# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:49:41 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: [(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H]1C(=O)Nc2ccccc12
#
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
 OIA  OIA  '[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]acetic acid'  ligand  22  14  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OIA
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
 OIA  O14  O  OC    -1  -0.617  -3.6862  -0.7793  -0.9620
 OIA  C11  C  C      0   0.421  -2.8602  -0.7390  -0.0296
 OIA  O13  O  O      0  -0.609  -3.1114  -0.6157   1.1849
 OIA  C10  C  CH2    0  -0.563  -1.3781  -0.9287  -0.4104
 OIA  C3   C  CR15   0  -0.453  -0.4181  -0.0695   0.4096
 OIA  C9   C  CR5    0   0.082   1.0376  -0.3825   0.2377
 OIA  C4   C  C1     0  -0.339   1.7502  -1.5493   0.4191
 OIA  C5   C  C1     0  -0.264   3.1259  -1.5486   0.1825
 OIA  C6   C  C1     0  -0.270   3.7663  -0.3876  -0.2306
 OIA  C7   C  C1     0  -0.309   3.0589   0.7985  -0.4186
 OIA  C8   C  CR5    0   0.378   1.6979   0.7733  -0.1784
 OIA  N1   N  NR15   0  -0.742   0.7755   1.8053  -0.2919
 OIA  C2   C  CR5    0   0.540  -0.4918   1.3995   0.0067
 OIA  O12  O  O      0  -0.454  -1.4847   2.0936  -0.0622
 OIA  H2   H  HCH2   0   0.248  -1.1288  -1.9800  -0.2277
 OIA  H3   H  HCH2   0   0.225  -1.2210  -0.7591  -1.4780
 OIA  H4   H  HCR5   0   0.297  -0.7113  -0.1463   1.4627
 OIA  H5   H  H      0   0.251   1.2541  -2.4561   0.7430
 OIA  H6   H  H      0   0.252   3.6965  -2.4571   0.3230
 OIA  H7   H  H      0   0.256   4.8336  -0.3997  -0.4104
 OIA  H8   H  H      0   0.264   3.5600   1.7019  -0.7414
 OIA  H9   H  HNR5   0   0.407   0.9991   2.7369  -0.6079

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
 OIA  O12  C2   double    1.213  0.020  1.213
 OIA  C2   C3   single    1.525  0.020  1.525
 OIA  C2   N1   single    1.364  0.020  1.364
 OIA  C10  C11  single    1.542  0.020  1.542
 OIA  C10  C3   single    1.527  0.020  1.527
 OIA  O13  C11  deloc     1.246  0.020  1.246
 OIA  C11  O14  deloc     1.246  0.020  1.246
 OIA  C3   C9   single    1.499  0.020  1.499
 OIA  N1   C8   single    1.389  0.020  1.389
 OIA  C8   C9   aromatic  1.395  0.020  1.395
 OIA  C8   C7   aromatic  1.382  0.020  1.382
 OIA  C9   C4   aromatic  1.379  0.020  1.379
 OIA  C7   C6   aromatic  1.394  0.020  1.394
 OIA  C4   C5   aromatic  1.396  0.020  1.396
 OIA  C6   C5   aromatic  1.389  0.020  1.389
 OIA  C10  H2   single    0.970  0.020  1.090
 OIA  C10  H3   single    0.970  0.020  1.090
 OIA  C3   H4   single    0.970  0.020  1.090
 OIA  C4   H5   single    0.930  0.020  1.080
 OIA  C5   H6   single    0.930  0.020  1.080
 OIA  C6   H7   single    0.930  0.020  1.080
 OIA  C7   H8   single    0.930  0.020  1.080
 OIA  N1   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
 OIA  C10  C11  O13  116.52  3.000
 OIA  O13  C11  O14  126.77  3.000
 OIA  C10  C11  O14  116.64  3.000
 OIA  H3   C10  H2   106.21  3.000
 OIA  H3   C10  C3   110.30  3.000
 OIA  H2   C10  C3   107.90  3.000
 OIA  H3   C10  C11  111.13  3.000
 OIA  H2   C10  C11  107.19  3.000
 OIA  C3   C10  C11  113.73  3.000
 OIA  H4   C3   C2   107.97  3.000
 OIA  H4   C3   C9   110.82  3.000
 OIA  C2   C3   C9   102.58  3.000
 OIA  H4   C3   C10  107.96  3.000
 OIA  C9   C3   C10  115.56  3.000
 OIA  C2   C3   C10  111.70  3.000
 OIA  C8   C9   C4   119.72  3.000
 OIA  C4   C9   C3   131.56  3.000
 OIA  C8   C9   C3   108.72  3.000
 OIA  H5   C4   C5   120.17  3.000
 OIA  H5   C4   C9   120.72  3.000
 OIA  C5   C4   C9   119.11  3.000
 OIA  H6   C5   C6   119.82  3.000
 OIA  H6   C5   C4   119.82  3.000
 OIA  C6   C5   C4   120.36  3.000
 OIA  H7   C6   C7   119.18  3.000
 OIA  H7   C6   C5   119.66  3.000
 OIA  C7   C6   C5   121.16  3.000
 OIA  H8   C7   C8   121.53  3.000
 OIA  H8   C7   C6   121.04  3.000
 OIA  C8   C7   C6   117.44  3.000
 OIA  N1   C8   C7   128.77  3.000
 OIA  C7   C8   C9   122.22  3.000
 OIA  N1   C8   C9   109.01  3.000
 OIA  H9   N1   C2   123.32  3.000
 OIA  H9   N1   C8   124.37  3.000
 OIA  C2   N1   C8   112.22  3.000
 OIA  O12  C2   N1   125.29  3.000
 OIA  N1   C2   C3   107.43  3.000
 OIA  O12  C2   C3   127.26  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
 OIA  CONST_01  C6   C7   C8   C9     0.00   0.0  0
 OIA  CONST_02  C6   C5   C4   C9     0.00   0.0  0
 OIA  CONST_03  C7   C8   C9   C4     0.00   0.0  0
 OIA  CONST_04  C7   C6   C5   C4     0.00   0.0  0
 OIA  CONST_05  C8   C9   C4   C5     0.00   0.0  0
 OIA  CONST_06  C8   C7   C6   C5     0.00   0.0  0
 OIA  CONST_07  C8   N1   C2   C3     0.00   0.0  0
 OIA  CONST_08  O12  C2   N1   C8   180.00   0.0  0
 OIA  CONST_09  H5   C4   C9   C3     0.00   0.0  0
 OIA  CONST_10  H8   C7   C8   C9   180.00   0.0  0
 OIA  CONST_11  H6   C5   C4   C9   180.00   0.0  0
 OIA  CONST_12  H7   C6   C5   C4   180.00   0.0  0
 OIA  CONST_13  H9   N1   C2   C3   180.00   0.0  0
 OIA  Var_01    C3   C10  C11  O14  143.30  30.0  2

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
 OIA  chir_01  C3  C2  C10  C9  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
 OIA  plan-1  C3   0.020
 OIA  plan-1  C9   0.020
 OIA  plan-1  C4   0.020
 OIA  plan-1  C5   0.020
 OIA  plan-1  C6   0.020
 OIA  plan-1  C7   0.020
 OIA  plan-1  C8   0.020
 OIA  plan-1  N1   0.020
 OIA  plan-1  C2   0.020
 OIA  plan-1  O12  0.020
 OIA  plan-1  H5   0.020
 OIA  plan-1  H6   0.020
 OIA  plan-1  H7   0.020
 OIA  plan-1  H8   0.020
 OIA  plan-1  H9   0.020
 OIA  plan-2  O14  0.020
 OIA  plan-2  C11  0.020
 OIA  plan-2  O13  0.020
 OIA  plan-2  C10  0.020

