# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:04:58 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-4-nitro-isoindole-1,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cccc2C(=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
 JOH  JOH  2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-4-nitro-isoindole-1,3-dione  ligand  28  21  .  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_JOH
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
 JOH  O3   O  O      0  -0.387  -1.4126   1.9673  -0.1451
 JOH  C5   C  CR5    0   0.623  -0.5152   1.1714  -0.0560
 JOH  N2   N  NR5    0  -0.614  -0.6814  -0.1945   0.0782
 JOH  C1   C  CR15   0  -0.256  -1.9702  -0.8227   0.1041
 JOH  C4   C  CH2    0  -0.590  -2.8427  -0.5232   1.3218
 JOH  C3   C  CR5    0   0.551  -4.2113  -0.2562   0.7450
 JOH  O1   O  O      0  -0.414  -5.2429  -0.1052   1.3465
 JOH  N1   N  NR15   0  -0.674  -4.0864  -0.1955  -0.6260
 JOH  C2   C  CR5    0   0.574  -2.8190  -0.4021  -1.0941
 JOH  O2   O  O      0  -0.402  -2.4494  -0.3063  -2.2337
 JOH  C6   C  CR56   0  -0.058   0.9457   1.4034  -0.0659
 JOH  C7   C  CR56   0  -0.008   1.5785   0.1809   0.0876
 JOH  C8   C  CR5    0   0.620   0.5265  -0.8785   0.1372
 JOH  O4   O  O      0  -0.366   0.6391  -2.0706   0.1839
 JOH  C9   C  CR16   0  -0.269   1.6338   2.5899  -0.2048
 JOH  C10  C  CR16   0  -0.253   3.0226   2.5298  -0.2098
 JOH  C11  C  CR16   0  -0.247   3.6838   1.3159  -0.0758
 JOH  C12  C  CR6    0   0.210   2.9582   0.1438   0.0877
 JOH  N3   N  N      1   0.323   3.6901  -1.0979   0.2893
 JOH  O5   O  O      0  -0.358   4.6636  -1.2812  -0.3991
 JOH  O6   O  O     -1  -0.350   3.2881  -1.8443   1.1438
 JOH  H1   H  HCR5   0   0.358  -1.8088  -1.8994   0.0123
 JOH  H2   H  HCH2   0   0.321  -2.8802  -1.3492   2.0298
 JOH  H3   H  HCH2   0   0.320  -2.5133   0.3626   1.8671
 JOH  H4   H  HNR5   0   0.433  -4.8641   0.0283  -1.2349
 JOH  H5   H  HCR6   0   0.294   1.1151   3.5324  -0.3149
 JOH  H6   H  HCR6   0   0.302   3.6035   3.4343  -0.3206
 JOH  H7   H  HCR6   0   0.318   4.7646   1.2929  -0.0790

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
 JOH  O1   C3   double    1.204  0.020  1.204
 JOH  C3   N1   single    1.378  0.020  1.378
 JOH  C3   C4   single    1.509  0.020  1.509
 JOH  N1   C2   single    1.367  0.020  1.367
 JOH  C4   C1   single    1.528  0.020  1.528
 JOH  C2   C1   single    1.527  0.020  1.527
 JOH  C2   O2   double    1.202  0.020  1.202
 JOH  C1   N2   single    1.434  0.020  1.434
 JOH  O4   C8   double    1.198  0.020  1.198
 JOH  N2   C8   single    1.389  0.020  1.389
 JOH  N2   C5   single    1.383  0.020  1.383
 JOH  C8   C7   single    1.494  0.020  1.494
 JOH  O3   C5   double    1.203  0.020  1.203
 JOH  C5   C6   single    1.479  0.020  1.479
 JOH  O6   N3   single    1.204  0.020  1.204
 JOH  C7   C6   aromatic  1.385  0.020  1.385
 JOH  C7   C12  aromatic  1.380  0.020  1.380
 JOH  C6   C9   aromatic  1.379  0.020  1.379
 JOH  N3   O5   double    1.206  0.020  1.206
 JOH  N3   C12  single    1.455  0.020  1.455
 JOH  C12  C11  aromatic  1.388  0.020  1.388
 JOH  C9   C10  aromatic  1.390  0.020  1.390
 JOH  C11  C10  aromatic  1.389  0.020  1.389
 JOH  C1   H1   single    0.970  0.020  1.090
 JOH  C4   H2   single    0.970  0.020  1.090
 JOH  C4   H3   single    0.970  0.020  1.090
 JOH  N1   H4   single    0.860  0.020  1.020
 JOH  C9   H5   single    0.930  0.020  1.080
 JOH  C10  H6   single    0.930  0.020  1.080
 JOH  C11  H7   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
 JOH  C6   C5   N2   105.92  3.000
 JOH  C6   C5   O3   129.24  3.000
 JOH  N2   C5   O3   124.84  3.000
 JOH  C8   N2   C1   124.40  3.000
 JOH  C8   N2   C5   112.71  3.000
 JOH  C1   N2   C5   122.86  3.000
 JOH  H1   C1   C2   106.71  3.000
 JOH  H1   C1   C4   110.15  3.000
 JOH  C2   C1   C4   104.71  3.000
 JOH  H1   C1   N2   107.30  3.000
 JOH  C2   C1   N2   111.39  3.000
 JOH  C4   C1   N2   116.22  3.000
 JOH  H3   C4   H2   107.55  3.000
 JOH  H3   C4   C3   108.73  3.000
 JOH  H2   C4   C3   110.59  3.000
 JOH  H3   C4   C1   112.65  3.000
 JOH  H2   C4   C1   112.92  3.000
 JOH  C3   C4   C1   104.35  3.000
 JOH  N1   C3   O1   124.71  3.000
 JOH  N1   C3   C4   107.81  3.000
 JOH  O1   C3   C4   127.47  3.000
 JOH  H4   N1   C2   122.65  3.000
 JOH  H4   N1   C3   122.57  3.000
 JOH  C2   N1   C3   114.72  3.000
 JOH  O2   C2   N1   126.71  3.000
 JOH  O2   C2   C1   126.51  3.000
 JOH  N1   C2   C1   106.75  3.000
 JOH  C9   C6   C7   122.87  3.000
 JOH  C9   C6   C5   128.94  3.000
 JOH  C7   C6   C5   108.18  3.000
 JOH  C12  C7   C8   133.23  3.000
 JOH  C12  C7   C6   118.71  3.000
 JOH  C8   C7   C6   107.93  3.000
 JOH  O4   C8   C7   129.84  3.000
 JOH  C7   C8   N2   105.17  3.000
 JOH  O4   C8   N2   124.97  3.000
 JOH  H5   C9   C10  121.10  3.000
 JOH  H5   C9   C6   121.40  3.000
 JOH  C10  C9   C6   117.50  3.000
 JOH  H6   C10  C11  119.05  3.000
 JOH  H6   C10  C9   120.08  3.000
 JOH  C11  C10  C9   120.87  3.000
 JOH  H7   C11  C12  120.33  3.000
 JOH  H7   C11  C10  119.63  3.000
 JOH  C12  C11  C10  120.03  3.000
 JOH  N3   C12  C11  118.28  3.000
 JOH  C11  C12  C7   119.99  3.000
 JOH  N3   C12  C7   121.71  3.000
 JOH  O6   N3   O5   125.48  3.000
 JOH  O5   N3   C12  117.16  3.000
 JOH  O6   N3   C12  117.35  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
 JOH  CONST_01  C11  C12  C7   C6     0.00   0.0  0
 JOH  CONST_02  C11  C10  C9   C6     0.00   0.0  0
 JOH  CONST_03  C10  C9   C6   C7     0.00   0.0  0
 JOH  CONST_04  C10  C11  C12  C7     0.00   0.0  0
 JOH  CONST_05  C12  C7   C6   C9     0.00   0.0  0
 JOH  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 JOH  CONST_07  C6   C5   N2   C1   180.00   0.0  0
 JOH  CONST_08  C2   N1   C3   C4     0.00   0.0  0
 JOH  CONST_09  C8   N2   C5   C6     0.00   0.0  0
 JOH  CONST_10  N3   C12  C7   C6   180.00   0.0  0
 JOH  CONST_11  N3   C12  C7   C8     0.00   0.0  0
 JOH  CONST_12  N3   C12  C11  C10  180.00   0.0  0
 JOH  CONST_13  C1   N2   C5   O3     0.00   0.0  0
 JOH  CONST_14  C8   N2   C5   O3   180.00   0.0  0
 JOH  CONST_15  C2   N1   C3   O1   180.00   0.0  0
 JOH  CONST_16  H5   C9   C6   C5     0.00   0.0  0
 JOH  CONST_17  H6   C10  C9   C6   180.00   0.0  0
 JOH  CONST_18  H7   C11  C12  C7   180.00   0.0  0
 JOH  CONST_19  H4   N1   C3   C4   180.00   0.0  0
 JOH  Var_01    N1   C3   C4   C1    -8.57  30.0  1
 JOH  Var_02    C3   N1   C2   C1     7.31  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
 JOH  chir_01  C1  C4  C2  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
 JOH  plan-1  O3   0.020
 JOH  plan-1  C5   0.020
 JOH  plan-1  N2   0.020
 JOH  plan-1  C1   0.020
 JOH  plan-1  C6   0.020
 JOH  plan-1  C7   0.020
 JOH  plan-1  C8   0.020
 JOH  plan-1  O4   0.020
 JOH  plan-1  C9   0.020
 JOH  plan-1  C10  0.020
 JOH  plan-1  C11  0.020
 JOH  plan-1  C12  0.020
 JOH  plan-1  N3   0.020
 JOH  plan-1  H5   0.020
 JOH  plan-1  H6   0.020
 JOH  plan-1  H7   0.020
 JOH  plan-2  C12  0.020
 JOH  plan-2  N3   0.020
 JOH  plan-2  O5   0.020
 JOH  plan-2  O6   0.020
 JOH  plan-3  C1   0.020
 JOH  plan-3  N1   0.020
 JOH  plan-3  C2   0.020
 JOH  plan-3  O2   0.020
 JOH  plan-4  C4   0.020
 JOH  plan-4  C3   0.020
 JOH  plan-4  O1   0.020
 JOH  plan-4  N1   0.020
 JOH  plan-4  C2   0.020
 JOH  plan-4  H4   0.020

