# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 00:37:50 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-3-(pyridin-3-yl)azetidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc(CN2C(=O)c3ccccc3C2=O)cc1)N4CC(C4)c5cccnc5
#
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
 OE4  OE4  N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-3-(pyridin-3-yl)azetidine-1-carboxamide  ligand  51  31  .  2021-08-17  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OE4
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
 OE4  C1   C  CR16  0  -0.310  -8.5589   1.8191   0.7286
 OE4  C2   C  CR16  0  -0.078  -7.8583   2.9195   0.2623
 OE4  C11  C  C     0   0.714  -2.6847  -1.4000  -0.8331
 OE4  C14  C  CR6   0   0.376  -0.3501  -1.5583   0.0147
 OE4  C15  C  CR16  0  -0.307   0.3271  -1.6864  -1.1999
 OE4  C16  C  CR16  0  -0.287   1.7031  -1.8682  -1.2061
 OE4  C17  C  CR6   0   0.122   2.4427  -1.9261  -0.0319
 OE4  C18  C  CR16  0  -0.284   1.7585  -1.8087   1.1750
 OE4  C19  C  CR16  0  -0.345   0.3884  -1.6284   1.2008
 OE4  C20  C  CH2   0  -0.430   3.9397  -2.0742  -0.0614
 OE4  C22  C  CR5   0   0.584   5.0279  -0.1856   1.1831
 OE4  C23  C  CR56  0  -0.024   5.6091   1.1201   0.7905
 OE4  C24  C  CR56  0  -0.025   5.5084   1.2364  -0.5860
 OE4  C25  C  CR5   0   0.585   4.8615   0.0066  -1.1013
 OE4  C26  C  CR16  0  -0.296   6.1677   2.1153   1.5629
 OE4  C27  C  CR16  0  -0.241   6.6299   3.2508   0.8994
 OE4  C28  C  CR16  0  -0.241   6.5296   3.3672  -0.4840
 OE4  C29  C  CR16  0  -0.296   5.9627   2.3529  -1.2541
 OE4  N3   N  N     0  -0.400  -6.6118   2.8440  -0.1932
 OE4  C4   C  CR16  0  -0.109  -6.0224   1.6573  -0.1957
 OE4  C5   C  CR6   0   0.103  -6.6271   0.4821   0.2498
 OE4  C6   C  CR16  0  -0.209  -7.9299   0.5829   0.7206
 OE4  C7   C  C     0  -0.428  -5.8994  -0.8241   0.2250
 OE4  C8   C  C     0  -0.234  -5.1764  -1.1866  -1.1007
 OE4  N9   N  N     0  -0.493  -3.9151  -1.0690  -0.3985
 OE4  C10  C  C     0  -0.271  -4.5066  -0.8389   0.9092
 OE4  N12  N  NH1   0  -0.791  -1.7194  -1.3396   0.1400
 OE4  O13  O  O     0  -0.522  -2.4758  -1.7070  -1.9993
 OE4  N21  N  NR5   0  -0.586   4.6193  -0.7913   0.0056
 OE4  O31  O  O     0  -0.403   4.9172  -0.6557   2.2875
 OE4  H1   H  HCR6  0   0.272  -9.5723   1.9298   1.0892
 OE4  H2   H  HCR6  0   0.264  -8.3196   3.9009   0.2554
 OE4  H3   H  HCR6  0   0.277  -0.2038  -1.6408  -2.1362
 OE4  H4   H  HCR6  0   0.252   2.2064  -1.9633  -2.1606
 OE4  H5   H  HCR6  0   0.254   2.2994  -1.8623   2.1119
 OE4  H6   H  HCR6  0   0.268  -0.1194  -1.5427   2.1548
 OE4  H7   H  HCH2  0   0.288   4.2912  -2.6750   0.7766
 OE4  H8   H  HCH2  0   0.289   4.2644  -2.5750  -0.9727
 OE4  H9   H  HCR6  0   0.275   6.2469   2.0251   2.6381
 OE4  H10  H  HCR6  0   0.279   7.0741   4.0573   1.4669
 OE4  H11  H  HCR6  0   0.279   6.8993   4.2611  -0.9677
 OE4  H12  H  HCR6  0   0.276   5.8840   2.4450  -2.3291
 OE4  H13  H  HCR6  0   0.258  -5.0043   1.6339  -0.5760
 OE4  H14  H  HCR6  0   0.270  -8.4493  -0.2985   1.0777
 OE4  H15  H  H     0   0.282  -6.5504  -1.6198   0.5833
 OE4  H16  H  H     0   0.257  -5.3908  -2.1930  -1.4663
 OE4  H17  H  H     0   0.247  -5.3082  -0.4761  -1.9192
 OE4  H18  H  H     0   0.257  -4.2059   0.0974   1.3857
 OE4  H19  H  H     0   0.266  -4.3677  -1.6608   1.6162
 OE4  H20  H  HNH1  0   0.422  -2.0252  -1.1351   1.0791
 OE4  O30  O  O     0  -0.399   4.5883  -0.2793  -2.2396

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
 OE4  C1   C2   aromatic  1.385  0.020  1.385
 OE4  C1   C6   aromatic  1.387  0.020  1.387
 OE4  C2   N3   aromatic  1.329  0.020  1.329
 OE4  C11  N9   single    1.346  0.020  1.346
 OE4  C11  N12  single    1.372  0.020  1.372
 OE4  C11  O13  double    1.224  0.020  1.224
 OE4  C14  C15  aromatic  1.396  0.020  1.396
 OE4  C14  C19  aromatic  1.399  0.020  1.399
 OE4  C14  N12  single    1.392  0.020  1.392
 OE4  C15  C16  aromatic  1.388  0.020  1.388
 OE4  C16  C17  aromatic  1.389  0.020  1.389
 OE4  C17  C18  aromatic  1.392  0.020  1.392
 OE4  C17  C20  single    1.505  0.020  1.505
 OE4  C18  C19  aromatic  1.382  0.020  1.382
 OE4  C20  N21  single    1.453  0.020  1.453
 OE4  C22  C23  single    1.482  0.020  1.482
 OE4  C22  N21  single    1.386  0.020  1.386
 OE4  C22  O31  double    1.205  0.020  1.205
 OE4  C23  C24  aromatic  1.385  0.020  1.385
 OE4  C23  C26  aromatic  1.378  0.020  1.378
 OE4  C24  C25  single    1.482  0.020  1.482
 OE4  C24  C29  aromatic  1.378  0.020  1.378
 OE4  C25  N21  single    1.386  0.020  1.386
 OE4  C25  O30  double    1.205  0.020  1.205
 OE4  C26  C27  aromatic  1.394  0.020  1.394
 OE4  C27  C28  aromatic  1.392  0.020  1.392
 OE4  C28  C29  aromatic  1.394  0.020  1.394
 OE4  N3   C4   aromatic  1.325  0.020  1.325
 OE4  C4   C5   aromatic  1.395  0.020  1.395
 OE4  C5   C6   aromatic  1.389  0.020  1.389
 OE4  C5   C7   single    1.495  0.020  1.495
 OE4  C7   C8   single    1.553  0.020  1.553
 OE4  C7   C10  single    1.552  0.020  1.552
 OE4  C8   N9   single    1.448  0.020  1.448
 OE4  N9   C10  single    1.454  0.020  1.454
 OE4  C1   H1   single    0.930  0.020  1.080
 OE4  C2   H2   single    0.930  0.020  1.080
 OE4  C15  H3   single    0.930  0.020  1.080
 OE4  C16  H4   single    0.930  0.020  1.080
 OE4  C18  H5   single    0.930  0.020  1.080
 OE4  C19  H6   single    0.930  0.020  1.080
 OE4  C20  H7   single    0.970  0.020  1.090
 OE4  C20  H8   single    0.970  0.020  1.090
 OE4  C26  H9   single    0.930  0.020  1.080
 OE4  C27  H10  single    0.930  0.020  1.080
 OE4  C28  H11  single    0.930  0.020  1.080
 OE4  C29  H12  single    0.930  0.020  1.080
 OE4  C4   H13  single    0.930  0.020  1.080
 OE4  C6   H14  single    0.930  0.020  1.080
 OE4  C7   H15  single    0.970  0.020  1.090
 OE4  C8   H16  single    0.970  0.020  1.090
 OE4  C8   H17  single    0.970  0.020  1.090
 OE4  C10  H18  single    0.970  0.020  1.090
 OE4  C10  H19  single    0.970  0.020  1.090
 OE4  N12  H20  single    0.860  0.020  1.020

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
 OE4  H1   C1   C6   121.20  3.000
 OE4  H1   C1   C2   120.32  3.000
 OE4  C6   C1   C2   118.47  3.000
 OE4  H2   C2   N3   116.63  3.000
 OE4  H2   C2   C1   120.39  3.000
 OE4  N3   C2   C1   122.98  3.000
 OE4  O13  C11  N12  124.53  3.000
 OE4  O13  C11  N9   121.69  3.000
 OE4  N12  C11  N9   113.78  3.000
 OE4  N12  C14  C19  116.79  3.000
 OE4  N12  C14  C15  124.72  3.000
 OE4  C19  C14  C15  118.48  3.000
 OE4  H3   C15  C16  119.35  3.000
 OE4  H3   C15  C14  120.87  3.000
 OE4  C16  C15  C14  119.78  3.000
 OE4  H4   C16  C17  119.59  3.000
 OE4  H4   C16  C15  118.43  3.000
 OE4  C17  C16  C15  121.98  3.000
 OE4  C20  C17  C18  120.94  3.000
 OE4  C20  C17  C16  121.16  3.000
 OE4  C18  C17  C16  117.88  3.000
 OE4  H5   C18  C19  119.03  3.000
 OE4  H5   C18  C17  120.02  3.000
 OE4  C19  C18  C17  120.95  3.000
 OE4  H6   C19  C18  119.41  3.000
 OE4  H6   C19  C14  119.66  3.000
 OE4  C18  C19  C14  120.93  3.000
 OE4  H8   C20  H7   107.09  3.000
 OE4  H8   C20  N21  107.75  3.000
 OE4  H7   C20  N21  107.49  3.000
 OE4  H8   C20  C17  110.99  3.000
 OE4  H7   C20  C17  111.12  3.000
 OE4  N21  C20  C17  112.17  3.000
 OE4  O31  C22  N21  125.52  3.000
 OE4  O31  C22  C23  128.49  3.000
 OE4  N21  C22  C23  105.99  3.000
 OE4  C26  C23  C24  121.73  3.000
 OE4  C26  C23  C22  130.29  3.000
 OE4  C24  C23  C22  107.98  3.000
 OE4  C29  C24  C25  130.36  3.000
 OE4  C29  C24  C23  121.72  3.000
 OE4  C25  C24  C23  107.91  3.000
 OE4  O30  C25  N21  125.33  3.000
 OE4  O30  C25  C24  128.63  3.000
 OE4  N21  C25  C24  106.04  3.000
 OE4  H9   C26  C27  121.11  3.000
 OE4  H9   C26  C23  121.77  3.000
 OE4  C27  C26  C23  117.12  3.000
 OE4  H10  C27  C28  119.26  3.000
 OE4  H10  C27  C26  119.59  3.000
 OE4  C28  C27  C26  121.15  3.000
 OE4  H11  C28  C29  119.56  3.000
 OE4  H11  C28  C27  119.28  3.000
 OE4  C29  C28  C27  121.17  3.000
 OE4  H12  C29  C28  121.10  3.000
 OE4  H12  C29  C24  121.78  3.000
 OE4  C28  C29  C24  117.11  3.000
 OE4  C4   N3   C2   117.95  3.000
 OE4  H13  C4   C5   119.98  3.000
 OE4  H13  C4   N3   115.88  3.000
 OE4  C5   C4   N3   124.14  3.000
 OE4  C7   C5   C6   121.70  3.000
 OE4  C7   C5   C4   121.31  3.000
 OE4  C6   C5   C4   116.99  3.000
 OE4  H14  C6   C5   120.15  3.000
 OE4  H14  C6   C1   120.38  3.000
 OE4  C5   C6   C1   119.47  3.000
 OE4  H15  C7   C10  112.62  3.000
 OE4  H15  C7   C8   112.88  3.000
 OE4  C10  C7   C8    87.49  3.000
 OE4  H15  C7   C5   109.99  3.000
 OE4  C10  C7   C5   115.96  3.000
 OE4  C8   C7   C5   116.40  3.000
 OE4  H17  C8   H16  108.96  3.000
 OE4  H17  C8   N9   114.57  3.000
 OE4  H16  C8   N9   114.09  3.000
 OE4  H17  C8   C7   115.59  3.000
 OE4  H16  C8   C7   114.18  3.000
 OE4  N9   C8   C7    88.43  3.000
 OE4  C10  N9   C8    95.43  3.000
 OE4  C10  N9   C11  134.53  3.000
 OE4  C8   N9   C11  128.28  3.000
 OE4  H19  C10  H18  109.10  3.000
 OE4  H19  C10  N9   114.28  3.000
 OE4  H18  C10  N9   114.58  3.000
 OE4  H19  C10  C7   113.98  3.000
 OE4  H18  C10  C7   115.53  3.000
 OE4  N9   C10  C7    88.29  3.000
 OE4  H20  N12  C14  114.45  3.000
 OE4  H20  N12  C11  117.13  3.000
 OE4  C14  N12  C11  128.40  3.000
 OE4  C25  N21  C22  112.06  3.000
 OE4  C25  N21  C20  123.59  3.000
 OE4  C22  N21  C20  124.25  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
 OE4  CONST_01  C4   N3   C2   C1     0.00   0.0  0
 OE4  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 OE4  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 OE4  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 OE4  CONST_05  C17  C16  C15  C14    0.00   0.0  0
 OE4  CONST_06  C17  C18  C19  C14    0.00   0.0  0
 OE4  CONST_07  C18  C19  C14  C15    0.00   0.0  0
 OE4  CONST_08  C18  C17  C16  C15    0.00   0.0  0
 OE4  CONST_09  C19  C14  C15  C16    0.00   0.0  0
 OE4  CONST_10  C19  C18  C17  C16    0.00   0.0  0
 OE4  CONST_11  C28  C29  C24  C23    0.00   0.0  0
 OE4  CONST_12  C28  C27  C26  C23    0.00   0.0  0
 OE4  CONST_13  C27  C26  C23  C24    0.00   0.0  0
 OE4  CONST_14  C27  C28  C29  C24    0.00   0.0  0
 OE4  CONST_15  C29  C24  C23  C26    0.00   0.0  0
 OE4  CONST_16  C29  C28  C27  C26    0.00   0.0  0
 OE4  CONST_17  C6   C1   C2   N3     0.00   0.0  0
 OE4  CONST_18  C6   C5   C4   N3     0.00   0.0  0
 OE4  CONST_19  C7   C5   C6   C1   180.00   0.0  0
 OE4  CONST_20  C7   C5   C4   N3   180.00   0.0  0
 OE4  CONST_21  C25  N21  C22  C23    0.00   0.0  0
 OE4  CONST_22  C20  C17  C16  C15  180.00   0.0  0
 OE4  CONST_23  N12  C14  C15  C16  180.00   0.0  0
 OE4  CONST_24  N12  C14  C19  C18  180.00   0.0  0
 OE4  CONST_25  C20  C17  C18  C19  180.00   0.0  0
 OE4  CONST_26  C23  C22  N21  C20  180.00   0.0  0
 OE4  CONST_27  O31  C22  N21  C25  180.00   0.0  0
 OE4  CONST_28  H14  C6   C1   C2   180.00   0.0  0
 OE4  CONST_29  H13  C4   N3   C2   180.00   0.0  0
 OE4  CONST_30  H4   C16  C15  C14  180.00   0.0  0
 OE4  CONST_31  H5   C18  C19  C14  180.00   0.0  0
 OE4  CONST_32  H6   C19  C14  C15  180.00   0.0  0
 OE4  CONST_33  H3   C15  C16  C17  180.00   0.0  0
 OE4  CONST_34  H9   C26  C23  C22    0.00   0.0  0
 OE4  CONST_35  H12  C29  C24  C23  180.00   0.0  0
 OE4  CONST_36  H10  C27  C26  C23  180.00   0.0  0
 OE4  CONST_37  H11  C28  C29  C24  180.00   0.0  0
 OE4  CONST_38  H1   C1   C2   N3   180.00   0.0  0
 OE4  CONST_39  H2   C2   N3   C4   180.00   0.0  0
 OE4  CONST_40  O13  C11  N9   C8     0.00   0.0  0
 OE4  CONST_41  O13  C11  N9   C10  180.00   0.0  0
 OE4  CONST_42  C15  C14  N12  C11    0.00   0.0  0
 OE4  CONST_43  C19  C14  N12  C11  180.00   0.0  0
 OE4  CONST_44  N9   C11  N12  C14  180.00   0.0  0
 OE4  CONST_45  O31  C22  N21  C20    0.00   0.0  0
 OE4  CONST_46  N12  C11  N9   C8   180.00   0.0  0
 OE4  CONST_47  N12  C11  N9   C10    0.00   0.0  0
 OE4  CONST_48  H20  N12  C14  C15  180.00   0.0  0
 OE4  CONST_49  O13  C11  N12  C14    0.00   0.0  0
 OE4  Var_01    C10  N9   C8   C7     4.68  30.0  1
 OE4  Var_02    N21  C20  C17  C16   94.05  30.0  2
 OE4  Var_03    C22  N21  C20  C17   91.59  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
 OE4  chir_01  C7  C5  C8  C10  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
 OE4  plan-1  C1   0.020
 OE4  plan-1  C2   0.020
 OE4  plan-1  N3   0.020
 OE4  plan-1  C4   0.020
 OE4  plan-1  C5   0.020
 OE4  plan-1  C6   0.020
 OE4  plan-1  C7   0.020
 OE4  plan-1  H1   0.020
 OE4  plan-1  H2   0.020
 OE4  plan-1  H13  0.020
 OE4  plan-1  H14  0.020
 OE4  plan-2  C14  0.020
 OE4  plan-2  C15  0.020
 OE4  plan-2  C16  0.020
 OE4  plan-2  C17  0.020
 OE4  plan-2  C18  0.020
 OE4  plan-2  C19  0.020
 OE4  plan-2  C20  0.020
 OE4  plan-2  N12  0.020
 OE4  plan-2  H3   0.020
 OE4  plan-2  H4   0.020
 OE4  plan-2  H5   0.020
 OE4  plan-2  H6   0.020
 OE4  plan-3  C20  0.020
 OE4  plan-3  C22  0.020
 OE4  plan-3  C23  0.020
 OE4  plan-3  C24  0.020
 OE4  plan-3  C25  0.020
 OE4  plan-3  C26  0.020
 OE4  plan-3  C27  0.020
 OE4  plan-3  C28  0.020
 OE4  plan-3  C29  0.020
 OE4  plan-3  N21  0.020
 OE4  plan-3  O31  0.020
 OE4  plan-3  H9   0.020
 OE4  plan-3  H10  0.020
 OE4  plan-3  H11  0.020
 OE4  plan-3  H12  0.020
 OE4  plan-3  O30  0.020
 OE4  plan-4  C11  0.020
 OE4  plan-4  C14  0.020
 OE4  plan-4  C8   0.020
 OE4  plan-4  N9   0.020
 OE4  plan-4  C10  0.020
 OE4  plan-4  N12  0.020
 OE4  plan-4  O13  0.020
 OE4  plan-4  H20  0.020

