# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 06:32:49 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: (2S)-2,3-dihydroxy-3-methylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)[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
 89V  89V  '(2S)-2,3-dihydroxy-3-methylbutanoic acid'  ligand  18  9  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_89V
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
 89V  OXT  O  OC    -1  -0.579  -1.8323  -1.1574  -0.4522
 89V  C    C  C      0   0.386  -1.4529  -0.0274  -0.1217
 89V  O    O  O      0  -0.618  -2.0806   0.8089   0.5747
 89V  CA   C  CH1    0  -0.066  -0.0679   0.4750  -0.6016
 89V  CB   C  CT     0   0.184   1.1110  -0.2305   0.1047
 89V  CG2  C  CH3    0  -0.673   2.4285   0.3874  -0.3655
 89V  CG1  C  CH3    0  -0.679   1.0015  -0.1169   1.6241
 89V  O1   O  OH1    0  -0.670   1.0622  -1.5912  -0.2946
 89V  O2   O  OH1    0  -0.698  -0.0031   1.8597  -0.3783
 89V  H2   H  HCH1   0   0.202   0.0283   0.2668  -1.6777
 89V  H3   H  HCH3   0   0.228   2.5066   1.4382  -0.0918
 89V  H4   H  HCH3   0   0.221   3.2763  -0.1328   0.0891
 89V  H5   H  HCH3   0   0.224   2.5310   0.3109  -1.4503
 89V  H6   H  HCH3   0   0.232   0.1155  -0.6270   2.0046
 89V  H7   H  HCH3   0   0.221   1.8753  -0.5662   2.1030
 89V  H8   H  HCH3   0   0.222   0.9593   0.9243   1.9438
 89V  H9   H  HOH1   0   0.437   1.8422  -2.0257   0.0662
 89V  H10  H  HOH1   0   0.427  -0.7895   1.9993   0.1868

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
 89V  CG2  CB   single  1.529  0.020  1.529
 89V  O1   CB   single  1.419  0.020  1.419
 89V  CG1  CB   single  1.528  0.020  1.528
 89V  CB   CA   single  1.545  0.020  1.545
 89V  CA   O2   single  1.404  0.020  1.404
 89V  CA   C    single  1.550  0.020  1.550
 89V  C    O    deloc   1.256  0.020  1.256
 89V  C    OXT  deloc   1.237  0.020  1.237
 89V  CA   H2   single  0.970  0.020  1.090
 89V  CG2  H3   single  0.970  0.020  1.090
 89V  CG2  H4   single  0.970  0.020  1.090
 89V  CG2  H5   single  0.970  0.020  1.090
 89V  CG1  H6   single  0.970  0.020  1.090
 89V  CG1  H7   single  0.970  0.020  1.090
 89V  CG1  H8   single  0.970  0.020  1.090
 89V  O1   H9   single  0.850  0.020  0.980
 89V  O2   H10  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
 89V  CA   C    O    113.73  3.000
 89V  O    C    OXT  127.08  3.000
 89V  CA   C    OXT  119.18  3.000
 89V  H2   CA   O2   109.76  3.000
 89V  H2   CA   CB   107.10  3.000
 89V  O2   CA   CB   110.03  3.000
 89V  H2   CA   C    108.64  3.000
 89V  O2   CA   C    108.16  3.000
 89V  CB   CA   C    113.11  3.000
 89V  O1   CB   CG1  110.41  3.000
 89V  CG1  CB   CG2  109.73  3.000
 89V  O1   CB   CG2  109.30  3.000
 89V  CG1  CB   CA   111.47  3.000
 89V  O1   CB   CA   106.44  3.000
 89V  CG2  CB   CA   109.41  3.000
 89V  H5   CG2  H4   107.87  3.000
 89V  H5   CG2  H3   108.09  3.000
 89V  H4   CG2  H3   107.39  3.000
 89V  H5   CG2  CB   110.97  3.000
 89V  H4   CG2  CB   110.36  3.000
 89V  H3   CG2  CB   112.00  3.000
 89V  H8   CG1  H7   107.16  3.000
 89V  H8   CG1  H6   108.24  3.000
 89V  H7   CG1  H6   107.71  3.000
 89V  H8   CG1  CB   111.45  3.000
 89V  H7   CG1  CB   110.36  3.000
 89V  H6   CG1  CB   111.74  3.000
 89V  H9   O1   CB   107.42  3.000
 89V  H10  O2   CA   101.27  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
 89V  Var_01  H3  CG2  CB  CA  63.10  30.0  3
 89V  Var_02  H6  CG1  CB  CA  63.75  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
 89V  chir_01  CA  CB  O2  C  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
 89V  plan-1  OXT  0.020
 89V  plan-1  C    0.020
 89V  plan-1  O    0.020
 89V  plan-1  CA   0.020

