# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 14:08:42 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: D-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@@H](N)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
 DTH  DTH  'D-threonine              '  D-peptide  17  8  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DTH
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
 DTH  N     N  NH2   0  -0.786   0.3274  -1.7579  -0.3276
 DTH  CA    C  CH1   0  -0.238   0.0319  -0.3726  -0.6077
 DTH  CB    C  CH1   0   0.041   1.0476   0.6611  -0.0840
 DTH  CG2   C  CH3   0  -0.700   2.4659   0.3418  -0.5249
 DTH  OG1   O  OH1   0  -0.673   0.9178   0.6646   1.3243
 DTH  C     C  C     0   0.549  -1.3387  -0.0309  -0.0506
 DTH  O     O  O     0  -0.437  -1.9754  -0.7300   0.6942
 DTH  OXT   O  OH1   0  -0.597  -1.7646   1.1518  -0.4815
 DTH  H     H  HNH2  0   0.360   1.1473  -2.0416  -0.8467
 DTH  HN2   H  HNH2  0   0.346   0.5445  -1.8869   0.6529
 DTH  HA    H  HCH1  0   0.283  -0.0159  -0.2497  -1.6945
 DTH  HB    H  HCH1  0   0.214   0.7747   1.6392  -0.4998
 DTH  HG21  H  HCH3  0   0.243   3.1533   1.1214  -0.1917
 DTH  HG22  H  HCH3  0   0.226   2.8129  -0.6062  -0.1119
 DTH  HG23  H  HCH3  0   0.232   2.5354   0.2896  -1.6125
 DTH  HG1   H  HOH1  0   0.456   1.5220   1.3205   1.6858
 DTH  HXT   H  HOH1  0   0.481  -2.6268   1.3567  -0.0896

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
 DTH  N    CA    single  1.458  0.019  1.458
 DTH  N    H     single  0.860  0.020  0.860
 DTH  N    HN2   single  0.890  0.020  1.040
 DTH  CA   CB    single  1.521  0.033  1.521
 DTH  CA   C     single  1.525  0.021  1.525
 DTH  CA   HA    single  0.970  0.020  0.970
 DTH  CB   CG2   single  1.519  0.020  1.519
 DTH  CB   OG1   single  1.414  0.020  1.414
 DTH  CB   HB    single  0.970  0.020  1.090
 DTH  CG2  HG21  single  0.970  0.020  1.090
 DTH  CG2  HG22  single  0.970  0.020  1.090
 DTH  CG2  HG23  single  0.970  0.020  1.090
 DTH  OG1  HG1   single  0.850  0.020  0.980
 DTH  C    O     double  1.231  0.020  1.231
 DTH  C    OXT   single  1.329  0.020  1.329
 DTH  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
 DTH  HN2   N    H     106.71  3.000
 DTH  HN2   N    CA    110.73  3.000
 DTH  H     N    CA    114.00  3.000
 DTH  HA    CA   C     110.00  3.000
 DTH  HA    CA   CB    109.00  3.000
 DTH  C     CA   CB    110.50  1.500
 DTH  HA    CA   N     110.00  3.000
 DTH  C     CA   N     111.00  2.800
 DTH  CB    CA   N     110.40  1.500
 DTH  HB    CB   OG1   110.63  3.000
 DTH  HB    CB   CG2   108.03  3.000
 DTH  OG1   CB   CG2   112.04  3.000
 DTH  HB    CB   CA    107.77  3.000
 DTH  OG1   CB   CA    106.23  3.000
 DTH  CG2   CB   CA    112.07  3.000
 DTH  HG23  CG2  HG22  108.39  3.000
 DTH  HG23  CG2  HG21  107.36  3.000
 DTH  HG22  CG2  HG21  107.75  3.000
 DTH  HG23  CG2  CB    111.03  3.000
 DTH  HG22  CG2  CB    111.71  3.000
 DTH  HG21  CG2  CB    110.44  3.000
 DTH  HG1   OG1  CB    108.55  3.000
 DTH  OXT   C    O     123.23  3.000
 DTH  OXT   C    CA    120.80  1.700
 DTH  O     C    CA    120.80  1.700
 DTH  HXT   OXT  C     110.01  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
 DTH  CONST_01  HXT  OXT  C  CA  180.00  0.0  0

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
 DTH  chir_01  CA  N    CB  C    positiv
 DTH  chir_02  CB  OG1  CA  CG2  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
 DTH  plan-1  CA   0.020
 DTH  plan-1  C    0.020
 DTH  plan-1  O    0.020
 DTH  plan-1  OXT  0.020
 DTH  plan-1  HXT  0.020

