# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 04:59:33 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 2-methyl-3~{H}-isoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1Cc2ccccc2C1=O
#
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
 5WV  5WV  2-methyl-3~{H}-isoindol-1-one  ligand  20  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5WV
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
 5WV  OAB  O  O     0  -0.486  -1.6613  -1.9111   0.0668
 5WV  CAH  C  CR5   0   0.539  -1.1255  -0.8143   0.0294
 5WV  CAJ  C  CR56  0  -0.069   0.3246  -0.5233   0.0133
 5WV  CAF  C  CR16  0  -0.302   1.3958  -1.4007   0.0396
 5WV  CAD  C  CR16  0  -0.260   2.6741  -0.8607   0.0165
 5WV  CAC  C  CR16  0  -0.243   2.8598   0.5212  -0.0318
 5WV  CAE  C  CR16  0  -0.319   1.7769   1.3933  -0.0584
 5WV  CAI  C  CR56  0   0.087   0.5048   0.8490  -0.0352
 5WV  CAG  C  CH2   0  -0.270  -0.8362   1.5119  -0.0540
 5WV  NAK  N  NR5   0  -0.496  -1.7455   0.3882  -0.0057
 5WV  CAA  C  CH3   0  -0.516  -3.1700   0.5776  -0.0156
 5WV  H1   H  HCR6  0   0.260   1.2425  -2.4718   0.0759
 5WV  H2   H  HCR6  0   0.264   3.5358  -1.5146   0.0370
 5WV  H3   H  HCR6  0   0.265   3.8656   0.9206  -0.0479
 5WV  H4   H  HCR6  0   0.260   1.9309   2.4642  -0.0962
 5WV  H5   H  HCH2  0   0.271  -0.9816   2.1761   0.8034
 5WV  H6   H  HCH2  0   0.270  -0.9895   2.1081  -0.9588
 5WV  H7   H  HCH3  0   0.244  -3.5042   1.0082  -0.9613
 5WV  H8   H  HCH3  0   0.257  -3.6651  -0.3799   0.1229
 5WV  H9   H  HCH3  0   0.245  -3.4746   1.2443   0.7920

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
 5WV  CAG  CAI  single    1.496  0.020  1.496
 5WV  CAG  NAK  single    1.446  0.020  1.446
 5WV  CAE  CAI  aromatic  1.384  0.020  1.384
 5WV  CAE  CAC  aromatic  1.391  0.020  1.391
 5WV  CAI  CAJ  aromatic  1.385  0.020  1.385
 5WV  CAA  NAK  single    1.437  0.020  1.437
 5WV  NAK  CAH  single    1.353  0.020  1.353
 5WV  CAC  CAD  aromatic  1.395  0.020  1.395
 5WV  CAJ  CAH  single    1.479  0.020  1.479
 5WV  CAJ  CAF  aromatic  1.385  0.020  1.385
 5WV  CAH  OAB  double    1.221  0.020  1.221
 5WV  CAD  CAF  aromatic  1.388  0.020  1.388
 5WV  CAF  H1   single    0.930  0.020  1.080
 5WV  CAD  H2   single    0.930  0.020  1.080
 5WV  CAC  H3   single    0.930  0.020  1.080
 5WV  CAE  H4   single    0.930  0.020  1.080
 5WV  CAG  H5   single    0.970  0.020  1.090
 5WV  CAG  H6   single    0.970  0.020  1.090
 5WV  CAA  H7   single    0.970  0.020  1.090
 5WV  CAA  H8   single    0.970  0.020  1.090
 5WV  CAA  H9   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
 5WV  NAK  CAH  CAJ  105.90  3.000
 5WV  CAJ  CAH  OAB  127.38  3.000
 5WV  NAK  CAH  OAB  126.71  3.000
 5WV  CAI  CAJ  CAF  121.86  3.000
 5WV  CAF  CAJ  CAH  129.30  3.000
 5WV  CAI  CAJ  CAH  108.84  3.000
 5WV  H1   CAF  CAD  121.06  3.000
 5WV  H1   CAF  CAJ  121.19  3.000
 5WV  CAD  CAF  CAJ  117.74  3.000
 5WV  H2   CAD  CAC  119.56  3.000
 5WV  H2   CAD  CAF  119.87  3.000
 5WV  CAC  CAD  CAF  120.57  3.000
 5WV  H3   CAC  CAE  119.47  3.000
 5WV  H3   CAC  CAD  119.32  3.000
 5WV  CAE  CAC  CAD  121.21  3.000
 5WV  H4   CAE  CAI  121.36  3.000
 5WV  H4   CAE  CAC  120.68  3.000
 5WV  CAI  CAE  CAC  117.96  3.000
 5WV  CAG  CAI  CAE  130.50  3.000
 5WV  CAE  CAI  CAJ  120.66  3.000
 5WV  CAG  CAI  CAJ  108.84  3.000
 5WV  H6   CAG  H5   107.38  3.000
 5WV  H6   CAG  NAK  111.28  3.000
 5WV  H5   CAG  NAK  111.22  3.000
 5WV  H6   CAG  CAI  112.17  3.000
 5WV  H5   CAG  CAI  112.22  3.000
 5WV  NAK  CAG  CAI  102.64  3.000
 5WV  CAA  NAK  CAG  121.36  3.000
 5WV  CAA  NAK  CAH  124.85  3.000
 5WV  CAG  NAK  CAH  113.78  3.000
 5WV  H9   CAA  H8   108.48  3.000
 5WV  H9   CAA  H7   108.36  3.000
 5WV  H8   CAA  H7   108.57  3.000
 5WV  H9   CAA  NAK  110.63  3.000
 5WV  H8   CAA  NAK  109.55  3.000
 5WV  H7   CAA  NAK  111.19  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
 5WV  CONST_01  CAC  CAE  CAI  CAJ     0.00   0.0  0
 5WV  CONST_02  CAC  CAD  CAF  CAJ     0.00   0.0  0
 5WV  CONST_03  CAE  CAI  CAJ  CAF     0.00   0.0  0
 5WV  CONST_04  CAE  CAC  CAD  CAF     0.00   0.0  0
 5WV  CONST_05  CAI  CAE  CAC  CAD     0.00   0.0  0
 5WV  CONST_06  CAI  CAJ  CAF  CAD     0.00   0.0  0
 5WV  CONST_07  CAG  NAK  CAH  CAJ     0.00   0.0  0
 5WV  CONST_08  CAG  NAK  CAH  OAB   180.00   0.0  0
 5WV  CONST_09  CAA  NAK  CAH  CAJ   180.00   0.0  0
 5WV  CONST_10  H1   CAF  CAJ  CAH     0.00   0.0  0
 5WV  CONST_11  H4   CAE  CAI  CAJ   180.00   0.0  0
 5WV  CONST_12  H2   CAD  CAF  CAJ   180.00   0.0  0
 5WV  CONST_13  H3   CAC  CAD  CAF   180.00   0.0  0
 5WV  CONST_14  CAA  NAK  CAH  OAB     0.00   0.0  0
 5WV  Var_01    H5   CAG  NAK  CAH  -120.57  30.0  1
 5WV  Var_02    H7   CAA  NAK  CAH  -113.63  30.0  3

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
 5WV  plan-1  OAB  0.020
 5WV  plan-1  CAH  0.020
 5WV  plan-1  CAJ  0.020
 5WV  plan-1  CAF  0.020
 5WV  plan-1  CAD  0.020
 5WV  plan-1  CAC  0.020
 5WV  plan-1  CAE  0.020
 5WV  plan-1  CAI  0.020
 5WV  plan-1  CAG  0.020
 5WV  plan-1  NAK  0.020
 5WV  plan-1  CAA  0.020
 5WV  plan-1  H1   0.020
 5WV  plan-1  H2   0.020
 5WV  plan-1  H3   0.020
 5WV  plan-1  H4   0.020

