# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:57:24 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-bromo-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)c(Br)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
 BYR  BYR  '3-bromo-L-tyrosine       '  L-peptide  23  14  .  2016-04-22  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_BYR
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
 BYR  N    N   NH2    0  -0.785  -31.5327  -5.9284  -32.0181
 BYR  CA   C   CH1    0  -0.216  -30.0830  -5.8264  -31.9654
 BYR  CB   C   CH2    0  -0.487  -29.5397  -5.4797  -33.3622
 BYR  CG   C   CR6    0   0.091  -30.0414  -4.1616  -33.8817
 BYR  CD2  C   CR16   0  -0.270  -29.4533  -2.9661  -33.4847
 BYR  CE2  C   CR6    0  -0.215  -29.9391  -1.7476  -33.9369
 BYR  BR   BR  BR     0  -0.048  -29.0970  -0.1552  -33.3492
 BYR  CZ   C   CR6    0   0.377  -31.0285  -1.6754  -34.8069
 BYR  OH   O   OH1    0  -0.614  -31.5563  -0.5428  -35.2975
 BYR  CE1  C   CR16   0  -0.324  -31.6136  -2.8766  -35.2039
 BYR  CD1  C   CR16   0  -0.295  -31.1317  -4.0893  -34.7465
 BYR  C    C   C      0   0.391  -29.5029  -4.8569  -30.8991
 BYR  O    O   O      0  -0.596  -30.3067  -4.1650  -30.2466
 BYR  OXT  O   OC    -1  -0.617  -28.2570  -4.8589  -30.7918
 BYR  H    H   HNH2   0   0.334  -31.8659  -6.2505  -31.1176
 BYR  H2   H   HNH2   0   0.328  -31.9155  -4.9938  -32.1052
 BYR  HA   H   HCH1   0   0.221  -29.6961  -6.8249  -31.7304
 BYR  HB2  H   HCH2   0   0.233  -29.8329  -6.2709  -34.0558
 BYR  HB3  H   HCH2   0   0.237  -28.4502  -5.4768  -33.3246
 BYR  HD2  H   HCR6   0   0.266  -28.6007  -2.9890  -32.8173
 BYR  HH   H   HOH1   0   0.470  -31.0938   0.2433  -34.9830
 BYR  HE1  H   HCR6   0   0.268  -32.4576  -2.8430  -35.8819
 BYR  HD1  H   HCR6   0   0.251  -31.6112  -5.0021  -35.0783

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
 BYR  OH   CZ   single    1.342  0.020  1.342
 BYR  CE1  CZ   aromatic  1.394  0.020  1.394
 BYR  CE1  CD1  aromatic  1.383  0.020  1.383
 BYR  CZ   CE2  aromatic  1.396  0.020  1.396
 BYR  CD1  CG   aromatic  1.393  0.020  1.393
 BYR  CE2  CD2  aromatic  1.388  0.020  1.388
 BYR  CE2  BR   single    1.895  0.020  1.895
 BYR  CG   CD2  aromatic  1.390  0.020  1.390
 BYR  CG   CB   single    1.503  0.020  1.503
 BYR  CB   CA   single    1.530  0.020  1.530
 BYR  N    CA   single    1.458  0.019  1.458
 BYR  CA   C    single    1.525  0.021  1.525
 BYR  C    O    deloc     1.231  0.020  1.231
 BYR  C    OXT  deloc     1.251  0.020  1.251
 BYR  N    H    single    0.860  0.020  0.860
 BYR  N    H2   single    0.890  0.020  1.040
 BYR  CA   HA   single    0.970  0.020  0.970
 BYR  CB   HB2  single    0.970  0.020  1.090
 BYR  CB   HB3  single    0.970  0.020  1.090
 BYR  CD2  HD2  single    0.930  0.020  1.080
 BYR  OH   HH   single    0.850  0.020  0.980
 BYR  CE1  HE1  single    0.930  0.020  1.080
 BYR  CD1  HD1  single    0.930  0.020  1.080

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
 BYR  H2   N    H    104.20  3.000
 BYR  H2   N    CA   108.35  3.000
 BYR  H    N    CA   114.00  3.000
 BYR  HA   CA   C    109.00  3.000
 BYR  HA   CA   CB   109.00  3.000
 BYR  C    CA   CB   110.10  1.900
 BYR  HA   CA   N    110.00  3.000
 BYR  C    CA   N    111.00  2.800
 BYR  CB   CA   N    110.50  1.700
 BYR  HB3  CB   HB2  106.98  3.000
 BYR  HB3  CB   CG   110.07  3.000
 BYR  HB2  CB   CG   109.03  3.000
 BYR  HB3  CB   CA   108.80  3.000
 BYR  HB2  CB   CA   108.57  3.000
 BYR  CG   CB   CA   113.18  3.000
 BYR  CD1  CG   CD2  117.62  3.000
 BYR  CD2  CG   CB   120.94  3.000
 BYR  CD1  CG   CB   121.42  3.000
 BYR  HD2  CD2  CE2  119.67  3.000
 BYR  HD2  CD2  CG   119.40  3.000
 BYR  CE2  CD2  CG   120.93  3.000
 BYR  CZ   CE2  BR   119.78  3.000
 BYR  BR   CE2  CD2  118.77  3.000
 BYR  CZ   CE2  CD2  121.45  3.000
 BYR  CE1  CZ   OH   117.26  3.000
 BYR  CE1  CZ   CE2  117.42  3.000
 BYR  OH   CZ   CE2  125.32  3.000
 BYR  HH   OH   CZ   112.32  3.000
 BYR  HE1  CE1  CD1  120.39  3.000
 BYR  HE1  CE1  CZ   118.60  3.000
 BYR  CD1  CE1  CZ   121.02  3.000
 BYR  HD1  CD1  CE1  118.91  3.000
 BYR  HD1  CD1  CG   119.52  3.000
 BYR  CE1  CD1  CG   121.57  3.000
 BYR  OXT  C    O    126.80  3.000
 BYR  OXT  C    CA   115.46  3.000
 BYR  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
 BYR  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 BYR  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 BYR  CONST_03  CE1  CZ   CE2  CD2    0.00   0.0  0
 BYR  CONST_04  CE1  CD1  CG   CD2    0.00   0.0  0
 BYR  CONST_05  CD1  CE1  CZ   CE2    0.00   0.0  0
 BYR  CONST_06  CD1  CG   CD2  CE2    0.00   0.0  0
 BYR  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 BYR  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 BYR  CONST_09  BR   CE2  CD2  CG   180.00   0.0  0
 BYR  CONST_10  OH   CZ   CE2  CD2  180.00   0.0  0
 BYR  CONST_11  CE1  CZ   CE2  BR   180.00   0.0  0
 BYR  CONST_12  CD1  CE1  CZ   OH   180.00   0.0  0
 BYR  CONST_13  HE1  CE1  CD1  CG   180.00   0.0  0
 BYR  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 BYR  CONST_15  HD2  CD2  CE2  CZ   180.00   0.0  0
 BYR  Var_01    CD1  CG   CB   CA   -96.85  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
 BYR  chir_01  CA  CB  N  C  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
 BYR  plan-1  CB   0.020
 BYR  plan-1  CG   0.020
 BYR  plan-1  CD2  0.020
 BYR  plan-1  CE2  0.020
 BYR  plan-1  BR   0.020
 BYR  plan-1  CZ   0.020
 BYR  plan-1  OH   0.020
 BYR  plan-1  CE1  0.020
 BYR  plan-1  CD1  0.020
 BYR  plan-1  HD2  0.020
 BYR  plan-1  HE1  0.020
 BYR  plan-1  HD1  0.020
 BYR  plan-2  CA   0.020
 BYR  plan-2  C    0.020
 BYR  plan-2  O    0.020
 BYR  plan-2  OXT  0.020

