# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:27:13 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (2S,3S)-2-hydroxy-3-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](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
 OIL  OIL  '(2S,3S)-2-hydroxy-3-methylpentanoic acid'  ligand  20  9  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OIL
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
 OIL  C     C  C      0   0.394   1.7340  -0.0029   0.0792
 OIL  O     O  O      0  -0.614   2.2861  -0.7892   0.8862
 OIL  O1    O  OH1    0  -0.700   0.3121  -1.8959  -0.2583
 OIL  CA    C  CH1    0  -0.046   0.3731  -0.5024  -0.4638
 OIL  CB    C  CH1    0  -0.251  -0.8282   0.2046   0.1988
 OIL  CG1   C  CH2    0  -0.405  -2.1400  -0.4406  -0.2655
 OIL  CG2   C  CH3    0  -0.664  -0.8388   1.7065  -0.0720
 OIL  OXT   O  OC    -1  -0.588   2.1700   1.0915  -0.3092
 OIL  HO1   H  HOH1   0   0.423   1.0313  -2.0353   0.3858
 OIL  HA    H  HCH1   0   0.184   0.3298  -0.2951  -1.5431
 OIL  HB    H  HCH1   0   0.200  -0.7418   0.0486   1.2836
 OIL  HD1   H  HCH3   0   0.213  -3.2857  -0.0564   1.5381
 OIL  HD1A  H  HCH3   0   0.217  -3.5766   1.1226   0.2630
 OIL  HD1B  H  HCH3   0   0.226  -4.2670  -0.4875   0.1421
 OIL  HG1   H  HCH2   0   0.199  -2.2517  -0.2757  -1.3438
 OIL  HG1A  H  HCH2   0   0.223  -2.0766  -1.5207  -0.1264
 OIL  HG2   H  HCH3   0   0.220  -1.6908   2.1850   0.4110
 OIL  HG2A  H  HCH3   0   0.234   0.0614   2.1961   0.2906
 OIL  HG2B  H  HCH3   0   0.204  -0.9147   1.9069  -1.1440
 OIL  CD1   C  CH3    0  -0.669  -3.3822   0.0674   0.4572

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
 OIL  C    CA    single  1.548  0.020  1.548
 OIL  C    OXT   deloc   1.240  0.020  1.240
 OIL  O    C     deloc   1.255  0.020  1.255
 OIL  O1   HO1   single  0.850  0.020  0.980
 OIL  CA   O1    single  1.410  0.020  1.410
 OIL  CA   CB    single  1.543  0.020  1.543
 OIL  CA   HA    single  0.970  0.020  1.090
 OIL  CB   CG1   single  1.534  0.020  1.534
 OIL  CB   HB    single  0.970  0.020  1.090
 OIL  CD1  HD1   single  0.970  0.020  1.090
 OIL  CD1  HD1A  single  0.970  0.020  1.090
 OIL  CD1  HD1B  single  0.970  0.020  1.090
 OIL  CG1  CD1   single  1.524  0.020  1.524
 OIL  CG1  HG1   single  0.970  0.020  1.090
 OIL  CG1  HG1A  single  0.970  0.020  1.090
 OIL  CG2  CB    single  1.526  0.020  1.526
 OIL  CG2  HG2   single  0.970  0.020  1.090
 OIL  CG2  HG2A  single  0.970  0.020  1.090
 OIL  CG2  HG2B  single  0.970  0.020  1.090

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
 OIL  OXT   C    CA    118.94  3.000
 OIL  OXT   C    O     126.84  3.000
 OIL  CA    C    O     114.22  3.000
 OIL  HO1   O1   CA    101.87  3.000
 OIL  HA    CA   CB    107.72  3.000
 OIL  HA    CA   O1    109.13  3.000
 OIL  CB    CA   O1    110.89  3.000
 OIL  HA    CA   C     108.54  3.000
 OIL  CB    CA   C     112.70  3.000
 OIL  O1    CA   C     107.80  3.000
 OIL  HB    CB   CG2   108.38  3.000
 OIL  CG2   CB   CG1   110.75  3.000
 OIL  HB    CB   CG1   107.83  3.000
 OIL  CG2   CB   CA    112.34  3.000
 OIL  HB    CB   CA    107.30  3.000
 OIL  CG1   CB   CA    110.06  3.000
 OIL  HG1A  CG1  HG1   106.27  3.000
 OIL  HG1A  CG1  CD1   108.48  3.000
 OIL  HG1   CG1  CD1   109.46  3.000
 OIL  HG1A  CG1  CB    109.16  3.000
 OIL  HG1   CG1  CB    108.75  3.000
 OIL  CD1   CG1  CB    114.41  3.000
 OIL  HG2B  CG2  HG2A  107.58  3.000
 OIL  HG2B  CG2  HG2   107.45  3.000
 OIL  HG2A  CG2  HG2   107.56  3.000
 OIL  HG2B  CG2  CB    110.78  3.000
 OIL  HG2A  CG2  CB    112.23  3.000
 OIL  HG2   CG2  CB    111.03  3.000
 OIL  HD1B  CD1  HD1A  107.23  3.000
 OIL  HD1B  CD1  HD1   107.44  3.000
 OIL  HD1A  CD1  HD1   107.56  3.000
 OIL  HD1B  CD1  CG1   110.77  3.000
 OIL  HD1A  CD1  CG1   112.55  3.000
 OIL  HD1   CD1  CG1   111.07  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
 OIL  Var_01  HD1  CD1  CG1  CB  -55.94  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
 OIL  chir_01  CA  C   O1   CB   negativ
 OIL  chir_02  CB  CA  CG1  CG2  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
 OIL  plan-1  C    0.020
 OIL  plan-1  O    0.020
 OIL  plan-1  CA   0.020
 OIL  plan-1  OXT  0.020

