# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:55:03 2022
#   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
 DBB  DBB  '(2R)-2-aminobutanoic acid'  D-peptide  15  7  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_DBB
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
 DBB  N    N  NH2    0  -0.800   0.4087  -3.9159  -0.0002
 DBB  CA   C  CH1    0  -0.192   1.3489  -4.4938   0.9474
 DBB  C    C  C      0   0.400   2.6809  -4.8457   0.2437
 DBB  O    O  O      0  -0.614   3.3504  -5.7633   0.7597
 DBB  CB   C  CH2    0  -0.429   1.6610  -3.6089   2.1668
 DBB  CG   C  CH3    0  -0.669   0.4433  -3.2842   3.0217
 DBB  OXT  O  OC    -1  -0.605   2.9947  -4.1556  -0.7476
 DBB  H    H  HNH2   0   0.330  -0.3811  -3.5090   0.4851
 DBB  H1   H  HNH2   0   0.323   0.8734  -3.1612  -0.4899
 DBB  HA   H  HCH1   0   0.190   0.9126  -5.4253   1.3282
 DBB  HB2  H  HCH2   0   0.208   2.4045  -4.1175   2.7865
 DBB  HB3  H  HCH2   0   0.204   2.1286  -2.6795   1.8230
 DBB  HG1  H  HCH3   0   0.228   0.7209  -2.6975   3.8983
 DBB  HG2  H  HCH3   0   0.211  -0.3013  -2.7031   2.4745
 DBB  HG3  H  HCH3   0   0.215  -0.0435  -4.1955   3.3755

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
 DBB  N   CA   single  1.458  0.019  1.458
 DBB  CA  C    single  1.525  0.021  1.525
 DBB  CA  CB   single  1.521  0.033  1.521
 DBB  C   O    deloc   1.231  0.020  1.231
 DBB  CB  CG   single  1.523  0.020  1.523
 DBB  C   OXT  deloc   1.248  0.020  1.248
 DBB  N   H    single  0.860  0.020  0.860
 DBB  N   H1   single  0.890  0.020  1.040
 DBB  CA  HA   single  0.970  0.020  0.970
 DBB  CB  HB2  single  0.970  0.020  1.090
 DBB  CB  HB3  single  0.970  0.020  1.090
 DBB  CG  HG1  single  0.970  0.020  1.090
 DBB  CG  HG2  single  0.970  0.020  1.090
 DBB  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
 DBB  H1   N   H    106.87  3.000
 DBB  H1   N   CA   108.34  3.000
 DBB  H    N   CA   114.00  3.000
 DBB  HA   CA  CB   109.00  3.000
 DBB  HA   CA  C    110.00  3.000
 DBB  CB   CA  C    110.50  1.500
 DBB  HA   CA  N    110.00  3.000
 DBB  CB   CA  N    110.40  1.500
 DBB  C    CA  N    111.00  2.800
 DBB  OXT  C   O    126.89  3.000
 DBB  OXT  C   CA   120.80  1.700
 DBB  O    C   CA   120.80  1.700
 DBB  HB3  CB  HB2  106.40  3.000
 DBB  HB3  CB  CG   109.67  3.000
 DBB  HB2  CB  CG   108.95  3.000
 DBB  HB3  CB  CA   109.01  3.000
 DBB  HB2  CB  CA   108.63  3.000
 DBB  CG   CB  CA   113.91  3.000
 DBB  HG3  CG  HG2  107.61  3.000
 DBB  HG3  CG  HG1  107.57  3.000
 DBB  HG2  CG  HG1  106.87  3.000
 DBB  HG3  CG  CB   111.13  3.000
 DBB  HG2  CG  CB   112.19  3.000
 DBB  HG1  CG  CB   111.24  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
 DBB  Var_01  HG1  CG  CB  CA  177.21  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
 DBB  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
 DBB  plan-1  CA   0.020
 DBB  plan-1  C    0.020
 DBB  plan-1  O    0.020
 DBB  plan-1  OXT  0.020

