# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:16:03 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3,5-dibromo-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(Br)c(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
 DBY  DBY  '3,5-dibromo-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_DBY
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
 DBY  N    N   NH2    0  -0.793   6.8414  24.8623  10.1366
 DBY  CA   C   CH1    0  -0.195   7.0419  23.6392  10.8862
 DBY  C    C   C      0   0.401   6.5840  23.8059  12.3568
 DBY  O    O   O      0  -0.596   6.5571  24.9657  12.8110
 DBY  CB   C   CH2    0  -0.524   8.5033  23.1263  10.9115
 DBY  CG   C   CR6    0   0.113   9.0657  22.9087   9.5386
 DBY  CD1  C   CR16   0  -0.288   9.8238  23.8894   8.9066
 DBY  CE1  C   CR6    0  -0.202  10.2900  23.7028   7.6164
 DBY  CD2  C   CR16   0  -0.277   8.7960  21.7390   8.8369
 DBY  CE2  C   CR6    0  -0.212   9.2699  21.5585   7.5479
 DBY  CZ   C   CR6    0   0.431  10.0228  22.5385   6.8934
 DBY  OH   O   OH1    0  -0.592  10.5057  22.4440   5.6520
 DBY  BR1  BR  BR     0  -0.022  11.3193  25.0519   6.7976
 DBY  BR2  BR  BR     0  -0.024   8.8961  19.9328   6.6584
 DBY  OXT  O   OC    -1  -0.610   6.3285  22.7511  12.9696
 DBY  H    H   HNH2   0   0.335   7.3051  24.8160   9.2374
 DBY  H2   H   HNH2   0   0.327   7.2570  25.6311  10.6475
 DBY  HA   H   HCH1   0   0.210   6.4331  22.8523  10.4269
 DBY  HB2  H   HCH2   0   0.239   9.1231  23.8511  11.4479
 DBY  HB3  H   HCH2   0   0.243   8.5368  22.1934  11.4775
 DBY  HD1  H   HCR6   0   0.280  10.0596  24.8057   9.4337
 DBY  HD2  H   HCR6   0   0.278   8.2127  20.9576   9.3086
 DBY  HH   H   HOH1   0   0.479  10.2380  21.6272   5.2120

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
 DBY  N    CA   single    1.458  0.019  1.458
 DBY  N    H    single    0.860  0.020  0.860
 DBY  N    H2   single    0.890  0.020  1.040
 DBY  CA   C    single    1.525  0.021  1.525
 DBY  CA   CB   single    1.530  0.020  1.530
 DBY  CA   HA   single    0.970  0.020  0.970
 DBY  C    O    deloc     1.231  0.020  1.231
 DBY  C    OXT  deloc     1.246  0.020  1.246
 DBY  CB   CG   single    1.500  0.020  1.500
 DBY  CB   HB2  single    0.970  0.020  1.090
 DBY  CB   HB3  single    0.970  0.020  1.090
 DBY  CG   CD1  aromatic  1.391  0.020  1.391
 DBY  CG   CD2  aromatic  1.390  0.020  1.390
 DBY  CD1  CE1  aromatic  1.384  0.020  1.384
 DBY  CD1  HD1  single    0.930  0.020  1.080
 DBY  CE1  CZ   aromatic  1.396  0.020  1.396
 DBY  CE1  BR1  single    1.884  0.020  1.884
 DBY  CD2  CE2  aromatic  1.385  0.020  1.385
 DBY  CD2  HD2  single    0.930  0.020  1.080
 DBY  CE2  CZ   aromatic  1.398  0.020  1.398
 DBY  CE2  BR2  single    1.890  0.020  1.890
 DBY  CZ   OH   single    1.335  0.020  1.335
 DBY  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
 DBY  H2   N    H    107.15  3.000
 DBY  H2   N    CA   108.86  3.000
 DBY  H    N    CA   114.00  3.000
 DBY  HA   CA   CB   109.00  3.000
 DBY  HA   CA   C    109.00  3.000
 DBY  CB   CA   C    110.10  1.900
 DBY  HA   CA   N    110.00  3.000
 DBY  CB   CA   N    110.50  1.700
 DBY  C    CA   N    111.00  2.800
 DBY  OXT  C    O    127.17  3.000
 DBY  OXT  C    CA   115.87  3.000
 DBY  O    C    CA   120.80  1.700
 DBY  HB3  CB   HB2  107.13  3.000
 DBY  HB3  CB   CG   109.82  3.000
 DBY  HB2  CB   CG   109.42  3.000
 DBY  HB3  CB   CA   108.69  3.000
 DBY  HB2  CB   CA   108.85  3.000
 DBY  CG   CB   CA   112.77  3.000
 DBY  CD2  CG   CD1  118.00  3.000
 DBY  CD2  CG   CB   120.75  3.000
 DBY  CD1  CG   CB   121.19  3.000
 DBY  HD1  CD1  CE1  119.62  3.000
 DBY  HD1  CD1  CG   119.59  3.000
 DBY  CE1  CD1  CG   120.78  3.000
 DBY  BR1  CE1  CZ   118.46  3.000
 DBY  BR1  CE1  CD1  119.50  3.000
 DBY  CZ   CE1  CD1  122.04  3.000
 DBY  HD2  CD2  CE2  119.70  3.000
 DBY  HD2  CD2  CG   119.44  3.000
 DBY  CE2  CD2  CG   120.85  3.000
 DBY  BR2  CE2  CZ   119.27  3.000
 DBY  BR2  CE2  CD2  118.83  3.000
 DBY  CZ   CE2  CD2  121.90  3.000
 DBY  OH   CZ   CE2  125.46  3.000
 DBY  OH   CZ   CE1  118.11  3.000
 DBY  CE2  CZ   CE1  116.43  3.000
 DBY  HH   OH   CZ   112.53  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
 DBY  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 DBY  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 DBY  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 DBY  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 DBY  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 DBY  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 DBY  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 DBY  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 DBY  CONST_09  BR1  CE1  CD1  CG   180.00   0.0  0
 DBY  CONST_10  BR2  CE2  CD2  CG   180.00   0.0  0
 DBY  CONST_11  OH   CZ   CE1  CD1  180.00   0.0  0
 DBY  CONST_12  BR2  CE2  CZ   CE1  180.00   0.0  0
 DBY  CONST_13  OH   CZ   CE2  CD2  180.00   0.0  0
 DBY  CONST_14  BR1  CE1  CZ   CE2  180.00   0.0  0
 DBY  CONST_15  HD2  CD2  CG   CD1  180.00   0.0  0
 DBY  CONST_16  HD1  CD1  CG   CD2  180.00   0.0  0
 DBY  Var_01    CD1  CG   CB   CA    95.29  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
 DBY  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
 DBY  plan-1  CB   0.020
 DBY  plan-1  CG   0.020
 DBY  plan-1  CD1  0.020
 DBY  plan-1  CE1  0.020
 DBY  plan-1  CD2  0.020
 DBY  plan-1  CE2  0.020
 DBY  plan-1  CZ   0.020
 DBY  plan-1  OH   0.020
 DBY  plan-1  BR1  0.020
 DBY  plan-1  BR2  0.020
 DBY  plan-1  HD1  0.020
 DBY  plan-1  HD2  0.020
 DBY  plan-2  CA   0.020
 DBY  plan-2  C    0.020
 DBY  plan-2  O    0.020
 DBY  plan-2  OXT  0.020

