# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 02:40:34 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (2S)-2-hydroxy-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)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
 1LU  1LU  '(2S)-2-hydroxy-4-methylpentanoic acid'  ligand  21  9  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1LU
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
 1LU  OS    O  OH1   0  -0.651   0.5407   1.6639   0.5459
 1LU  CA    C  CH1   0  -0.076   0.5475   0.2720   0.4183
 1LU  C     C  C     0   0.512   1.8929  -0.2116  -0.0993
 1LU  O     O  O     0  -0.438   2.7251   0.5048  -0.5944
 1LU  CB    C  CH2   0  -0.461  -0.5775  -0.2605  -0.4762
 1LU  CG    C  CH1   0  -0.227  -1.9794   0.1861  -0.0564
 1LU  CD1   C  CH3   0  -0.652  -2.9999  -0.3404  -1.0609
 1LU  CD2   C  CH3   0  -0.665  -2.3328  -0.2733   1.3544
 1LU  OXT   O  OH1   0  -0.591   2.0343  -1.5225   0.0409
 1LU  HOS   H  HOH1  0   0.447   0.6439   2.0584  -0.3270
 1LU  HA    H  HCH1  0   0.273   0.4208  -0.1287   1.4287
 1LU  HB1   H  HCH2  0   0.241  -0.3941   0.0593  -1.5086
 1LU  HB2   H  HCH2  0   0.238  -0.5400  -1.3536  -0.4819
 1LU  HG    H  HCH1  0   0.222  -2.0168   1.2796  -0.0814
 1LU  HD11  H  HCH3  0   0.226  -2.7787   0.0008  -2.0737
 1LU  HD12  H  HCH3  0   0.214  -3.0076  -1.4331  -1.0728
 1LU  HD13  H  HCH3  0   0.228  -4.0078  -0.0049  -0.8113
 1LU  HD21  H  HCH3  0   0.230  -1.6776   0.1602   2.1109
 1LU  HD22  H  HCH3  0   0.231  -3.3533   0.0158   1.6099
 1LU  HD23  H  HCH3  0   0.215  -2.2672  -1.3610   1.4393
 1LU  HXT   H  HOH1  0   0.485   2.8847  -1.8105  -0.3239

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
 1LU  OS   CA    single  1.398  0.020  1.398
 1LU  OS   HOS   single  0.850  0.020  0.980
 1LU  CA   C     single  1.520  0.020  1.520
 1LU  CA   CB    single  1.533  0.020  1.533
 1LU  CA   HA    single  0.970  0.020  1.090
 1LU  C    O     double  1.205  0.020  1.205
 1LU  C    OXT   single  1.326  0.020  1.326
 1LU  CB   CG    single  1.530  0.020  1.530
 1LU  CB   HB1   single  0.970  0.020  1.090
 1LU  CB   HB2   single  0.970  0.020  1.090
 1LU  CG   CD1   single  1.526  0.020  1.526
 1LU  CG   CD2   single  1.525  0.020  1.525
 1LU  CG   HG    single  0.970  0.020  1.090
 1LU  CD1  HD11  single  0.970  0.020  1.090
 1LU  CD1  HD12  single  0.970  0.020  1.090
 1LU  CD1  HD13  single  0.970  0.020  1.090
 1LU  CD2  HD21  single  0.970  0.020  1.090
 1LU  CD2  HD22  single  0.970  0.020  1.090
 1LU  CD2  HD23  single  0.970  0.020  1.090
 1LU  OXT  HXT   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
 1LU  HOS   OS   CA    108.93  3.000
 1LU  HA    CA   CB    109.06  3.000
 1LU  HA    CA   C     107.48  3.000
 1LU  CB    CA   C     109.89  3.000
 1LU  HA    CA   OS    106.24  3.000
 1LU  CB    CA   OS    113.31  3.000
 1LU  C     CA   OS    110.62  3.000
 1LU  OXT   C    O     123.90  3.000
 1LU  OXT   C    CA    111.89  3.000
 1LU  O     C    CA    124.20  3.000
 1LU  HB2   CB   HB1   106.31  3.000
 1LU  HB2   CB   CG    108.94  3.000
 1LU  HB1   CB   CG    109.05  3.000
 1LU  HB2   CB   CA    108.97  3.000
 1LU  HB1   CB   CA    109.00  3.000
 1LU  CG    CB   CA    114.27  3.000
 1LU  HG    CG   CD2   108.31  3.000
 1LU  HG    CG   CD1   107.87  3.000
 1LU  CD2   CG   CD1   110.49  3.000
 1LU  HG    CG   CB    108.46  3.000
 1LU  CD2   CG   CB    112.22  3.000
 1LU  CD1   CG   CB    109.36  3.000
 1LU  HD13  CD1  HD12  107.67  3.000
 1LU  HD13  CD1  HD11  107.66  3.000
 1LU  HD12  CD1  HD11  107.70  3.000
 1LU  HD13  CD1  CG    111.16  3.000
 1LU  HD12  CD1  CG    110.92  3.000
 1LU  HD11  CD1  CG    111.56  3.000
 1LU  HD23  CD2  HD22  107.56  3.000
 1LU  HD23  CD2  HD21  107.79  3.000
 1LU  HD22  CD2  HD21  107.11  3.000
 1LU  HD23  CD2  CG    110.96  3.000
 1LU  HD22  CD2  CG    110.70  3.000
 1LU  HD21  CD2  CG    112.49  3.000
 1LU  HXT   OXT  C     110.34  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
 1LU  CONST_01  HXT   OXT  C   CA  180.00   0.0  0
 1LU  Var_01    CD1   CG   CB  CA  176.91  30.0  3
 1LU  Var_02    HD11  CD1  CG  CB  -57.55  30.0  3
 1LU  Var_03    HD21  CD2  CG  CB   62.96  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
 1LU  chir_01  CA  OS  C  CB  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
 1LU  plan-1  CA   0.020
 1LU  plan-1  C    0.020
 1LU  plan-1  O    0.020
 1LU  plan-1  OXT  0.020
 1LU  plan-1  HXT  0.020

