# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 07:17:07 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: O-phosphono-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O[P](O)(O)=O)cc1)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
 PTR  PTR  'O-phosphono-L-tyrosine   '  L-peptide  26  17  .  2011-11-15  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_PTR
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
 PTR  N    N  NH2    0  -0.793  46.4111  11.2349  -0.6490
 PTR  CA   C  CH1    0  -0.199  45.0181  11.6394  -0.7142
 PTR  C    C  C      0   0.411  44.8516  13.0056  -1.4207
 PTR  O    O  O      0  -0.617  43.6833  13.3050  -1.7452
 PTR  OXT  O  OC    -1  -0.599  45.8744  13.6959  -1.5920
 PTR  CB   C  CH2    0  -0.522  44.3063  11.6630   0.6562
 PTR  CG   C  CR6    0   0.112  44.8681  12.6519   1.6379
 PTR  CD1  C  CR16   0  -0.319  45.8834  12.3084   2.5283
 PTR  CD2  C  CR16   0  -0.291  44.3913  13.9611   1.6940
 PTR  CE1  C  CR16   0  -0.358  46.3713  13.2151   3.4610
 PTR  CE2  C  CR16   0  -0.342  44.8711  14.8767   2.6171
 PTR  CZ   C  CR6    0   0.371  45.8641  14.5154   3.5352
 PTR  OH   O  O2     0  -0.668  46.3371  15.3760   4.4448
 PTR  P    P  P      0   1.206  45.2868  15.8559   5.7854
 PTR  O1P  O  O      0  -0.869  44.1599  16.6338   5.1217
 PTR  O2P  O  OP    -1  -0.871  46.2625  16.6886   6.5967
 PTR  O3P  O  OP    -1  -0.878  44.8787  14.5216   6.3877
 PTR  H    H  HNH2   0   0.328  46.5160  10.4660   0.0028
 PTR  HN2  H  HNH2   0   0.328  46.9584  12.0027  -0.2813
 PTR  HA   H  HCH1   0   0.206  44.4809  10.8974  -1.3177
 PTR  HB2  H  HCH2   0   0.224  43.2456  11.8670   0.4947
 PTR  HB3  H  HCH2   0   0.225  44.3619  10.6569   1.0841
 PTR  HD1  H  HCR6   0   0.228  46.2825  11.2996   2.5176
 PTR  HD2  H  HCR6   0   0.224  43.6137  14.2695   1.0042
 PTR  HE1  H  HCR6   0   0.230  47.1491  12.9102   4.1515
 PTR  HE2  H  HCR6   0   0.234  44.4690  15.8800   2.6437

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
 PTR  N    CA   single    1.458  0.019  1.458
 PTR  N    H    single    0.860  0.020  0.860
 PTR  N    HN2  single    0.890  0.020  1.040
 PTR  CA   C    single    1.525  0.021  1.525
 PTR  CA   CB   single    1.530  0.020  1.530
 PTR  CA   HA   single    0.970  0.020  0.970
 PTR  C    O    deloc     1.231  0.020  1.231
 PTR  C    OXT  deloc     1.246  0.020  1.246
 PTR  CB   CG   single    1.502  0.020  1.502
 PTR  CB   HB2  single    0.970  0.020  1.090
 PTR  CB   HB3  single    0.970  0.020  1.090
 PTR  CG   CD1  aromatic  1.393  0.020  1.393
 PTR  CG   CD2  aromatic  1.394  0.020  1.394
 PTR  CD1  CE1  aromatic  1.389  0.020  1.389
 PTR  CD1  HD1  single    0.930  0.020  1.080
 PTR  CD2  CE2  aromatic  1.386  0.020  1.386
 PTR  CD2  HD2  single    0.930  0.020  1.080
 PTR  CE1  CZ   aromatic  1.398  0.020  1.398
 PTR  CE1  HE1  single    0.930  0.020  1.080
 PTR  CE2  CZ   aromatic  1.400  0.020  1.400
 PTR  CE2  HE2  single    0.930  0.020  1.080
 PTR  CZ   OH   single    1.339  0.020  1.339
 PTR  OH   P    single    1.769  0.020  1.769
 PTR  P    O1P  deloc     1.522  0.020  1.522
 PTR  P    O2P  deloc     1.518  0.020  1.518
 PTR  P    O3P  deloc     1.520  0.020  1.520

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
 PTR  HN2  N    H    106.61  3.000
 PTR  HN2  N    CA   108.89  3.000
 PTR  H    N    CA   114.00  3.000
 PTR  HA   CA   CB   109.00  3.000
 PTR  HA   CA   C    109.00  3.000
 PTR  CB   CA   C    110.10  1.900
 PTR  HA   CA   N    110.00  3.000
 PTR  CB   CA   N    110.50  1.700
 PTR  C    CA   N    111.00  2.800
 PTR  OXT  C    O    126.83  3.000
 PTR  OXT  C    CA   117.63  3.000
 PTR  O    C    CA   120.80  1.700
 PTR  HB3  CB   HB2  106.19  3.000
 PTR  HB3  CB   CG   109.30  3.000
 PTR  HB2  CB   CG   109.69  3.000
 PTR  HB3  CB   CA   108.02  3.000
 PTR  HB2  CB   CA   108.61  3.000
 PTR  CG   CB   CA   114.67  3.000
 PTR  CD2  CG   CD1  117.06  3.000
 PTR  CD2  CG   CB   121.09  3.000
 PTR  CD1  CG   CB   121.85  3.000
 PTR  HD1  CD1  CE1  118.97  3.000
 PTR  HD1  CD1  CG   119.40  3.000
 PTR  CE1  CD1  CG   121.60  3.000
 PTR  HD2  CD2  CE2  118.95  3.000
 PTR  HD2  CD2  CG   119.12  3.000
 PTR  CE2  CD2  CG   121.92  3.000
 PTR  HE1  CE1  CZ   119.23  3.000
 PTR  HE1  CE1  CD1  119.74  3.000
 PTR  CZ   CE1  CD1  121.03  3.000
 PTR  HE2  CE2  CZ   119.16  3.000
 PTR  HE2  CE2  CD2  120.05  3.000
 PTR  CZ   CE2  CD2  120.79  3.000
 PTR  OH   CZ   CE2  122.03  3.000
 PTR  OH   CZ   CE1  120.40  3.000
 PTR  CE2  CZ   CE1  117.56  3.000
 PTR  P    OH   CZ   118.65  3.000
 PTR  O3P  P    O2P  116.26  3.000
 PTR  O3P  P    O1P  115.01  3.000
 PTR  O2P  P    O1P  115.39  3.000
 PTR  O3P  P    OH   102.80  3.000
 PTR  O2P  P    OH    99.92  3.000
 PTR  O1P  P    OH   104.35  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
 PTR  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PTR  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PTR  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PTR  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PTR  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PTR  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PTR  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PTR  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PTR  CONST_09  OH   CZ   CE1  CD1  180.00   0.0  0
 PTR  CONST_10  OH   CZ   CE2  CD2  180.00   0.0  0
 PTR  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 PTR  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 PTR  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 PTR  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 PTR  Var_01    CD1  CG   CB   CA   -90.53  30.0  2
 PTR  Var_02    O1P  P    OH   CZ   -65.82  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
 PTR  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
 PTR  plan-1  CB   0.020
 PTR  plan-1  CG   0.020
 PTR  plan-1  CD1  0.020
 PTR  plan-1  CD2  0.020
 PTR  plan-1  CE1  0.020
 PTR  plan-1  CE2  0.020
 PTR  plan-1  CZ   0.020
 PTR  plan-1  OH   0.020
 PTR  plan-1  HD1  0.020
 PTR  plan-1  HD2  0.020
 PTR  plan-1  HE1  0.020
 PTR  plan-1  HE2  0.020
 PTR  plan-2  CA   0.020
 PTR  plan-2  C    0.020
 PTR  plan-2  O    0.020
 PTR  plan-2  OXT  0.020

