# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 03:47:01 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (2S,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
 VLL  VLL  '(2S,3R)-2,3-diaminobutanoic acid'  L-peptide  17  8  .  2012-08-28  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_VLL
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
 VLL  N     N  NH2    0  -0.822  42.4765  32.8156  31.1966
 VLL  CA    C  CH1    0  -0.211  43.5632  32.2854  32.0095
 VLL  CB    C  CH1    0  -0.067  43.9534  33.2946  33.0981
 VLL  CG1   C  CH3    0  -0.669  44.5287  34.5727  32.4910
 VLL  C     C  C      0   0.412  43.2017  30.9120  32.6364
 VLL  OXT   O  OC    -1  -0.609  44.0667  30.4071  33.3783
 VLL  O     O  O      0  -0.600  42.0988  30.4132  32.3308
 VLL  NG2   N  NH2    0  -0.796  42.7977  33.5297  33.9557
 VLL  HN1   H  HNH2   0   0.333  42.8199  33.1466  30.3066
 VLL  HN2   H  HNH2   0   0.335  41.8333  32.0562  31.0120
 VLL  HA    H  HCH1   0   0.202  44.4642  32.1126  31.4018
 VLL  HB    H  HCH1   0   0.202  44.7333  32.8282  33.7059
 VLL  HG11  H  HCH3   0   0.217  44.8162  35.2796  33.2726
 VLL  HG12  H  HCH3   0   0.208  45.4170  34.3682  31.8890
 VLL  HG13  H  HCH3   0   0.210  43.7959  35.0686  31.8504
 VLL  HG21  H  HNH2   0   0.331  43.0088  34.2664  34.6182
 VLL  HG22  H  HNH2   0   0.324  42.0508  33.8863  33.3696

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
 VLL  N    CA    single  1.458  0.019  1.458
 VLL  N    HN1   single  0.890  0.020  1.040
 VLL  N    HN2   single  0.890  0.020  1.040
 VLL  CA   CB    single  1.521  0.033  1.521
 VLL  CA   C     single  1.525  0.021  1.525
 VLL  CA   HA    single  0.970  0.020  0.970
 VLL  CB   CG1   single  1.527  0.020  1.527
 VLL  CB   NG2   single  1.458  0.020  1.458
 VLL  CB   HB    single  0.970  0.020  1.090
 VLL  CG1  HG11  single  0.970  0.020  1.090
 VLL  CG1  HG12  single  0.970  0.020  1.090
 VLL  CG1  HG13  single  0.970  0.020  1.090
 VLL  C    OXT   deloc   1.246  0.020  1.246
 VLL  C    O     deloc   1.231  0.020  1.231
 VLL  NG2  HG21  single  0.890  0.020  1.040
 VLL  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
 VLL  HN2   N    HN1   107.54  3.000
 VLL  HN2   N    CA    107.62  3.000
 VLL  HN1   N    CA    110.94  3.000
 VLL  HA    CA   C     110.00  3.000
 VLL  HA    CA   CB    109.00  3.000
 VLL  C     CA   CB    110.50  1.500
 VLL  HA    CA   N     110.00  3.000
 VLL  C     CA   N     111.00  2.800
 VLL  CB    CA   N     110.40  1.500
 VLL  HB    CB   NG2   107.90  3.000
 VLL  HB    CB   CG1   108.02  3.000
 VLL  NG2   CB   CG1   113.41  3.000
 VLL  HB    CB   CA    107.16  3.000
 VLL  NG2   CB   CA    108.76  3.000
 VLL  CG1   CB   CA    111.34  3.000
 VLL  HG13  CG1  HG12  107.90  3.000
 VLL  HG13  CG1  HG11  107.60  3.000
 VLL  HG12  CG1  HG11  107.54  3.000
 VLL  HG13  CG1  CB    111.12  3.000
 VLL  HG12  CG1  CB    111.64  3.000
 VLL  HG11  CG1  CB    110.86  3.000
 VLL  O     C    OXT   126.65  3.000
 VLL  O     C    CA    120.80  1.700
 VLL  OXT   C    CA    120.80  1.700
 VLL  HG22  NG2  HG21  106.01  3.000
 VLL  HG22  NG2  CB    107.49  3.000
 VLL  HG21  NG2  CB    109.68  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
 VLL  chir_01  CA  N    CB  C    negativ
 VLL  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
 VLL  plan-1  CA   0.020
 VLL  plan-1  C    0.020
 VLL  plan-1  OXT  0.020
 VLL  plan-1  O    0.020

