# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 13:20:53 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 1,3-dioxo-2,3-dihydro-1H-indene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C(C#N)C(=O)c2ccccc12
#
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
 0FN  0FN  1,3-dioxo-2,3-dihydro-1H-indene-2-carbonitrile  ligand  18  13  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0FN
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
 0FN  OAH  O  O     0  -0.334  -1.0128  -2.3292   0.1346
 0FN  CAC  C  CR5   0   0.390  -0.6367  -1.1932   0.2140
 0FN  CAD  C  CR56  0  -0.000   0.7319  -0.6782   0.0538
 0FN  CAK  C  CR16  0  -0.260   1.9070  -1.3996  -0.0907
 0FN  CAL  C  CR16  0  -0.232   3.0852  -0.6848  -0.2468
 0FN  CAM  C  CR16  0  -0.232   3.0854   0.7124  -0.2630
 0FN  CAJ  C  CR16  0  -0.261   1.9074   1.4307  -0.1242
 0FN  CAE  C  CR56  0  -0.000   0.7320   0.7134   0.0374
 0FN  CAB  C  CR5   0   0.390  -0.6364   1.2324   0.1853
 0FN  OAI  O  O     0  -0.334  -1.0125   2.3662   0.0800
 0FN  CAA  C  CR15  0  -0.619  -1.5285   0.0231   0.5070
 0FN  CAF  C  CSP   0   0.169  -2.7878   0.0149  -0.1988
 0FN  NAG  N  NS    0  -0.239  -3.7827   0.0081  -0.7739
 0FN  H1   H  HCR6  0   0.285   1.9083  -2.4810  -0.0808
 0FN  H2   H  HCR6  0   0.288   4.0209  -1.2150  -0.3617
 0FN  H3   H  HCR6  0   0.288   4.0213   1.2396  -0.3900
 0FN  H4   H  HCR6  0   0.285   1.9089   2.5122  -0.1395
 0FN  H5   H  HCR5  0   0.418  -1.7269   0.0372   1.5879

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
 0FN  OAI  CAB  double    1.199  0.020  1.199
 0FN  CAJ  CAM  aromatic  1.387  0.020  1.387
 0FN  CAJ  CAE  aromatic  1.386  0.020  1.386
 0FN  CAM  CAL  aromatic  1.397  0.020  1.397
 0FN  CAB  CAE  single    1.471  0.020  1.471
 0FN  CAB  CAA  single    1.537  0.020  1.537
 0FN  CAE  CAD  aromatic  1.392  0.020  1.392
 0FN  CAL  CAK  aromatic  1.387  0.020  1.387
 0FN  CAA  CAF  single    1.444  0.020  1.444
 0FN  CAA  CAC  single    1.536  0.020  1.536
 0FN  CAF  NAG  triple    1.149  0.020  1.149
 0FN  CAD  CAK  aromatic  1.386  0.020  1.386
 0FN  CAD  CAC  single    1.471  0.020  1.471
 0FN  CAC  OAH  double    1.199  0.020  1.199
 0FN  CAK  H1   single    0.930  0.020  1.080
 0FN  CAL  H2   single    0.930  0.020  1.080
 0FN  CAM  H3   single    0.930  0.020  1.080
 0FN  CAJ  H4   single    0.930  0.020  1.080
 0FN  CAA  H5   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
 0FN  CAA  CAC  CAD  106.48  3.000
 0FN  CAD  CAC  OAH  128.04  3.000
 0FN  CAA  CAC  OAH  125.48  3.000
 0FN  CAE  CAD  CAK  121.26  3.000
 0FN  CAK  CAD  CAC  128.15  3.000
 0FN  CAE  CAD  CAC  110.58  3.000
 0FN  H1   CAK  CAL  121.02  3.000
 0FN  H1   CAK  CAD  121.36  3.000
 0FN  CAL  CAK  CAD  117.62  3.000
 0FN  H2   CAL  CAM  119.26  3.000
 0FN  H2   CAL  CAK  119.62  3.000
 0FN  CAM  CAL  CAK  121.12  3.000
 0FN  H3   CAM  CAJ  119.63  3.000
 0FN  H3   CAM  CAL  119.27  3.000
 0FN  CAJ  CAM  CAL  121.11  3.000
 0FN  H4   CAJ  CAE  121.35  3.000
 0FN  H4   CAJ  CAM  121.02  3.000
 0FN  CAE  CAJ  CAM  117.64  3.000
 0FN  CAB  CAE  CAJ  128.15  3.000
 0FN  CAB  CAE  CAD  110.58  3.000
 0FN  CAJ  CAE  CAD  121.26  3.000
 0FN  CAA  CAB  OAI  125.47  3.000
 0FN  CAA  CAB  CAE  106.46  3.000
 0FN  OAI  CAB  CAE  128.06  3.000
 0FN  H5   CAA  CAF  108.87  3.000
 0FN  H5   CAA  CAB  107.49  3.000
 0FN  CAF  CAA  CAB  114.11  3.000
 0FN  H5   CAA  CAC  107.61  3.000
 0FN  CAF  CAA  CAC  114.12  3.000
 0FN  CAB  CAA  CAC  104.25  3.000
 0FN  NAG  CAF  CAA  180.00  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
 0FN  CONST_01  CAM  CAJ  CAE  CAD    0.00   0.0  0
 0FN  CONST_02  CAM  CAL  CAK  CAD    0.00   0.0  0
 0FN  CONST_03  CAJ  CAM  CAL  CAK    0.00   0.0  0
 0FN  CONST_04  CAJ  CAE  CAD  CAK    0.00   0.0  0
 0FN  CONST_05  CAE  CAJ  CAM  CAL    0.00   0.0  0
 0FN  CONST_06  CAE  CAD  CAK  CAL    0.00   0.0  0
 0FN  CONST_07  H1   CAK  CAD  CAC    0.00   0.0  0
 0FN  CONST_08  H4   CAJ  CAE  CAD  180.00   0.0  0
 0FN  CONST_09  H2   CAL  CAK  CAD  180.00   0.0  0
 0FN  CONST_10  H3   CAM  CAL  CAK  180.00   0.0  0
 0FN  Var_01    CAA  CAB  CAE  CAD    8.03  30.0  1
 0FN  Var_02    CAA  CAC  CAD  CAK  173.06  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
 0FN  chir_01  CAA  CAB  CAF  CAC  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
 0FN  plan-1  OAH  0.020
 0FN  plan-1  CAC  0.020
 0FN  plan-1  CAD  0.020
 0FN  plan-1  CAA  0.020
 0FN  plan-2  CAC  0.020
 0FN  plan-2  CAD  0.020
 0FN  plan-2  CAK  0.020
 0FN  plan-2  CAL  0.020
 0FN  plan-2  CAM  0.020
 0FN  plan-2  CAJ  0.020
 0FN  plan-2  CAE  0.020
 0FN  plan-2  CAB  0.020
 0FN  plan-2  H1   0.020
 0FN  plan-2  H2   0.020
 0FN  plan-2  H3   0.020
 0FN  plan-2  H4   0.020
 0FN  plan-3  CAE  0.020
 0FN  plan-3  CAB  0.020
 0FN  plan-3  OAI  0.020
 0FN  plan-3  CAA  0.020

