# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 06:00:53 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: (2S)-2-amino-4,4-difluorobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(F)F)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
 OBF  OBF  '(2S)-2-amino-4,4-difluorobutanoic acid'  L-peptide  15  9  .  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_OBF
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
 OBF  N    N  NH2    0  -0.800   9.4466  -2.7057  -2.3457
 OBF  CA   C  CH1    0  -0.219   9.5764  -1.3229  -2.7670
 OBF  CB   C  CH2    0  -0.572   9.8377  -1.0997  -4.2709
 OBF  CG   C  CH1    0   0.539  11.2303  -1.4482  -4.7145
 OBF  FG1  F  F      0  -0.351  11.3999  -1.1541  -6.0401
 OBF  FG2  F  F      0  -0.351  11.4887  -2.7896  -4.6028
 OBF  C    C  C      0   0.406   8.3017  -0.5169  -2.3930
 OBF  O    O  O      0  -0.607   8.4462   0.7177  -2.3069
 OBF  HN   H  HNH2   0   0.330  10.1334  -3.2950  -2.7942
 OBF  HA   H  HCH1   0   0.210  10.4127  -0.8708  -2.2200
 OBF  H1B  H  HCH2   0   0.247   9.1066  -1.6533  -4.8687
 OBF  H2B  H  HCH2   0   0.249   9.7077  -0.0381  -4.4953
 OBF  HG   H  HCH1   0   0.185  11.9999  -0.9177  -4.1497
 OBF  HNA  H  HNH2   0   0.328   8.5345  -3.0422  -2.6268
 OBF  OXT  O  OC    -1  -0.594   7.2470  -1.1635  -2.2512

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
 OBF  N    HNA  single  0.890  0.020  1.040
 OBF  CA   N    single  1.458  0.019  1.458
 OBF  CA   C    single  1.525  0.021  1.525
 OBF  CA   HA   single  0.970  0.020  0.970
 OBF  CB   CA   single  1.521  0.033  1.521
 OBF  CG   CB   single  1.502  0.020  1.502
 OBF  CG   HG   single  0.970  0.020  1.090
 OBF  FG1  CG   single  1.368  0.020  1.368
 OBF  FG2  CG   single  1.371  0.020  1.371
 OBF  C    OXT  deloc   1.245  0.020  1.245
 OBF  O    C    deloc   1.231  0.020  1.231
 OBF  HN   N    single  0.890  0.020  1.040
 OBF  H1B  CB   single  0.970  0.020  1.090
 OBF  H2B  CB   single  0.970  0.020  1.090

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
 OBF  HNA  N   HN   107.18  3.000
 OBF  HN   N   CA   111.48  3.000
 OBF  HNA  N   CA   108.46  3.000
 OBF  HA   CA  C    110.00  3.000
 OBF  HA   CA  CB   109.00  3.000
 OBF  C    CA  CB   110.50  1.500
 OBF  CB   CA  N    110.40  1.500
 OBF  HA   CA  N    110.00  3.000
 OBF  C    CA  N    111.00  2.800
 OBF  H2B  CB  H1B  107.44  3.000
 OBF  H2B  CB  CG   105.96  3.000
 OBF  H1B  CB  CG   109.91  3.000
 OBF  H2B  CB  CA   108.70  3.000
 OBF  H1B  CB  CA   110.24  3.000
 OBF  CG   CB  CA   114.28  3.000
 OBF  HG   CG  FG2  107.48  3.000
 OBF  FG2  CG  FG1  105.42  3.000
 OBF  HG   CG  FG1  108.01  3.000
 OBF  FG2  CG  CB   112.19  3.000
 OBF  FG1  CG  CB   110.55  3.000
 OBF  HG   CG  CB   112.82  3.000
 OBF  OXT  C   O    127.22  3.000
 OBF  O    C   CA   120.80  1.700
 OBF  OXT  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
 OBF  Var_01  FG1  CG  CB  CA  -176.72  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
 OBF  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
 OBF  plan-1  CA   0.020
 OBF  plan-1  C    0.020
 OBF  plan-1  O    0.020
 OBF  plan-1  OXT  0.020

