# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:07:17 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 4-bromo-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc(Br)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
 BF7  BF7  '4-bromo-D-phenylalanine  '  D-peptide  22  13  .  2022-09-16  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_BF7
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
 BF7  N    N   NH2    0  -0.795   0.6569  6.0678   8.3931
 BF7  CA   C   CH1    0  -0.174  -0.5131  5.6098   9.1293
 BF7  C    C   C      0   0.412  -1.4318  4.8183   8.1703
 BF7  O    O   O      0  -0.601  -2.6183  5.1819   8.0745
 BF7  CB   C   CH2    0  -0.530  -0.1485  4.7370  10.3500
 BF7  CG   C   CR6    0   0.138  -1.3426  4.3527  11.1708
 BF7  CD1  C   CR16   0  -0.309  -1.8435  5.2195  12.1395
 BF7  CD2  C   CR16   0  -0.293  -2.0161  3.1523  10.9576
 BF7  CE1  C   CR16   0  -0.212  -2.9822  4.9127  12.8701
 BF7  CE2  C   CR16   0  -0.215  -3.1560  2.8222  11.6776
 BF7  CZ   C   CR6    0  -0.128  -3.6334  3.7131  12.6268
 BF7  BR   BR  BR     0  -0.061  -5.1954  3.2872  13.6052
 BF7  O1   O   OC    -1  -0.611  -0.8868  3.8616   7.5785
 BF7  H1   H   HNH2   0   0.333   1.3267  6.4801   9.0322
 BF7  H3   H   HNH2   0   0.327   1.1127  5.2592   7.9870
 BF7  HCA  H   HCH1   0   0.201  -1.0523  6.4909   9.4917
 BF7  HB2  H   HCH2   0   0.232   0.3718  3.8442   9.9945
 BF7  HB3  H   HCH2   0   0.235   0.5585  5.2922  10.9739
 BF7  HD1  H   HCR6   0   0.255  -1.3364  6.1573  12.3347
 BF7  HD2  H   HCR6   0   0.251  -1.6505  2.4594  10.2096
 BF7  HE1  H   HCR6   0   0.273  -3.3484  5.6054  13.6164
 BF7  HE2  H   HCR6   0   0.273  -3.6579  1.8821  11.4905

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
 BF7  C    O    deloc     1.231  0.020  1.231
 BF7  C    CA   single    1.525  0.021  1.525
 BF7  N    CA   single    1.458  0.019  1.458
 BF7  CA   CB   single    1.521  0.033  1.521
 BF7  CB   CG   single    1.499  0.020  1.499
 BF7  CG   CD2  aromatic  1.393  0.020  1.393
 BF7  CG   CD1  aromatic  1.393  0.020  1.393
 BF7  CD2  CE2  aromatic  1.388  0.020  1.388
 BF7  CD1  CE1  aromatic  1.387  0.020  1.387
 BF7  CE2  CZ   aromatic  1.387  0.020  1.387
 BF7  CE1  CZ   aromatic  1.387  0.020  1.387
 BF7  CZ   BR   single    1.892  0.020  1.892
 BF7  C    O1   deloc     1.250  0.020  1.250
 BF7  N    H1   single    0.890  0.020  1.040
 BF7  N    H3   single    0.890  0.020  1.040
 BF7  CA   HCA  single    0.970  0.020  1.090
 BF7  CB   HB2  single    0.970  0.020  1.090
 BF7  CB   HB3  single    0.970  0.020  1.090
 BF7  CD1  HD1  single    0.930  0.020  1.080
 BF7  CD2  HD2  single    0.930  0.020  1.080
 BF7  CE1  HE1  single    0.930  0.020  1.080
 BF7  CE2  HE2  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
 BF7  H3   N    H1   106.27  3.000
 BF7  H3   N    CA   108.25  3.000
 BF7  H1   N    CA   109.88  3.000
 BF7  HCA  CA   CB   108.03  3.000
 BF7  HCA  CA   C    108.95  3.000
 BF7  CB   CA   C    110.50  1.500
 BF7  HCA  CA   N    108.06  3.000
 BF7  CB   CA   N    110.40  1.500
 BF7  C    CA   N    111.00  2.800
 BF7  O1   C    O    127.07  3.000
 BF7  O1   C    CA   115.24  3.000
 BF7  O    C    CA   120.80  1.700
 BF7  HB3  CB   HB2  107.01  3.000
 BF7  HB3  CB   CG   109.42  3.000
 BF7  HB2  CB   CG   110.36  3.000
 BF7  HB3  CB   CA   108.45  3.000
 BF7  HB2  CB   CA   108.48  3.000
 BF7  CG   CB   CA   112.93  3.000
 BF7  CD2  CG   CD1  117.95  3.000
 BF7  CD1  CG   CB   120.51  3.000
 BF7  CD2  CG   CB   121.49  3.000
 BF7  HD1  CD1  CE1  118.72  3.000
 BF7  HD1  CD1  CG   119.70  3.000
 BF7  CE1  CD1  CG   121.59  3.000
 BF7  HD2  CD2  CE2  118.90  3.000
 BF7  HD2  CD2  CG   119.59  3.000
 BF7  CE2  CD2  CG   121.51  3.000
 BF7  HE1  CE1  CZ   121.06  3.000
 BF7  HE1  CE1  CD1  119.97  3.000
 BF7  CZ   CE1  CD1  118.97  3.000
 BF7  HE2  CE2  CZ   121.12  3.000
 BF7  HE2  CE2  CD2  119.86  3.000
 BF7  CZ   CE2  CD2  119.02  3.000
 BF7  BR   CZ   CE2  119.59  3.000
 BF7  BR   CZ   CE1  119.46  3.000
 BF7  CE2  CZ   CE1  120.95  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
 BF7  CONST_01  CZ   CE2  CD2  CG     0.00   0.0  0
 BF7  CONST_02  CZ   CE1  CD1  CG     0.00   0.0  0
 BF7  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 BF7  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 BF7  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 BF7  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 BF7  CONST_07  CE2  CD2  CG   CB   180.00   0.0  0
 BF7  CONST_08  CE1  CD1  CG   CB   180.00   0.0  0
 BF7  CONST_09  BR   CZ   CE1  CD1  180.00   0.0  0
 BF7  CONST_10  BR   CZ   CE2  CD2  180.00   0.0  0
 BF7  CONST_11  HE2  CE2  CD2  CG   180.00   0.0  0
 BF7  CONST_12  HE1  CE1  CD1  CG   180.00   0.0  0
 BF7  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 BF7  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 BF7  Var_01    CD2  CG   CB   CA    93.54  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
 BF7  chir_01  CA  C  N  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
 BF7  plan-1  CB   0.020
 BF7  plan-1  CG   0.020
 BF7  plan-1  CD1  0.020
 BF7  plan-1  CD2  0.020
 BF7  plan-1  CE1  0.020
 BF7  plan-1  CE2  0.020
 BF7  plan-1  CZ   0.020
 BF7  plan-1  BR   0.020
 BF7  plan-1  HD1  0.020
 BF7  plan-1  HD2  0.020
 BF7  plan-1  HE1  0.020
 BF7  plan-1  HE2  0.020
 BF7  plan-2  CA   0.020
 BF7  plan-2  C    0.020
 BF7  plan-2  O    0.020
 BF7  plan-2  O1   0.020

