# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 17:16:14 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: D-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc(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
 DTY  DTY  'D-tyrosine               '  D-peptide  23  13  .  2022-09-22  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_DTY
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
 DTY  N    N  NH2    0  -0.811  -0.3568  -1.8989   1.3446
 DTY  CA   C  CH1    0  -0.159   0.8999  -1.2372   0.9989
 DTY  C    C  C      0   0.407   2.0433  -2.2780   1.0221
 DTY  O    O  O      0  -0.608   1.9992  -3.1779   0.1606
 DTY  CB   C  CH2    0  -0.503   0.7513  -0.6118  -0.3890
 DTY  CG   C  CR6    0   0.099   1.9570   0.1810  -0.8072
 DTY  CD1  C  CR16   0  -0.302   2.1075   1.5125  -0.4306
 DTY  CD2  C  CR16   0  -0.286   2.9797  -0.3926  -1.5606
 DTY  CE1  C  CR16   0  -0.371   3.2285   2.2497  -0.7865
 DTY  CE2  C  CR16   0  -0.326   4.1061   0.3273  -1.9283
 DTY  CZ   C  CR6    0   0.333   4.2377   1.6581  -1.5408
 DTY  OH   O  OH1    0  -0.638   5.3512   2.3230  -1.9213
 DTY  OXT  O  OC    -1  -0.618   2.9089  -2.1450   1.9114
 DTY  H    H  HNH2   0   0.336  -1.0858  -1.1986   1.4198
 DTY  H2   H  HNH2   0   0.338  -0.2835  -2.3028   2.2710
 DTY  HA   H  HCH1   0   0.177   1.1552  -0.4336   1.7067
 DTY  HB2  H  HCH2   0   0.228   0.5563  -1.4098  -1.1077
 DTY  HB3  H  HCH2   0   0.227  -0.1278   0.0413  -0.3873
 DTY  HD1  H  HCR6   0   0.245   1.3301   1.9946   0.1514
 DTY  HD2  H  HCR6   0   0.243   2.8954  -1.4291  -1.8626
 DTY  HE1  H  HCR6   0   0.264   3.3127   3.2860  -0.4778
 DTY  HE2  H  HCR6   0   0.255   4.8851  -0.1411  -2.5175
 DTY  HH   H  HOH1   0   0.471   5.3240   3.2295  -1.5964

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
 DTY  N    CA   single    1.458  0.019  1.458
 DTY  N    H    single    0.860  0.020  0.860
 DTY  N    H2   single    0.890  0.020  1.040
 DTY  CA   C    single    1.525  0.021  1.525
 DTY  CA   CB   single    1.521  0.033  1.521
 DTY  CA   HA   single    0.970  0.020  0.970
 DTY  C    O    deloc     1.231  0.020  1.231
 DTY  C    OXT  deloc     1.248  0.020  1.248
 DTY  CB   CG   single    1.502  0.020  1.502
 DTY  CB   HB2  single    0.970  0.020  1.090
 DTY  CB   HB3  single    0.970  0.020  1.090
 DTY  CG   CD1  aromatic  1.392  0.020  1.392
 DTY  CG   CD2  aromatic  1.394  0.020  1.394
 DTY  CD1  CE1  aromatic  1.388  0.020  1.388
 DTY  CD1  HD1  single    0.930  0.020  1.080
 DTY  CD2  CE2  aromatic  1.386  0.020  1.386
 DTY  CD2  HD2  single    0.930  0.020  1.080
 DTY  CE1  CZ   aromatic  1.392  0.020  1.392
 DTY  CE1  HE1  single    0.930  0.020  1.080
 DTY  CE2  CZ   aromatic  1.392  0.020  1.392
 DTY  CE2  HE2  single    0.930  0.020  1.080
 DTY  CZ   OH   single    1.352  0.020  1.352
 DTY  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
 DTY  H2   N    H    105.05  3.000
 DTY  H2   N    CA   109.54  3.000
 DTY  H    N    CA   114.00  3.000
 DTY  HA   CA   CB   109.00  3.000
 DTY  HA   CA   C    110.00  3.000
 DTY  CB   CA   C    110.50  1.500
 DTY  HA   CA   N    110.00  3.000
 DTY  CB   CA   N    110.40  1.500
 DTY  C    CA   N    111.00  2.800
 DTY  OXT  C    O    126.44  3.000
 DTY  OXT  C    CA   120.80  1.700
 DTY  O    C    CA   120.80  1.700
 DTY  HB3  CB   HB2  107.08  3.000
 DTY  HB3  CB   CG   109.26  3.000
 DTY  HB2  CB   CG   110.24  3.000
 DTY  HB3  CB   CA   108.69  3.000
 DTY  HB2  CB   CA   108.42  3.000
 DTY  CG   CB   CA   112.97  3.000
 DTY  CD2  CG   CD1  117.43  3.000
 DTY  CD2  CG   CB   121.47  3.000
 DTY  CD1  CG   CB   121.09  3.000
 DTY  HD1  CD1  CE1  118.72  3.000
 DTY  HD1  CD1  CG   119.54  3.000
 DTY  CE1  CD1  CG   121.74  3.000
 DTY  HD2  CD2  CE2  119.09  3.000
 DTY  HD2  CD2  CG   119.18  3.000
 DTY  CE2  CD2  CG   121.72  3.000
 DTY  HE1  CE1  CZ   120.27  3.000
 DTY  HE1  CE1  CD1  119.81  3.000
 DTY  CZ   CE1  CD1  119.92  3.000
 DTY  HE2  CE2  CZ   119.78  3.000
 DTY  HE2  CE2  CD2  120.27  3.000
 DTY  CZ   CE2  CD2  119.95  3.000
 DTY  OH   CZ   CE2  118.02  3.000
 DTY  OH   CZ   CE1  122.74  3.000
 DTY  CE2  CZ   CE1  119.25  3.000
 DTY  HH   OH   CZ   110.16  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
 DTY  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 DTY  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 DTY  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 DTY  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 DTY  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 DTY  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 DTY  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 DTY  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 DTY  CONST_09  OH   CZ   CE1  CD1  180.00   0.0  0
 DTY  CONST_10  OH   CZ   CE2  CD2  180.00   0.0  0
 DTY  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 DTY  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 DTY  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 DTY  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 DTY  Var_01    CD1  CG   CB   CA   -85.17  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
 DTY  chir_01  CA  N  C  CB  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
 DTY  plan-1  CB   0.020
 DTY  plan-1  CG   0.020
 DTY  plan-1  CD1  0.020
 DTY  plan-1  CD2  0.020
 DTY  plan-1  CE1  0.020
 DTY  plan-1  CE2  0.020
 DTY  plan-1  CZ   0.020
 DTY  plan-1  OH   0.020
 DTY  plan-1  HD1  0.020
 DTY  plan-1  HD2  0.020
 DTY  plan-1  HE1  0.020
 DTY  plan-1  HE2  0.020
 DTY  plan-2  CA   0.020
 DTY  plan-2  C    0.020
 DTY  plan-2  O    0.020
 DTY  plan-2  OXT  0.020

