# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 00:32:13 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-amino-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)c(N)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
 TY2  TY2  '3-amino-L-tyrosine       '  L-peptide  25  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 PERFECT (side chain)
;

data_comp_TY2
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
 TY2  N     N  NH2    0  -0.798  1.5024  27.8639  41.2758
 TY2  CA    C  CH1    0  -0.173  2.0607  29.2050  41.4084
 TY2  C     C  C      0   0.412  1.3654  30.1315  40.3857
 TY2  O     O  O      0  -0.614  1.4469  29.7658  39.1926
 TY2  CB    C  CH2    0  -0.527  3.5883  29.2342  41.2098
 TY2  CG    C  CR6    0   0.125  4.2085  30.5845  41.4318
 TY2  CD1   C  CR16   0  -0.340  4.5815  30.9959  42.7050
 TY2  CD2   C  CR16   0  -0.372  4.4023  31.4666  40.3701
 TY2  CE1   C  CR16   0  -0.364  5.1339  32.2571  42.9049
 TY2  CE2   C  CR6    0   0.234  4.9495  32.7353  40.5447
 TY2  CZ    C  CR6    0   0.280  5.3183  33.1259  41.8429
 TY2  OH    O  OH1    0  -0.641  5.8553  34.3665  41.9734
 TY2  NE2   N  NH2    0  -0.852  5.0812  33.6258  39.4878
 TY2  OXT   O  OC    -1  -0.603  0.7943  31.1498  40.8175
 TY2  HN1   H  HNH2   0   0.325  1.6250  27.5651  40.3151
 TY2  HA2   H  HNH2   0   0.331  2.0362  27.2134  41.8411
 TY2  HB    H  HCH1   0   0.194  1.8441  29.5639  42.4196
 TY2  HA1   H  HCH2   0   0.225  4.0349  28.5130  41.9020
 TY2  HB2   H  HCH2   0   0.221  3.8072  28.8770  40.1998
 TY2  HA    H  HCR6   0   0.234  4.4523  30.3316  43.5512
 TY2  HC    H  HCR6   0   0.236  4.1145  31.1609  39.3694
 TY2  HD    H  HCR6   0   0.256  5.4275  32.5657  43.9031
 TY2  HE21  H  HNH2   0   0.370  5.8529  34.2698  39.5677
 TY2  HE22  H  HNH2   0   0.371  5.0827  33.1841  38.5814
 TY2  HH    H  HOH1   0   0.470  6.1164  34.5229  42.8874

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
 TY2  N    CA    single    1.458  0.019  1.458
 TY2  CA   C     single    1.525  0.021  1.525
 TY2  CA   CB    single    1.530  0.020  1.530
 TY2  C    O     deloc     1.231  0.020  1.231
 TY2  C    OXT   deloc     1.245  0.020  1.245
 TY2  CB   CG    single    1.502  0.020  1.502
 TY2  CG   CD1   aromatic  1.389  0.020  1.389
 TY2  CG   CD2   aromatic  1.394  0.020  1.394
 TY2  CD1  CE1   aromatic  1.391  0.020  1.391
 TY2  CD2  CE2   aromatic  1.393  0.020  1.393
 TY2  CE1  CZ    aromatic  1.384  0.020  1.384
 TY2  CE2  CZ    aromatic  1.405  0.020  1.405
 TY2  CE2  NE2   single    1.388  0.020  1.388
 TY2  CZ   OH    single    1.358  0.020  1.358
 TY2  N    HN1   single    0.890  0.020  1.040
 TY2  N    HA2   single    0.890  0.020  1.040
 TY2  CA   HB    single    0.970  0.020  1.090
 TY2  CB   HA1   single    0.970  0.020  1.090
 TY2  CB   HB2   single    0.970  0.020  1.090
 TY2  CD1  HA    single    0.930  0.020  1.080
 TY2  CD2  HC    single    0.930  0.020  1.080
 TY2  CE1  HD    single    0.930  0.020  1.080
 TY2  NE2  HE21  single    0.890  0.020  1.040
 TY2  NE2  HE22  single    0.890  0.020  1.040
 TY2  OH   HH    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
 TY2  HA2   N    HN1   106.01  3.000
 TY2  HA2   N    CA    109.74  3.000
 TY2  HN1   N    CA    108.11  3.000
 TY2  HB    CA   CB    108.00  3.000
 TY2  HB    CA   C     109.01  3.000
 TY2  CB    CA   C     110.10  1.900
 TY2  HB    CA   N     108.04  3.000
 TY2  CB    CA   N     110.50  1.700
 TY2  C     CA   N     111.00  2.800
 TY2  OXT   C    O     126.88  3.000
 TY2  OXT   C    CA    117.86  3.000
 TY2  O     C    CA    120.80  1.700
 TY2  HB2   CB   HA1   106.69  3.000
 TY2  HB2   CB   CG    110.33  3.000
 TY2  HA1   CB   CG    109.28  3.000
 TY2  HB2   CB   CA    108.14  3.000
 TY2  HA1   CB   CA    108.09  3.000
 TY2  CG    CB   CA    114.03  3.000
 TY2  CD2   CG   CD1   118.25  3.000
 TY2  CD2   CG   CB    120.91  3.000
 TY2  CD1   CG   CB    120.83  3.000
 TY2  HA    CD1  CE1   119.39  3.000
 TY2  HA    CD1  CG    120.15  3.000
 TY2  CE1   CD1  CG    120.45  3.000
 TY2  HC    CD2  CE2   118.45  3.000
 TY2  HC    CD2  CG    119.16  3.000
 TY2  CE2   CD2  CG    122.39  3.000
 TY2  HD    CE1  CZ    119.41  3.000
 TY2  HD    CE1  CD1   119.83  3.000
 TY2  CZ    CE1  CD1   120.77  3.000
 TY2  NE2   CE2  CZ    120.01  3.000
 TY2  NE2   CE2  CD2   121.75  3.000
 TY2  CZ    CE2  CD2   118.18  3.000
 TY2  OH    CZ   CE2   116.52  3.000
 TY2  OH    CZ   CE1   123.52  3.000
 TY2  CE2   CZ   CE1   119.96  3.000
 TY2  HH    OH   CZ    110.27  3.000
 TY2  HE22  NE2  HE21  110.48  3.000
 TY2  HE22  NE2  CE2   113.80  3.000
 TY2  HE21  NE2  CE2   114.96  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
 TY2  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 TY2  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 TY2  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 TY2  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 TY2  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 TY2  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 TY2  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 TY2  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 TY2  CONST_09  NE2  CE2  CD2  CG   180.00   0.0  0
 TY2  CONST_10  OH   CZ   CE1  CD1  180.00   0.0  0
 TY2  CONST_11  OH   CZ   CE2  CD2  180.00   0.0  0
 TY2  CONST_12  NE2  CE2  CZ   CE1  180.00   0.0  0
 TY2  CONST_13  HD   CE1  CD1  CG   180.00   0.0  0
 TY2  CONST_14  HC   CD2  CG   CD1  180.00   0.0  0
 TY2  CONST_15  HA   CD1  CG   CD2  180.00   0.0  0
 TY2  Var_01    CD1  CG   CB   CA    85.98  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
 TY2  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
 TY2  plan-1  CB    0.020
 TY2  plan-1  CG    0.020
 TY2  plan-1  CD1   0.020
 TY2  plan-1  CD2   0.020
 TY2  plan-1  CE1   0.020
 TY2  plan-1  CE2   0.020
 TY2  plan-1  CZ    0.020
 TY2  plan-1  OH    0.020
 TY2  plan-1  NE2   0.020
 TY2  plan-1  HA    0.020
 TY2  plan-1  HC    0.020
 TY2  plan-1  HD    0.020
 TY2  plan-2  CE2   0.020
 TY2  plan-2  NE2   0.020
 TY2  plan-2  HE21  0.020
 TY2  plan-2  HE22  0.020
 TY2  plan-3  CA    0.020
 TY2  plan-3  C     0.020
 TY2  plan-3  O     0.020
 TY2  plan-3  OXT   0.020

