# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:04:01 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-iodo-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(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
 IYR  IYR  '3-iodo-L-tyrosine        '  L-peptide  23  14  .  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_IYR
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
 IYR  N    N  NH2    0  -0.813  25.7690  60.6549  28.2543
 IYR  CA   C  CH1    0  -0.199  25.4802  59.2893  27.8322
 IYR  CB   C  CH2    0  -0.501  25.9133  58.3184  28.9367
 IYR  CC   C  CR6    0   0.132  26.1177  56.9001  28.4799
 IYR  CD   C  CR16   0  -0.269  27.2121  56.5807  27.6808
 IYR  CE   C  CR6    0  -0.320  27.4327  55.2802  27.2514
 IYR  IE   I  I      0   0.039  29.0991  54.8521  26.0443
 IYR  CF   C  CR6    0   0.401  26.5721  54.2477  27.6149
 IYR  OF   O  OH1    0  -0.617  26.8250  53.0014  27.1799
 IYR  CG   C  CR16   0  -0.369  25.4818  54.5631  28.4239
 IYR  CH   C  CR16   0  -0.284  25.2599  55.8657  28.8386
 IYR  C    C  C      0   0.417  23.9826  59.1763  27.4510
 IYR  O    O  O      0  -0.612  23.5043  60.1559  26.8411
 IYR  OXT  O  OC    -1  -0.586  23.3880  58.1238  27.7473
 IYR  H    H  HNH2   0   0.332  25.3190  61.2838  27.6020
 IYR  H2   H  HNH2   0   0.330  26.7640  60.8287  28.1869
 IYR  HA   H  HCH1   0   0.202  26.0419  59.0176  26.9196
 IYR  HB2  H  HCH2   0   0.228  26.8628  58.6786  29.3465
 IYR  HB3  H  HCH2   0   0.231  25.1962  58.3470  29.7597
 IYR  HD   H  HCR6   0   0.263  27.9052  57.3634  27.3958
 IYR  HF   H  HOH1   0   0.478  26.1609  52.3882  27.5160
 IYR  HG   H  HCR6   0   0.271  24.7984  53.7762  28.7244
 IYR  HH   H  HCR6   0   0.245  24.3997  56.0790  29.4581

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
 IYR  N   CA   single    1.458  0.019  1.458
 IYR  N   H    single    0.860  0.020  0.860
 IYR  N   H2   single    0.890  0.020  1.040
 IYR  CA  CB   single    1.530  0.020  1.530
 IYR  CA  C    single    1.525  0.021  1.525
 IYR  CA  HA   single    0.970  0.020  0.970
 IYR  CB  CC   single    1.504  0.020  1.504
 IYR  CB  HB2  single    0.970  0.020  1.090
 IYR  CB  HB3  single    0.970  0.020  1.090
 IYR  CC  CD   aromatic  1.392  0.020  1.392
 IYR  CC  CH   aromatic  1.391  0.020  1.391
 IYR  CD  CE   aromatic  1.387  0.020  1.387
 IYR  CD  HD   single    0.930  0.020  1.080
 IYR  CE  IE   single    2.102  0.020  2.102
 IYR  CE  CF   aromatic  1.392  0.020  1.392
 IYR  CF  OF   single    1.344  0.020  1.344
 IYR  CF  CG   aromatic  1.394  0.020  1.394
 IYR  OF  HF   single    0.850  0.020  0.980
 IYR  CG  CH   aromatic  1.385  0.020  1.385
 IYR  CG  HG   single    0.930  0.020  1.080
 IYR  CH  HH   single    0.930  0.020  1.080
 IYR  C   O    deloc     1.231  0.020  1.231
 IYR  C   OXT  deloc     1.245  0.020  1.245

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
 IYR  H2   N   H    106.71  3.000
 IYR  H2   N   CA   109.64  3.000
 IYR  H    N   CA   114.00  3.000
 IYR  HA   CA  C    109.00  3.000
 IYR  HA   CA  CB   109.00  3.000
 IYR  C    CA  CB   110.10  1.900
 IYR  HA   CA  N    110.00  3.000
 IYR  C    CA  N    111.00  2.800
 IYR  CB   CA  N    110.50  1.700
 IYR  HB3  CB  HB2  106.18  3.000
 IYR  HB3  CB  CC   110.05  3.000
 IYR  HB2  CB  CC   107.82  3.000
 IYR  HB3  CB  CA   109.94  3.000
 IYR  HB2  CB  CA   107.83  3.000
 IYR  CC   CB  CA   114.63  3.000
 IYR  CH   CC  CD   117.53  3.000
 IYR  CH   CC  CB   122.63  3.000
 IYR  CD   CC  CB   119.83  3.000
 IYR  HD   CD  CE   119.61  3.000
 IYR  HD   CD  CC   119.21  3.000
 IYR  CE   CD  CC   121.18  3.000
 IYR  CF   CE  IE   119.27  3.000
 IYR  CF   CE  CD   121.07  3.000
 IYR  IE   CE  CD   119.66  3.000
 IYR  CG   CF  OF   123.01  3.000
 IYR  CG   CF  CE   117.85  3.000
 IYR  OF   CF  CE   119.13  3.000
 IYR  HF   OF  CF   110.32  3.000
 IYR  HG   CG  CH   119.89  3.000
 IYR  HG   CG  CF   119.31  3.000
 IYR  CH   CG  CF   120.80  3.000
 IYR  HH   CH  CG   118.99  3.000
 IYR  HH   CH  CC   119.45  3.000
 IYR  CG   CH  CC   121.56  3.000
 IYR  OXT  C   O    126.62  3.000
 IYR  OXT  C   CA   117.70  3.000
 IYR  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
 IYR  CONST_01  CF  CE  CD  CC    0.00   0.0  0
 IYR  CONST_02  CF  CG  CH  CC    0.00   0.0  0
 IYR  CONST_03  CG  CH  CC  CD    0.00   0.0  0
 IYR  CONST_04  CG  CF  CE  CD    0.00   0.0  0
 IYR  CONST_05  CH  CC  CD  CE    0.00   0.0  0
 IYR  CONST_06  CH  CG  CF  CE    0.00   0.0  0
 IYR  CONST_07  CE  CD  CC  CB  180.00   0.0  0
 IYR  CONST_08  CG  CH  CC  CB  180.00   0.0  0
 IYR  CONST_09  IE  CE  CD  CC  180.00   0.0  0
 IYR  CONST_10  OF  CF  CE  CD  180.00   0.0  0
 IYR  CONST_11  CG  CF  CE  IE  180.00   0.0  0
 IYR  CONST_12  CH  CG  CF  OF  180.00   0.0  0
 IYR  CONST_13  HG  CG  CH  CC  180.00   0.0  0
 IYR  CONST_14  HH  CH  CC  CD  180.00   0.0  0
 IYR  CONST_15  HD  CD  CE  CF  180.00   0.0  0
 IYR  Var_01    CD  CC  CB  CA   71.24  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
 IYR  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
 IYR  plan-1  CB   0.020
 IYR  plan-1  CC   0.020
 IYR  plan-1  CD   0.020
 IYR  plan-1  CE   0.020
 IYR  plan-1  IE   0.020
 IYR  plan-1  CF   0.020
 IYR  plan-1  OF   0.020
 IYR  plan-1  CG   0.020
 IYR  plan-1  CH   0.020
 IYR  plan-1  HD   0.020
 IYR  plan-1  HG   0.020
 IYR  plan-1  HH   0.020
 IYR  plan-2  CA   0.020
 IYR  plan-2  C    0.020
 IYR  plan-2  O    0.020
 IYR  plan-2  OXT  0.020

