# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:43:48 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: O-phosphono-D-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O[P](O)(O)=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
 D11  D11  'O-phosphono-D-threonine  '  D-peptide  19  12  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_D11
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
 D11  N     N  NH2    0  -0.793  33.8286  29.2137  24.0206
 D11  CA    C  CH1    0  -0.207  33.5005  27.8502  24.4403
 D11  CB    C  CH1    0   0.110  32.0664  27.8099  24.9941
 D11  CG2   C  CH3    0  -0.693  31.7186  26.4518  25.5983
 D11  OG1   O  O2     0  -0.663  31.1695  28.1216  23.9616
 D11  P     P  P      0   1.210  29.7825  29.0640  24.2903
 D11  O1P   O  O      0  -0.904  30.3108  30.3382  24.9478
 D11  O2P   O  OP    -1  -0.898  28.9067  28.2123  25.2122
 D11  O3P   O  OP    -1  -0.896  29.2317  29.2425  22.8796
 D11  C     C  C      0   0.376  34.5081  27.2830  25.4666
 D11  O     O  O      0  -0.616  34.7418  28.0034  26.4636
 D11  OXT   O  OC    -1  -0.616  35.0098  26.1644  25.2303
 D11  H     H  HNH2   0   0.317  33.9842  29.7589  24.8619
 D11  H2    H  HNH2   0   0.328  34.7278  29.2021  23.5526
 D11  HA    H  HCH1   0   0.178  33.5212  27.2148  23.5473
 D11  HB    H  HCH1   0   0.145  32.0110  28.5602  25.7981
 D11  HG21  H  HCH3   0   0.197  31.8712  25.6449  24.8773
 D11  HG22  H  HCH3   0   0.203  32.3132  26.2258  26.4842
 D11  HG23  H  HCH3   0   0.224  30.6698  26.4560  25.8909

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
 D11  N    CA    single  1.458  0.019  1.458
 D11  N    H     single  0.860  0.020  0.860
 D11  N    H2    single  0.890  0.020  1.040
 D11  CA   CB    single  1.521  0.033  1.521
 D11  CA   C     single  1.525  0.021  1.525
 D11  CA   HA    single  0.970  0.020  0.970
 D11  CB   CG2   single  1.527  0.020  1.527
 D11  CB   OG1   single  1.403  0.020  1.403
 D11  CB   HB    single  0.970  0.020  1.090
 D11  CG2  HG21  single  0.970  0.020  1.090
 D11  CG2  HG22  single  0.970  0.020  1.090
 D11  CG2  HG23  single  0.970  0.020  1.090
 D11  OG1  P     single  1.709  0.020  1.709
 D11  P    O1P   deloc   1.528  0.020  1.528
 D11  P    O2P   deloc   1.530  0.020  1.530
 D11  P    O3P   deloc   1.525  0.020  1.525
 D11  C    O     deloc   1.231  0.020  1.231
 D11  C    OXT   deloc   1.249  0.020  1.249

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
 D11  H2    N    H     104.65  3.000
 D11  H2    N    CA    108.70  3.000
 D11  H     N    CA    114.00  3.000
 D11  HA    CA   C     110.00  3.000
 D11  HA    CA   CB    109.00  3.000
 D11  C     CA   CB    110.50  1.500
 D11  HA    CA   N     110.00  3.000
 D11  C     CA   N     111.00  2.800
 D11  CB    CA   N     110.40  1.500
 D11  HB    CB   OG1   110.72  3.000
 D11  HB    CB   CG2   107.81  3.000
 D11  OG1   CB   CG2   110.08  3.000
 D11  HB    CB   CA    106.98  3.000
 D11  OG1   CB   CA    108.98  3.000
 D11  CG2   CB   CA    112.23  3.000
 D11  HG23  CG2  HG22  107.92  3.000
 D11  HG23  CG2  HG21  108.35  3.000
 D11  HG22  CG2  HG21  107.86  3.000
 D11  HG23  CG2  CB    108.80  3.000
 D11  HG22  CG2  CB    112.43  3.000
 D11  HG21  CG2  CB    111.35  3.000
 D11  P     OG1  CB    120.00  3.000
 D11  O3P   P    O2P   114.57  3.000
 D11  O3P   P    O1P   115.17  3.000
 D11  O2P   P    O1P   113.75  3.000
 D11  O3P   P    OG1   100.36  3.000
 D11  O2P   P    OG1   105.87  3.000
 D11  O1P   P    OG1   105.19  3.000
 D11  OXT   C    O     126.24  3.000
 D11  OXT   C    CA    120.80  1.700
 D11  O     C    CA    120.80  1.700

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
 D11  Var_01  O1P  P  OG1  CB  54.66  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
 D11  chir_01  CA  N    CB  C    positiv
 D11  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
 D11  plan-1  CA   0.020
 D11  plan-1  C    0.020
 D11  plan-1  O    0.020
 D11  plan-1  OXT  0.020

