# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:55:19 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  15  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   0.560   0.0487  -0.0321  -1.2862
 AKB  O1    O  O     0  -0.419  -0.7146  -0.2776  -2.1792
 AKB  O2    O  OH1   0  -0.592   1.3467  -0.3040  -1.3186
 AKB  C2    C  CH1   0  -0.322  -0.3346   0.6207   0.0332
 AKB  C3    C  C     0   0.379   0.2551  -0.2237   1.1812
 AKB  C4    C  CH3   0  -0.775   1.4982   0.2907   1.8342
 AKB  O3    O  O     0  -0.384  -0.3165  -1.2292   1.5299
 AKB  N4    N  NH2   0  -0.769  -1.7591   0.8030   0.1018
 AKB  HO2   H  HOH1  0   0.489   1.5873  -0.7201  -2.1605
 AKB  H21   H  HCH1  0   0.308   0.1446   1.6057   0.0436
 AKB  H41   H  HCH3  0   0.264   1.8936  -0.4122   2.5639
 AKB  H42   H  HCH3  0   0.269   2.2615   0.5179   1.0895
 AKB  H43   H  HCH3  0   0.275   1.2659   1.2340   2.3355
 AKB  HN41  H  HNH2  0   0.353  -2.2225  -0.0834   0.2584
 AKB  HN42  H  HNH2  0   0.364  -1.9879   1.3951   0.8893

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    double  1.200  0.020  1.200
 AKB  C1  O2    single  1.327  0.020  1.327
 AKB  C1  C2    single  1.521  0.020  1.521
 AKB  O2  HO2   single  0.850  0.020  0.980
 AKB  C2  C3    single  1.542  0.020  1.542
 AKB  C2  N4    single  1.438  0.020  1.438
 AKB  C2  H21   single  0.970  0.020  1.090
 AKB  C3  C4    single  1.495  0.020  1.495
 AKB  C3  O3    double  1.208  0.020  1.208
 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    110.83  3.000
 AKB  C2    C1  O1    124.96  3.000
 AKB  O2    C1  O1    124.21  3.000
 AKB  HO2   O2  C1    110.61  3.000
 AKB  H21   C2  N4    108.60  3.000
 AKB  H21   C2  C3    108.54  3.000
 AKB  N4    C2  C3    114.38  3.000
 AKB  H21   C2  C1    106.49  3.000
 AKB  N4    C2  C1    110.21  3.000
 AKB  C3    C2  C1    108.32  3.000
 AKB  O3    C3  C4    123.61  3.000
 AKB  O3    C3  C2    119.32  3.000
 AKB  C4    C3  C2    117.04  3.000
 AKB  H43   C4  H42   106.39  3.000
 AKB  H43   C4  H41   109.11  3.000
 AKB  H42   C4  H41   109.78  3.000
 AKB  H43   C4  C3    108.69  3.000
 AKB  H42   C4  C3    110.81  3.000
 AKB  H41   C4  C3    111.89  3.000
 AKB  HN42  N4  HN41  106.77  3.000
 AKB  HN42  N4  C2    109.61  3.000
 AKB  HN41  N4  C2    110.48  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  CONST_01  HO2  O2  C1  O1     0.00   0.0  0
 AKB  Var_01    H41  C4  C3  C2  -174.55  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
 AKB  plan-2  HO2  0.020

