# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:43:52 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (3S)-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
 H7S  H7S  (3S)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione  ligand  26  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H7S
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
 H7S  C1   C  CH1   0  -0.540   1.3575   0.3771  -0.5503
 H7S  C2   C  C     0   0.583   1.8549   0.9633   0.7636
 H7S  C4   C  C     0   0.544   3.7641   0.4243  -0.4195
 H7S  C5   C  CH2   0  -0.581   2.6244  -0.1611  -1.2150
 H7S  CG   C  CR5   0   0.048   0.2261  -0.5760  -0.3634
 H7S  CD1  C  CR15  0  -0.067   0.2589  -1.9443  -0.3795
 H7S  NE1  N  NR15  0  -0.689  -0.9881  -2.4442  -0.1595
 H7S  CE2  C  CR56  0   0.351  -1.8681  -1.4136   0.0033
 H7S  CD2  C  CR56  0   0.055  -1.1347  -0.2137  -0.1165
 H7S  CE3  C  CR16  0  -0.536  -1.7949   1.0153   0.0087
 H7S  CZ3  C  CR6   0   0.525  -3.1474   0.9811   0.2368
 H7S  CH2  C  CR16  0  -0.438  -3.8809  -0.2027   0.3566
 H7S  CZ2  C  CR16  0  -0.282  -3.2405  -1.4204   0.2411
 H7S  N3   N  NH1   0  -0.672   3.2258   1.0040   0.7045
 H7S  O6   O  O     0  -0.426   4.9412   0.3852  -0.6784
 H7S  O7   O  O     0  -0.414   1.1882   1.3499   1.6892
 H7S  F8   F  F     0  -0.329  -3.8169   2.1464   0.3602
 H7S  H1   H  HCH1  0   0.327   0.9995   1.2389  -1.1282
 H7S  H2   H  HCH2  0   0.300   2.7069  -1.2483  -1.1544
 H7S  H3   H  HCH2  0   0.309   2.7087   0.1080  -2.2665
 H7S  H4   H  HCR5  0   0.287   1.0877  -2.6163  -0.5363
 H7S  H5   H  HNR5  0   0.414  -1.2178  -3.4235  -0.1406
 H7S  H6   H  HCR6  0   0.262  -1.2681   1.9579  -0.0696
 H7S  H7   H  HCR6  0   0.273  -4.9464  -0.1578   0.5393
 H7S  H8   H  HCR6  0   0.273  -3.7951  -2.3448   0.3343
 H7S  H9   H  HNH1  0   0.424   3.7941   1.4119   1.4363

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
 H7S  CH2  CZ2  aromatic  1.381  0.020  1.381
 H7S  CH2  CZ3  aromatic  1.398  0.020  1.398
 H7S  CZ2  CE2  aromatic  1.393  0.020  1.393
 H7S  F8   CZ3  single    1.350  0.020  1.350
 H7S  CZ3  CE3  aromatic  1.372  0.020  1.372
 H7S  CE2  NE1  aromatic  1.365  0.020  1.365
 H7S  CE2  CD2  aromatic  1.411  0.020  1.411
 H7S  CE3  CD2  aromatic  1.401  0.020  1.401
 H7S  NE1  CD1  aromatic  1.361  0.020  1.361
 H7S  CD2  CG   aromatic  1.430  0.020  1.430
 H7S  CD1  CG   aromatic  1.369  0.020  1.369
 H7S  CG   C1   single    1.491  0.020  1.491
 H7S  O7   C2   double    1.204  0.020  1.204
 H7S  C1   C2   single    1.522  0.020  1.522
 H7S  C1   C5   single    1.529  0.020  1.529
 H7S  C2   N3   single    1.373  0.020  1.373
 H7S  C5   C4   single    1.508  0.020  1.508
 H7S  N3   C4   single    1.374  0.020  1.374
 H7S  C4   O6   double    1.206  0.020  1.206
 H7S  C1   H1   single    0.970  0.020  1.090
 H7S  C5   H2   single    0.970  0.020  1.090
 H7S  C5   H3   single    0.970  0.020  1.090
 H7S  CD1  H4   single    0.930  0.020  1.080
 H7S  NE1  H5   single    0.860  0.020  1.020
 H7S  CE3  H6   single    0.930  0.020  1.080
 H7S  CH2  H7   single    0.930  0.020  1.080
 H7S  CZ2  H8   single    0.930  0.020  1.080
 H7S  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
 H7S  H1   C1   CG   108.69  3.000
 H7S  H1   C1   C5   108.53  3.000
 H7S  CG   C1   C5   117.28  3.000
 H7S  H1   C1   C2   104.99  3.000
 H7S  C5   C1   C2   103.89  3.000
 H7S  CG   C1   C2   112.70  3.000
 H7S  O7   C2   N3   125.19  3.000
 H7S  N3   C2   C1   107.49  3.000
 H7S  O7   C2   C1   127.30  3.000
 H7S  O6   C4   N3   124.86  3.000
 H7S  O6   C4   C5   127.72  3.000
 H7S  N3   C4   C5   107.41  3.000
 H7S  H3   C5   H2   107.09  3.000
 H7S  H3   C5   C4   110.80  3.000
 H7S  H2   C5   C4   107.46  3.000
 H7S  H3   C5   C1   113.40  3.000
 H7S  H2   C5   C1   112.89  3.000
 H7S  C4   C5   C1   105.08  3.000
 H7S  CD2  CG   CD1  106.15  3.000
 H7S  CD1  CG   C1   128.26  3.000
 H7S  CD2  CG   C1   125.58  3.000
 H7S  H4   CD1  NE1  119.91  3.000
 H7S  H4   CD1  CG   130.02  3.000
 H7S  NE1  CD1  CG   110.07  3.000
 H7S  H5   NE1  CE2  125.84  3.000
 H7S  H5   NE1  CD1  124.72  3.000
 H7S  CE2  NE1  CD1  109.42  3.000
 H7S  CZ2  CE2  CD2  122.05  3.000
 H7S  CD2  CE2  NE1  107.27  3.000
 H7S  CZ2  CE2  NE1  130.68  3.000
 H7S  CE3  CD2  CE2  119.57  3.000
 H7S  CE3  CD2  CG   133.35  3.000
 H7S  CE2  CD2  CG   107.09  3.000
 H7S  H6   CE3  CZ3  120.89  3.000
 H7S  H6   CE3  CD2  121.88  3.000
 H7S  CZ3  CE3  CD2  117.23  3.000
 H7S  F8   CZ3  CH2  117.59  3.000
 H7S  F8   CZ3  CE3  118.86  3.000
 H7S  CH2  CZ3  CE3  123.55  3.000
 H7S  H7   CH2  CZ2  120.50  3.000
 H7S  H7   CH2  CZ3  119.74  3.000
 H7S  CZ2  CH2  CZ3  119.76  3.000
 H7S  H8   CZ2  CH2  120.56  3.000
 H7S  H8   CZ2  CE2  121.60  3.000
 H7S  CH2  CZ2  CE2  117.84  3.000
 H7S  H9   N3   C4   122.77  3.000
 H7S  H9   N3   C2   122.78  3.000
 H7S  C4   N3   C2   114.45  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
 H7S  CONST_01  CZ2  CE2  CD2  CG   180.00   0.0  0
 H7S  CONST_02  NE1  CE2  CD2  CG     0.00   0.0  0
 H7S  CONST_03  CZ3  CE3  CD2  CG   180.00   0.0  0
 H7S  CONST_04  CE2  NE1  CD1  CG     0.00   0.0  0
 H7S  CONST_05  CZ2  CE2  NE1  CD1  180.00   0.0  0
 H7S  CONST_06  CD2  CE2  NE1  CD1    0.00   0.0  0
 H7S  CONST_07  CE2  CD2  CG   CD1    0.00   0.0  0
 H7S  CONST_08  CE3  CD2  CG   CD1  180.00   0.0  0
 H7S  CONST_09  CH2  CZ2  CE2  NE1  180.00   0.0  0
 H7S  CONST_10  CE3  CD2  CE2  NE1  180.00   0.0  0
 H7S  CONST_11  CD2  CG   CD1  NE1    0.00   0.0  0
 H7S  CONST_12  CZ3  CH2  CZ2  CE2    0.00   0.0  0
 H7S  CONST_13  CZ3  CE3  CD2  CE2    0.00   0.0  0
 H7S  CONST_14  CH2  CZ2  CE2  CD2    0.00   0.0  0
 H7S  CONST_15  CH2  CZ3  CE3  CD2    0.00   0.0  0
 H7S  CONST_16  CZ2  CH2  CZ3  CE3    0.00   0.0  0
 H7S  CONST_17  CZ2  CE2  CD2  CE3    0.00   0.0  0
 H7S  CONST_18  CE2  CD2  CG   C1   180.00   0.0  0
 H7S  CONST_19  CE3  CD2  CG   C1     0.00   0.0  0
 H7S  CONST_20  NE1  CD1  CG   C1   180.00   0.0  0
 H7S  CONST_21  C4   N3   C2   C1     0.00   0.0  0
 H7S  CONST_22  F8   CZ3  CE3  CD2  180.00   0.0  0
 H7S  CONST_23  F8   CZ3  CH2  CZ2  180.00   0.0  0
 H7S  CONST_24  O7   C2   N3   C4   180.00   0.0  0
 H7S  CONST_25  H4   CD1  CG   C1     0.00   0.0  0
 H7S  CONST_26  H6   CE3  CD2  CG     0.00   0.0  0
 H7S  CONST_27  H5   NE1  CD1  CG   180.00   0.0  0
 H7S  CONST_28  H8   CZ2  CE2  NE1    0.00   0.0  0
 H7S  CONST_29  H7   CH2  CZ2  CE2  180.00   0.0  0
 H7S  CONST_30  H9   N3   C2   C1   180.00   0.0  0
 H7S  Var_01    N3   C4   C5   C1    10.27  30.0  1
 H7S  Var_02    C5   C4   N3   C2    -3.31  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
 H7S  chir_01  C1  CG  C2  C5  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
 H7S  plan-1  C1   0.020
 H7S  plan-1  CG   0.020
 H7S  plan-1  CD1  0.020
 H7S  plan-1  NE1  0.020
 H7S  plan-1  CE2  0.020
 H7S  plan-1  CD2  0.020
 H7S  plan-1  CE3  0.020
 H7S  plan-1  CZ3  0.020
 H7S  plan-1  CH2  0.020
 H7S  plan-1  CZ2  0.020
 H7S  plan-1  F8   0.020
 H7S  plan-1  H4   0.020
 H7S  plan-1  H5   0.020
 H7S  plan-1  H6   0.020
 H7S  plan-1  H7   0.020
 H7S  plan-1  H8   0.020
 H7S  plan-2  C1   0.020
 H7S  plan-2  C2   0.020
 H7S  plan-2  C4   0.020
 H7S  plan-2  N3   0.020
 H7S  plan-2  O7   0.020
 H7S  plan-2  H9   0.020
 H7S  plan-3  C4   0.020
 H7S  plan-3  C5   0.020
 H7S  plan-3  N3   0.020
 H7S  plan-3  O6   0.020

