# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 22:55:53 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 3-(6,7-dioxo-6,7-dihydro-1H-indol-3-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH]c2C(=O)C(=O)C=Cc12)C(O)=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
 TRQ  TRQ  3-(6,7-dioxo-6,7-dihydro-1H-indol-3-yl)-L-alanine  L-peptide  26  17  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_TRQ
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
 TRQ  N    N  NH2    0  -0.795  80.7789  11.7108  17.0880
 TRQ  CA   C  CH1    0  -0.184  82.1776  11.9830  17.3703
 TRQ  C    C  C      0   0.402  82.4100  11.8932  18.8974
 TRQ  O    O  O      0  -0.611  81.6633  12.6101  19.5958
 TRQ  OXT  O  OC    -1  -0.599  83.3175  11.1403  19.2969
 TRQ  CB   C  CH2    0  -0.550  82.6711  13.3618  16.8704
 TRQ  CG   C  CR5    0   0.039  82.5521  13.5188  15.3939
 TRQ  CD1  C  CR15   0  -0.048  83.5113  13.1668  14.4503
 TRQ  NE1  N  NR15   0  -0.620  83.0311  13.3946  13.2148
 TRQ  CE2  C  CR5    0   0.225  81.7694  13.8910  13.3030
 TRQ  CZ2  C  C      0   0.270  80.8900  14.2740  12.2431
 TRQ  CH2  C  C      0   0.287  79.5162  14.8150  12.7273
 TRQ  CZ3  C  C1     0  -0.384  79.2445  14.8817  14.1637
 TRQ  CE3  C  C1     0  -0.289  80.1585  14.4869  15.0680
 TRQ  CD2  C  CR5    0  -0.018  81.4454  13.9777  14.6525
 TRQ  O6   O  O      0  -0.371  78.7176  15.1685  11.8891
 TRQ  O7   O  O      0  -0.384  81.1287  14.2106  11.0542
 TRQ  H    H  HNH2   0   0.341  80.5858  11.8062  16.0981
 TRQ  H2   H  HNH2   0   0.330  80.2075  12.3944  17.5701
 TRQ  HA   H  HCH1   0   0.204  82.7771  11.2151  16.8723
 TRQ  HB2  H  HCH2   0   0.236  82.0965  14.1407  17.3782
 TRQ  HB3  H  HCH2   0   0.243  83.7152  13.4964  17.1672
 TRQ  HD1  H  HCR5   0   0.296  84.5051  12.7748  14.5986
 TRQ  HE1  H  HNR5   0   0.426  83.5356  13.2306  12.3562
 TRQ  HZ3  H  H      0   0.276  78.2798  15.2652  14.4696
 TRQ  HE3  H  H      0   0.277  79.9361  14.5504  16.1263

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
 TRQ  N    CA   single    1.458  0.019  1.458
 TRQ  N    H    single    0.860  0.020  0.860
 TRQ  N    H2   single    0.890  0.020  1.040
 TRQ  CA   C    single    1.525  0.021  1.525
 TRQ  CA   CB   single    1.530  0.020  1.530
 TRQ  CA   HA   single    0.970  0.020  0.970
 TRQ  C    O    deloc     1.231  0.020  1.231
 TRQ  C    OXT  deloc     1.245  0.020  1.245
 TRQ  CB   CG   single    1.490  0.020  1.490
 TRQ  CB   HB2  single    0.970  0.020  1.090
 TRQ  CB   HB3  single    0.970  0.020  1.090
 TRQ  CG   CD1  aromatic  1.391  0.020  1.391
 TRQ  CG   CD2  aromatic  1.409  0.020  1.409
 TRQ  CD1  NE1  aromatic  1.345  0.020  1.345
 TRQ  CD1  HD1  single    0.930  0.020  1.080
 TRQ  NE1  CE2  aromatic  1.359  0.020  1.359
 TRQ  NE1  HE1  single    0.860  0.020  1.020
 TRQ  CE2  CZ2  single    1.430  0.020  1.430
 TRQ  CE2  CD2  aromatic  1.391  0.020  1.391
 TRQ  CZ2  CH2  single    1.554  0.020  1.554
 TRQ  CZ2  O7   double    1.214  0.020  1.214
 TRQ  CH2  CZ3  single    1.463  0.020  1.463
 TRQ  CH2  O6   double    1.211  0.020  1.211
 TRQ  CZ3  CE3  double    1.345  0.020  1.345
 TRQ  CZ3  HZ3  single    0.930  0.020  1.080
 TRQ  CE3  CD2  single    1.445  0.020  1.445
 TRQ  CE3  HE3  single    0.930  0.020  1.080

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
 TRQ  H2   N    H    107.10  3.000
 TRQ  H2   N    CA   108.92  3.000
 TRQ  H    N    CA   114.00  3.000
 TRQ  HA   CA   CB   109.00  3.000
 TRQ  HA   CA   C    109.00  3.000
 TRQ  CB   CA   C    110.10  1.900
 TRQ  HA   CA   N    110.00  3.000
 TRQ  CB   CA   N    110.50  1.700
 TRQ  C    CA   N    111.00  2.800
 TRQ  OXT  C    O    127.13  3.000
 TRQ  OXT  C    CA   117.47  3.000
 TRQ  O    C    CA   120.80  1.700
 TRQ  HB3  CB   HB2  106.74  3.000
 TRQ  HB3  CB   CG   109.41  3.000
 TRQ  HB2  CB   CG   110.09  3.000
 TRQ  HB3  CB   CA   109.05  3.000
 TRQ  HB2  CB   CA   108.49  3.000
 TRQ  CG   CB   CA   112.87  3.000
 TRQ  CD2  CG   CD1  105.49  3.000
 TRQ  CD2  CG   CB   128.22  3.000
 TRQ  CD1  CG   CB   126.21  3.000
 TRQ  HD1  CD1  NE1  121.13  3.000
 TRQ  HD1  CD1  CG   129.35  3.000
 TRQ  NE1  CD1  CG   109.52  3.000
 TRQ  HE1  NE1  CE2  125.37  3.000
 TRQ  HE1  NE1  CD1  125.13  3.000
 TRQ  CE2  NE1  CD1  109.50  3.000
 TRQ  CD2  CE2  CZ2  124.02  3.000
 TRQ  CD2  CE2  NE1  107.59  3.000
 TRQ  CZ2  CE2  NE1  128.39  3.000
 TRQ  O7   CZ2  CH2  119.81  3.000
 TRQ  O7   CZ2  CE2  126.23  3.000
 TRQ  CH2  CZ2  CE2  113.96  3.000
 TRQ  O6   CH2  CZ3  122.94  3.000
 TRQ  O6   CH2  CZ2  117.98  3.000
 TRQ  CZ3  CH2  CZ2  119.07  3.000
 TRQ  HZ3  CZ3  CE3  121.32  3.000
 TRQ  HZ3  CZ3  CH2  117.33  3.000
 TRQ  CE3  CZ3  CH2  121.36  3.000
 TRQ  HE3  CE3  CD2  118.97  3.000
 TRQ  HE3  CE3  CZ3  120.01  3.000
 TRQ  CD2  CE3  CZ3  121.02  3.000
 TRQ  CE3  CD2  CE2  120.57  3.000
 TRQ  CE3  CD2  CG   131.53  3.000
 TRQ  CE2  CD2  CG   107.90  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
 TRQ  CONST_01  CE2  NE1  CD1  CG     0.00   0.0  0
 TRQ  CONST_02  NE1  CE2  CD2  CG     0.00   0.0  0
 TRQ  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 TRQ  CONST_04  CD2  CE2  NE1  CD1    0.00   0.0  0
 TRQ  CONST_05  CD2  CG   CD1  NE1    0.00   0.0  0
 TRQ  CONST_06  NE1  CD1  CG   CB   180.00   0.0  0
 TRQ  CONST_07  CE2  CD2  CG   CB   180.00   0.0  0
 TRQ  CONST_08  CE3  CD2  CG   CB     0.00   0.0  0
 TRQ  CONST_09  HE1  NE1  CD1  CG   180.00   0.0  0
 TRQ  CONST_10  HD1  CD1  NE1  CE2  180.00   0.0  0
 TRQ  Var_01    CD1  CG   CB   CA   -88.77  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
 TRQ  chir_01  CA  N  C  CB  positiv

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
 TRQ  plan-1  CB   0.020
 TRQ  plan-1  CG   0.020
 TRQ  plan-1  CD1  0.020
 TRQ  plan-1  NE1  0.020
 TRQ  plan-1  CE2  0.020
 TRQ  plan-1  CZ2  0.020
 TRQ  plan-1  CH2  0.020
 TRQ  plan-1  CZ3  0.020
 TRQ  plan-1  CE3  0.020
 TRQ  plan-1  CD2  0.020
 TRQ  plan-1  O6   0.020
 TRQ  plan-1  O7   0.020
 TRQ  plan-1  HD1  0.020
 TRQ  plan-1  HE1  0.020
 TRQ  plan-1  HZ3  0.020
 TRQ  plan-1  HE3  0.020
 TRQ  plan-2  CA   0.020
 TRQ  plan-2  C    0.020
 TRQ  plan-2  O    0.020
 TRQ  plan-2  OXT  0.020

