# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:38:58 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (2S)-2,4-diaminobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[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
 DAB  DAB  '(2S)-2,4-diaminobutanoic acid'  L-peptide  17  8  .  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_DAB
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
 DAB  N    N  NH2    0  -0.801  4.9404  19.4802  15.6016
 DAB  CA   C  CH1    0  -0.213  3.8496  20.2492  16.1807
 DAB  C    C  C      0   0.405  2.6241  20.2585  15.2359
 DAB  O    O  O      0  -0.603  2.8449  20.0998  14.0185
 DAB  CB   C  CH2    0  -0.430  4.2022  21.7118  16.5119
 DAB  CG   C  CH2    0  -0.300  5.3351  21.8948  17.5129
 DAB  ND   N  NH2    0  -0.800  4.9882  21.3587  18.8229
 DAB  OXT  O  OC    -1  -0.613  1.5201  20.4726  15.7753
 DAB  H    H  HNH2   0   0.331  5.8036  19.6504  16.1029
 DAB  H2   H  HNH2   0   0.323  5.0862  19.8018  14.6525
 DAB  HA   H  HCH1   0   0.197  3.5385  19.7541  17.1077
 DAB  HB2  H  HCH2   0   0.207  4.4745  22.2243  15.5825
 DAB  HB3  H  HCH2   0   0.207  3.3124  22.2133  16.9022
 DAB  HG2  H  HCH2   0   0.181  6.2653  21.4763  17.0999
 DAB  HG3  H  HCH2   0   0.223  5.5219  22.9656  17.6261
 DAB  HD1  H  HNH2   0   0.343  5.7376  21.5551  19.4741
 DAB  HD2  H  HNH2   0   0.340  4.9352  20.3489  18.7738

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
 DAB  N   CA   single  1.458  0.019  1.458
 DAB  N   H    single  0.860  0.020  0.860
 DAB  N   H2   single  0.890  0.020  1.040
 DAB  CA  C    single  1.525  0.021  1.525
 DAB  CA  CB   single  1.521  0.033  1.521
 DAB  CA  HA   single  0.970  0.020  0.970
 DAB  C   O    deloc   1.231  0.020  1.231
 DAB  C   OXT  deloc   1.247  0.020  1.247
 DAB  CB  CG   single  1.523  0.020  1.523
 DAB  CB  HB2  single  0.970  0.020  1.090
 DAB  CB  HB3  single  0.970  0.020  1.090
 DAB  CG  ND   single  1.457  0.020  1.457
 DAB  CG  HG2  single  0.970  0.020  1.090
 DAB  CG  HG3  single  0.970  0.020  1.090
 DAB  ND  HD1  single  0.890  0.020  1.040
 DAB  ND  HD2  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
 DAB  H2   N   H    106.73  3.000
 DAB  H2   N   CA   108.25  3.000
 DAB  H    N   CA   114.00  3.000
 DAB  HA   CA  CB   109.00  3.000
 DAB  HA   CA  C    109.00  3.000
 DAB  CB   CA  C    110.50  1.500
 DAB  HA   CA  N    110.00  3.000
 DAB  CB   CA  N    110.40  1.500
 DAB  C    CA  N    111.00  2.800
 DAB  OXT  C   O    126.91  3.000
 DAB  OXT  C   CA   115.98  3.000
 DAB  O    C   CA   120.80  1.700
 DAB  HB3  CB  HB2  106.89  3.000
 DAB  HB3  CB  CG   108.40  3.000
 DAB  HB2  CB  CG   108.45  3.000
 DAB  HB3  CB  CA   109.02  3.000
 DAB  HB2  CB  CA   108.58  3.000
 DAB  CG   CB  CA   115.20  3.000
 DAB  HG3  CG  HG2  105.48  3.000
 DAB  HG3  CG  ND   107.94  3.000
 DAB  HG2  CG  ND   113.50  3.000
 DAB  HG3  CG  CB   108.24  3.000
 DAB  HG2  CG  CB   109.66  3.000
 DAB  ND   CG  CB   111.69  3.000
 DAB  HD2  ND  HD1  105.28  3.000
 DAB  HD2  ND  CG   109.62  3.000
 DAB  HD1  ND  CG   109.31  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
 DAB  Var_01  ND   CG  CB  CA   -64.06  30.0  3
 DAB  Var_02  HD1  ND  CG  CB  -176.16  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
 DAB  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
 DAB  plan-1  CA   0.020
 DAB  plan-1  C    0.020
 DAB  plan-1  O    0.020
 DAB  plan-1  OXT  0.020

