# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 19:45:50 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: (2S)-2-amino-3-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H](N)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
 AKB  AKB  '(2S)-2-amino-3-oxobutanoic acid'  ligand  14  8  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AKB
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
 AKB  C1    C  C      0   0.412   0.2201  -0.1145  -1.1261
 AKB  O1    O  O      0  -0.583  -0.5658  -0.9444  -1.6111
 AKB  O2    O  OC    -1  -0.589   1.3907   0.1201  -1.4677
 AKB  C2    C  CH1    0  -0.300  -0.3320   0.7044   0.0954
 AKB  C3    C  C      0   0.355   0.1198  -0.0373   1.3417
 AKB  C4    C  CH3    0  -0.774   1.5436   0.1777   1.7712
 AKB  O3    O  O      0  -0.413  -0.6398  -0.7502   1.9634
 AKB  N4    N  NH2    0  -0.793  -1.7598   0.8796  -0.0186
 AKB  H21   H  HCH1   0   0.241   0.1685   1.6787   0.0897
 AKB  H41   H  HCH3   0   0.251   1.8858  -0.6108   2.4392
 AKB  H42   H  HCH3   0   0.257   2.2075   0.2570   0.9124
 AKB  H43   H  HCH3   0   0.265   1.6027   1.1295   2.3062
 AKB  HN41  H  HNH2   0   0.336  -2.1719  -0.0060  -0.2824
 AKB  HN42  H  HNH2   0   0.336  -2.1601   1.1315   0.8764

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
 AKB  C1  O1    deloc   1.242  0.020  1.242
 AKB  C1  O2    deloc   1.242  0.020  1.242
 AKB  C1  C2    single  1.571  0.020  1.571
 AKB  C2  C3    single  1.519  0.020  1.519
 AKB  C2  N4    single  1.443  0.020  1.443
 AKB  C2  H21   single  0.970  0.020  1.090
 AKB  C3  C4    single  1.503  0.020  1.503
 AKB  C3  O3    double  1.213  0.020  1.213
 AKB  C4  H41   single  0.970  0.020  1.090
 AKB  C4  H42   single  0.970  0.020  1.090
 AKB  C4  H43   single  0.970  0.020  1.090
 AKB  N4  HN41  single  0.890  0.020  1.040
 AKB  N4  HN42  single  0.890  0.020  1.040

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
 AKB  C2    C1  O2    116.53  3.000
 AKB  C2    C1  O1    115.45  3.000
 AKB  O2    C1  O1    127.99  3.000
 AKB  H21   C2  N4    110.10  3.000
 AKB  H21   C2  C3    107.62  3.000
 AKB  N4    C2  C3    114.73  3.000
 AKB  H21   C2  C1    107.40  3.000
 AKB  N4    C2  C1    110.46  3.000
 AKB  C3    C2  C1    106.20  3.000
 AKB  O3    C3  C4    122.06  3.000
 AKB  O3    C3  C2    121.41  3.000
 AKB  C4    C3  C2    116.52  3.000
 AKB  H43   C4  H42   106.84  3.000
 AKB  H43   C4  H41   108.26  3.000
 AKB  H42   C4  H41   110.20  3.000
 AKB  H43   C4  C3    108.39  3.000
 AKB  H42   C4  C3    111.27  3.000
 AKB  H41   C4  C3    111.70  3.000
 AKB  HN42  N4  HN41  106.69  3.000
 AKB  HN42  N4  C2    110.59  3.000
 AKB  HN41  N4  C2    108.50  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
 AKB  Var_01  H41  C4  C3  C2  -160.88  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
 AKB  chir_01  C2  C1  C3  N4  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
 AKB  plan-1  C2  0.020
 AKB  plan-1  C3  0.020
 AKB  plan-1  C4  0.020
 AKB  plan-1  O3  0.020
 AKB  plan-2  C1  0.020
 AKB  plan-2  O1  0.020
 AKB  plan-2  O2  0.020
 AKB  plan-2  C2  0.020

