# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 07:40:05 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 7-methyl-1~{H}-indole-2,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2C(=O)C(=O)Nc12
#
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
 72S  72S  7-methyl-1~{H}-indole-2,3-dione  ligand  19  12  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_72S
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
 72S  C10  C  CH3   0  -0.737  -2.2760   2.1596   0.0302
 72S  C5   C  CR6   0   0.068  -1.7780   0.7476   0.0287
 72S  C4   C  CR16  0  -0.290  -2.6343  -0.3547   0.0469
 72S  C3   C  CR16  0  -0.255  -2.1799  -1.6722   0.0468
 72S  C2   C  CR16  0  -0.299  -0.8203  -1.9406   0.0286
 72S  C1   C  CR56  0  -0.067   0.0502  -0.8620   0.0099
 72S  C6   C  CR56  0   0.380  -0.4248   0.4511   0.0094
 72S  N7   N  NR15  0  -0.769   0.6361   1.3577  -0.0133
 72S  C8   C  CR5   0   0.451   1.8357   0.7262  -0.0286
 72S  O11  O  O     0  -0.401   2.9403   1.2074  -0.0497
 72S  C9   C  CR5   0   0.247   1.5033  -0.7911  -0.0127
 72S  O12  O  O     0  -0.341   2.3402  -1.6550  -0.0192
 72S  H1   H  HCH3  0   0.256  -1.9370   2.7036  -0.8534
 72S  H2   H  HCH3  0   0.262  -3.3640   2.1907   0.0404
 72S  H3   H  HCH3  0   0.256  -1.9204   2.7072   0.9050
 72S  H4   H  HCR6  0   0.269  -3.7024  -0.1736   0.0612
 72S  H5   H  HCR6  0   0.268  -2.8960  -2.4819   0.0609
 72S  H6   H  HCR6  0   0.273  -0.4466  -2.9563   0.0280
 72S  H7   H  HNR5  0   0.428   0.5286   2.3614  -0.0207

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
 72S  C4   C3   aromatic  1.394  0.020  1.394
 72S  C4   C5   aromatic  1.396  0.020  1.396
 72S  C3   C2   aromatic  1.386  0.020  1.386
 72S  C10  C5   single    1.497  0.020  1.497
 72S  C5   C6   aromatic  1.385  0.020  1.385
 72S  C2   C1   aromatic  1.386  0.020  1.386
 72S  C6   C1   aromatic  1.396  0.020  1.396
 72S  C6   N7   single    1.396  0.020  1.396
 72S  C1   C9   single    1.455  0.020  1.455
 72S  N7   C8   single    1.356  0.020  1.356
 72S  O12  C9   double    1.203  0.020  1.203
 72S  C9   C8   single    1.553  0.020  1.553
 72S  C8   O11  double    1.205  0.020  1.205
 72S  C10  H1   single    0.970  0.020  1.090
 72S  C10  H2   single    0.970  0.020  1.090
 72S  C10  H3   single    0.970  0.020  1.090
 72S  C4   H4   single    0.930  0.020  1.080
 72S  C3   H5   single    0.930  0.020  1.080
 72S  C2   H6   single    0.930  0.020  1.080
 72S  N7   H7   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
 72S  H3   C10  H2   107.69  3.000
 72S  H3   C10  H1   107.30  3.000
 72S  H2   C10  H1   107.68  3.000
 72S  H3   C10  C5   111.44  3.000
 72S  H2   C10  C5   111.07  3.000
 72S  H1   C10  C5   111.46  3.000
 72S  C6   C5   C4   115.49  3.000
 72S  C6   C5   C10  121.78  3.000
 72S  C4   C5   C10  122.73  3.000
 72S  H4   C4   C3   118.65  3.000
 72S  H4   C4   C5   118.23  3.000
 72S  C3   C4   C5   123.13  3.000
 72S  H5   C3   C2   120.33  3.000
 72S  H5   C3   C4   119.48  3.000
 72S  C2   C3   C4   120.19  3.000
 72S  H6   C2   C1   120.89  3.000
 72S  H6   C2   C3   121.37  3.000
 72S  C1   C2   C3   117.74  3.000
 72S  C9   C1   C6   107.09  3.000
 72S  C9   C1   C2   131.70  3.000
 72S  C6   C1   C2   121.21  3.000
 72S  N7   C6   C1   110.63  3.000
 72S  N7   C6   C5   127.13  3.000
 72S  C1   C6   C5   122.24  3.000
 72S  H7   N7   C8   123.87  3.000
 72S  H7   N7   C6   124.40  3.000
 72S  C8   N7   C6   111.73  3.000
 72S  C9   C8   O11  125.90  3.000
 72S  O11  C8   N7   128.70  3.000
 72S  C9   C8   N7   105.40  3.000
 72S  O12  C9   C8   123.55  3.000
 72S  C8   C9   C1   105.16  3.000
 72S  O12  C9   C1   131.30  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
 72S  CONST_01  C2   C3   C4  C5      0.00   0.0  0
 72S  CONST_02  C2   C1   C6  C5      0.00   0.0  0
 72S  CONST_03  C1   C2   C3  C4      0.00   0.0  0
 72S  CONST_04  C1   C6   C5  C4      0.00   0.0  0
 72S  CONST_05  C6   C5   C4  C3      0.00   0.0  0
 72S  CONST_06  C6   C1   C2  C3      0.00   0.0  0
 72S  CONST_07  C9   C8   N7  C6      0.00   0.0  0
 72S  CONST_08  C3   C4   C5  C10   180.00   0.0  0
 72S  CONST_09  C1   C6   C5  C10   180.00   0.0  0
 72S  CONST_10  N7   C6   C5  C10     0.00   0.0  0
 72S  CONST_11  O11  C8   N7  C6    180.00   0.0  0
 72S  CONST_12  H5   C3   C4  C5    180.00   0.0  0
 72S  CONST_13  H6   C2   C3  C4    180.00   0.0  0
 72S  CONST_14  H4   C4   C3  C2    180.00   0.0  0
 72S  CONST_15  H7   N7   C8  C9    180.00   0.0  0
 72S  Var_01    H1   C10  C5  C4   -120.45  30.0  2

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
 72S  plan-1  C10  0.020
 72S  plan-1  C5   0.020
 72S  plan-1  C4   0.020
 72S  plan-1  C3   0.020
 72S  plan-1  C2   0.020
 72S  plan-1  C1   0.020
 72S  plan-1  C6   0.020
 72S  plan-1  N7   0.020
 72S  plan-1  C8   0.020
 72S  plan-1  O11  0.020
 72S  plan-1  C9   0.020
 72S  plan-1  O12  0.020
 72S  plan-1  H4   0.020
 72S  plan-1  H5   0.020
 72S  plan-1  H6   0.020
 72S  plan-1  H7   0.020

