# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 00:26:43 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (2R,3R)-2,3-diaminobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)[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
 VDL  VDL  '(2R,3R)-2,3-diaminobutanoic acid'  D-peptide  17  8  .  2016-04-26  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_VDL
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
 VDL  N     N  NH2    0  -0.802  35.5463  31.1834  34.4391
 VDL  CA    C  CH1    0  -0.150  35.9497  30.1038  35.3319
 VDL  CB    C  CH1    0  -0.102  34.8014  29.7632  36.2988
 VDL  CG1   C  CH3    0  -0.668  35.1591  28.5720  37.1872
 VDL  C     C  C      0   0.388  37.2490  30.4636  36.0984
 VDL  OXT   O  OC    -1  -0.602  37.3119  31.5955  36.6251
 VDL  O     O  O      0  -0.605  38.1244  29.5770  36.1450
 VDL  NG2   N  NH2    0  -0.799  34.3596  30.9348  37.0487
 VDL  HN1   H  HNH2   0   0.332  36.2489  31.3015  33.7196
 VDL  HN2   H  HNH2   0   0.327  34.7041  30.9052  33.9489
 VDL  HA    H  HCH1   0   0.174  36.1534  29.1715  34.7842
 VDL  HB    H  HCH1   0   0.202  33.9583  29.4445  35.6692
 VDL  HG11  H  HCH3   0   0.218  34.2909  28.2637  37.7730
 VDL  HG12  H  HCH3   0   0.211  35.4805  27.7097  36.6000
 VDL  HG13  H  HCH3   0   0.216  35.9590  28.8152  37.8889
 VDL  HG21  H  HNH2   0   0.329  33.7866  30.6330  37.8274
 VDL  HG22  H  HNH2   0   0.330  35.1736  31.3884  37.4465

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
 VDL  N    CA    single  1.458  0.019  1.458
 VDL  N    HN1   single  0.890  0.020  1.040
 VDL  N    HN2   single  0.890  0.020  1.040
 VDL  CA   CB    single  1.521  0.033  1.521
 VDL  CA   C     single  1.525  0.021  1.525
 VDL  CA   HA    single  0.970  0.020  0.970
 VDL  CB   CG1   single  1.528  0.020  1.528
 VDL  CB   NG2   single  1.460  0.020  1.460
 VDL  CB   HB    single  0.970  0.020  1.090
 VDL  CG1  HG11  single  0.970  0.020  1.090
 VDL  CG1  HG12  single  0.970  0.020  1.090
 VDL  CG1  HG13  single  0.970  0.020  1.090
 VDL  C    OXT   deloc   1.250  0.020  1.250
 VDL  C    O     deloc   1.231  0.020  1.231
 VDL  NG2  HG21  single  0.890  0.020  1.040
 VDL  NG2  HG22  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
 VDL  HN2   N    HN1   105.36  3.000
 VDL  HN2   N    CA    108.83  3.000
 VDL  HN1   N    CA    109.24  3.000
 VDL  HA    CA   C     110.00  3.000
 VDL  HA    CA   CB    109.00  3.000
 VDL  C     CA   CB    110.50  1.500
 VDL  HA    CA   N     110.00  3.000
 VDL  C     CA   N     111.00  2.800
 VDL  CB    CA   N     110.40  1.500
 VDL  HB    CB   NG2   107.15  3.000
 VDL  HB    CB   CG1   106.64  3.000
 VDL  NG2   CB   CG1   113.44  3.000
 VDL  HB    CB   CA    106.05  3.000
 VDL  NG2   CB   CA    111.77  3.000
 VDL  CG1   CB   CA    111.28  3.000
 VDL  HG13  CG1  HG12  107.82  3.000
 VDL  HG13  CG1  HG11  107.50  3.000
 VDL  HG12  CG1  HG11  107.44  3.000
 VDL  HG13  CG1  CB    111.81  3.000
 VDL  HG12  CG1  CB    111.83  3.000
 VDL  HG11  CG1  CB    110.23  3.000
 VDL  O     C    OXT   126.36  3.000
 VDL  O     C    CA    120.80  1.700
 VDL  OXT   C    CA    120.80  1.700
 VDL  HG22  NG2  HG21  106.62  3.000
 VDL  HG22  NG2  CB    108.54  3.000
 VDL  HG21  NG2  CB    109.09  3.000

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
 VDL  chir_01  CA  N    CB  C    positiv
 VDL  chir_02  CB  NG2  CA  CG1  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
 VDL  plan-1  CA   0.020
 VDL  plan-1  C    0.020
 VDL  plan-1  OXT  0.020
 VDL  plan-1  O    0.020

