  0.020  1.390
 Z93  C8   C13   aromatic  1.394  0.020  1.394
 Z93  C9   C10   aromatic  1.386  0.020  1.386
 Z93  C10  C11   aromatic  1.393  0.020  1.393
 Z93  C11  C12   aromatic  1.395  0.020  1.395
 Z93  C11  C14   single    1.473  0.020  1.473
 Z93  C12  C13   aromatic  1.384  0.020  1.384
 Z93  C14  C15   aromatic  1.393  0.020  1.393
 Z93  C14  C19   aromatic  1.395  0.020  1.395
 Z93  C15  C16   aromatic  1.384  0.020  1.384
 Z93  C16  C17   aromatic  1.387  0.020  1.387
 Z93  C17  N18   aromatic  1.328  0.020  1.328
 Z93  N18  C19   aromatic  1.325  0.020  1.325
 Z93  N20  C21   double    1.318  0.020  1.318
 Z93  N20  C22   single    1.447  0.020  1.447
 Z93  N20  C23   single    1.447  0.020  1.447
 Z93  C21  C25   single    1.412  0.020  1.412
 Z93  C22  C24   single    1.479  0.020  1.479
 Z93  C22  O30   double    1.188  0.020  1.188
 Z93  C24  C25   aromatic  1.403  0.020  1.403
 Z93  C24  C29   aromatic  1.357  0.020  1.357
 Z93  C25  C26   aromatic  1.387  0.020  1.387
 Z93  C26  C27   aromatic  1.385  0.020  1.385
 Z93  C27  C28   aromatic  1.403  0.020  1.403
 Z93  C28  C29   aromatic  1.423  0.020  1.423
 Z93  C28  O31   single    1.315  0.020  1.315
 Z93  O31  C32   single    1.426  0.020  1.426
 Z93  N1   HN1   single    0.860  0.020  1.020
 Z93  N4   HN4   single    0.860  0.020  1.020
 Z93  C9   H9    single    0.930  0.020  1.080
 Z93  C10  H10   single    0.930  0.020  1.080
 Z93  C12  H12   single    0.930  0.020  1.080
 Z93  C13  H13   single    0.930  0.020  1.080
 Z93  C15  H15   single    0.930  0.020  1.080
 Z93  C16  H16   single    0.930  0.020  1.080
 Z93  C17  H17   single    0.930  0.020  1.080
 Z93  C19  H19   single    0.930  0.020  1.080
 Z93  C21  H21   single    0.930  0.020  1.080
 Z93  C23  H23   single    0.970  0.020  1.090
 Z93  C23  H23A  single    0.970  0.020  1.090
 Z93  C26  H26   single    0.930  0.020  1.080
 Z93  C27  H27   single    0.930  0.020  1.080
 Z93  C29  H29   single    0.930  0.020  1.080
 Z93  C32  H32   single    0.970  0.020  1.090
 Z93  C32  H32A  single    0.970  0.020  1.090
 Z93  C32  H32B  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
 Z93  HN1   N1   C5    122.64  3.000
 Z93  HN1   N1   C2    124.26  3.000
 Z93  C5    N1   C2    113.03  3.000
 Z93  O7    C2   C3    125.93  3.000
 Z93  O7    C2   N1    127.97  3.000
 Z93  C3    C2   N1    106.09  3.000
 Z93  C23   C3   C8    110.38  3.000
 Z93  C23   C3   N4    110.40  3.000
 Z93  C8    C3   N4    114.41  3.000
 Z93  C23   C3   C2    110.66  3.000
 Z93  C8    C3   C2    109.44  3.000
 Z93  N4    C3   C2    101.20  3.000
 Z93  HN4   N4   C5    121.18  3.000
 Z93  HN4   N4   C3    123.51  3.000
 Z93  C5    N4   C3    113.44  3.000
 Z93  O6    C5   N4    128.11  3.000
 Z93  O6    C5   N1    125.85  3.000
 Z93  N4    C5   N1    106.03  3.000
 Z93  C13   C8   C9    118.63  3.000
 Z93  C13   C8   C3    120.30  3.000
 Z93  C9    C8   C3    121.05  3.000
 Z93  H9    C9   C10   118.47  3.000
 Z93  H9    C9   C8    120.87  3.000
 Z93  C10   C9   C8    120.66  3.000
 Z93  H10   C10  C11   120.19  3.000
 Z93  H10   C10  C9    118.81  3.000
 Z93  C11   C10  C9    120.98  3.000
 Z93  C14   C11  C12   120.82  3.000
 Z93  C14   C11  C10   121.07  3.000
 Z93  C12   C11  C10   118.11  3.000
 Z93  H12   C12  C13   118.90  3.000
 Z93  H12   C12  C11   120.08  3.000
 Z93  C13   C12  C11   121.01  3.000
 Z93  H13   C13  C12   118.25  3.000
 Z93  H13   C13  C8    121.15  3.000
 Z93  C12   C13  C8    120.60  3.000
 Z93  C19   C14  C15   117.02  3.000
 Z93  C19   C14  C11   121.12  3.000
 Z93  C15   C14  C11   121.87  3.000
 Z93  H15   C15  C16   120.09  3.000
 Z93  H15   C15  C14   120.55  3.000
 Z93  C16   C15  C14   119.35  3.000
 Z93  H16   C16  C17   120.37  3.000
 Z93  H16   C16  C15   121.04  3.000
 Z93  C17   C16  C15   118.59  3.000
 Z93  H17   C17  N18   116.67  3.000
 Z93  H17   C17  C16   120.37  3.000
 Z93  N18   C17  C16   122.96  3.000
 Z93  C19   N18  C17   118.06  3.000
 Z93  H19   C19  N18   116.09  3.000
 Z93  H19   C19  C14   119.87  3.000
 Z93  N18   C19  C14   124.03  3.000
 Z93  C23   N20  C22   124.37  3.000
 Z93  C23   N20  C21   125.74  3.000
 Z93  C22   N20  C21   109.84  3.000
 Z93  H21   C21  C25   127.01  3.000
 Z93  H21   C21  N20   121.75  3.000
 Z93  C25   C21  N20   111.21  3.000
 Z93  O30   C22  C24   131.86  3.000
 Z93  O30   C22  N20   123.84  3.000
 Z93  C24   C22  N20   104.30  3.000
 Z93  H23A  C23  H23   107.97  3.000
 Z93  H23A  C23  N20   108.19  3.000
 Z93  H23   C23  N20   108.76  3.000
 Z93  H23A  C23  C3    111.39  3.000
 Z93  H23   C23  C3    109.27  3.000
 Z93  N20   C23  C3    111.17  3.000
 Z93  C29   C24  C25   122.61  3.000
 Z93  C29   C24  C22   130.17  3.000
 Z93  C25   C24  C22   107.22  3.000
 Z93  C26   C25  C24   120.65  3.000
 Z93  C26   C25  C21   131.94  3.000
 Z93  C24   C25  C21   107.41  3.000
 Z93  H26   C26  C27   120.31  3.000
 Z93  H26   C26  C25   121.49  3.000
 Z93  C27   C26  C25   118.21  3.000
 Z93  H27   C27  C28   120.64  3.000
 Z93  H27   C27  C26   118.63  3.000
 Z93  C28   C27  C26   120.73  3.000
 Z93  O31   C28  C29   114.84  3.000
 Z93  O31   C28  C27   124.24  3.000
 Z93  C29   C28  C27   120.91  3.000
 Z93  H29   C29  C28   120.27  3.000
 Z93  H29   C29  C24   122.85  3.000
 Z93  C28   C29  C24   116.88  3.000
 Z93  C32   O31  C28   120.03  3.000
 Z93  H32B  C32  H32A  109.73  3.000
 Z93  H32B  C32  H32   109.37  3.000
 Z93  H32A  C32  H32   109.38  3.000
 Z93  H32B  C32  O31   111.18  3.000
 Z93  H32A  C32  O31   111.10  3.000
 Z93  H32   C32  O31   105.99  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
 Z93  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 Z93  CONST_02  C11  C12  C13  C8      0.00   0.0  0
 Z93  CONST_03  C12  C13  C8   C9      0.00   0.0  0
 Z93  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 Z93  CONST_05  C14  C11  C10  C9    180.00   0.0  0
 Z93  CONST_06  C13  C8   C9   C10     0.00   0.0  0
 Z93  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 Z93  CONST_10  C16  C15  C14  C11   180.00   0.0  0
 Z93  CONST_11  N18  C19  C14  C11   180.00   0.0  0
 Z93  CONST_14  C14  C11  C12  C13   180.00   0.0  0
 Z93  CONST_15  C17  C16  C15  C14     0.00   0.0  0
 Z93  CONST_16  C17  N18  C19  C14     0.00   0.0  0
 Z93  CONST_17  N18  C19  C14  C15     0.00   0.0  0
 Z93  CONST_18  N18  C17  C16  C15     0.00   0.0  0
 Z93  CONST_19  C19  C14  C15  C16     0.00   0.0  0
 Z93  CONST_20  C19  N18  C17  C16     0.00   0.0  0
 Z93  CONST_21  C27  C26  C25  C24     0.00   0.0  0
 Z93  CONST_22  C27  C28  C29  C24     0.00   0.0  0
 Z93  CONST_23  C28  C29  C24  C25     0.00   0.0  0
 Z93  CONST_24  C28  C27  C26  C25     0.00   0.0  0
 Z93  CONST_25  C29  C24  C25  C26     0.00   0.0  0
 Z93  CONST_26  C29  C28  C27  C26     0.00   0.0  0
 Z93  CONST_27  C10  C9   C8   C3    180.00   0.0  0
 Z93  CONST_28  C12  C13  C8   C3    180.00   0.0  0
 Z93  CONST_29  C3   N4   C5   N1      0.00   0.0  0
 Z93  CONST_30  N4   C5   N1   C2      0.00   0.0  0
 Z93  CONST_31  C5   N1   C2   C3      0.00   0.0  0
 Z93  CONST_32  C24  C22  N20  C21     0.00   0.0  0
 Z93  CONST_33  O31  C28  C29  C24   180.00   0.0  0
 Z93  CONST_34  O31  C28  C27  C26   180.00   0.0  0
 Z93  CONST_35  O6   C5   N1   C2    180.00   0.0  0
 Z93  CONST_36  O6   C5   N4   C3    180.00   0.0  0
 Z93  CONST_37  O7   C2   N1   C5    180.00   0.0  0
 Z93  CONST_38  O30  C22  N20  C21   180.00   0.0  0
 Z93  CONST_39  C24  C22  N20  C23   180.00   0.0  0
 Z93  CONST_40  H9   C9   C8   C3      0.00   0.0  0
 Z93  CONST_41  H13  C13  C8   C3      0.00   0.0  0
 Z93  CONST_42  H10  C10  C9   C8    180.00   0.0  0
 Z93  CONST_43  H12  C12  C13  C8    180.00   0.0  0
 Z93  CONST_44  H15  C15  C14  C11     0.00   0.0  0
 Z93  CONST_45  H19  C19  C14  C11     0.00   0.0  0
 Z93  CONST_46  H16  C16  C15  C14   180.00   0.0  0
 Z93  CONST_47  H17  C17  C16  C15   180.00   0.0  0
 Z93  CONST_48  H26  C26  C25  C21     0.00   0.0  0
 Z93  CONST_49  H29  C29  C24  C22     0.00   0.0  0
 Z93  CONST_50  H27  C27  C26  C25   180.00   0.0  0
 Z93  CONST_51  HN4  N4   C5   N1    180.00   0.0  0
 Z93  CONST_52  HN1  N1   C2   C3    180.00   0.0  0
 Z93  CONST_53  O30  C22  N20  C23     0.00   0.0  0
 Z93  Var_01    C21  N20  C23  C3     79.41  30.0  2
 Z93  Var_02    H32  C32  O31  C28  -179.99  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
 Z93  chir_01  C3  N4  C8  C2  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
 Z93  plan-1  C3   0.020
 Z93  plan-1  C8   0.020
 Z93  plan-1  C9   0.020
 Z93  plan-1  C10  0.020
 Z93  plan-1  C11  0.020
 Z93  plan-1  C12  0.020
 Z93  plan-1  C13  0.020
 Z93  plan-1  C14  0.020
 Z93  plan-1  H9   0.020
 Z93  plan-1  H10  0.020
 Z93  plan-1  H12  0.020
 Z93  plan-1  H13  0.020
 Z93  plan-2  C11  0.020
 Z93  plan-2  C14  0.020
 Z93  plan-2  C15  0.020
 Z93  plan-2  C16  0.020
 Z93  plan-2  C17  0.020
 Z93  plan-2  N18  0.020
 Z93  plan-2  C19  0.020
 Z93  plan-2  H15  0.020
 Z93  plan-2  H16  0.020
 Z93  plan-2  H17  0.020
 Z93  plan-2  H19  0.020
 Z93  plan-3  N20  0.020
 Z93  plan-3  C21  0.020
 Z93  plan-3  C22  0.020
 Z93  plan-3  C23  0.020
 Z93  plan-3  C24  0.020
 Z93  plan-3  C25  0.020
 Z93  plan-3  C26  0.020
 Z93  plan-3  C27  0.020
 Z93  plan-3  C28  0.020
 Z93  plan-3  C29  0.020
 Z93  plan-3  O30  0.020
 Z93  plan-3  O31  0.020
 Z93  plan-3  H21  0.020
 Z93  plan-3  H26  0.020
 Z93  plan-3  H27  0.020
 Z93  plan-3  H29  0.020
 Z93  plan-4  N1   0.020
 Z93  plan-4  C2   0.020
 Z93  plan-4  C3   0.020
 Z93  plan-4  N4   0.020
 Z93  plan-4  C5   0.020
 Z93  plan-4  O6   0.020
 Z93  plan-4  O7   0.020
 Z93  plan-4  HN1  0.020
 Z93  plan-4  HN4  0.020

