# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 20:02:33 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@](O)(CC(O)=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
 VPM  VPM  '(2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid'  ligand  24  12  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VPM
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
 VPM  CAA  C  CH3   0  -0.651   2.8856  -0.1252  -0.7889
 VPM  CAK  C  CH1   0  -0.276   1.6841  -0.9286  -0.2959
 VPM  CAB  C  CH3   0  -0.663   2.0020  -1.5639   1.0551
 VPM  CAL  C  CT    0   0.136   0.3603  -0.1101  -0.3541
 VPM  CAJ  C  C     0   0.556   0.4899   1.1596   0.4811
 VPM  OAF  O  OH1   0  -0.592   0.3109   0.9258   1.7738
 VPM  OAD  O  O     0  -0.434   0.7793   2.2374   0.0339
 VPM  OAG  O  OH1   0  -0.656   0.1328   0.3390  -1.6656
 VPM  CAH  C  CH2   0  -0.604  -0.8214  -0.9726   0.0979
 VPM  CAI  C  C     0   0.569  -2.1315  -0.2386   0.0152
 VPM  OAE  O  O     0  -0.435  -2.2513   0.9600   0.0671
 VPM  OAC  O  OH1   0  -0.594  -3.1601  -1.0702  -0.0832
 VPM  H1   H  HCH3  0   0.223   3.1647   0.6631  -0.0873
 VPM  H2   H  HCH3  0   0.234   3.7479  -0.7853  -0.8875
 VPM  H3   H  HCH3  0   0.236   2.7094   0.3343  -1.7601
 VPM  H4   H  HCH1  0   0.240   1.5229  -1.7499  -1.0066
 VPM  H5   H  HCH3  0   0.229   2.2217  -0.8164   1.8171
 VPM  H6   H  HCH3  0   0.234   1.1981  -2.1987   1.4265
 VPM  H7   H  HCH3  0   0.238   2.8850  -2.1953   0.9534
 VPM  H8   H  HOH1  0   0.482   0.4497   1.7413   2.2785
 VPM  H9   H  HOH1  0   0.449   0.2026  -0.4177  -2.2582
 VPM  H10  H  HCH2  0   0.287  -0.8585  -1.8740  -0.5197
 VPM  H11  H  HCH2  0   0.305  -0.7110  -1.3220   1.1269
 VPM  H12  H  HOH1  0   0.485  -3.9919  -0.5723  -0.0848

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
 VPM  CAB  CAK  single  1.526  0.020  1.526
 VPM  CAA  CAK  single  1.527  0.020  1.527
 VPM  OAG  CAL  single  1.405  0.020  1.405
 VPM  CAK  CAL  single  1.557  0.020  1.557
 VPM  CAL  CAJ  single  1.525  0.020  1.525
 VPM  CAL  CAH  single  1.531  0.020  1.531
 VPM  OAD  CAJ  double  1.202  0.020  1.202
 VPM  CAJ  OAF  single  1.326  0.020  1.326
 VPM  OAE  CAI  double  1.206  0.020  1.206
 VPM  OAC  CAI  single  1.326  0.020  1.326
 VPM  CAI  CAH  single  1.504  0.020  1.504
 VPM  CAA  H1   single  0.970  0.020  1.090
 VPM  CAA  H2   single  0.970  0.020  1.090
 VPM  CAA  H3   single  0.970  0.020  1.090
 VPM  CAK  H4   single  0.970  0.020  1.090
 VPM  CAB  H5   single  0.970  0.020  1.090
 VPM  CAB  H6   single  0.970  0.020  1.090
 VPM  CAB  H7   single  0.970  0.020  1.090
 VPM  OAF  H8   single  0.850  0.020  0.980
 VPM  OAG  H9   single  0.850  0.020  0.980
 VPM  CAH  H10  single  0.970  0.020  1.090
 VPM  CAH  H11  single  0.970  0.020  1.090
 VPM  OAC  H12  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
 VPM  H3   CAA  H2   107.63  3.000
 VPM  H3   CAA  H1   108.05  3.000
 VPM  H2   CAA  H1   107.04  3.000
 VPM  H3   CAA  CAK  112.50  3.000
 VPM  H2   CAA  CAK  109.44  3.000
 VPM  H1   CAA  CAK  111.94  3.000
 VPM  H4   CAK  CAL  104.13  3.000
 VPM  H4   CAK  CAB  106.98  3.000
 VPM  CAL  CAK  CAB  115.40  3.000
 VPM  H4   CAK  CAA  107.46  3.000
 VPM  CAL  CAK  CAA  112.35  3.000
 VPM  CAB  CAK  CAA  109.93  3.000
 VPM  H7   CAB  H6   106.97  3.000
 VPM  H7   CAB  H5   107.41  3.000
 VPM  H6   CAB  H5   108.06  3.000
 VPM  H7   CAB  CAK  109.10  3.000
 VPM  H6   CAB  CAK  112.98  3.000
 VPM  H5   CAB  CAK  112.04  3.000
 VPM  CAH  CAL  OAG  109.31  3.000
 VPM  CAH  CAL  CAJ  111.89  3.000
 VPM  OAG  CAL  CAJ  105.00  3.000
 VPM  CAH  CAL  CAK  110.42  3.000
 VPM  CAJ  CAL  CAK  110.17  3.000
 VPM  OAG  CAL  CAK  109.91  3.000
 VPM  OAD  CAJ  OAF  123.59  3.000
 VPM  OAF  CAJ  CAL  112.06  3.000
 VPM  OAD  CAJ  CAL  124.27  3.000
 VPM  H8   OAF  CAJ  109.89  3.000
 VPM  H9   OAG  CAL  108.14  3.000
 VPM  H11  CAH  H10  105.77  3.000
 VPM  H11  CAH  CAI  107.22  3.000
 VPM  H10  CAH  CAI  109.98  3.000
 VPM  H11  CAH  CAL  112.35  3.000
 VPM  H10  CAH  CAL  108.89  3.000
 VPM  CAI  CAH  CAL  112.41  3.000
 VPM  OAC  CAI  OAE  123.33  3.000
 VPM  OAC  CAI  CAH  111.94  3.000
 VPM  OAE  CAI  CAH  124.71  3.000
 VPM  H12  OAC  CAI  110.09  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
 VPM  CONST_01  H8   OAF  CAJ  CAL  180.00   0.0  0
 VPM  CONST_02  H12  OAC  CAI  CAH  180.00   0.0  0
 VPM  Var_01    OAE  CAI  CAH  CAL  -25.23  30.0  2
 VPM  Var_02    H5   CAB  CAK  CAA   61.06  30.0  3
 VPM  Var_03    H1   CAA  CAK  CAB  -59.02  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
 VPM  chir_01  CAL  CAK  CAJ  CAH  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
 VPM  plan-1  CAL  0.020
 VPM  plan-1  CAJ  0.020
 VPM  plan-1  OAF  0.020
 VPM  plan-1  OAD  0.020
 VPM  plan-1  H8   0.020
 VPM  plan-2  CAH  0.020
 VPM  plan-2  CAI  0.020
 VPM  plan-2  OAE  0.020
 VPM  plan-2  OAC  0.020
 VPM  plan-2  H12  0.020

