# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:34:20 2022
#   Inital geometry file: a 48 line input string
#   Ligand name: (2S)-2-amino-4-bromopent-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(Br)=C)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
 A8E  A8E  '(2S)-2-amino-4-bromopent-4-enoic acid'  L-peptide  16  9  .  2012-08-28  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A8E
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
 A8E  O     O   O      0  -0.609  7.6718  -0.4421  -1.6176
 A8E  C     C   C      0   0.440  6.5280  -0.4959  -1.1228
 A8E  N     N   NH2    0  -0.800  5.9811  -2.3795  -2.5815
 A8E  OXT   O   OC    -1  -0.589  6.1768  -0.0790  -0.0046
 A8E  BR    BR  BR     0  -0.093  1.3210  -1.9073  -1.2847
 A8E  CA    C   CH1    0  -0.258  5.4502  -1.1263  -2.0503
 A8E  CB    C   CH2    0  -0.433  4.1279  -1.3733  -1.3364
 A8E  CG    C   C      0  -0.013  2.9495  -1.5723  -2.2395
 A8E  CD1   C   C2     0  -0.539  2.8927  -1.5194  -3.5619
 A8E  HN    H   HNH2   0   0.333  5.3974  -2.7184  -3.3366
 A8E  HNA   H   HNH2   0   0.335  6.8849  -2.1826  -2.9914
 A8E  HA    H   HCH1   0   0.200  5.2773  -0.3784  -2.8436
 A8E  HB    H   HCH2   0   0.244  4.2334  -2.2540  -0.6947
 A8E  HBA   H   HCH2   0   0.256  3.9147  -0.5387  -0.6656
 A8E  HD1   H   H      0   0.258  3.7892  -1.3276  -4.1375
 A8E  HD1A  H   H      0   0.270  1.9790  -1.6598  -4.1217

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
 A8E  OXT  C     deloc   1.244  0.020  1.244
 A8E  CA   C     single  1.525  0.021  1.525
 A8E  C    O     deloc   1.231  0.020  1.231
 A8E  N    CA    single  1.458  0.019  1.458
 A8E  N    HN    single  0.890  0.020  1.040
 A8E  N    HNA   single  0.890  0.020  1.040
 A8E  CG   BR    single  1.917  0.020  1.917
 A8E  CA   CB    single  1.540  0.027  1.540
 A8E  CA   HA    single  0.970  0.020  0.970
 A8E  CG   CB    single  1.498  0.020  1.498
 A8E  CB   HB    single  0.970  0.020  1.090
 A8E  CB   HBA   single  0.970  0.020  1.090
 A8E  CD1  CG    double  1.325  0.020  1.325
 A8E  CD1  HD1   single  0.930  0.020  1.080
 A8E  CD1  HD1A  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
 A8E  CA    C    OXT  118.44  3.000
 A8E  CA    C    O    120.80  1.700
 A8E  OXT   C    O    126.94  3.000
 A8E  HNA   N    HN   106.13  3.000
 A8E  HNA   N    CA   107.76  3.000
 A8E  HN    N    CA   110.41  3.000
 A8E  HA    CA   CB   109.00  3.000
 A8E  HA    CA   N    110.00  3.000
 A8E  CB    CA   N    111.50  1.700
 A8E  HA    CA   C    109.00  3.000
 A8E  CB    CA   C    111.40  1.900
 A8E  N     CA   C    111.00  2.800
 A8E  HBA   CB   HB   105.88  3.000
 A8E  HBA   CB   CG   108.56  3.000
 A8E  HB    CB   CG   108.81  3.000
 A8E  HBA   CB   CA   109.49  3.000
 A8E  HB    CB   CA   108.76  3.000
 A8E  CG    CB   CA   114.96  3.000
 A8E  CD1   CG   CB   129.07  3.000
 A8E  CD1   CG   BR   117.89  3.000
 A8E  CB    CG   BR   113.03  3.000
 A8E  HD1A  CD1  HD1  116.60  3.000
 A8E  HD1A  CD1  CG   123.24  3.000
 A8E  HD1   CD1  CG   120.16  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
 A8E  Var_01  CA   CB   CG  BR  179.05  30.0  3
 A8E  Var_02  HD1  CD1  CG  BR  179.70   0.0  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
 A8E  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
 A8E  plan-1  O     0.020
 A8E  plan-1  C     0.020
 A8E  plan-1  OXT   0.020
 A8E  plan-1  CA    0.020
 A8E  plan-2  BR    0.020
 A8E  plan-2  CB    0.020
 A8E  plan-2  CG    0.020
 A8E  plan-2  CD1   0.020
 A8E  plan-2  HD1   0.020
 A8E  plan-2  HD1A  0.020

