# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 10:10:55 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 3-(hydroxymethyl)-O-phosphono-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O[P](O)(O)=O)c(CO)c1)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
 PTH  PTH  3-(hydroxymethyl)-O-phosphono-L-tyrosine  L-peptide  30  19  .  2012-08-28  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_PTH
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
 PTH  N    N  NH2    0  -0.797  41.8108   7.7987  22.7189
 PTH  CA   C  CH1    0  -0.194  42.2046   8.0796  21.3507
 PTH  C    C  C      0   0.399  41.1351   7.5857  20.3459
 PTH  O    O  O      0  -0.599  40.3405   6.7112  20.7445
 PTH  OXT  O  OC    -1  -0.613  41.1907   8.0826  19.2031
 PTH  CB   C  CH2    0  -0.519  43.5691   7.4719  20.9456
 PTH  CG   C  C      0   0.121  44.6995   7.9382  21.8182
 PTH  CD1  C  C1     0  -0.364  45.3020   9.1783  21.5944
 PTH  CD2  C  C1     0  -0.333  45.1519   7.1880  22.8967
 PTH  CE1  C  C      0  -0.077  46.3224   9.6631  22.3986
 PTH  CE2  C  C1     0  -0.345  46.1651   7.6599  23.7241
 PTH  CZ   C  C      0   0.357  46.7681   8.8937  23.4891
 PTH  CF   C  CH2    0  -0.190  46.9905  10.9887  22.1258
 PTH  OH   O  O2     0  -0.664  47.7927   9.3257  24.2352
 PTH  P    P  P      0   1.213  47.5256  10.1582  25.7721
 PTH  O1P  O  O      0  -0.869  47.0377   9.0620  26.7054
 PTH  O2P  O  OP    -1  -0.869  46.4835  11.2164  25.4379
 PTH  O3P  O  OP    -1  -0.871  48.9350  10.6632  26.0212
 PTH  OF   O  OH1    0  -0.658  46.5180  11.6547  20.9786
 PTH  H    H  HNH2   0   0.333  42.6104   7.8846  23.3353
 PTH  H2   H  HNH2   0   0.322  41.5033   6.8354  22.7702
 PTH  HA   H  HCH1   0   0.202  42.2957   9.1662  21.2352
 PTH  HB2  H  HCH2   0   0.223  43.4934   6.3802  20.9887
 PTH  HB3  H  HCH2   0   0.225  43.7706   7.7363  19.9050
 PTH  HD1  H  H      0   0.224  44.9536   9.7757  20.7590
 PTH  HD2  H  H      0   0.232  44.7144   6.2152  23.0937
 PTH  HE2  H  H      0   0.231  46.5124   7.0547  24.5522
 PTH  HF1  H  HCH2   0   0.234  46.8130  11.6470  22.9778
 PTH  HF2  H  HCH2   0   0.201  48.0771  10.8411  22.0775
 PTH  HOF  H  HOH1   0   0.446  46.7963  11.1583  20.2030

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
 PTH  N    CA   single    1.458  0.019  1.458
 PTH  N    H    single    0.860  0.020  0.860
 PTH  N    H2   single    0.890  0.020  1.040
 PTH  CA   C    single    1.525  0.021  1.525
 PTH  CA   CB   single    1.530  0.020  1.530
 PTH  CA   HA   single    0.970  0.020  0.970
 PTH  C    O    deloc     1.231  0.020  1.231
 PTH  C    OXT  deloc     1.247  0.020  1.247
 PTH  CB   CG   single    1.502  0.020  1.502
 PTH  CB   HB2  single    0.970  0.020  1.090
 PTH  CB   HB3  single    0.970  0.020  1.090
 PTH  CG   CD1  aromatic  1.397  0.020  1.397
 PTH  CG   CD2  aromatic  1.390  0.020  1.390
 PTH  CD1  CE1  aromatic  1.387  0.020  1.387
 PTH  CD1  HD1  single    0.930  0.020  1.080
 PTH  CD2  CE2  aromatic  1.391  0.020  1.391
 PTH  CD2  HD2  single    0.930  0.020  1.080
 PTH  CE1  CZ   aromatic  1.407  0.020  1.407
 PTH  CE1  CF   single    1.509  0.020  1.509
 PTH  CE2  CZ   aromatic  1.393  0.020  1.393
 PTH  CE2  HE2  single    0.930  0.020  1.080
 PTH  CZ   OH   single    1.339  0.020  1.339
 PTH  CF   OF   single    1.408  0.020  1.408
 PTH  CF   HF1  single    0.970  0.020  1.090
 PTH  CF   HF2  single    0.970  0.020  1.090
 PTH  OH   P    single    1.768  0.020  1.768
 PTH  P    O1P  deloc     1.520  0.020  1.520
 PTH  P    O2P  deloc     1.522  0.020  1.522
 PTH  P    O3P  deloc     1.518  0.020  1.518
 PTH  OF   HOF  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
 PTH  H2   N    H    106.83  3.000
 PTH  H2   N    CA   108.32  3.000
 PTH  H    N    CA   114.00  3.000
 PTH  HA   CA   CB   109.00  3.000
 PTH  HA   CA   C    109.00  3.000
 PTH  CB   CA   C    110.10  1.900
 PTH  HA   CA   N    110.00  3.000
 PTH  CB   CA   N    110.50  1.700
 PTH  C    CA   N    111.00  2.800
 PTH  OXT  C    O    126.91  3.000
 PTH  OXT  C    CA   115.89  3.000
 PTH  O    C    CA   120.80  1.700
 PTH  HB3  CB   HB2  106.95  3.000
 PTH  HB3  CB   CG   109.84  3.000
 PTH  HB2  CB   CG   109.79  3.000
 PTH  HB3  CB   CA   108.48  3.000
 PTH  HB2  CB   CA   108.67  3.000
 PTH  CG   CB   CA   112.92  3.000
 PTH  CD2  CG   CD1  117.60  3.000
 PTH  CD2  CG   CB   121.89  3.000
 PTH  CD1  CG   CB   120.47  3.000
 PTH  HD1  CD1  CE1  119.37  3.000
 PTH  HD1  CD1  CG   118.29  3.000
 PTH  CE1  CD1  CG   122.34  3.000
 PTH  HD2  CD2  CE2  119.35  3.000
 PTH  HD2  CD2  CG   119.59  3.000
 PTH  CE2  CD2  CG   121.05  3.000
 PTH  CF   CE1  CZ   118.70  3.000
 PTH  CF   CE1  CD1  121.87  3.000
 PTH  CZ   CE1  CD1  119.43  3.000
 PTH  HE2  CE2  CZ   119.02  3.000
 PTH  HE2  CE2  CD2  119.93  3.000
 PTH  CZ   CE2  CD2  121.03  3.000
 PTH  OH   CZ   CE2  121.53  3.000
 PTH  OH   CZ   CE1  119.85  3.000
 PTH  CE2  CZ   CE1  118.55  3.000
 PTH  HF2  CF   HF1  106.05  3.000
 PTH  HF2  CF   OF   111.10  3.000
 PTH  HF1  CF   OF   107.23  3.000
 PTH  HF2  CF   CE1  109.15  3.000
 PTH  HF1  CF   CE1  108.46  3.000
 PTH  OF   CF   CE1  114.47  3.000
 PTH  P    OH   CZ   121.37  3.000
 PTH  O3P  P    O2P  116.13  3.000
 PTH  O3P  P    O1P  115.93  3.000
 PTH  O2P  P    O1P  114.60  3.000
 PTH  O3P  P    OH    99.15  3.000
 PTH  O2P  P    OH   103.88  3.000
 PTH  O1P  P    OH   104.04  3.000
 PTH  HOF  OF   CF   108.40  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
 PTH  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PTH  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PTH  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PTH  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PTH  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PTH  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PTH  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PTH  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PTH  CONST_09  CF   CE1  CD1  CG   180.00   0.0  0
 PTH  CONST_10  OH   CZ   CE1  CD1  180.00   0.0  0
 PTH  CONST_11  OH   CZ   CE2  CD2  180.00   0.0  0
 PTH  CONST_12  CF   CE1  CZ   CE2  180.00   0.0  0
 PTH  CONST_13  HE2  CE2  CD2  CG   180.00   0.0  0
 PTH  CONST_14  HD2  CD2  CG   CD1  180.00   0.0  0
 PTH  CONST_15  HD1  CD1  CG   CD2  180.00   0.0  0
 PTH  Var_01    CD1  CG   CB   CA   -81.02  30.0  2
 PTH  Var_02    OF   CF   CE1  CD1   -1.77  30.0  2
 PTH  Var_03    O1P  P    OH   CZ    71.53  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
 PTH  chir_01  CA  N  C  CB  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
 PTH  plan-1  CB   0.020
 PTH  plan-1  CG   0.020
 PTH  plan-1  CD1  0.020
 PTH  plan-1  CD2  0.020
 PTH  plan-1  CE1  0.020
 PTH  plan-1  CE2  0.020
 PTH  plan-1  CZ   0.020
 PTH  plan-1  CF   0.020
 PTH  plan-1  OH   0.020
 PTH  plan-1  HD1  0.020
 PTH  plan-1  HD2  0.020
 PTH  plan-1  HE2  0.020
 PTH  plan-2  CA   0.020
 PTH  plan-2  C    0.020
 PTH  plan-2  O    0.020
 PTH  plan-2  OXT  0.020

