# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:26:01 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  22  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    4.004   2.8499  -0.1409  -0.8080
 VPM  CAK  C  CH1    0    4.056   1.6572  -0.9632  -0.3240
 VPM  CAB  C  CH3    0    4.008   1.9887  -1.6101   1.0176
 VPM  CAL  C  CT     0    2.216   0.3273  -0.1580  -0.3592
 VPM  CAJ  C  C      0    4.261   0.4748   1.1387   0.4693
 VPM  OAF  O  OC    -1    6.001   0.5030   0.9946   1.7103
 VPM  OAD  O  O      0    5.998   0.6221   2.2087  -0.1463
 VPM  OAG  O  OH1    0    2.442   0.0746   0.2109  -1.7097
 VPM  CAH  C  CH2    0   -1.861  -0.8301  -1.0238   0.1424
 VPM  CAI  C  C      0  -19.630  -2.2109  -0.4209  -0.1491
 VPM  OAE  O  O      0   -0.016  -2.4062   0.7538   0.2226
 VPM  OAC  O  OC    -1  -21.321  -3.0491  -1.1575  -0.7138
 VPM  H1   H  HCH3   0    0.999   3.1070   0.6472  -0.0974
 VPM  H2   H  HCH3   0    1.000   3.7302  -0.7780  -0.9158
 VPM  H3   H  HCH3   0    0.999   2.6581   0.3285  -1.7719
 VPM  H4   H  HCH1   0    1.032   1.5154  -1.7844  -1.0425
 VPM  H5   H  HCH3   0    0.999   2.1709  -0.8577   1.7830
 VPM  H6   H  HCH3   0    1.004   1.1870  -2.2579   1.3724
 VPM  H7   H  HCH3   0    1.000   2.8860  -2.2252   0.9234
 VPM  H9   H  HOH1   0   -1.763  -0.0118  -0.6073  -2.2106
 VPM  H10  H  HCH2   0    1.598  -0.7583  -2.0216  -0.3066
 VPM  H11  H  HCH2   0    0.972  -0.7306  -1.1635   1.2208

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  1.423  0.020  1.423
 VPM  CAK  CAL  single  1.555  0.020  1.555
 VPM  CAL  CAJ  single  1.546  0.020  1.546
 VPM  CAL  CAH  single  1.530  0.020  1.530
 VPM  OAD  CAJ  deloc   1.243  0.020  1.243
 VPM  CAJ  OAF  deloc   1.250  0.020  1.250
 VPM  OAE  CAI  deloc   1.248  0.020  1.248
 VPM  OAC  CAI  deloc   1.251  0.020  1.251
 VPM  CAI  CAH  single  1.535  0.020  1.535
 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  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

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   107.83  3.000
 VPM  H3   CAA  H1   107.84  3.000
 VPM  H2   CAA  H1   107.19  3.000
 VPM  H3   CAA  CAK  112.02  3.000
 VPM  H2   CAA  CAK  110.28  3.000
 VPM  H1   CAA  CAK  111.48  3.000
 VPM  H4   CAK  CAL  105.15  3.000
 VPM  H4   CAK  CAB  106.60  3.000
 VPM  CAL  CAK  CAB  115.17  3.000
 VPM  H4   CAK  CAA  107.19  3.000
 VPM  CAL  CAK  CAA  112.45  3.000
 VPM  CAB  CAK  CAA  109.71  3.000
 VPM  H7   CAB  H6   107.32  3.000
 VPM  H7   CAB  H5   108.21  3.000
 VPM  H6   CAB  H5   107.76  3.000
 VPM  H7   CAB  CAK  109.97  3.000
 VPM  H6   CAB  CAK  112.23  3.000
 VPM  H5   CAB  CAK  111.19  3.000
 VPM  CAH  CAL  OAG  108.88  3.000
 VPM  CAH  CAL  CAJ  111.78  3.000
 VPM  OAG  CAL  CAJ  107.95  3.000
 VPM  CAH  CAL  CAK  110.28  3.000
 VPM  CAJ  CAL  CAK  109.91  3.000
 VPM  OAG  CAL  CAK  107.92  3.000
 VPM  OAD  CAJ  OAF  126.03  3.000
 VPM  OAF  CAJ  CAL  115.96  3.000
 VPM  OAD  CAJ  CAL  117.90  3.000
 VPM  H9   OAG  CAL  106.82  3.000
 VPM  H11  CAH  H10  106.38  3.000
 VPM  H11  CAH  CAI  108.66  3.000
 VPM  H10  CAH  CAI  109.79  3.000
 VPM  H11  CAH  CAL  109.10  3.000
 VPM  H10  CAH  CAL  109.34  3.000
 VPM  CAI  CAH  CAL  113.33  3.000
 VPM  OAC  CAI  OAE  125.75  3.000
 VPM  OAC  CAI  CAH  117.22  3.000
 VPM  OAE  CAI  CAH  117.01  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  Var_01  OAE  CAI  CAH  CAL  -52.61  30.0  2
 VPM  Var_02  H5   CAB  CAK  CAA   62.75  30.0  3
 VPM  Var_03  H1   CAA  CAK  CAB  -59.78  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-2  CAH  0.020
 VPM  plan-2  CAI  0.020
 VPM  plan-2  OAE  0.020
 VPM  plan-2  OAC  0.020

