# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 21:02:41 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 6,7-dihydroxy-L-tryptophan
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH]c2c(O)c(O)ccc12)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
 TOQ  TOQ  6,7-dihydroxy-L-tryptophan  L-peptide  28  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_TOQ
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
 TOQ  C     C  C      0   0.413  11.3449  29.6902  61.4095
 TOQ  N     N  NH2    0  -0.799  12.5154  27.7719  60.3470
 TOQ  O     O  O      0  -0.600  10.9189  28.8465  62.2224
 TOQ  O6    O  OH1    0  -0.643   9.1015  25.3312  54.8760
 TOQ  O7    O  OH1    0  -0.657   7.3474  27.1381  55.9906
 TOQ  CA    C  CH1    0  -0.206  12.3940  29.2192  60.3733
 TOQ  CB    C  CH2    0  -0.518  12.0838  29.7549  58.9700
 TOQ  CG    C  CR5    0   0.045  10.7867  29.2907  58.3892
 TOQ  CD1   C  CR15   0  -0.093   9.5501  29.8326  58.5926
 TOQ  CD2   C  CR56   0  -0.017  10.5898  28.1945  57.4820
 TOQ  NE1   N  NR15   0  -0.689   8.6028  29.1419  57.8760
 TOQ  CE2   C  CR56   0   0.311   9.2123  28.1400  57.1856
 TOQ  CE3   C  CR16   0  -0.378  11.4456  27.2690  56.8753
 TOQ  CH2   C  CR6    0   0.274   9.5468  26.2813  55.7326
 TOQ  CZ2   C  CR6    0   0.161   8.6755  27.1866  56.3179
 TOQ  CZ3   C  CR16   0  -0.367  10.9259  26.3327  56.0059
 TOQ  OXT   O  OC    -1  -0.612  11.0463  30.9019  61.3692
 TOQ  HN    H  HNH2   0   0.326  13.4094  27.5121  59.9508
 TOQ  HNA   H  HNH2   0   0.329  12.5000  27.4248  61.2962
 TOQ  HO6   H  HOH1   0   0.462   8.1409  25.3911  54.8046
 TOQ  HO7   H  HOH1   0   0.473   6.8118  27.0302  56.7860
 TOQ  HA    H  HCH1   0   0.194  13.3380  29.7057  60.6782
 TOQ  HB    H  HCH2   0   0.225  12.1046  30.8446  59.0113
 TOQ  HBA   H  HCH2   0   0.219  12.8990  29.4651  58.2990
 TOQ  HD1   H  HCR5   0   0.263   9.2643  30.6722  59.2053
 TOQ  HE3   H  HCR6   0   0.234  12.5088  27.2848  57.0803
 TOQ  HZ3   H  HCR6   0   0.248  11.5746  25.6092  55.5273
 TOQ  HNE1  H  HNR5   0   0.401   7.6248  29.3738  57.8430

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
 TOQ  C    O     deloc     1.231  0.020  1.231
 TOQ  C    OXT   deloc     1.249  0.020  1.249
 TOQ  N    CA    single    1.458  0.019  1.458
 TOQ  N    HN    single    0.890  0.020  1.040
 TOQ  N    HNA   single    0.890  0.020  1.040
 TOQ  O6   CH2   single    1.354  0.020  1.354
 TOQ  O6   HO6   single    0.850  0.020  0.980
 TOQ  O7   CZ2   single    1.369  0.020  1.369
 TOQ  O7   HO7   single    0.850  0.020  0.980
 TOQ  CA   C     single    1.525  0.021  1.525
 TOQ  CA   HA    single    0.970  0.020  0.970
 TOQ  CB   CA    single    1.530  0.020  1.530
 TOQ  CB   HB    single    0.970  0.020  1.090
 TOQ  CB   HBA   single    0.970  0.020  1.090
 TOQ  CG   CB    single    1.495  0.020  1.495
 TOQ  CG   CD1   aromatic  1.365  0.020  1.365
 TOQ  CD1  HD1   single    0.930  0.020  1.080
 TOQ  CD2  CG    aromatic  1.437  0.020  1.437
 TOQ  NE1  CD1   aromatic  1.374  0.020  1.374
 TOQ  NE1  HNE1  single    0.860  0.020  1.020
 TOQ  CE2  CD2   aromatic  1.410  0.020  1.410
 TOQ  CE2  NE1   aromatic  1.361  0.020  1.361
 TOQ  CE3  CD2   aromatic  1.399  0.020  1.399
 TOQ  CE3  HE3   single    0.930  0.020  1.080
 TOQ  CH2  CZ3   aromatic  1.407  0.020  1.407
 TOQ  CH2  CZ2   aromatic  1.386  0.020  1.386
 TOQ  CZ2  CE2   aromatic  1.396  0.020  1.396
 TOQ  CZ3  CE3   aromatic  1.379  0.020  1.379
 TOQ  CZ3  HZ3   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
 TOQ  OXT   C    CA   115.83  3.000
 TOQ  CA    C    O    120.80  1.700
 TOQ  OXT   C    O    126.60  3.000
 TOQ  HNA   N    HN   107.04  3.000
 TOQ  HNA   N    CA   108.90  3.000
 TOQ  HN    N    CA   109.68  3.000
 TOQ  HO6   O6   CH2  109.30  3.000
 TOQ  HO7   O7   CZ2  110.21  3.000
 TOQ  HA    CA   CB   109.00  3.000
 TOQ  CB    CA   N    110.50  1.700
 TOQ  HA    CA   N    110.00  3.000
 TOQ  CB    CA   C    110.10  1.900
 TOQ  HA    CA   C    109.00  3.000
 TOQ  N     CA   C    111.00  2.800
 TOQ  HBA   CB   HB   105.87  3.000
 TOQ  HBA   CB   CG   109.01  3.000
 TOQ  HB    CB   CG   109.96  3.000
 TOQ  CG    CB   CA   114.99  3.000
 TOQ  HBA   CB   CA   108.52  3.000
 TOQ  HB    CB   CA   108.09  3.000
 TOQ  CD2   CG   CD1  105.83  3.000
 TOQ  CD2   CG   CB   126.96  3.000
 TOQ  CD1   CG   CB   127.20  3.000
 TOQ  HD1   CD1  NE1  120.34  3.000
 TOQ  NE1   CD1  CG   110.32  3.000
 TOQ  HD1   CD1  CG   129.34  3.000
 TOQ  CE3   CD2  CE2  118.75  3.000
 TOQ  CE3   CD2  CG   134.02  3.000
 TOQ  CE2   CD2  CG   107.23  3.000
 TOQ  HNE1  NE1  CE2  126.06  3.000
 TOQ  CE2   NE1  CD1  109.02  3.000
 TOQ  HNE1  NE1  CD1  124.87  3.000
 TOQ  CZ2   CE2  NE1  130.22  3.000
 TOQ  CZ2   CE2  CD2  122.18  3.000
 TOQ  NE1   CE2  CD2  107.60  3.000
 TOQ  HE3   CE3  CZ3  119.94  3.000
 TOQ  CZ3   CE3  CD2  119.47  3.000
 TOQ  HE3   CE3  CD2  120.59  3.000
 TOQ  CZ3   CH2  CZ2  120.68  3.000
 TOQ  CZ2   CH2  O6   121.23  3.000
 TOQ  CZ3   CH2  O6   118.08  3.000
 TOQ  CH2   CZ2  CE2  117.82  3.000
 TOQ  CE2   CZ2  O7   123.08  3.000
 TOQ  CH2   CZ2  O7   119.07  3.000
 TOQ  HZ3   CZ3  CH2  118.48  3.000
 TOQ  HZ3   CZ3  CE3  120.42  3.000
 TOQ  CH2   CZ3  CE3  121.10  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
 TOQ  CONST_01  CE2   NE1  CD1  CG     0.00   0.0  0
 TOQ  CONST_02  NE1   CE2  CD2  CG     0.00   0.0  0
 TOQ  CONST_03  CZ2   CE2  CD2  CG   180.00   0.0  0
 TOQ  CONST_04  CZ3   CE3  CD2  CG   180.00   0.0  0
 TOQ  CONST_05  CE2   CD2  CG   CD1    0.00   0.0  0
 TOQ  CONST_06  CE3   CD2  CG   CD1  180.00   0.0  0
 TOQ  CONST_07  CD2   CE2  NE1  CD1    0.00   0.0  0
 TOQ  CONST_08  CZ2   CE2  NE1  CD1  180.00   0.0  0
 TOQ  CONST_09  NE1   CD1  CG   CD2    0.00   0.0  0
 TOQ  CONST_10  CH2   CZ2  CE2  CD2    0.00   0.0  0
 TOQ  CONST_11  CH2   CZ3  CE3  CD2    0.00   0.0  0
 TOQ  CONST_12  CE3   CD2  CE2  NE1  180.00   0.0  0
 TOQ  CONST_13  CH2   CZ2  CE2  NE1  180.00   0.0  0
 TOQ  CONST_14  CZ3   CE3  CD2  CE2    0.00   0.0  0
 TOQ  CONST_15  CZ3   CH2  CZ2  CE2    0.00   0.0  0
 TOQ  CONST_16  CZ2   CE2  CD2  CE3    0.00   0.0  0
 TOQ  CONST_17  CZ2   CH2  CZ3  CE3    0.00   0.0  0
 TOQ  CONST_18  CE3   CZ3  CH2  O6   180.00   0.0  0
 TOQ  CONST_19  CE2   CZ2  CH2  O6   180.00   0.0  0
 TOQ  CONST_20  CZ3   CH2  CZ2  O7   180.00   0.0  0
 TOQ  CONST_21  CD2   CE2  CZ2  O7   180.00   0.0  0
 TOQ  CONST_22  NE1   CE2  CZ2  O7     0.00   0.0  0
 TOQ  CONST_23  NE1   CD1  CG   CB   180.00   0.0  0
 TOQ  CONST_24  CE2   CD2  CG   CB   180.00   0.0  0
 TOQ  CONST_25  CE3   CD2  CG   CB     0.00   0.0  0
 TOQ  CONST_26  HNE1  NE1  CD1  CG   180.00   0.0  0
 TOQ  CONST_27  HE3   CE3  CD2  CG     0.00   0.0  0
 TOQ  CONST_28  HD1   CD1  CG   CD2  180.00   0.0  0
 TOQ  CONST_29  HZ3   CZ3  CE3  CD2  180.00   0.0  0
 TOQ  Var_01    CD1   CG   CB   CA    84.44  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
 TOQ  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
 TOQ  plan-1  O6    0.020
 TOQ  plan-1  O7    0.020
 TOQ  plan-1  CB    0.020
 TOQ  plan-1  CG    0.020
 TOQ  plan-1  CD1   0.020
 TOQ  plan-1  CD2   0.020
 TOQ  plan-1  NE1   0.020
 TOQ  plan-1  CE2   0.020
 TOQ  plan-1  CE3   0.020
 TOQ  plan-1  CH2   0.020
 TOQ  plan-1  CZ2   0.020
 TOQ  plan-1  CZ3   0.020
 TOQ  plan-1  HD1   0.020
 TOQ  plan-1  HE3   0.020
 TOQ  plan-1  HZ3   0.020
 TOQ  plan-1  HNE1  0.020
 TOQ  plan-2  C     0.020
 TOQ  plan-2  O     0.020
 TOQ  plan-2  CA    0.020
 TOQ  plan-2  OXT   0.020

