# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 00:48:07 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: O-sulfo-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O[S](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
 TYS  TYS  'O-sulfo-L-tyrosine       '  L-peptide  26  17  .  2013-08-12  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_TYS
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
 TYS  N    N  NH2    0  -0.780  15.8632   1.7649  -4.6295
 TYS  CA   C  CH1    0  -0.209  16.5342   1.7829  -3.3402
 TYS  CB   C  CH2    0  -0.517  15.4953   1.7642  -2.2104
 TYS  CG   C  C      0   0.164  14.5635   2.9421  -2.2238
 TYS  CD1  C  C1     0  -0.307  15.0107   4.1988  -1.8181
 TYS  CD2  C  C1     0  -0.327  13.2400   2.8260  -2.6372
 TYS  CE1  C  C1     0  -0.296  14.1661   5.2977  -1.8042
 TYS  CE2  C  C1     0  -0.301  12.3785   3.9149  -2.6217
 TYS  CZ   C  C      0   0.315  12.8428   5.1535  -2.2033
 TYS  OH   O  OC2    0  -0.633  12.0050   6.2381  -2.2137
 TYS  S    S  S      0   1.552  11.1881   6.5797  -0.7876
 TYS  O1   O  OS     0  -0.720  12.2391   6.8170   0.2006
 TYS  O2   O  OS     0  -0.720  10.3813   5.3896  -0.5269
 TYS  O3   O  OS    -1  -0.718  10.4412   7.7641  -1.1949
 TYS  C    C  C      0   0.381  17.5729   0.6506  -3.1027
 TYS  O    O  O      0  -0.615  18.2568   0.7567  -2.0632
 TYS  OXT  O  OC    -1  -0.597  17.6329  -0.2598  -3.9506
 TYS  H    H  HNH2   0   0.332  16.5603   1.8727  -5.3565
 TYS  HN2  H  HNH2   0   0.321  15.4919   0.8328  -4.7775
 TYS  HA   H  HCH1   0   0.215  17.0771   2.7334  -3.2668
 TYS  HB2  H  HCH2   0   0.230  14.9141   0.8381  -2.2754
 TYS  HB3  H  HCH2   0   0.240  16.0251   1.7335  -1.2569
 TYS  HD1  H  H      0   0.242  16.0392   4.3204  -1.4962
 TYS  HD2  H  H      0   0.241  12.8679   1.8627  -2.9652
 TYS  HE1  H  H      0   0.254  14.5319   6.2653  -1.4860
 TYS  HE2  H  H      0   0.254  11.3506   3.8044  -2.9427

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
 TYS  N    CA   single    1.458  0.019  1.458
 TYS  N    H    single    0.860  0.020  0.860
 TYS  N    HN2  single    0.890  0.020  1.040
 TYS  CA   CB   single    1.530  0.020  1.530
 TYS  CA   C    single    1.525  0.021  1.525
 TYS  CA   HA   single    0.970  0.020  0.970
 TYS  CB   CG   single    1.502  0.020  1.502
 TYS  CB   HB2  single    0.970  0.020  1.090
 TYS  CB   HB3  single    0.970  0.020  1.090
 TYS  CG   CD1  aromatic  1.394  0.020  1.394
 TYS  CG   CD2  aromatic  1.391  0.020  1.391
 TYS  CD1  CE1  aromatic  1.386  0.020  1.386
 TYS  CD1  HD1  single    0.930  0.020  1.080
 TYS  CD2  CE2  aromatic  1.389  0.020  1.389
 TYS  CD2  HD2  single    0.930  0.020  1.080
 TYS  CE1  CZ   aromatic  1.390  0.020  1.390
 TYS  CE1  HE1  single    0.930  0.020  1.080
 TYS  CE2  CZ   aromatic  1.387  0.020  1.387
 TYS  CE2  HE2  single    0.930  0.020  1.080
 TYS  CZ   OH   single    1.371  0.020  1.371
 TYS  OH   S    single    1.679  0.020  1.679
 TYS  S    O1   deloc     1.462  0.020  1.462
 TYS  S    O2   deloc     1.461  0.020  1.461
 TYS  S    O3   deloc     1.458  0.020  1.458
 TYS  C    O    deloc     1.231  0.020  1.231
 TYS  C    OXT  deloc     1.246  0.020  1.246

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
 TYS  HN2  N    H    104.18  3.000
 TYS  HN2  N    CA   108.05  3.000
 TYS  H    N    CA   114.00  3.000
 TYS  HA   CA   C    109.00  3.000
 TYS  HA   CA   CB   109.00  3.000
 TYS  C    CA   CB   110.10  1.900
 TYS  HA   CA   N    110.00  3.000
 TYS  C    CA   N    111.00  2.800
 TYS  CB   CA   N    110.50  1.700
 TYS  HB3  CB   HB2  106.60  3.000
 TYS  HB3  CB   CG   109.33  3.000
 TYS  HB2  CB   CG   109.47  3.000
 TYS  HB3  CB   CA   108.36  3.000
 TYS  HB2  CB   CA   109.01  3.000
 TYS  CG   CB   CA   113.82  3.000
 TYS  CD2  CG   CD1  117.82  3.000
 TYS  CD2  CG   CB   121.83  3.000
 TYS  CD1  CG   CB   120.36  3.000
 TYS  HD1  CD1  CE1  119.08  3.000
 TYS  HD1  CD1  CG   119.44  3.000
 TYS  CE1  CD1  CG   121.48  3.000
 TYS  HD2  CD2  CE2  119.18  3.000
 TYS  HD2  CD2  CG   119.39  3.000
 TYS  CE2  CD2  CG   121.43  3.000
 TYS  HE1  CE1  CZ   119.94  3.000
 TYS  HE1  CE1  CD1  120.38  3.000
 TYS  CZ   CE1  CD1  119.68  3.000
 TYS  HE2  CE2  CZ   119.89  3.000
 TYS  HE2  CE2  CD2  120.38  3.000
 TYS  CZ   CE2  CD2  119.73  3.000
 TYS  OH   CZ   CE2  119.98  3.000
 TYS  OH   CZ   CE1  120.14  3.000
 TYS  CE2  CZ   CE1  119.86  3.000
 TYS  S    OH   CZ   116.88  3.000
 TYS  O3   S    O2   115.38  3.000
 TYS  O3   S    O1   115.16  3.000
 TYS  O2   S    O1   114.11  3.000
 TYS  O3   S    OH   100.21  3.000
 TYS  O2   S    OH   104.74  3.000
 TYS  O1   S    OH   104.92  3.000
 TYS  OXT  C    O    127.04  3.000
 TYS  OXT  C    CA   117.42  3.000
 TYS  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
 TYS  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 TYS  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 TYS  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 TYS  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 TYS  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 TYS  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 TYS  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 TYS  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 TYS  CONST_09  OH   CZ   CE1  CD1  180.00   0.0  0
 TYS  CONST_10  OH   CZ   CE2  CD2  180.00   0.0  0
 TYS  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 TYS  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 TYS  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 TYS  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 TYS  Var_01    CD1  CG   CB   CA   -73.98  30.0  2
 TYS  Var_02    O1   S    OH   CZ    59.89  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
 TYS  chir_01  CA  N  CB  C  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
 TYS  plan-1  CB   0.020
 TYS  plan-1  CG   0.020
 TYS  plan-1  CD1  0.020
 TYS  plan-1  CD2  0.020
 TYS  plan-1  CE1  0.020
 TYS  plan-1  CE2  0.020
 TYS  plan-1  CZ   0.020
 TYS  plan-1  OH   0.020
 TYS  plan-1  HD1  0.020
 TYS  plan-1  HD2  0.020
 TYS  plan-1  HE1  0.020
 TYS  plan-1  HE2  0.020
 TYS  plan-2  CA   0.020
 TYS  plan-2  C    0.020
 TYS  plan-2  O    0.020
 TYS  plan-2  OXT  0.020

