# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 06:38:17 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: (3S)-3-amino-5,5-difluoro-2-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(F)F)C(=O)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
 ABK  ABK  '(3S)-3-amino-5,5-difluoro-2-oxopentanoic acid'  ligand  17  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ABK
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
 ABK  N    N  NH2    0  -0.786   1.9515   1.0298  -0.3717
 ABK  CA   C  CH1    0  -0.214   0.6328   0.5640  -0.0003
 ABK  CB   C  CH2    0  -0.581   0.0424  -0.5496  -0.8904
 ABK  CG   C  CH1    0   0.544  -0.1069  -0.1376  -2.3290
 ABK  FG1  F  F      0  -0.348  -0.6853  -1.1475  -3.0452
 ABK  FG2  F  F      0  -0.349  -0.9426   0.9382  -2.4424
 ABK  O21  O  OC    -1  -0.577  -0.6633  -0.7294   3.2394
 ABK  O22  O  O      0  -0.574  -1.6760   0.4481   1.6266
 ABK  C1   C  C      0   0.245   0.6527   0.0308   1.4224
 ABK  HN1  H  HNH2   0   0.351   1.9382   1.4576  -1.2874
 ABK  HN2  H  HNH2   0   0.344   2.6096   0.2619  -0.4122
 ABK  HA   H  HCH1   0   0.266  -0.0522   1.4141  -0.0210
 ABK  HB1  H  HCH2   0   0.261   0.6995  -1.4242  -0.8641
 ABK  HB2  H  HCH2   0   0.269  -0.9351  -0.8556  -0.5130
 ABK  HG   H  HCH1   0   0.184   0.8341   0.1174  -2.8182
 ABK  O12  O  O      0  -0.382   1.6882  -0.2937   1.9504
 ABK  C2   C  C      0   0.347  -0.7048  -0.1016   2.1739

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
 ABK  N    CA   single  1.447  0.020  1.447
 ABK  N    HN1  single  0.890  0.020  1.040
 ABK  N    HN2  single  0.890  0.020  1.040
 ABK  CA   CB   single  1.543  0.020  1.543
 ABK  CA   C1   single  1.519  0.020  1.519
 ABK  CA   HA   single  0.970  0.020  1.090
 ABK  CB   CG   single  1.504  0.020  1.504
 ABK  CB   HB1  single  0.970  0.020  1.090
 ABK  CB   HB2  single  0.970  0.020  1.090
 ABK  CG   FG1  single  1.366  0.020  1.366
 ABK  CG   FG2  single  1.367  0.020  1.367
 ABK  CG   HG   single  0.970  0.020  1.090
 ABK  O12  C1   double  1.207  0.020  1.207
 ABK  C2   O21  deloc   1.237  0.020  1.237
 ABK  C2   O22  deloc   1.243  0.020  1.243
 ABK  C2   C1   single  1.557  0.020  1.557

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
 ABK  HN2  N   HN1  107.06  3.000
 ABK  HN2  N   CA   111.01  3.000
 ABK  HN1  N   CA   110.91  3.000
 ABK  HA   CA  C1   107.41  3.000
 ABK  HA   CA  CB   108.11  3.000
 ABK  C1   CA  CB   106.97  3.000
 ABK  HA   CA  N    108.43  3.000
 ABK  C1   CA  N    109.96  3.000
 ABK  CB   CA  N    115.65  3.000
 ABK  HB2  CB  HB1  107.78  3.000
 ABK  HB2  CB  CG   108.58  3.000
 ABK  HB1  CB  CG   107.55  3.000
 ABK  HB2  CB  CA   110.21  3.000
 ABK  HB1  CB  CA   109.47  3.000
 ABK  CG   CB  CA   113.08  3.000
 ABK  HG   CG  FG2  107.84  3.000
 ABK  HG   CG  FG1  107.63  3.000
 ABK  FG2  CG  FG1  106.22  3.000
 ABK  HG   CG  CB   114.04  3.000
 ABK  FG2  CG  CB   110.83  3.000
 ABK  FG1  CG  CB   109.93  3.000
 ABK  C2   C1  O12  120.93  3.000
 ABK  C2   C1  CA   118.05  3.000
 ABK  O12  C1  CA   121.02  3.000
 ABK  C1   C2  O22  115.53  3.000
 ABK  C1   C2  O21  115.43  3.000
 ABK  O22  C2  O21  129.03  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
 ABK  Var_01  FG1  CG  CB  CA  -177.45  30.0  3
 ABK  Var_02  O21  C2  C1  CA   169.16  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
 ABK  chir_01  CA  N  CB  C1  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
 ABK  plan-1  CA   0.020
 ABK  plan-1  C1   0.020
 ABK  plan-1  O12  0.020
 ABK  plan-1  C2   0.020
 ABK  plan-2  O21  0.020
 ABK  plan-2  O22  0.020
 ABK  plan-2  C1   0.020
 ABK  plan-2  C2   0.020

