# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 12:27:44 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: (2R)-2-hydroxy-3-methylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](O)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
 VAD  VAD  '(2R)-2-hydroxy-3-methylbutanoic acid'  L-peptide  18  8  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VAD
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
 VAD  CA    C  CH1   0  -0.023  -0.4654  -0.4141   0.0840
 VAD  CB    C  CH1   0  -0.295   0.2162   0.3996   1.1970
 VAD  CG1   C  CH3   0  -0.650  -0.3404  -0.0064   2.5578
 VAD  CG2   C  CH3   0  -0.664   1.7346   0.2417   1.1791
 VAD  C     C  C     0   0.509   0.0779  -0.0126  -1.2797
 VAD  O     O  O     0  -0.442  -0.2965   0.9681  -1.8734
 VAD  OXT   O  OH1   0  -0.585   0.9996  -0.8454  -1.7366
 VAD  OE    O  OH1   0  -0.656  -1.8615  -0.2730   0.0834
 VAD  HA    H  HCH1  0   0.257  -0.2616  -1.4758   0.2512
 VAD  HB    H  HCH1  0   0.235  -0.0189   1.4571   1.0226
 VAD  HG11  H  HCH3  0   0.233   0.1282   0.5813   3.3480
 VAD  HG12  H  HCH3  0   0.235  -1.4166   0.1447   2.6275
 VAD  HG13  H  HCH3  0   0.219  -0.1330  -1.0595   2.7614
 VAD  HG21  H  HCH3  0   0.225   2.0254  -0.8059   1.2839
 VAD  HG22  H  HCH3  0   0.235   2.1950   0.6283   0.2695
 VAD  HG23  H  HCH3  0   0.238   2.1722   0.7885   2.0147
 VAD  HXT   H  HOH1  0   0.483   1.3426  -0.5353  -2.5893
 VAD  HOE   H  HOH1  0   0.447  -2.0775   0.6616  -0.0129

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
 VAD  CA   CB    single  1.540  0.027  1.540
 VAD  CA   C     single  1.525  0.021  1.525
 VAD  CA   OE    single  1.403  0.020  1.403
 VAD  CA   HA    single  0.970  0.020  0.970
 VAD  CB   CG1   single  1.525  0.020  1.525
 VAD  CB   CG2   single  1.527  0.020  1.527
 VAD  CB   HB    single  0.970  0.020  1.090
 VAD  CG1  HG11  single  0.970  0.020  1.090
 VAD  CG1  HG12  single  0.970  0.020  1.090
 VAD  CG1  HG13  single  0.970  0.020  1.090
 VAD  CG2  HG21  single  0.970  0.020  1.090
 VAD  CG2  HG22  single  0.970  0.020  1.090
 VAD  CG2  HG23  single  0.970  0.020  1.090
 VAD  C    O     double  1.231  0.020  1.231
 VAD  C    OXT   single  1.324  0.020  1.324
 VAD  OXT  HXT   single  0.850  0.020  0.980
 VAD  OE   HOE   single  0.850  0.020  0.980

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
 VAD  HA    CA   OE    106.44  3.000
 VAD  HA    CA   C     109.00  3.000
 VAD  OE    CA   C     109.17  3.000
 VAD  HA    CA   CB    109.00  3.000
 VAD  OE    CA   CB    112.84  3.000
 VAD  C     CA   CB    111.40  1.900
 VAD  HB    CB   CG2   108.11  3.000
 VAD  HB    CB   CG1   108.67  3.000
 VAD  CG2   CB   CG1   110.24  3.000
 VAD  HB    CB   CA    107.45  3.000
 VAD  CG2   CB   CA    112.19  3.000
 VAD  CG1   CB   CA    110.06  3.000
 VAD  HG13  CG1  HG12  108.03  3.000
 VAD  HG13  CG1  HG11  107.63  3.000
 VAD  HG12  CG1  HG11  107.67  3.000
 VAD  HG13  CG1  CB    110.71  3.000
 VAD  HG12  CG1  CB    112.38  3.000
 VAD  HG11  CG1  CB    110.25  3.000
 VAD  HG23  CG2  HG22  106.98  3.000
 VAD  HG23  CG2  HG21  107.50  3.000
 VAD  HG22  CG2  HG21  107.92  3.000
 VAD  HG23  CG2  CB    109.78  3.000
 VAD  HG22  CG2  CB    113.14  3.000
 VAD  HG21  CG2  CB    111.27  3.000
 VAD  OXT   C    O     123.91  3.000
 VAD  OXT   C    CA    113.08  3.000
 VAD  O     C    CA    120.80  1.700
 VAD  HXT   OXT  C     110.40  3.000
 VAD  HOE   OE   CA    108.69  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
 VAD  CONST_01  HXT   OXT  C   CA   180.00   0.0  0
 VAD  Var_01    HG11  CG1  CB  CA  -179.00  30.0  3
 VAD  Var_02    HG21  CG2  CB  CA   -58.02  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
 VAD  chir_01  CA  CB  C  OE  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
 VAD  plan-1  CA   0.020
 VAD  plan-1  C    0.020
 VAD  plan-1  O    0.020
 VAD  plan-1  OXT  0.020
 VAD  plan-1  HXT  0.020

