# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 13:59:09 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: (2R,3R)-3-hydroxy-2,4-dimethylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](O)[C@@H](C)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
 28H  28H  '(2R,3R)-3-hydroxy-2,4-dimethylpentanoic acid'  ligand  24  10  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_28H
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
 28H  CCB  C  CH3   0  -0.680  -2.1963   0.8462  -1.2855
 28H  CCA  C  CH1   0  -0.271  -1.9273   0.4008   0.1496
 28H  CCC  C  CH3   0  -0.647  -3.0216  -0.5481   0.6322
 28H  CBZ  C  CH1   0   0.071  -0.5453  -0.2375   0.3437
 28H  OCF  O  OH1   0  -0.667  -0.4269  -1.4842  -0.3124
 28H  CBY  C  CH1   0  -0.408   0.6294   0.6740  -0.0512
 28H  CCE  C  CH3   0  -0.669   0.6762   1.9670   0.7601
 28H  CBX  C  C     0   0.562   1.9025  -0.1099   0.1725
 28H  OCD  O  O     0  -0.452   2.2946  -0.4597   1.2592
 28H  H1   H  HCH3  0   0.235  -1.5111   1.6259  -1.6201
 28H  H2   H  HCH3  0   0.215  -2.1288   0.0153  -1.9923
 28H  H3   H  HCH3  0   0.241  -3.2059   1.2494  -1.3718
 28H  H4   H  HCH1  0   0.235  -1.9560   1.2862   0.7912
 28H  H5   H  HCH3  0   0.219  -3.1012  -1.4268  -0.0087
 28H  H6   H  HCH3  0   0.225  -2.8329  -0.8928   1.6508
 28H  H7   H  HCH3  0   0.228  -3.9904  -0.0469   0.6275
 28H  H8   H  HCH1  0   0.235  -0.4398  -0.4641   1.4104
 28H  H9   H  HOH1  0   0.443  -0.5215  -1.3476  -1.2612
 28H  H10  H  HCH1  0   0.265   0.5532   0.9225  -1.1137
 28H  H11  H  HCH3  0   0.235   0.6612   1.7652   1.8315
 28H  H12  H  HCH3  0   0.249   1.5772   2.5389   0.5377
 28H  H13  H  HCH3  0   0.245  -0.1738   2.6055   0.5245
 28H  OXT  O  OH1   0  -0.586   2.5603  -0.3714  -0.9502
 28H  HXT  H  HOH1  0   0.477   3.3634  -0.8764  -0.7501

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
 28H  OCD  CBX  double  1.207  0.020  1.207
 28H  CCC  CCA  single  1.527  0.020  1.527
 28H  CBX  CBY  single  1.512  0.020  1.512
 28H  CCB  CCA  single  1.527  0.020  1.527
 28H  CBY  CCE  single  1.527  0.020  1.527
 28H  CBY  CBZ  single  1.538  0.020  1.538
 28H  CCA  CBZ  single  1.535  0.020  1.535
 28H  CBZ  OCF  single  1.414  0.020  1.414
 28H  CCB  H1   single  0.970  0.020  1.090
 28H  CCB  H2   single  0.970  0.020  1.090
 28H  CCB  H3   single  0.970  0.020  1.090
 28H  CCA  H4   single  0.970  0.020  1.090
 28H  CCC  H5   single  0.970  0.020  1.090
 28H  CCC  H6   single  0.970  0.020  1.090
 28H  CCC  H7   single  0.970  0.020  1.090
 28H  CBZ  H8   single  0.970  0.020  1.090
 28H  OCF  H9   single  0.850  0.020  0.980
 28H  CBY  H10  single  0.970  0.020  1.090
 28H  CCE  H11  single  0.970  0.020  1.090
 28H  CCE  H12  single  0.970  0.020  1.090
 28H  CCE  H13  single  0.970  0.020  1.090
 28H  CBX  OXT  single  1.327  0.020  1.327
 28H  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
 28H  H3   CCB  H2   106.68  3.000
 28H  H3   CCB  H1   107.04  3.000
 28H  H2   CCB  H1   107.84  3.000
 28H  H3   CCB  CCA  110.21  3.000
 28H  H2   CCB  CCA  112.04  3.000
 28H  H1   CCB  CCA  112.73  3.000
 28H  H4   CCA  CBZ  106.63  3.000
 28H  H4   CCA  CCC  107.39  3.000
 28H  CBZ  CCA  CCC  110.30  3.000
 28H  H4   CCA  CCB  108.09  3.000
 28H  CBZ  CCA  CCB  113.52  3.000
 28H  CCC  CCA  CCB  110.62  3.000
 28H  H7   CCC  H6   107.61  3.000
 28H  H7   CCC  H5   107.63  3.000
 28H  H6   CCC  H5   107.85  3.000
 28H  H7   CCC  CCA  110.47  3.000
 28H  H6   CCC  CCA  111.55  3.000
 28H  H5   CCC  CCA  111.55  3.000
 28H  H8   CBZ  CBY  107.39  3.000
 28H  H8   CBZ  OCF  105.15  3.000
 28H  CBY  CBZ  OCF  109.84  3.000
 28H  H8   CBZ  CCA  107.22  3.000
 28H  OCF  CBZ  CCA  112.55  3.000
 28H  CBY  CBZ  CCA  114.13  3.000
 28H  H9   OCF  CBZ  108.89  3.000
 28H  H10  CBY  CBX  108.67  3.000
 28H  H10  CBY  CCE  109.01  3.000
 28H  CBX  CBY  CCE  109.55  3.000
 28H  H10  CBY  CBZ  109.31  3.000
 28H  CCE  CBY  CBZ  112.87  3.000
 28H  CBX  CBY  CBZ  107.33  3.000
 28H  H13  CCE  H12  107.06  3.000
 28H  H13  CCE  H11  108.08  3.000
 28H  H12  CCE  H11  108.00  3.000
 28H  H13  CCE  CBY  110.95  3.000
 28H  H12  CCE  CBY  111.17  3.000
 28H  H11  CCE  CBY  111.40  3.000
 28H  OXT  CBX  OCD  122.92  3.000
 28H  OXT  CBX  CBY  113.23  3.000
 28H  OCD  CBX  CBY  123.85  3.000
 28H  HXT  OXT  CBX  109.79  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
 28H  CONST_01  HXT  OXT  CBX  CBY  180.00   0.0  0
 28H  Var_01    H5   CCC  CCA  CCB   58.13  30.0  3
 28H  Var_02    H1   CCB  CCA  CCC  172.36  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
 28H  chir_01  CBZ  CBY  CCA  OCF  negativ
 28H  chir_02  CBY  CBZ  CCE  CBX  negativ

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
 28H  plan-1  CBY  0.020
 28H  plan-1  CBX  0.020
 28H  plan-1  OCD  0.020
 28H  plan-1  OXT  0.020
 28H  plan-1  HXT  0.020

