# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:26:25 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 5-azanyl-2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]isoindole-1,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2C(=O)N([C@H]3CC(=O)NC3=O)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
 JOB  JOB  5-azanyl-2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]isoindole-1,3-dione  ligand  28  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JOB
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
 JOB  C4   C  C     0   0.572   2.5497   0.4486  -1.0031
 JOB  C5   C  CR5   0   0.588  -0.6516   1.2737   0.4427
 JOB  C6   C  CR56  0  -0.018  -1.8767   0.4698   0.2006
 JOB  C11  C  CR16  0  -0.332  -3.7740  -1.4198  -0.3721
 JOB  C7   C  CR56  0  -0.076  -1.4847  -0.8018  -0.2006
 JOB  C8   C  CR5   0   0.586  -0.0268  -0.8462  -0.2278
 JOB  C9   C  CR16  0  -0.396  -3.1876   0.8410   0.3268
 JOB  C10  C  CR6   0   0.400  -4.1772  -0.1273   0.0348
 JOB  C12  C  CR16  0  -0.288  -2.4407  -1.7612  -0.4911
 JOB  N1   N  NH1   0  -0.674   3.7367  -0.1225  -0.6347
 JOB  N2   N  NR5   0  -0.614   0.4064   0.4229   0.1700
 JOB  C3   C  CH1   0  -0.251   1.7904   0.7673   0.2827
 JOB  N3   N  NH2   0  -0.862  -5.4813   0.1790   0.1478
 JOB  C1   C  C     0   0.550   3.8562  -0.3844   0.7117
 JOB  C2   C  CH2   0  -0.591   2.5795   0.0569   1.3832
 JOB  O1   O  O     0  -0.407   2.1917   0.6890  -2.1256
 JOB  O2   O  O     0  -0.418   4.8208  -0.8868   1.2292
 JOB  O3   O  O     0  -0.399  -0.5567   2.4197   0.8009
 JOB  O4   O  O     0  -0.416   0.7314  -1.7404  -0.5209
 JOB  H1   H  HCR6  0   0.275  -4.5356  -2.1572  -0.5930
 JOB  H2   H  HCR6  0   0.278  -3.4697   1.8379   0.6418
 JOB  H3   H  HCR6  0   0.271  -2.1613  -2.7587  -0.8044
 JOB  H4   H  HNH1  0   0.430   4.4511  -0.3783  -1.3052
 JOB  H5   H  HCH1  0   0.349   1.8463   1.8502   0.4204
 JOB  H6   H  HNH2  0   0.406  -5.7796   1.1000   0.4146
 JOB  H7   H  HNH2  0   0.406  -6.1967  -0.4862  -0.0856
 JOB  H8   H  HCH2  0   0.317   2.8002   0.7037   2.2309
 JOB  H9   H  HCH2  0   0.316   2.0629  -0.8227   1.7697

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
 JOB  N3   C10  single    1.344  0.020  1.344
 JOB  C9   C10  aromatic  1.415  0.020  1.415
 JOB  C9   C6   aromatic  1.368  0.020  1.368
 JOB  O3   C5   double    1.204  0.020  1.204
 JOB  C10  C11  aromatic  1.414  0.020  1.414
 JOB  C6   C5   single    1.485  0.020  1.485
 JOB  C6   C7   aromatic  1.390  0.020  1.390
 JOB  C5   N2   single    1.385  0.020  1.385
 JOB  C11  C12  aromatic  1.381  0.020  1.381
 JOB  O1   C4   double    1.202  0.020  1.202
 JOB  N1   C4   single    1.368  0.020  1.368
 JOB  N1   C1   single    1.377  0.020  1.377
 JOB  C4   C3   single    1.527  0.020  1.527
 JOB  C7   C12  aromatic  1.385  0.020  1.385
 JOB  C7   C8   single    1.459  0.020  1.459
 JOB  N2   C3   single    1.431  0.020  1.431
 JOB  N2   C8   single    1.399  0.020  1.399
 JOB  C1   O2   double    1.204  0.020  1.204
 JOB  C1   C2   single    1.509  0.020  1.509
 JOB  C3   C2   single    1.529  0.020  1.529
 JOB  C8   O4   double    1.208  0.020  1.208
 JOB  C11  H1   single    0.930  0.020  1.080
 JOB  C9   H2   single    0.930  0.020  1.080
 JOB  C12  H3   single    0.930  0.020  1.080
 JOB  N1   H4   single    0.860  0.020  1.020
 JOB  C3   H5   single    0.970  0.020  1.090
 JOB  N3   H6   single    0.860  0.020  1.020
 JOB  N3   H7   single    0.860  0.020  1.020
 JOB  C2   H8   single    0.970  0.020  1.090
 JOB  C2   H9   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
 JOB  O1   C4   C3   126.61  3.000
 JOB  C3   C4   N1   106.97  3.000
 JOB  O1   C4   N1   126.39  3.000
 JOB  O3   C5   N2   125.66  3.000
 JOB  N2   C5   C6   105.40  3.000
 JOB  O3   C5   C6   128.94  3.000
 JOB  C9   C6   C7   123.03  3.000
 JOB  C7   C6   C5   108.04  3.000
 JOB  C9   C6   C5   128.93  3.000
 JOB  H1   C11  C12  119.53  3.000
 JOB  H1   C11  C10  118.73  3.000
 JOB  C12  C11  C10  121.74  3.000
 JOB  C12  C7   C8   131.66  3.000
 JOB  C8   C7   C6   108.37  3.000
 JOB  C12  C7   C6   119.97  3.000
 JOB  O4   C8   N2   123.10  3.000
 JOB  O4   C8   C7   130.85  3.000
 JOB  N2   C8   C7   106.06  3.000
 JOB  H2   C9   C10  120.52  3.000
 JOB  H2   C9   C6   121.75  3.000
 JOB  C10  C9   C6   117.73  3.000
 JOB  N3   C10  C9   120.34  3.000
 JOB  C9   C10  C11  119.05  3.000
 JOB  N3   C10  C11  120.61  3.000
 JOB  H3   C12  C7   121.39  3.000
 JOB  H3   C12  C11  120.12  3.000
 JOB  C7   C12  C11  118.48  3.000
 JOB  H4   N1   C1   122.56  3.000
 JOB  H4   N1   C4   122.64  3.000
 JOB  C1   N1   C4   114.72  3.000
 JOB  C3   N2   C8   122.71  3.000
 JOB  C8   N2   C5   112.14  3.000
 JOB  C3   N2   C5   125.15  3.000
 JOB  H5   C3   C2   110.07  3.000
 JOB  H5   C3   N2   107.33  3.000
 JOB  C2   C3   N2   116.37  3.000
 JOB  H5   C3   C4   106.70  3.000
 JOB  C2   C3   C4   104.62  3.000
 JOB  N2   C3   C4   111.37  3.000
 JOB  H7   N3   H6   117.23  3.000
 JOB  H7   N3   C10  121.37  3.000
 JOB  H6   N3   C10  121.30  3.000
 JOB  O2   C1   C2   127.49  3.000
 JOB  C2   C1   N1   107.83  3.000
 JOB  O2   C1   N1   124.68  3.000
 JOB  H9   C2   H8   107.40  3.000
 JOB  H9   C2   C1   108.82  3.000
 JOB  H8   C2   C1   110.42  3.000
 JOB  H9   C2   C3   112.65  3.000
 JOB  H8   C2   C3   112.89  3.000
 JOB  C1   C2   C3   104.62  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
 JOB  CONST_01  C11  C10  C9   C6     0.00   0.0  0
 JOB  CONST_02  C11  C12  C7   C6     0.00   0.0  0
 JOB  CONST_03  C10  C9   C6   C7     0.00   0.0  0
 JOB  CONST_04  C10  C11  C12  C7     0.00   0.0  0
 JOB  CONST_05  C12  C11  C10  C9     0.00   0.0  0
 JOB  CONST_06  C12  C7   C6   C9     0.00   0.0  0
 JOB  CONST_07  C3   N2   C5   C6   180.00   0.0  0
 JOB  CONST_08  C8   N2   C5   C6     0.00   0.0  0
 JOB  CONST_09  C1   N1   C4   C3     0.00   0.0  0
 JOB  CONST_10  N3   C10  C9   C6   180.00   0.0  0
 JOB  CONST_11  N3   C10  C11  C12  180.00   0.0  0
 JOB  CONST_12  O3   C5   N2   C8   180.00   0.0  0
 JOB  CONST_13  O3   C5   N2   C3     0.00   0.0  0
 JOB  CONST_14  O1   C4   N1   C1   180.00   0.0  0
 JOB  CONST_15  H2   C9   C6   C5     0.00   0.0  0
 JOB  CONST_16  H3   C12  C7   C6   180.00   0.0  0
 JOB  CONST_17  H1   C11  C12  C7   180.00   0.0  0
 JOB  CONST_18  H4   N1   C4   C3   180.00   0.0  0
 JOB  CONST_19  H6   N3   C10  C11  180.00   0.0  0
 JOB  CONST_20  H7   N3   C10  C11    0.00   0.0  0
 JOB  Var_01    C2   C1   N1   C4     0.23  30.0  1
 JOB  Var_02    C3   C2   C1   N1    -7.08  30.0  1

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
 JOB  chir_01  C3  C4  N2  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
 JOB  plan-1  C5   0.020
 JOB  plan-1  C6   0.020
 JOB  plan-1  C11  0.020
 JOB  plan-1  C7   0.020
 JOB  plan-1  C8   0.020
 JOB  plan-1  C9   0.020
 JOB  plan-1  C10  0.020
 JOB  plan-1  C12  0.020
 JOB  plan-1  N2   0.020
 JOB  plan-1  C3   0.020
 JOB  plan-1  N3   0.020
 JOB  plan-1  O3   0.020
 JOB  plan-1  O4   0.020
 JOB  plan-1  H1   0.020
 JOB  plan-1  H2   0.020
 JOB  plan-1  H3   0.020
 JOB  plan-2  C10  0.020
 JOB  plan-2  N3   0.020
 JOB  plan-2  H6   0.020
 JOB  plan-2  H7   0.020
 JOB  plan-3  N1   0.020
 JOB  plan-3  C1   0.020
 JOB  plan-3  C2   0.020
 JOB  plan-3  O2   0.020
 JOB  plan-4  C4   0.020
 JOB  plan-4  N1   0.020
 JOB  plan-4  C3   0.020
 JOB  plan-4  C1   0.020
 JOB  plan-4  O1   0.020
 JOB  plan-4  H4   0.020

