# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 14:27:14 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: O-phosphono-L-allothreonine
#   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
 YTH  YTH  O-phosphono-L-allothreonine  L-peptide  19  12  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_YTH
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
 YTH  N     N  NH2    0  -0.843  14.4883  56.9665  154.6267
 YTH  CA    C  CH1    0  -0.195  14.1413  56.2441  155.8458
 YTH  CB    C  CH1    0   0.065  14.2221  54.7282  155.5619
 YTH  CG2   C  CH3    0  -0.674  13.2726  53.9033  156.4180
 YTH  OG1   O  O2     0  -0.662  15.5266  54.2310  155.7337
 YTH  P     P  P      0   1.220  16.5172  53.8885  154.3887
 YTH  O1P   O  O      0  -0.898  15.6612  53.0143  153.4737
 YTH  O2P   O  OP    -1  -0.878  16.8713  55.2569  153.7892
 YTH  O3P   O  OP    -1  -0.888  17.6836  53.1791  155.0647
 YTH  C     C  C      0   0.382  14.9668  56.6203  157.1029
 YTH  O     O  O      0  -0.611  15.9948  57.3081  156.9375
 YTH  OXT   O  OC    -1  -0.621  14.5227  56.2122  158.1992
 YTH  H     H  HNH2   0   0.309  14.7323  57.9170  154.8768
 YTH  H2    H  HNH2   0   0.335  15.3479  56.5563  154.2605
 YTH  HA    H  HCH1   0   0.176  13.0913  56.4673  156.0824
 YTH  HB    H  HCH1   0   0.166  13.9008  54.6039  154.5176
 YTH  HG21  H  HCH3   0   0.197  12.2425  54.2494  156.3108
 YTH  HG22  H  HCH3   0   0.204  13.3026  52.8553  156.1128
 YTH  HG23  H  HCH3   0   0.215  13.5377  53.9635  157.4722

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
 YTH  O1P  P     deloc   1.528  0.020  1.528
 YTH  O2P  P     deloc   1.535  0.020  1.535
 YTH  P    O3P   deloc   1.523  0.020  1.523
 YTH  P    OG1   single  1.705  0.020  1.705
 YTH  N    CA    single  1.458  0.019  1.458
 YTH  OG1  CB    single  1.407  0.020  1.407
 YTH  CB   CA    single  1.540  0.027  1.540
 YTH  CB   CG2   single  1.522  0.020  1.522
 YTH  CA   C     single  1.525  0.021  1.525
 YTH  C    O     deloc   1.231  0.020  1.231
 YTH  C    OXT   deloc   1.251  0.020  1.251
 YTH  N    H     single  0.860  0.020  0.860
 YTH  N    H2    single  0.890  0.020  1.040
 YTH  CA   HA    single  0.970  0.020  0.970
 YTH  CB   HB    single  0.970  0.020  1.090
 YTH  CG2  HG21  single  0.970  0.020  1.090
 YTH  CG2  HG22  single  0.970  0.020  1.090
 YTH  CG2  HG23  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
 YTH  H2    N    H     105.24  3.000
 YTH  H2    N    CA    107.53  3.000
 YTH  H     N    CA    114.00  3.000
 YTH  HA    CA   C     109.00  3.000
 YTH  HA    CA   CB    109.00  3.000
 YTH  C     CA   CB    109.10  2.200
 YTH  HA    CA   N     110.00  3.000
 YTH  C     CA   N     111.00  2.800
 YTH  CB    CA   N     111.50  1.700
 YTH  HB    CB   OG1   110.31  3.000
 YTH  HB    CB   CG2   106.90  3.000
 YTH  OG1   CB   CG2   108.57  3.000
 YTH  HB    CB   CA    105.68  3.000
 YTH  CG2   CB   CA    113.33  3.000
 YTH  OG1   CB   CA    111.90  3.000
 YTH  HG23  CG2  HG22  108.48  3.000
 YTH  HG23  CG2  HG21  107.89  3.000
 YTH  HG22  CG2  HG21  107.62  3.000
 YTH  HG23  CG2  CB    111.28  3.000
 YTH  HG22  CG2  CB    110.24  3.000
 YTH  HG21  CG2  CB    111.20  3.000
 YTH  P     OG1  CB    120.89  3.000
 YTH  O3P   P    O2P   114.31  3.000
 YTH  O3P   P    O1P   115.36  3.000
 YTH  O2P   P    O1P   113.91  3.000
 YTH  O3P   P    OG1   100.85  3.000
 YTH  O2P   P    OG1   105.25  3.000
 YTH  O1P   P    OG1   105.18  3.000
 YTH  OXT   C    O     126.04  3.000
 YTH  OXT   C    CA    116.25  3.000
 YTH  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
 YTH  Var_01  O1P  P  OG1  CB  -50.67  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
 YTH  chir_01  CA  N    CB  C    negativ
 YTH  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
 YTH  plan-1  CA   0.020
 YTH  plan-1  C    0.020
 YTH  plan-1  O    0.020
 YTH  plan-1  OXT  0.020

