# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 00:26:32 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3,5-diiodo-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(I)c(O)c(I)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
 TYI  TYI  '3,5-diiodo-L-tyrosine    '  L-peptide  23  15  .  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_TYI
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
 TYI  N    N  NH2    0  -0.809  13.8210  18.8244  29.3110
 TYI  CA   C  CH1    0  -0.208  14.4317  17.9896  30.3312
 TYI  CB   C  CH2    0  -0.490  14.0516  16.5204  30.1123
 TYI  CG   C  C      0   0.119  12.5677  16.2968  30.1764
 TYI  CD1  C  C1     0  -0.266  11.7707  16.3805  29.0384
 TYI  CE1  C  C      0  -0.323  10.4003  16.2097  29.1201
 TYI  CD2  C  C1     0  -0.277  11.9419  16.0424  31.3907
 TYI  CE2  C  C      0  -0.332  10.5673  15.8724  31.4666
 TYI  CZ   C  C      0   0.457   9.7554  15.9510  30.3322
 TYI  OH   O  OH1    0  -0.596   8.4286  15.7958  30.3147
 TYI  C    C  C      0   0.414  15.9740  18.1748  30.3578
 TYI  O    O  O      0  -0.602  16.6229  17.3002  30.9629
 TYI  OXT  O  OC    -1  -0.596  16.4284  19.1977  29.8088
 TYI  I1   I  I      0   0.069   9.2441  16.3324  27.3704
 TYI  I2   I  I      0   0.078   9.7128  15.4747  33.3520
 TYI  H    H  HNH2   0   0.336  14.3535  19.6824  29.2504
 TYI  H2   H  HNH2   0   0.333  12.8779  19.0745  29.5762
 TYI  HA   H  HCH1   0   0.204  14.0901  18.2594  31.3461
 TYI  HB2  H  HCH2   0   0.230  14.4294  16.1994  29.1379
 TYI  HB3  H  HCH2   0   0.237  14.5441  15.9098  30.8689
 TYI  HD1  H  H      0   0.271  12.2346  16.5780  28.0812
 TYI  HD2  H  H      0   0.276  12.5431  15.9723  32.2888
 TYI  HH   H  HOH1   0   0.475   8.0670  15.6119  31.1913

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
 TYI  N    CA   single    1.458  0.019  1.458
 TYI  N    H    single    0.860  0.020  0.860
 TYI  N    H2   single    0.890  0.020  1.040
 TYI  CA   CB   single    1.530  0.020  1.530
 TYI  CA   C    single    1.525  0.021  1.525
 TYI  CA   HA   single    0.970  0.020  0.970
 TYI  CB   CG   single    1.502  0.020  1.502
 TYI  CB   HB2  single    0.970  0.020  1.090
 TYI  CB   HB3  single    0.970  0.020  1.090
 TYI  CG   CD1  aromatic  1.392  0.020  1.392
 TYI  CG   CD2  aromatic  1.390  0.020  1.390
 TYI  CD1  CE1  aromatic  1.383  0.020  1.383
 TYI  CD1  HD1  single    0.930  0.020  1.080
 TYI  CE1  CZ   aromatic  1.397  0.020  1.397
 TYI  CE1  I1   single    2.101  0.020  2.101
 TYI  CD2  CE2  aromatic  1.387  0.020  1.387
 TYI  CD2  HD2  single    0.930  0.020  1.080
 TYI  CE2  CZ   aromatic  1.397  0.020  1.397
 TYI  CE2  I2   single    2.108  0.020  2.108
 TYI  CZ   OH   single    1.336  0.020  1.336
 TYI  OH   HH   single    0.850  0.020  0.980
 TYI  C    O    deloc     1.231  0.020  1.231
 TYI  C    OXT  deloc     1.247  0.020  1.247

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
 TYI  H2   N    H    107.28  3.000
 TYI  H2   N    CA   110.49  3.000
 TYI  H    N    CA   114.00  3.000
 TYI  HA   CA   C    109.00  3.000
 TYI  HA   CA   CB   109.00  3.000
 TYI  C    CA   CB   110.10  1.900
 TYI  HA   CA   N    110.00  3.000
 TYI  C    CA   N    111.00  2.800
 TYI  CB   CA   N    110.50  1.700
 TYI  HB3  CB   HB2  107.35  3.000
 TYI  HB3  CB   CG   109.47  3.000
 TYI  HB2  CB   CG   109.62  3.000
 TYI  HB3  CB   CA   109.01  3.000
 TYI  HB2  CB   CA   108.84  3.000
 TYI  CG   CB   CA   112.42  3.000
 TYI  CD2  CG   CD1  117.88  3.000
 TYI  CD2  CG   CB   120.63  3.000
 TYI  CD1  CG   CB   121.46  3.000
 TYI  HD1  CD1  CE1  119.97  3.000
 TYI  HD1  CD1  CG   119.26  3.000
 TYI  CE1  CD1  CG   120.77  3.000
 TYI  I1   CE1  CZ   118.64  3.000
 TYI  I1   CE1  CD1  119.26  3.000
 TYI  CZ   CE1  CD1  122.09  3.000
 TYI  HD2  CD2  CE2  119.79  3.000
 TYI  HD2  CD2  CG   119.11  3.000
 TYI  CE2  CD2  CG   121.10  3.000
 TYI  I2   CE2  CZ   120.08  3.000
 TYI  I2   CE2  CD2  118.28  3.000
 TYI  CZ   CE2  CD2  121.64  3.000
 TYI  OH   CZ   CE2  125.54  3.000
 TYI  OH   CZ   CE1  117.94  3.000
 TYI  CE2  CZ   CE1  116.52  3.000
 TYI  HH   OH   CZ   112.46  3.000
 TYI  OXT  C    O    126.87  3.000
 TYI  OXT  C    CA   116.88  3.000
 TYI  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
 TYI  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 TYI  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 TYI  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 TYI  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 TYI  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 TYI  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 TYI  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 TYI  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 TYI  CONST_09  I1   CE1  CD1  CG   180.00   0.0  0
 TYI  CONST_10  I2   CE2  CD2  CG   180.00   0.0  0
 TYI  CONST_11  OH   CZ   CE1  CD1  180.00   0.0  0
 TYI  CONST_12  I2   CE2  CZ   CE1  180.00   0.0  0
 TYI  CONST_13  OH   CZ   CE2  CD2  180.00   0.0  0
 TYI  CONST_14  I1   CE1  CZ   CE2  180.00   0.0  0
 TYI  CONST_15  HD2  CD2  CG   CD1  180.00   0.0  0
 TYI  CONST_16  HD1  CD1  CG   CD2  180.00   0.0  0
 TYI  Var_01    CD1  CG   CB   CA    90.14  30.0  2

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
 TYI  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
 TYI  plan-1  CB   0.020
 TYI  plan-1  CG   0.020
 TYI  plan-1  CD1  0.020
 TYI  plan-1  CE1  0.020
 TYI  plan-1  CD2  0.020
 TYI  plan-1  CE2  0.020
 TYI  plan-1  CZ   0.020
 TYI  plan-1  OH   0.020
 TYI  plan-1  I1   0.020
 TYI  plan-1  I2   0.020
 TYI  plan-1  HD1  0.020
 TYI  plan-1  HD2  0.020
 TYI  plan-2  CA   0.020
 TYI  plan-2  C    0.020
 TYI  plan-2  O    0.020
 TYI  plan-2  OXT  0.020

