# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:42:08 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN1C(=O)c2ccccc2C1=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
 51X  51X  '(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)acetic acid'  ligand  22  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_51X
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
 51X  C3   C  C     0   0.552  -2.9009  -0.0254   0.4596
 51X  C4   C  CH2   0  -0.456  -2.1384   0.0222  -0.8461
 51X  C5   C  CR5   0   0.581   0.0243   1.1636  -0.4065
 51X  C6   C  CR56  0  -0.034   1.3938   0.6939  -0.0934
 51X  C7   C  CR16  0  -0.294   2.5417   1.4111   0.1685
 51X  C8   C  CR16  0  -0.241   3.6980   0.6833   0.4427
 51X  C9   C  CR16  0  -0.241   3.6875  -0.7089   0.4514
 51X  C10  C  CR16  0  -0.293   2.5204  -1.4226   0.1856
 51X  C11  C  CR56  0  -0.032   1.3836  -0.6918  -0.0854
 51X  C12  C  CR5   0   0.574   0.0069  -1.1443  -0.3950
 51X  O    O  O     0  -0.423  -2.3885  -0.0306   1.5458
 51X  N1   N  NR5   0  -0.593  -0.7273   0.0200  -0.6164
 51X  O2   O  O     0  -0.400  -0.3906   2.2925  -0.4769
 51X  H4   H  HCH2  0   0.326  -2.4145  -0.8336  -1.4642
 51X  H5   H  HCH2  0   0.325  -2.4220   0.9172  -1.4023
 51X  H6   H  HCR6  0   0.276   2.5504   2.4927   0.1633
 51X  H7   H  HCR6  0   0.279   4.6201   1.2074   0.6554
 51X  H8   H  HCR6  0   0.279   4.6017  -1.2439   0.6707
 51X  H9   H  HCR6  0   0.277   2.5108  -2.5042   0.1933
 51X  OXT  O  OH1   0  -0.575  -4.2071  -0.0579   0.2434
 51X  HXT  H  HOH1  0   0.465  -4.6805  -0.0886   1.0861
 51X  O1   O  O     0  -0.352  -0.4332  -2.2584  -0.4565

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
 51X  O1   C12  double    1.199  0.020  1.199
 51X  C10  C9   aromatic  1.394  0.020  1.394
 51X  C10  C11  aromatic  1.378  0.020  1.378
 51X  C9   C8   aromatic  1.392  0.020  1.392
 51X  C12  C11  single    1.482  0.020  1.482
 51X  C12  N1   single    1.394  0.020  1.394
 51X  C11  C6   aromatic  1.386  0.020  1.386
 51X  C8   C7   aromatic  1.394  0.020  1.394
 51X  C3   O    double    1.201  0.020  1.201
 51X  C3   C4   single    1.513  0.020  1.513
 51X  N1   C4   single    1.430  0.020  1.430
 51X  N1   C5   single    1.384  0.020  1.384
 51X  C6   C7   aromatic  1.379  0.020  1.379
 51X  C6   C5   single    1.481  0.020  1.481
 51X  C5   O2   double    1.205  0.020  1.205
 51X  C4   H4   single    0.970  0.020  1.090
 51X  C4   H5   single    0.970  0.020  1.090
 51X  C7   H6   single    0.930  0.020  1.080
 51X  C8   H7   single    0.930  0.020  1.080
 51X  C9   H8   single    0.930  0.020  1.080
 51X  C10  H9   single    0.930  0.020  1.080
 51X  C3   OXT  single    1.324  0.020  1.324
 51X  OXT  HXT  single    0.850  0.020  0.980

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
 51X  OXT  C3   O    124.64  3.000
 51X  OXT  C3   C4   110.92  3.000
 51X  O    C3   C4   124.45  3.000
 51X  H5   C4   H4   106.79  3.000
 51X  H5   C4   N1   109.86  3.000
 51X  H4   C4   N1   109.85  3.000
 51X  H5   C4   C3   109.55  3.000
 51X  H4   C4   C3   109.68  3.000
 51X  N1   C4   C3   111.02  3.000
 51X  O2   C5   N1   125.32  3.000
 51X  O2   C5   C6   128.89  3.000
 51X  N1   C5   C6   105.79  3.000
 51X  C11  C6   C7   121.69  3.000
 51X  C7   C6   C5   130.16  3.000
 51X  C11  C6   C5   108.15  3.000
 51X  H6   C7   C8   121.10  3.000
 51X  H6   C7   C6   121.73  3.000
 51X  C8   C7   C6   117.16  3.000
 51X  H7   C8   C9   119.32  3.000
 51X  H7   C8   C7   119.54  3.000
 51X  C9   C8   C7   121.15  3.000
 51X  H8   C9   C10  119.55  3.000
 51X  H8   C9   C8   119.31  3.000
 51X  C10  C9   C8   121.15  3.000
 51X  H9   C10  C11  121.62  3.000
 51X  H9   C10  C9   121.21  3.000
 51X  C11  C10  C9   117.17  3.000
 51X  C12  C11  C10  130.20  3.000
 51X  C12  C11  C6   108.12  3.000
 51X  C10  C11  C6   121.68  3.000
 51X  O1   C12  N1   125.05  3.000
 51X  N1   C12  C11  105.51  3.000
 51X  O1   C12  C11  129.44  3.000
 51X  C12  N1   C5   112.32  3.000
 51X  C5   N1   C4   123.98  3.000
 51X  C12  N1   C4   123.13  3.000
 51X  HXT  OXT  C3   109.96  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
 51X  CONST_01  C9   C10  C11  C6     0.00   0.0  0
 51X  CONST_02  C9   C8   C7   C6     0.00   0.0  0
 51X  CONST_03  C10  C9   C8   C7     0.00   0.0  0
 51X  CONST_04  C10  C11  C6   C7     0.00   0.0  0
 51X  CONST_05  C11  C10  C9   C8     0.00   0.0  0
 51X  CONST_06  C11  C6   C7   C8     0.00   0.0  0
 51X  CONST_07  C12  N1   C5   C6     0.00   0.0  0
 51X  CONST_08  C6   C5   N1   C4   180.00   0.0  0
 51X  CONST_09  O2   C5   N1   C12  180.00   0.0  0
 51X  CONST_10  H6   C7   C6   C5     0.00   0.0  0
 51X  CONST_11  H9   C10  C11  C6   180.00   0.0  0
 51X  CONST_12  H7   C8   C7   C6   180.00   0.0  0
 51X  CONST_13  H8   C9   C8   C7   180.00   0.0  0
 51X  CONST_14  O2   C5   N1   C4     0.00   0.0  0
 51X  CONST_15  HXT  OXT  C3   C4   180.00   0.0  0
 51X  Var_01    C12  N1   C4   C3    83.10  30.0  2
 51X  Var_02    N1   C4   C3   O      1.71  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
 51X  plan-1  C4   0.020
 51X  plan-1  C5   0.020
 51X  plan-1  C6   0.020
 51X  plan-1  C7   0.020
 51X  plan-1  C8   0.020
 51X  plan-1  C9   0.020
 51X  plan-1  C10  0.020
 51X  plan-1  C11  0.020
 51X  plan-1  C12  0.020
 51X  plan-1  N1   0.020
 51X  plan-1  O2   0.020
 51X  plan-1  H6   0.020
 51X  plan-1  H7   0.020
 51X  plan-1  H8   0.020
 51X  plan-1  H9   0.020
 51X  plan-1  O1   0.020
 51X  plan-2  C3   0.020
 51X  plan-2  C4   0.020
 51X  plan-2  O    0.020
 51X  plan-2  OXT  0.020
 51X  plan-2  HXT  0.020

