# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 19:50:48 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: O-phosphono-L-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
 TPO  TPO  'O-phosphono-L-threonine  '  L-peptide  19  12  .  2009-03-25  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TPO
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
 TPO  N     N  NH2    0  -0.814  22.0275  1.9288  -14.6067
 TPO  CA    C  CH1    0  -0.171  22.4387  2.9324  -13.6322
 TPO  CB    C  CH1    0   0.097  21.2808  3.9150  -13.4025
 TPO  CG2   C  CH3    0  -0.686  21.6626  5.0002  -12.4017
 TPO  OG1   O  O2     0  -0.672  20.9292  4.4951  -14.6341
 TPO  P     P  P      0   1.214  19.2698  4.6816  -15.0319
 TPO  O1P   O  O      0  -0.894  19.3843  5.4743  -16.3292
 TPO  O2P   O  OP    -1  -0.902  18.7332  3.2594  -15.1908
 TPO  O3P   O  OP    -1  -0.897  18.6528  5.4429  -13.8590
 TPO  C     C  C      0   0.379  22.8508  2.2590  -12.3002
 TPO  O     O  O      0  -0.609  22.0321  1.4659  -11.7914
 TPO  OXT   O  OC    -1  -0.618  23.9657  2.5750  -11.8321
 TPO  H     H  HNH2   0   0.325  22.8309  1.3832  -14.8920
 TPO  H2    H  HNH2   0   0.326  21.7071  2.4111  -15.4370
 TPO  HA    H  HCH1   0   0.148  23.2974  3.5264  -13.9869
 TPO  HB    H  HCH1   0   0.149  20.4448  3.3348  -12.9871
 TPO  HG21  H  HCH3   0   0.220  20.8479  5.7173  -12.3085
 TPO  HG22  H  HCH3   0   0.207  21.8624  4.5947  -11.4090
 TPO  HG23  H  HCH3   0   0.198  22.5566  5.5379  -12.7271

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
 TPO  N    CA    single  1.458  0.019  1.458
 TPO  N    H     single  0.860  0.020  0.860
 TPO  N    H2    single  0.890  0.020  1.040
 TPO  CA   CB    single  1.540  0.027  1.540
 TPO  CA   C     single  1.525  0.021  1.525
 TPO  CA   HA    single  0.970  0.020  0.970
 TPO  CB   CG2   single  1.525  0.020  1.525
 TPO  CB   OG1   single  1.406  0.020  1.406
 TPO  CB   HB    single  0.970  0.020  1.090
 TPO  CG2  HG21  single  0.970  0.020  1.090
 TPO  CG2  HG22  single  0.970  0.020  1.090
 TPO  CG2  HG23  single  0.970  0.020  1.090
 TPO  OG1  P     single  1.717  0.020  1.717
 TPO  P    O1P   deloc   1.525  0.020  1.525
 TPO  P    O2P   deloc   1.528  0.020  1.528
 TPO  P    O3P   deloc   1.528  0.020  1.528
 TPO  C    O     deloc   1.231  0.020  1.231
 TPO  C    OXT   deloc   1.250  0.020  1.250

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
 TPO  H2    N    H     106.07  3.000
 TPO  H2    N    CA    108.03  3.000
 TPO  H     N    CA    114.00  3.000
 TPO  HA    CA   C     109.00  3.000
 TPO  HA    CA   CB    109.00  3.000
 TPO  C     CA   CB    109.10  2.200
 TPO  HA    CA   N     110.00  3.000
 TPO  C     CA   N     111.00  2.800
 TPO  CB    CA   N     111.50  1.700
 TPO  HB    CB   OG1   111.01  3.000
 TPO  HB    CB   CG2   108.55  3.000
 TPO  OG1   CB   CG2   110.11  3.000
 TPO  HB    CB   CA    106.99  3.000
 TPO  OG1   CB   CA    108.75  3.000
 TPO  CG2   CB   CA    111.39  3.000
 TPO  HG23  CG2  HG22  107.70  3.000
 TPO  HG23  CG2  HG21  108.26  3.000
 TPO  HG22  CG2  HG21  107.69  3.000
 TPO  HG23  CG2  CB    111.08  3.000
 TPO  HG22  CG2  CB    112.25  3.000
 TPO  HG21  CG2  CB    109.72  3.000
 TPO  P     OG1  CB    119.31  3.000
 TPO  O3P   P    O2P   113.68  3.000
 TPO  O3P   P    O1P   115.11  3.000
 TPO  O2P   P    O1P   114.94  3.000
 TPO  O3P   P    OG1   105.46  3.000
 TPO  O2P   P    OG1   105.22  3.000
 TPO  O1P   P    OG1   100.43  3.000
 TPO  OXT   C    O     126.37  3.000
 TPO  OXT   C    CA    116.72  3.000
 TPO  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
 TPO  Var_01  O1P  P  OG1  CB  173.72  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
 TPO  chir_01  CA  N    CB  C    negativ
 TPO  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
 TPO  plan-1  CA   0.020
 TPO  plan-1  C    0.020
 TPO  plan-1  O    0.020
 TPO  plan-1  OXT  0.020

