# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:44:55 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 4-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: Nc1cccc2C(=O)N([C@H]3CC(=O)NC3=O)C(=O)c12
#
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
 JO5  JO5  4-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_JO5
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
 JO5  C4   C  CR16  0  -0.322   4.2484  -0.5654   0.0008
 JO5  C5   C  CR16  0  -0.243   3.7654  -1.8307   0.2521
 JO5  C6   C  CR16  0  -0.340   2.3900  -2.1052   0.3159
 JO5  C11  C  CR5   0   0.550  -3.7725  -0.1053  -0.7400
 JO5  C7   C  CR56  0  -0.045   1.5559  -1.0380   0.1146
 JO5  C8   C  CR5   0   0.595   0.0771  -0.9865   0.1241
 JO5  C9   C  CR15  0  -0.252  -1.6128   0.7908  -0.1906
 JO5  C10  C  CH2   0  -0.592  -2.4540   0.2830  -1.3614
 JO5  C12  C  CR5   0   0.572  -2.3996   0.3851   1.0534
 JO5  N2   N  NR5   0  -0.613  -0.2601   0.3303  -0.1290
 JO5  C3   C  CR6   0   0.333   3.3855   0.5396  -0.2108
 JO5  N3   N  NR15  0  -0.675  -3.6345  -0.0210   0.6277
 JO5  C1   C  CR5   0   0.609   0.8683   1.1370  -0.2946
 JO5  C2   C  CR56  0  -0.119   2.0209   0.2513  -0.1413
 JO5  O2   O  O     0  -0.408  -0.7223  -1.8712   0.3100
 JO5  O3   O  O     0  -0.417  -4.7791  -0.4448  -1.3071
 JO5  O4   O  O     0  -0.406  -2.0211   0.4463   2.1930
 JO5  H1   H  HCR6  0   0.280   5.3188  -0.4042  -0.0382
 JO5  H2   H  HCR6  0   0.276   4.4747  -2.6330   0.4064
 JO5  H3   H  HCR6  0   0.268   2.0204  -3.1013   0.5149
 JO5  H4   H  HCR5  0   0.350  -1.5853   1.8836  -0.1991
 JO5  H5   H  HCH2  0   0.318  -2.0211  -0.5958  -1.8422
 JO5  H6   H  HCH2  0   0.317  -2.6034   1.0357  -2.1337
 JO5  H7   H  HNH2  0   0.404   4.8590   1.9394  -0.3680
 JO5  H8   H  HNH2  0   0.403   3.2731   2.5666  -0.4906
 JO5  H9   H  HNR5  0   0.431  -4.3718  -0.2893   1.2678
 JO5  N1   N  NH2   0  -0.856   3.8762   1.7627  -0.4836
 JO5  O1   O  O     0  -0.417   0.8312   2.3244  -0.5180

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
 JO5  O3   C11  double    1.204  0.020  1.204
 JO5  C11  N3   single    1.377  0.020  1.377
 JO5  C11  C10  single    1.508  0.020  1.508
 JO5  N3   C12  single    1.368  0.020  1.368
 JO5  C10  C9   single    1.528  0.020  1.528
 JO5  C12  C9   single    1.527  0.020  1.527
 JO5  C12  O4   double    1.202  0.020  1.202
 JO5  C9   N2   single    1.430  0.020  1.430
 JO5  O1   C1   double    1.209  0.020  1.209
 JO5  N2   C1   single    1.397  0.020  1.397
 JO5  N2   C8   single    1.383  0.020  1.383
 JO5  C1   C2   single    1.462  0.020  1.462
 JO5  O2   C8   double    1.207  0.020  1.207
 JO5  C8   C7   single    1.480  0.020  1.480
 JO5  C2   C7   aromatic  1.394  0.020  1.394
 JO5  C2   C3   aromatic  1.397  0.020  1.397
 JO5  C7   C6   aromatic  1.369  0.020  1.369
 JO5  N1   C3   single    1.346  0.020  1.346
 JO5  C3   C4   aromatic  1.418  0.020  1.418
 JO5  C6   C5   aromatic  1.404  0.020  1.404
 JO5  C4   C5   aromatic  1.378  0.020  1.378
 JO5  C4   H1   single    0.930  0.020  1.080
 JO5  C5   H2   single    0.930  0.020  1.080
 JO5  C6   H3   single    0.930  0.020  1.080
 JO5  C9   H4   single    0.970  0.020  1.090
 JO5  C10  H5   single    0.970  0.020  1.090
 JO5  C10  H6   single    0.970  0.020  1.090
 JO5  N1   H7   single    0.890  0.020  1.040
 JO5  N1   H8   single    0.890  0.020  1.040
 JO5  N3   H9   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
 JO5  H1   C4   C3   118.69  3.000
 JO5  H1   C4   C5   119.33  3.000
 JO5  C3   C4   C5   121.98  3.000
 JO5  H2   C5   C6   119.39  3.000
 JO5  H2   C5   C4   118.51  3.000
 JO5  C6   C5   C4   122.10  3.000
 JO5  H3   C6   C7   122.48  3.000
 JO5  H3   C6   C5   121.57  3.000
 JO5  C7   C6   C5   115.96  3.000
 JO5  O3   C11  N3   124.66  3.000
 JO5  N3   C11  C10  107.80  3.000
 JO5  O3   C11  C10  127.53  3.000
 JO5  C2   C7   C8   107.60  3.000
 JO5  C2   C7   C6   122.99  3.000
 JO5  C8   C7   C6   129.41  3.000
 JO5  O2   C8   N2   124.39  3.000
 JO5  O2   C8   C7   129.60  3.000
 JO5  N2   C8   C7   106.01  3.000
 JO5  H4   C9   N2   107.36  3.000
 JO5  H4   C9   C12  106.55  3.000
 JO5  N2   C9   C12  111.51  3.000
 JO5  H4   C9   C10  109.88  3.000
 JO5  N2   C9   C10  116.52  3.000
 JO5  C12  C9   C10  104.61  3.000
 JO5  H6   C10  H5   107.38  3.000
 JO5  H6   C10  C9   112.90  3.000
 JO5  H5   C10  C9   112.75  3.000
 JO5  H6   C10  C11  110.50  3.000
 JO5  H5   C10  C11  108.72  3.000
 JO5  C9   C10  C11  104.54  3.000
 JO5  O4   C12  N3   126.46  3.000
 JO5  O4   C12  C9   126.62  3.000
 JO5  N3   C12  C9   106.89  3.000
 JO5  C1   N2   C9   124.95  3.000
 JO5  C1   N2   C8   112.00  3.000
 JO5  C9   N2   C8   123.04  3.000
 JO5  C2   C3   N1   123.64  3.000
 JO5  N1   C3   C4   121.11  3.000
 JO5  C2   C3   C4   115.24  3.000
 JO5  H9   N3   C12  122.63  3.000
 JO5  H9   N3   C11  122.58  3.000
 JO5  C12  N3   C11  114.69  3.000
 JO5  C2   C1   O1   129.70  3.000
 JO5  C2   C1   N2   105.94  3.000
 JO5  O1   C1   N2   124.36  3.000
 JO5  C1   C2   C3   129.81  3.000
 JO5  C3   C2   C7   121.74  3.000
 JO5  C1   C2   C7   108.45  3.000
 JO5  H8   N1   H7   116.55  3.000
 JO5  H8   N1   C3   120.63  3.000
 JO5  H7   N1   C3   119.53  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
 JO5  CONST_01  C7   C2   C3   C4     0.00   0.0  0
 JO5  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 JO5  CONST_03  C2   C7   C6   C5     0.00   0.0  0
 JO5  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 JO5  CONST_05  C3   C2   C7   C6     0.00   0.0  0
 JO5  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 JO5  CONST_07  C9   N2   C8   C7   180.00   0.0  0
 JO5  CONST_08  C1   N2   C8   C7     0.00   0.0  0
 JO5  CONST_09  C12  N3   C11  C10    0.00   0.0  0
 JO5  CONST_10  N1   C3   C4   C5   180.00   0.0  0
 JO5  CONST_11  N1   C3   C2   C7   180.00   0.0  0
 JO5  CONST_12  C1   C2   C3   N1     0.00   0.0  0
 JO5  CONST_13  O2   C8   N2   C9     0.00   0.0  0
 JO5  CONST_14  O3   C11  N3   C12  180.00   0.0  0
 JO5  CONST_15  O2   C8   N2   C1   180.00   0.0  0
 JO5  CONST_16  H3   C6   C5   C4   180.00   0.0  0
 JO5  CONST_17  H1   C4   C5   C6   180.00   0.0  0
 JO5  CONST_18  H2   C5   C6   C7   180.00   0.0  0
 JO5  CONST_19  H9   N3   C11  C10  180.00   0.0  0
 JO5  CONST_20  H7   N1   C3   C4     0.00   0.0  0
 JO5  CONST_21  H8   N1   C3   C4   180.00   0.0  0
 JO5  Var_01    C9   C12  N3   C11    7.18  30.0  1
 JO5  Var_02    N3   C11  C10  C9    -7.88  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
 JO5  chir_01  C9  C10  C12  N2  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
 JO5  plan-1  C4   0.020
 JO5  plan-1  C5   0.020
 JO5  plan-1  C6   0.020
 JO5  plan-1  C7   0.020
 JO5  plan-1  C8   0.020
 JO5  plan-1  C9   0.020
 JO5  plan-1  N2   0.020
 JO5  plan-1  C3   0.020
 JO5  plan-1  C1   0.020
 JO5  plan-1  C2   0.020
 JO5  plan-1  O2   0.020
 JO5  plan-1  H1   0.020
 JO5  plan-1  H2   0.020
 JO5  plan-1  H3   0.020
 JO5  plan-1  N1   0.020
 JO5  plan-1  O1   0.020
 JO5  plan-2  C3   0.020
 JO5  plan-2  H7   0.020
 JO5  plan-2  H8   0.020
 JO5  plan-2  N1   0.020
 JO5  plan-3  C9   0.020
 JO5  plan-3  C12  0.020
 JO5  plan-3  N3   0.020
 JO5  plan-3  O4   0.020
 JO5  plan-4  C11  0.020
 JO5  plan-4  C10  0.020
 JO5  plan-4  C12  0.020
 JO5  plan-4  N3   0.020
 JO5  plan-4  O3   0.020
 JO5  plan-4  H9   0.020

