# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 04:12:13 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: (2R)-2-aminobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[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
 AA3  AA3  '(2R)-2-aminobutanoic acid'  L-peptide  15  7  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AA3
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
 AA3  N    N  NH2    0  -0.786   0.6604   1.5853   0.3767
 AA3  CA   C  CH1    0  -0.202   0.2735   0.1828   0.3974
 AA3  C    C  C      0   0.383  -1.1824  -0.1122  -0.0399
 AA3  O    O  O      0  -0.610  -1.7991   0.7872  -0.6455
 AA3  CB   C  CH2    0  -0.420   1.2327  -0.6413  -0.4672
 AA3  CG   C  CH3    0  -0.654   2.6885  -0.5389  -0.0382
 AA3  OXT  O  OC    -1  -0.627  -1.6155  -1.2523   0.2324
 AA3  H    H  HNH2   0   0.321   0.4127   1.9663  -0.5299
 AA3  HN   H  HNH2   0   0.332   0.0754   2.0927   1.0298
 AA3  HA   H  HCH1   0   0.202   0.3836  -0.1691   1.4305
 AA3  HB1  H  HCH2   0   0.215   0.9135  -1.6849  -0.4388
 AA3  HB2  H  HCH2   0   0.203   1.1349  -0.3214  -1.5116
 AA3  HG1  H  HCH3   0   0.217   3.0479   0.4875  -0.0977
 AA3  HG2  H  HCH3   0   0.208   2.8182  -0.8738   0.9933
 AA3  HG3  H  HCH3   0   0.217   3.3304  -1.1580  -0.6669

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
 AA3  N   CA   single  1.458  0.019  1.458
 AA3  N   H    single  0.860  0.020  0.860
 AA3  N   HN   single  0.890  0.020  1.040
 AA3  CA  C    single  1.525  0.021  1.525
 AA3  CA  CB   single  1.521  0.033  1.521
 AA3  CA  HA   single  0.970  0.020  0.970
 AA3  C   O    deloc   1.231  0.020  1.231
 AA3  C   OXT  deloc   1.250  0.020  1.250
 AA3  CB  CG   single  1.521  0.020  1.521
 AA3  CB  HB1  single  0.970  0.020  1.090
 AA3  CB  HB2  single  0.970  0.020  1.090
 AA3  CG  HG1  single  0.970  0.020  1.090
 AA3  CG  HG2  single  0.970  0.020  1.090
 AA3  CG  HG3  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
 AA3  HN   N   H    104.31  3.000
 AA3  HN   N   CA   108.66  3.000
 AA3  H    N   CA   114.00  3.000
 AA3  HA   CA  CB   109.00  3.000
 AA3  HA   CA  C    109.00  3.000
 AA3  CB   CA  C    110.50  1.500
 AA3  HA   CA  N    110.00  3.000
 AA3  CB   CA  N    110.40  1.500
 AA3  C    CA  N    111.00  2.800
 AA3  OXT  C   O    126.32  3.000
 AA3  OXT  C   CA   115.98  3.000
 AA3  O    C   CA   120.80  1.700
 AA3  HB2  CB  HB1  106.11  3.000
 AA3  HB2  CB  CG   109.53  3.000
 AA3  HB1  CB  CG   109.68  3.000
 AA3  HB2  CB  CA   108.95  3.000
 AA3  HB1  CB  CA   108.45  3.000
 AA3  CG   CB  CA   113.82  3.000
 AA3  HG3  CG  HG2  107.48  3.000
 AA3  HG3  CG  HG1  108.01  3.000
 AA3  HG2  CG  HG1  107.54  3.000
 AA3  HG3  CG  CB   111.24  3.000
 AA3  HG2  CG  CB   111.06  3.000
 AA3  HG1  CG  CB   111.33  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
 AA3  Var_01  HG1  CG  CB  CA  -60.74  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
 AA3  chir_01  CA  N  C  CB  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
 AA3  plan-1  CA   0.020
 AA3  plan-1  C    0.020
 AA3  plan-1  O    0.020
 AA3  plan-1  OXT  0.020

