# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:59:09 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-bromo-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1Br)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
 6DU  6DU  '2-bromo-L-phenylalanine  '  L-peptide  22  13  .  2017-07-04  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_6DU
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
 6DU  O    O   O      0  -0.604  -10.8859  -38.8817  -29.5091
 6DU  C    C   C      0   0.395  -10.1898  -37.8498  -29.4378
 6DU  CA   C   CH1    0  -0.159  -10.3315  -36.9921  -28.1561
 6DU  N    N   NH2    0  -0.805  -11.7321  -36.7700  -27.8131
 6DU  CB   C   CH2    0  -0.519   -9.6759  -37.7184  -26.9717
 6DU  CG   C   CR6    0   0.193   -8.2166  -38.0060  -27.1696
 6DU  CD1  C   CR6    0  -0.195   -7.1976  -37.0770  -26.9608
 6DU  CD2  C   CR16   0  -0.302   -7.8228  -39.2731  -27.6050
 6DU  BR   BR  BR     0  -0.067   -7.6036  -35.3231  -26.3589
 6DU  CE1  C   CR16   0  -0.214   -5.8584  -37.3824  -27.1685
 6DU  CE2  C   CR16   0  -0.234   -6.4944  -39.5997  -27.8231
 6DU  CZ   C   CR16   0  -0.273   -5.5065  -38.6509  -27.6029
 6DU  H4   H   HCH1   0   0.185   -9.7911  -36.0518  -28.3287
 6DU  H5   H   HNH2   0   0.334  -11.7798  -36.1036  -27.0509
 6DU  H6   H   HNH2   0   0.337  -12.2045  -36.3225  -28.5892
 6DU  H8   H   HCH2   0   0.240   -9.8290  -37.1312  -26.0614
 6DU  H9   H   HCH2   0   0.245  -10.2054  -38.6616  -26.8229
 6DU  H10  H   HCR6   0   0.253   -8.5903  -40.0167  -27.7802
 6DU  H11  H   HCR6   0   0.274   -5.0903  -36.6407  -26.9931
 6DU  H12  H   HCR6   0   0.258   -6.2318  -40.5936  -28.1610
 6DU  H13  H   HCR6   0   0.263   -4.4637  -38.8908  -27.7637
 6DU  OXT  O   OC    -1  -0.606   -9.3653  -37.4410  -30.2791

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
 6DU  O    C    deloc     1.231  0.020  1.231
 6DU  C    CA   single    1.525  0.021  1.525
 6DU  CA   N    single    1.458  0.019  1.458
 6DU  CA   CB   single    1.521  0.033  1.521
 6DU  CE2  CZ   aromatic  1.387  0.020  1.387
 6DU  CE2  CD2  aromatic  1.385  0.020  1.385
 6DU  CZ   CE1  aromatic  1.386  0.020  1.386
 6DU  CD2  CG   aromatic  1.396  0.020  1.396
 6DU  CE1  CD1  aromatic  1.389  0.020  1.389
 6DU  CG   CD1  aromatic  1.395  0.020  1.395
 6DU  CG   CB   single    1.500  0.020  1.500
 6DU  CD1  BR   single    1.898  0.020  1.898
 6DU  CA   H4   single    0.970  0.020  1.090
 6DU  N    H5   single    0.890  0.020  1.040
 6DU  N    H6   single    0.890  0.020  1.040
 6DU  CB   H8   single    0.970  0.020  1.090
 6DU  CB   H9   single    0.970  0.020  1.090
 6DU  CD2  H10  single    0.930  0.020  1.080
 6DU  CE1  H11  single    0.930  0.020  1.080
 6DU  CE2  H12  single    0.930  0.020  1.080
 6DU  CZ   H13  single    0.930  0.020  1.080
 6DU  C    OXT  deloc     1.247  0.020  1.247

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
 6DU  OXT  C    CA   120.80  1.700
 6DU  OXT  C    O    127.02  3.000
 6DU  CA   C    O    120.80  1.700
 6DU  H4   CA   CB   108.41  3.000
 6DU  H4   CA   N    112.27  3.000
 6DU  CB   CA   N    110.40  1.500
 6DU  H4   CA   C    107.40  3.000
 6DU  CB   CA   C    110.50  1.500
 6DU  N    CA   C    111.00  2.800
 6DU  H6   N    H5   105.30  3.000
 6DU  H6   N    CA   109.57  3.000
 6DU  H5   N    CA   108.79  3.000
 6DU  H9   CB   H8   106.40  3.000
 6DU  H9   CB   CG   108.91  3.000
 6DU  H8   CB   CG   110.41  3.000
 6DU  H9   CB   CA   107.84  3.000
 6DU  H8   CB   CA   109.15  3.000
 6DU  CG   CB   CA   113.83  3.000
 6DU  CD2  CG   CD1  116.43  3.000
 6DU  CD1  CG   CB   124.27  3.000
 6DU  CD2  CG   CB   119.29  3.000
 6DU  CE1  CD1  BR   117.17  3.000
 6DU  BR   CD1  CG   120.45  3.000
 6DU  CE1  CD1  CG   122.38  3.000
 6DU  H10  CD2  CE2  119.49  3.000
 6DU  H10  CD2  CG   118.27  3.000
 6DU  CE2  CD2  CG   122.23  3.000
 6DU  H11  CE1  CZ   119.85  3.000
 6DU  H11  CE1  CD1  120.63  3.000
 6DU  CZ   CE1  CD1  119.52  3.000
 6DU  H12  CE2  CZ   120.33  3.000
 6DU  H12  CE2  CD2  119.89  3.000
 6DU  CZ   CE2  CD2  119.78  3.000
 6DU  H13  CZ   CE2  120.73  3.000
 6DU  H13  CZ   CE1  119.61  3.000
 6DU  CE2  CZ   CE1  119.66  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
 6DU  CONST_01  CZ   CE2  CD2  CG     0.00   0.0  0
 6DU  CONST_02  CZ   CE1  CD1  CG     0.00   0.0  0
 6DU  CONST_03  CE2  CZ   CE1  CD1    0.00   0.0  0
 6DU  CONST_04  CE2  CD2  CG   CD1    0.00   0.0  0
 6DU  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 6DU  CONST_06  CE1  CD1  CG   CD2    0.00   0.0  0
 6DU  CONST_07  CE2  CD2  CG   CB   180.00   0.0  0
 6DU  CONST_08  CE1  CD1  CG   CB   180.00   0.0  0
 6DU  CONST_09  BR   CD1  CG   CD2  180.00   0.0  0
 6DU  CONST_10  CZ   CE1  CD1  BR   180.00   0.0  0
 6DU  CONST_11  H12  CE2  CD2  CG   180.00   0.0  0
 6DU  CONST_12  H11  CE1  CD1  CG   180.00   0.0  0
 6DU  CONST_13  H13  CZ   CE1  CD1  180.00   0.0  0
 6DU  CONST_14  H10  CD2  CG   CD1  180.00   0.0  0
 6DU  Var_01    CD2  CG   CB   CA   -98.01  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
 6DU  chir_01  CA  C  N  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
 6DU  plan-1  CB   0.020
 6DU  plan-1  CG   0.020
 6DU  plan-1  CD1  0.020
 6DU  plan-1  CD2  0.020
 6DU  plan-1  BR   0.020
 6DU  plan-1  CE1  0.020
 6DU  plan-1  CE2  0.020
 6DU  plan-1  CZ   0.020
 6DU  plan-1  H10  0.020
 6DU  plan-1  H11  0.020
 6DU  plan-1  H12  0.020
 6DU  plan-1  H13  0.020
 6DU  plan-2  O    0.020
 6DU  plan-2  C    0.020
 6DU  plan-2  CA   0.020
 6DU  plan-2  OXT  0.020

