# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:51:06 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (3S)-3-amino-4,4-dihydroxybutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(O)=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
 AKZ  AKZ  '(3S)-3-amino-4,4-dihydroxybutanoic acid'  peptide  17  9  .  2016-04-22  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AKZ
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
 AKZ  C    C  CH1    0   0.299  34.8435  33.8504  31.6532
 AKZ  N    N  NH2    0  -0.831  35.9532  32.6120  29.9407
 AKZ  O    O  OH1    0  -0.666  33.6448  34.0521  32.3233
 AKZ  CA   C  CH1    0  -0.161  34.6204  32.9143  30.4575
 AKZ  CB   C  CH2    0  -0.583  33.9088  31.6213  30.8370
 AKZ  CG   C  C      0   0.421  33.5922  30.6478  29.6791
 AKZ  OD1  O  O      0  -0.601  34.0492  30.9078  28.5440
 AKZ  OD2  O  OC    -1  -0.611  32.9001  29.6586  29.9862
 AKZ  HA   H  HCH1   0   0.203  33.9996  33.4557  29.7298
 AKZ  HB2  H  HCH2   0   0.218  34.5089  31.0783  31.5760
 AKZ  HB3  H  HCH2   0   0.231  32.9680  31.8547  31.3406
 AKZ  HO   H  HOH1   0   0.455  33.7251  34.8271  32.8879
 AKZ  H1   H  HCH1   0   0.174  35.2176  34.8149  31.2645
 AKZ  OXT  O  OH1    0  -0.686  35.7979  33.3025  32.5233
 AKZ  HXT  H  HOH1   0   0.436  36.3826  32.7888  31.9396
 AKZ  H    H  HNH2   0   0.358  35.8400  31.9155  29.2136
 AKZ  H2   H  HNH2   0   0.343  36.3442  33.4324  29.4907

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
 AKZ  C    O    single  1.231  0.020  1.231
 AKZ  N    CA   single  1.458  0.019  1.458
 AKZ  N    H    single  0.860  0.020  0.860
 AKZ  N    H2   single  0.890  0.020  1.040
 AKZ  CA   C    single  1.525  0.021  1.525
 AKZ  CA   CB   single  1.530  0.020  1.530
 AKZ  CA   HA   single  0.970  0.020  0.970
 AKZ  CB   HB2  single  0.970  0.020  1.090
 AKZ  CB   HB3  single  0.970  0.020  1.090
 AKZ  CG   CB   single  1.546  0.020  1.546
 AKZ  CG   OD2  deloc   1.246  0.020  1.246
 AKZ  OD1  CG   deloc   1.251  0.020  1.251
 AKZ  O    HO   single  0.850  0.020  0.980
 AKZ  C    H1   single  0.970  0.020  1.090
 AKZ  C    OXT  single  1.403  0.020  1.403
 AKZ  OXT  HXT  single  0.850  0.020  0.980

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
 AKZ  OXT  C    H1   109.20  3.000
 AKZ  OXT  C    CA   110.11  3.000
 AKZ  H1   C    CA   107.91  3.000
 AKZ  OXT  C    O    110.17  3.000
 AKZ  H1   C    O    109.59  3.000
 AKZ  CA   C    O    120.80  1.700
 AKZ  H2   N    H    106.31  3.000
 AKZ  H2   N    CA   109.95  3.000
 AKZ  H    N    CA   114.00  3.000
 AKZ  HO   O    C    109.16  3.000
 AKZ  HA   CA   CB   109.00  3.000
 AKZ  HA   CA   N    110.00  3.000
 AKZ  CB   CA   N    110.50  1.700
 AKZ  HA   CA   C    109.00  3.000
 AKZ  CB   CA   C    110.10  1.900
 AKZ  N    CA   C    111.00  2.800
 AKZ  HB3  CB   HB2  105.47  3.000
 AKZ  HB3  CB   CG   107.67  3.000
 AKZ  HB2  CB   CG   107.77  3.000
 AKZ  CG   CB   CA   116.33  3.000
 AKZ  HB3  CB   CA   109.61  3.000
 AKZ  HB2  CB   CA   109.43  3.000
 AKZ  OD2  CG   OD1  126.28  3.000
 AKZ  OD1  CG   CB   118.30  3.000
 AKZ  OD2  CG   CB   115.42  3.000
 AKZ  HXT  OXT  C    104.06  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
 AKZ  Var_01  OD2  CG  CB  CA  -173.45  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
 AKZ  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
 AKZ  plan-1  CB   0.020
 AKZ  plan-1  CG   0.020
 AKZ  plan-1  OD1  0.020
 AKZ  plan-1  OD2  0.020

