# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 20:13:31 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (2R)-2,4-dihydroxy-3,3-dimethylbutanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO)[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
 PAF  PAF  (2R)-2,4-dihydroxy-3,3-dimethylbutanoate  ligand  21  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PAF
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
 PAF  O1    O  OC    -1  -0.613   2.4762  -0.7555  -0.6155
 PAF  C1    C  C      0   0.401   1.8504   0.0794   0.0808
 PAF  O2    O  O      0  -0.583   2.2211   1.2239   0.3811
 PAF  C2    C  CH1    0  -0.049   0.4887  -0.4348   0.6115
 PAF  O3    O  OH1    0  -0.700   0.4682  -1.8333   0.4501
 PAF  C3    C  CT     0  -0.142  -0.7336   0.2263  -0.0775
 PAF  C4    C  CH3    0  -0.656  -0.6784   0.0170  -1.5916
 PAF  C5    C  CH3    0  -0.643  -0.7880   1.7223   0.2367
 PAF  C6    C  CH2    0  -0.116  -1.9796  -0.4508   0.5063
 PAF  O4    O  OH1    0  -0.676  -3.1514   0.1295  -0.0285
 PAF  H21   H  HCH1   0   0.198   0.4245  -0.1956   1.6841
 PAF  HO31  H  HOH1   0   0.426   1.2328  -1.9729  -0.1426
 PAF  H41   H  HCH3   0   0.221   0.1709   0.5407  -2.0341
 PAF  H42   H  HCH3   0   0.218  -0.5915  -1.0397  -1.8507
 PAF  H43   H  HCH3   0   0.224  -1.5795   0.3996  -2.0719
 PAF  H51   H  HCH3   0   0.217  -1.6925   2.1711  -0.1745
 PAF  H52   H  HCH3   0   0.208  -0.7915   1.9011   1.3151
 PAF  H53   H  HCH3   0   0.230   0.0672   2.2488  -0.1805
 PAF  H61   H  HCH2   0   0.203  -1.9474  -1.5240   0.2919
 PAF  H62   H  HCH2   0   0.181  -1.9540  -0.3410   1.6020
 PAF  HO41  H  HOH1   0   0.451  -3.8965  -0.4163   0.2360

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
 PAF  O1  C1    deloc   1.254  0.020  1.254
 PAF  C1  O2    deloc   1.240  0.020  1.240
 PAF  C1  C2    single  1.549  0.020  1.549
 PAF  C2  O3    single  1.408  0.020  1.408
 PAF  C2  C3    single  1.551  0.020  1.551
 PAF  C2  H21   single  0.970  0.020  1.090
 PAF  O3  HO31  single  0.850  0.020  0.980
 PAF  C3  C4    single  1.530  0.020  1.530
 PAF  C3  C5    single  1.530  0.020  1.530
 PAF  C3  C6    single  1.534  0.020  1.534
 PAF  C4  H41   single  0.970  0.020  1.090
 PAF  C4  H42   single  0.970  0.020  1.090
 PAF  C4  H43   single  0.970  0.020  1.090
 PAF  C5  H51   single  0.970  0.020  1.090
 PAF  C5  H52   single  0.970  0.020  1.090
 PAF  C5  H53   single  0.970  0.020  1.090
 PAF  C6  O4    single  1.413  0.020  1.413
 PAF  C6  H61   single  0.970  0.020  1.090
 PAF  C6  H62   single  0.970  0.020  1.090
 PAF  O4  HO41  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
 PAF  C2    C1  O2   119.09  3.000
 PAF  C2    C1  O1   114.06  3.000
 PAF  O2    C1  O1   126.84  3.000
 PAF  H21   C2  C3   107.11  3.000
 PAF  H21   C2  O3   109.07  3.000
 PAF  C3    C2  O3   111.16  3.000
 PAF  H21   C2  C1   108.23  3.000
 PAF  C3    C2  C1   113.51  3.000
 PAF  O3    C2  C1   107.65  3.000
 PAF  HO31  O3  C2   101.54  3.000
 PAF  C6    C3  C5   108.95  3.000
 PAF  C6    C3  C4   110.23  3.000
 PAF  C5    C3  C4   109.78  3.000
 PAF  C6    C3  C2   106.44  3.000
 PAF  C5    C3  C2   110.71  3.000
 PAF  C4    C3  C2   110.67  3.000
 PAF  H43   C4  H42  107.52  3.000
 PAF  H43   C4  H41  107.22  3.000
 PAF  H42   C4  H41  107.84  3.000
 PAF  H43   C4  C3   110.99  3.000
 PAF  H42   C4  C3   111.74  3.000
 PAF  H41   C4  C3   111.33  3.000
 PAF  H53   C5  H52  107.57  3.000
 PAF  H53   C5  H51  107.97  3.000
 PAF  H52   C5  H51  107.59  3.000
 PAF  H53   C5  C3   111.51  3.000
 PAF  H52   C5  C3   111.26  3.000
 PAF  H51   C5  C3   110.77  3.000
 PAF  H62   C6  H61  106.97  3.000
 PAF  H62   C6  O4   110.78  3.000
 PAF  H61   C6  O4   110.66  3.000
 PAF  H62   C6  C3   108.41  3.000
 PAF  H61   C6  C3   109.54  3.000
 PAF  O4    C6  C3   110.39  3.000
 PAF  HO41  O4  C6   107.80  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
 PAF  Var_01  O4   C6  C3  C2   177.66  30.0  3
 PAF  Var_02  H41  C4  C3  C2   -65.82  30.0  3
 PAF  Var_03  H51  C5  C3  C2  -175.08  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
 PAF  chir_01  C2  C1  O3  C3  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
 PAF  plan-1  O1  0.020
 PAF  plan-1  C1  0.020
 PAF  plan-1  O2  0.020
 PAF  plan-1  C2  0.020

