# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 04:43:22 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (3R)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc2[nH]cc([C@H]3CC(=O)NC3=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
 AOJ  AOJ  (3R)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione  ligand  26  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AOJ
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
 AOJ  N1   N  NR15  0  -0.672   3.2021   1.0206  -0.7464
 AOJ  C4   C  CR5   0   0.583   1.8314   0.9692  -0.7998
 AOJ  C5   C  CR15  0  -0.067   0.2525  -1.9329   0.3831
 AOJ  C6   C  CR56  0   0.351  -1.8788  -1.4129   0.0095
 AOJ  C7   C  CR16  0  -0.282  -3.2531  -1.4263  -0.2170
 AOJ  C8   C  CR16  0  -0.438  -3.8981  -0.2117  -0.3401
 AOJ  C10  C  CR16  0  -0.537  -1.8132   1.0161  -0.0214
 AOJ  C11  C  CR6   0   0.525  -3.1673   0.9755  -0.2382
 AOJ  C9   C  CR56  0   0.054  -1.1485  -0.2096   0.1112
 AOJ  N2   N  NR15  0  -0.689  -0.9944  -2.4391   0.1763
 AOJ  C12  C  CR5   0   0.048   0.2151  -0.5649   0.3528
 AOJ  C1   C  CR15  0  -0.540   1.3436   0.3946   0.5227
 AOJ  O2   O  O     0  -0.414   1.1580   1.3403  -1.7271
 AOJ  C3   C  CR5   0   0.544   3.7487   0.4555   0.3811
 AOJ  O1   O  O     0  -0.425   4.9271   0.4275   0.6356
 AOJ  C2   C  CH2   0  -0.581   2.6164  -0.1313   1.1861
 AOJ  H4   H  HNR5  0   0.424   3.7650   1.4260  -1.4839
 AOJ  H7   H  HCR6  0   0.273  -3.8060  -2.3532  -0.2957
 AOJ  H8   H  HCR6  0   0.274  -4.9652  -0.1715  -0.5145
 AOJ  H9   H  HCR6  0   0.262  -1.2886   1.9609   0.0439
 AOJ  H6   H  HNR5  0   0.414  -1.2223  -3.4191   0.1734
 AOJ  H1   H  HCR5  0   0.327   0.9855   1.2605   1.0944
 AOJ  H3   H  HCH2  0   0.309   2.7035   0.1455   2.2354
 AOJ  H2   H  HCH2  0   0.300   2.7050  -1.2184   1.1322
 AOJ  H5   H  HCR5  0   0.287   1.0847  -2.6003   0.5419
 AOJ  F1   F  F     0  -0.329  -3.8413   2.1374  -0.3688

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
 AOJ  C7   C8   aromatic  1.381  0.020  1.381
 AOJ  C7   C6   aromatic  1.393  0.020  1.393
 AOJ  C8   C11  aromatic  1.398  0.020  1.398
 AOJ  N2   C6   aromatic  1.365  0.020  1.365
 AOJ  N2   C5   aromatic  1.362  0.020  1.362
 AOJ  C6   C9   aromatic  1.411  0.020  1.411
 AOJ  C5   C12  aromatic  1.369  0.020  1.369
 AOJ  C11  F1   single    1.350  0.020  1.350
 AOJ  C11  C10  aromatic  1.372  0.020  1.372
 AOJ  C9   C10  aromatic  1.401  0.020  1.401
 AOJ  C9   C12  aromatic  1.430  0.020  1.430
 AOJ  C12  C1   single    1.491  0.020  1.491
 AOJ  O2   C4   double    1.205  0.020  1.205
 AOJ  C4   C1   single    1.522  0.020  1.522
 AOJ  C4   N1   single    1.373  0.020  1.373
 AOJ  C1   C2   single    1.529  0.020  1.529
 AOJ  N1   C3   single    1.375  0.020  1.375
 AOJ  C2   C3   single    1.508  0.020  1.508
 AOJ  C3   O1   double    1.206  0.020  1.206
 AOJ  N1   H4   single    0.860  0.020  1.020
 AOJ  C5   H5   single    0.930  0.020  1.080
 AOJ  C7   H7   single    0.930  0.020  1.080
 AOJ  C8   H8   single    0.930  0.020  1.080
 AOJ  C10  H9   single    0.930  0.020  1.080
 AOJ  N2   H6   single    0.860  0.020  1.020
 AOJ  C1   H1   single    0.970  0.020  1.090
 AOJ  C2   H3   single    0.970  0.020  1.090
 AOJ  C2   H2   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
 AOJ  H4   N1   C3   122.75  3.000
 AOJ  H4   N1   C4   122.81  3.000
 AOJ  C3   N1   C4   114.43  3.000
 AOJ  O2   C4   C1   127.29  3.000
 AOJ  C1   C4   N1   107.48  3.000
 AOJ  O2   C4   N1   125.21  3.000
 AOJ  H5   C5   C12  130.00  3.000
 AOJ  H5   C5   N2   119.93  3.000
 AOJ  C12  C5   N2   110.07  3.000
 AOJ  N2   C6   C9   107.27  3.000
 AOJ  C9   C6   C7   122.04  3.000
 AOJ  N2   C6   C7   130.69  3.000
 AOJ  H7   C7   C8   120.56  3.000
 AOJ  H7   C7   C6   121.61  3.000
 AOJ  C8   C7   C6   117.83  3.000
 AOJ  H8   C8   C11  119.73  3.000
 AOJ  H8   C8   C7   120.51  3.000
 AOJ  C11  C8   C7   119.76  3.000
 AOJ  H9   C10  C9   121.87  3.000
 AOJ  H9   C10  C11  120.90  3.000
 AOJ  C9   C10  C11  117.22  3.000
 AOJ  F1   C11  C10  118.86  3.000
 AOJ  C10  C11  C8   123.55  3.000
 AOJ  F1   C11  C8   117.58  3.000
 AOJ  C12  C9   C10  133.32  3.000
 AOJ  C12  C9   C6   107.09  3.000
 AOJ  C10  C9   C6   119.58  3.000
 AOJ  H6   N2   C6   125.81  3.000
 AOJ  H6   N2   C5   124.75  3.000
 AOJ  C6   N2   C5   109.42  3.000
 AOJ  C1   C12  C9   125.54  3.000
 AOJ  C1   C12  C5   128.31  3.000
 AOJ  C9   C12  C5   106.15  3.000
 AOJ  H1   C1   C2   108.48  3.000
 AOJ  H1   C1   C12  108.67  3.000
 AOJ  C2   C1   C12  117.28  3.000
 AOJ  H1   C1   C4   105.02  3.000
 AOJ  C2   C1   C4   103.89  3.000
 AOJ  C12  C1   C4   112.74  3.000
 AOJ  C2   C3   O1   127.74  3.000
 AOJ  O1   C3   N1   124.84  3.000
 AOJ  C2   C3   N1   107.41  3.000
 AOJ  H2   C2   H3   107.11  3.000
 AOJ  H2   C2   C3   107.46  3.000
 AOJ  H3   C2   C3   110.82  3.000
 AOJ  H2   C2   C1   112.87  3.000
 AOJ  H3   C2   C1   113.42  3.000
 AOJ  C3   C2   C1   105.05  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
 AOJ  CONST_01  C7   C6   N2   C5   180.00   0.0  0
 AOJ  CONST_02  C9   C6   N2   C5     0.00   0.0  0
 AOJ  CONST_03  C6   C9   C12  C5     0.00   0.0  0
 AOJ  CONST_04  C10  C9   C12  C5   180.00   0.0  0
 AOJ  CONST_05  C11  C8   C7   C6     0.00   0.0  0
 AOJ  CONST_06  C12  C5   N2   C6     0.00   0.0  0
 AOJ  CONST_07  C11  C10  C9   C6     0.00   0.0  0
 AOJ  CONST_08  C10  C11  C8   C7     0.00   0.0  0
 AOJ  CONST_09  C10  C9   C6   C7     0.00   0.0  0
 AOJ  CONST_10  C12  C9   C6   C7   180.00   0.0  0
 AOJ  CONST_11  N2   C6   C7   C8   180.00   0.0  0
 AOJ  CONST_12  C9   C6   C7   C8     0.00   0.0  0
 AOJ  CONST_13  C9   C10  C11  C8     0.00   0.0  0
 AOJ  CONST_14  N2   C6   C9   C10  180.00   0.0  0
 AOJ  CONST_15  C12  C9   C10  C11  180.00   0.0  0
 AOJ  CONST_16  N2   C5   C12  C9     0.00   0.0  0
 AOJ  CONST_17  C12  C9   C6   N2     0.00   0.0  0
 AOJ  CONST_18  C1   C12  C9   C6   180.00   0.0  0
 AOJ  CONST_19  C1   C12  C9   C10    0.00   0.0  0
 AOJ  CONST_20  C1   C12  C5   N2   180.00   0.0  0
 AOJ  CONST_21  C3   N1   C4   C1     0.00   0.0  0
 AOJ  CONST_22  F1   C11  C8   C7   180.00   0.0  0
 AOJ  CONST_23  C9   C10  C11  F1   180.00   0.0  0
 AOJ  CONST_24  C3   N1   C4   O2   180.00   0.0  0
 AOJ  CONST_25  H8   C8   C7   C6   180.00   0.0  0
 AOJ  CONST_26  H5   C5   N2   C6   180.00   0.0  0
 AOJ  CONST_27  H9   C10  C9   C6   180.00   0.0  0
 AOJ  CONST_28  H6   N2   C6   C7     0.00   0.0  0
 AOJ  CONST_29  H7   C7   C8   C11  180.00   0.0  0
 AOJ  CONST_30  H4   N1   C4   C1   180.00   0.0  0
 AOJ  Var_01    C1   C2   C3   N1   -10.43  30.0  1
 AOJ  Var_02    C2   C3   N1   C4     3.33  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
 AOJ  chir_01  C1  C12  C4  C2  positiv

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
 AOJ  plan-1  C5   0.020
 AOJ  plan-1  C6   0.020
 AOJ  plan-1  C7   0.020
 AOJ  plan-1  C8   0.020
 AOJ  plan-1  C10  0.020
 AOJ  plan-1  C11  0.020
 AOJ  plan-1  C9   0.020
 AOJ  plan-1  N2   0.020
 AOJ  plan-1  C12  0.020
 AOJ  plan-1  C1   0.020
 AOJ  plan-1  H7   0.020
 AOJ  plan-1  H8   0.020
 AOJ  plan-1  H9   0.020
 AOJ  plan-1  H6   0.020
 AOJ  plan-1  H5   0.020
 AOJ  plan-1  F1   0.020
 AOJ  plan-2  N1   0.020
 AOJ  plan-2  C4   0.020
 AOJ  plan-2  C1   0.020
 AOJ  plan-2  O2   0.020
 AOJ  plan-2  C3   0.020
 AOJ  plan-2  H4   0.020
 AOJ  plan-3  N1   0.020
 AOJ  plan-3  C3   0.020
 AOJ  plan-3  O1   0.020
 AOJ  plan-3  C2   0.020

