# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:51:44 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: O-methyl-D-allothreonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H](C)[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
 XDT  XDT  'O-methyl-D-allothreonine '  D-peptide  19  9  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XDT
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
 XDT  N     N  NH2    0  -0.820  6.9250  38.4721  4.8899
 XDT  CA    C  CH1    0  -0.297  6.8465  37.1550  4.2771
 XDT  C     C  C      0   0.441  5.6629  36.3455  4.8737
 XDT  O     O  O      0  -0.505  4.7245  36.9941  5.3845
 XDT  CB    C  CH1    0   0.097  6.8704  37.2158  2.7315
 XDT  OG1   O  O2     0  -0.413  5.8865  38.0849  2.1891
 XDT  CG2   C  CH3    0  -0.695  6.9355  35.8614  2.0410
 XDT  CD1   C  CH3    0  -0.376  4.5934  37.5737  1.9913
 XDT  OXT   O  OC    -1  -0.677  5.7451  35.1069  4.7783
 XDT  H     H  HNH2   0   0.316  7.3425  39.1448  4.2594
 XDT  H2    H  HNH2   0   0.340  5.9751  38.7745  5.0675
 XDT  HCA   H  HCH1   0   0.202  7.7481  36.5831  4.5351
 XDT  HB    H  HCH1   0   0.217  7.8098  37.7289  2.4888
 XDT  HG21  H  HCH3   0   0.266  7.0975  35.9953  0.9701
 XDT  HG22  H  HCH3   0   0.230  7.7764  35.2929  2.4385
 XDT  HG23  H  HCH3   0   0.192  6.0448  35.2518  2.1793
 XDT  HD11  H  HCH3   0   0.203  3.9722  38.4070  1.6591
 XDT  HD12  H  HCH3   0   0.172  4.5489  36.8032  1.2144
 XDT  HD13  H  HCH3   0   0.107  4.1391  37.1696  2.8978

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
 XDT  N    CA    single  1.458  0.019  1.458
 XDT  N    H     single  0.860  0.020  0.860
 XDT  N    H2    single  0.890  0.020  1.040
 XDT  CA   C     single  1.525  0.021  1.525
 XDT  CA   CB    single  1.521  0.033  1.521
 XDT  CA   HCA   single  0.970  0.020  1.090
 XDT  C    O     deloc   1.231  0.020  1.231
 XDT  C    OXT   deloc   1.245  0.020  1.245
 XDT  CB   OG1   single  1.420  0.020  1.420
 XDT  CB   CG2   single  1.522  0.020  1.522
 XDT  CB   HB    single  0.970  0.020  1.090
 XDT  OG1  CD1   single  1.404  0.020  1.404
 XDT  CG2  HG21  single  0.970  0.020  1.090
 XDT  CG2  HG22  single  0.970  0.020  1.090
 XDT  CG2  HG23  single  0.970  0.020  1.090
 XDT  CD1  HD11  single  0.970  0.020  1.090
 XDT  CD1  HD12  single  0.970  0.020  1.090
 XDT  CD1  HD13  single  0.970  0.020  1.090

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
 XDT  H2    N    H     107.32  3.000
 XDT  H2    N    CA    107.07  3.000
 XDT  H     N    CA    114.00  3.000
 XDT  HCA   CA   CB    104.03  3.000
 XDT  HCA   CA   C     105.30  3.000
 XDT  CB    CA   C     110.50  1.500
 XDT  HCA   CA   N     109.16  3.000
 XDT  CB    CA   N     110.40  1.500
 XDT  C     CA   N     111.00  2.800
 XDT  OXT   C    O     126.67  3.000
 XDT  OXT   C    CA    120.80  1.700
 XDT  O     C    CA    120.80  1.700
 XDT  HB    CB   CG2   106.21  3.000
 XDT  HB    CB   OG1   102.85  3.000
 XDT  CG2   CB   OG1   113.64  3.000
 XDT  HB    CB   CA    104.63  3.000
 XDT  CG2   CB   CA    114.77  3.000
 XDT  OG1   CB   CA    113.25  3.000
 XDT  CD1   OG1  CB    117.96  3.000
 XDT  HG23  CG2  HG22  107.03  3.000
 XDT  HG23  CG2  HG21  108.36  3.000
 XDT  HG22  CG2  HG21  107.90  3.000
 XDT  HG23  CG2  CB    113.95  3.000
 XDT  HG22  CG2  CB    109.37  3.000
 XDT  HG21  CG2  CB    110.02  3.000
 XDT  HD13  CD1  HD12  108.17  3.000
 XDT  HD13  CD1  HD11  107.38  3.000
 XDT  HD12  CD1  HD11  107.35  3.000
 XDT  HD13  CD1  OG1   113.64  3.000
 XDT  HD12  CD1  OG1   113.17  3.000
 XDT  HD11  CD1  OG1   106.80  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
 XDT  Var_01  HD11  CD1  OG1  CB  174.99  30.0  3

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
 XDT  chir_01  CA  N    C   CB   negativ
 XDT  chir_02  CB  OG1  CA  CG2  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
 XDT  plan-1  CA   0.020
 XDT  plan-1  C    0.020
 XDT  plan-1  O    0.020
 XDT  plan-1  OXT  0.020

