# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 16:28:50 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: D-tryptophan
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1c[nH]c2ccccc12)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
 DTR  DTR  'D-tryptophan             '  D-peptide  27  15  .  2022-03-18  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DTR
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
 DTR  N    N  NH2   0  -0.782  -4.0752   2.8407  6.6919
 DTR  CA   C  CH1   0  -0.190  -3.6244   1.8177  5.7736
 DTR  CB   C  CH2   0  -0.530  -4.4190   1.9235  4.4606
 DTR  CG   C  CR5   0  -0.004  -4.0828   0.8635  3.4677
 DTR  CD1  C  CR15  0  -0.078  -4.8652  -0.1957  3.1044
 DTR  NE1  N  NR15  0  -0.688  -4.2083  -0.9798  2.1985
 DTR  CE2  C  CR56  0   0.352  -2.9768  -0.4474  1.9516
 DTR  CZ2  C  CR16  0  -0.306  -1.9541  -0.8819  1.1096
 DTR  CH2  C  CR16  0  -0.285  -0.7989  -0.1247  1.0665
 DTR  CZ3  C  CR16  0  -0.268  -0.6598   1.0402  1.8396
 DTR  CE3  C  CR16  0  -0.378  -1.6767   1.4676  2.6713
 DTR  CD2  C  CR56  0   0.034  -2.8581   0.7203  2.7379
 DTR  C    C  C     0   0.531  -3.7829   0.4050  6.3152
 DTR  O    O  O     0  -0.450  -4.7834   0.0103  6.8640
 DTR  OXT  O  OH1   0  -0.582  -2.7145  -0.3519  6.1146
 DTR  H    H  HNH2  0   0.346  -5.0129   2.6323  7.0141
 DTR  HN2  H  HNH2  0   0.357  -3.4861   2.8666  7.5144
 DTR  HA   H  HCH1  0   0.262  -2.5677   1.9934  5.5612
 DTR  HB2  H  HCH2  0   0.247  -5.4859   1.8797  4.6970
 DTR  HB3  H  HCH2  0   0.254  -4.2279   2.9188  4.0516
 DTR  HD1  H  HCR5  0   0.282  -5.8616  -0.4503  3.4310
 DTR  HE1  H  HNR5  0   0.408  -4.5849  -1.8100  1.7739
 DTR  HZ2  H  HCR6  0   0.258  -2.0580  -1.7785  0.5116
 DTR  HH2  H  HCR6  0   0.248   0.0150  -0.4354  0.4239
 DTR  HZ3  H  HCR6  0   0.245   0.2599   1.6081  1.7810
 DTR  HE3  H  HCR6  0   0.240  -1.5608   2.3684  3.2622
 DTR  HXT  H  HOH1  0   0.475  -2.8785  -1.2504  6.4397

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
 DTR  N    CA   single    1.458  0.019  1.458
 DTR  N    H    single    0.860  0.020  0.860
 DTR  N    HN2  single    0.890  0.020  1.040
 DTR  CA   CB   single    1.521  0.033  1.521
 DTR  CA   C    single    1.525  0.021  1.525
 DTR  CA   HA   single    0.970  0.020  0.970
 DTR  CB   CG   single    1.491  0.020  1.491
 DTR  CB   HB2  single    0.970  0.020  1.090
 DTR  CB   HB3  single    0.970  0.020  1.090
 DTR  CG   CD1  aromatic  1.366  0.020  1.366
 DTR  CG   CD2  aromatic  1.433  0.020  1.433
 DTR  CD1  NE1  aromatic  1.366  0.020  1.366
 DTR  CD1  HD1  single    0.930  0.020  1.080
 DTR  NE1  CE2  aromatic  1.364  0.020  1.364
 DTR  NE1  HE1  single    0.860  0.020  1.020
 DTR  CE2  CZ2  aromatic  1.394  0.020  1.394
 DTR  CE2  CD2  aromatic  1.413  0.020  1.413
 DTR  CZ2  CH2  aromatic  1.382  0.020  1.382
 DTR  CZ2  HZ2  single    0.930  0.020  1.080
 DTR  CH2  CZ3  aromatic  1.405  0.020  1.405
 DTR  CH2  HH2  single    0.930  0.020  1.080
 DTR  CZ3  CE3  aromatic  1.381  0.020  1.381
 DTR  CZ3  HZ3  single    0.930  0.020  1.080
 DTR  CE3  CD2  aromatic  1.399  0.020  1.399
 DTR  CE3  HE3  single    0.930  0.020  1.080
 DTR  C    O    double    1.231  0.020  1.231
 DTR  C    OXT  single    1.325  0.020  1.325
 DTR  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
 DTR  HN2  N    H    106.59  3.000
 DTR  HN2  N    CA   110.64  3.000
 DTR  H    N    CA   114.00  3.000
 DTR  HA   CA   C    110.00  3.000
 DTR  HA   CA   CB   109.00  3.000
 DTR  C    CA   CB   110.50  1.500
 DTR  HA   CA   N    110.00  3.000
 DTR  C    CA   N    111.00  2.800
 DTR  CB   CA   N    110.40  1.500
 DTR  HB3  CB   HB2  106.73  3.000
 DTR  HB3  CB   CG   111.03  3.000
 DTR  HB2  CB   CG   109.61  3.000
 DTR  HB3  CB   CA   106.96  3.000
 DTR  HB2  CB   CA   108.46  3.000
 DTR  CG   CB   CA   113.77  3.000
 DTR  CD2  CG   CD1  106.05  3.000
 DTR  CD2  CG   CB   127.09  3.000
 DTR  CD1  CG   CB   126.82  3.000
 DTR  HD1  CD1  NE1  120.62  3.000
 DTR  HD1  CD1  CG   129.15  3.000
 DTR  NE1  CD1  CG   110.24  3.000
 DTR  HE1  NE1  CE2  125.72  3.000
 DTR  HE1  NE1  CD1  125.00  3.000
 DTR  CE2  NE1  CD1  109.27  3.000
 DTR  CD2  CE2  CZ2  122.14  3.000
 DTR  CD2  CE2  NE1  107.32  3.000
 DTR  CZ2  CE2  NE1  130.54  3.000
 DTR  HZ2  CZ2  CH2  121.11  3.000
 DTR  HZ2  CZ2  CE2  121.42  3.000
 DTR  CH2  CZ2  CE2  117.47  3.000
 DTR  HH2  CH2  CZ3  119.35  3.000
 DTR  HH2  CH2  CZ2  119.32  3.000
 DTR  CZ3  CH2  CZ2  121.32  3.000
 DTR  HZ3  CZ3  CE3  119.72  3.000
 DTR  HZ3  CZ3  CH2  119.29  3.000
 DTR  CE3  CZ3  CH2  120.99  3.000
 DTR  HE3  CE3  CD2  120.55  3.000
 DTR  HE3  CE3  CZ3  120.44  3.000
 DTR  CD2  CE3  CZ3  119.00  3.000
 DTR  CE3  CD2  CE2  119.07  3.000
 DTR  CE3  CD2  CG   133.82  3.000
 DTR  CE2  CD2  CG   107.11  3.000
 DTR  OXT  C    O    123.39  3.000
 DTR  OXT  C    CA   120.80  1.700
 DTR  O    C    CA   120.80  1.700
 DTR  HXT  OXT  C    110.02  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
 DTR  CONST_01  CE2  NE1  CD1  CG     0.00   0.0  0
 DTR  CONST_02  NE1  CE2  CD2  CG     0.00   0.0  0
 DTR  CONST_03  CZ2  CE2  CD2  CG   180.00   0.0  0
 DTR  CONST_04  CZ3  CE3  CD2  CG   180.00   0.0  0
 DTR  CONST_05  CE2  CD2  CG   CD1    0.00   0.0  0
 DTR  CONST_06  CE3  CD2  CG   CD1  180.00   0.0  0
 DTR  CONST_07  CZ2  CE2  NE1  CD1  180.00   0.0  0
 DTR  CONST_08  CD2  CE2  NE1  CD1    0.00   0.0  0
 DTR  CONST_09  CD2  CG   CD1  NE1    0.00   0.0  0
 DTR  CONST_10  CH2  CZ2  CE2  NE1  180.00   0.0  0
 DTR  CONST_11  CE3  CD2  CE2  NE1  180.00   0.0  0
 DTR  CONST_12  CZ3  CH2  CZ2  CE2    0.00   0.0  0
 DTR  CONST_13  CZ3  CE3  CD2  CE2    0.00   0.0  0
 DTR  CONST_14  CE3  CD2  CE2  CZ2    0.00   0.0  0
 DTR  CONST_15  CE3  CZ3  CH2  CZ2    0.00   0.0  0
 DTR  CONST_16  CD2  CE2  CZ2  CH2    0.00   0.0  0
 DTR  CONST_17  CD2  CE3  CZ3  CH2    0.00   0.0  0
 DTR  CONST_18  NE1  CD1  CG   CB   180.00   0.0  0
 DTR  CONST_19  CE2  CD2  CG   CB   180.00   0.0  0
 DTR  CONST_20  CE3  CD2  CG   CB     0.00   0.0  0
 DTR  CONST_21  HE1  NE1  CD1  CG   180.00   0.0  0
 DTR  CONST_22  HE3  CE3  CD2  CG     0.00   0.0  0
 DTR  CONST_23  HZ2  CZ2  CE2  NE1    0.00   0.0  0
 DTR  CONST_24  HD1  CD1  NE1  CE2  180.00   0.0  0
 DTR  CONST_25  HH2  CH2  CZ2  CE2  180.00   0.0  0
 DTR  CONST_26  HZ3  CZ3  CH2  CZ2  180.00   0.0  0
 DTR  CONST_27  HXT  OXT  C    CA   180.00   0.0  0
 DTR  Var_01    CD1  CG   CB   CA   108.13  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
 DTR  chir_01  CA  N  CB  C  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
 DTR  plan-1  CB   0.020
 DTR  plan-1  CG   0.020
 DTR  plan-1  CD1  0.020
 DTR  plan-1  NE1  0.020
 DTR  plan-1  CE2  0.020
 DTR  plan-1  CZ2  0.020
 DTR  plan-1  CH2  0.020
 DTR  plan-1  CZ3  0.020
 DTR  plan-1  CE3  0.020
 DTR  plan-1  CD2  0.020
 DTR  plan-1  HD1  0.020
 DTR  plan-1  HE1  0.020
 DTR  plan-1  HZ2  0.020
 DTR  plan-1  HH2  0.020
 DTR  plan-1  HZ3  0.020
 DTR  plan-1  HE3  0.020
 DTR  plan-2  CA   0.020
 DTR  plan-2  C    0.020
 DTR  plan-2  O    0.020
 DTR  plan-2  OXT  0.020
 DTR  plan-2  HXT  0.020

