# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 20:38:02 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2S,4S)-4-hydroxy-2,5-dimethyl-3-oxohexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](O)C(=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
 HIT  HIT  '(2S,4S)-4-hydroxy-2,5-dimethyl-3-oxohexanoic acid'  ligand  25  12  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HIT
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
 HIT  CA1   C  CH1    0  -0.037   3.1858   1.0734  -3.3066
 HIT  C3    C  CH1    0  -0.297   3.0636  -0.3352  -3.9210
 HIT  C5    C  CH3    0  -0.658   3.9765  -1.3446  -3.2319
 HIT  C9    C  CH3    0  -0.667   3.3325  -0.2920  -5.4238
 HIT  C13   C  C      0   0.399   2.7263   1.1032  -1.8586
 HIT  O14   O  O      0  -0.405   3.4949   1.3704  -0.9645
 HIT  CA2   C  CH1    0  -0.487   1.2658   0.8196  -1.6251
 HIT  C17   C  CH3    0  -0.654   0.7164   1.6600  -0.4728
 HIT  C21   C  C      0   0.441   1.0455  -0.6931  -1.2943
 HIT  O22   O  OC    -1  -0.598   0.1661  -1.2815  -1.9475
 HIT  O1    O  O      0  -0.588   1.7470  -1.1560  -0.3787
 HIT  O25   O  OH1    0  -0.664   4.4904   1.5831  -3.3597
 HIT  HA1   H  HCH1   0   0.236   2.4861   1.7265  -3.8548
 HIT  H3    H  HCH1   0   0.242   2.0261  -0.6550  -3.7872
 HIT  H51   H  HCH3   0   0.235   3.7293  -1.4689  -2.1772
 HIT  H52   H  HCH3   0   0.217   5.0228  -1.0451  -3.3033
 HIT  H53   H  HCH3   0   0.227   3.8836  -2.3234  -3.7045
 HIT  H91   H  HCH3   0   0.232   2.6964   0.4399  -5.9249
 HIT  H92   H  HCH3   0   0.214   4.3733  -0.0482  -5.6501
 HIT  H93   H  HCH3   0   0.240   3.1330  -1.2654  -5.8733
 HIT  HA2   H  HCH1   0   0.236   0.7129   1.0554  -2.5379
 HIT  H171  H  HCH3   0   0.226   1.2194   1.4187   0.4616
 HIT  H172  H  HCH3   0   0.230  -0.3495   1.4689  -0.3419
 HIT  H173  H  HCH3   0   0.228   0.8389   2.7281  -0.6592
 HIT  HO2   H  HOH1   0   0.452   4.7454   1.6548  -4.2843

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
 HIT  CA1  C3    single  1.542  0.020  1.542
 HIT  CA1  C13   single  1.519  0.020  1.519
 HIT  CA1  O25   single  1.402  0.020  1.402
 HIT  CA1  HA1   single  0.970  0.020  1.090
 HIT  C3   C5    single  1.525  0.020  1.525
 HIT  C3   C9    single  1.527  0.020  1.527
 HIT  C3   H3    single  0.970  0.020  1.090
 HIT  C5   H51   single  0.970  0.020  1.090
 HIT  C5   H52   single  0.970  0.020  1.090
 HIT  C5   H53   single  0.970  0.020  1.090
 HIT  C9   H91   single  0.970  0.020  1.090
 HIT  C9   H92   single  0.970  0.020  1.090
 HIT  C9   H93   single  0.970  0.020  1.090
 HIT  C13  O14   double  1.209  0.020  1.209
 HIT  C13  CA2   single  1.506  0.020  1.506
 HIT  CA2  C17   single  1.528  0.020  1.528
 HIT  CA2  C21   single  1.564  0.020  1.564
 HIT  CA2  HA2   single  0.970  0.020  1.090
 HIT  C17  H171  single  0.970  0.020  1.090
 HIT  C17  H172  single  0.970  0.020  1.090
 HIT  C17  H173  single  0.970  0.020  1.090
 HIT  C21  O22   deloc   1.243  0.020  1.243
 HIT  C21  O1    deloc   1.243  0.020  1.243
 HIT  O25  HO2   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
 HIT  HA1   CA1  O25   110.88  3.000
 HIT  HA1   CA1  C13   105.68  3.000
 HIT  O25   CA1  C13   108.09  3.000
 HIT  HA1   CA1  C3    107.02  3.000
 HIT  O25   CA1  C3    113.01  3.000
 HIT  C13   CA1  C3    111.95  3.000
 HIT  H3    C3   C9    107.19  3.000
 HIT  H3    C3   C5    108.60  3.000
 HIT  C9    C3   C5    110.97  3.000
 HIT  H3    C3   CA1   107.07  3.000
 HIT  C9    C3   CA1   110.63  3.000
 HIT  C5    C3   CA1   112.16  3.000
 HIT  H53   C5   H52   107.44  3.000
 HIT  H53   C5   H51   107.31  3.000
 HIT  H52   C5   H51   108.19  3.000
 HIT  H53   C5   C3    110.31  3.000
 HIT  H52   C5   C3    111.27  3.000
 HIT  H51   C5   C3    112.13  3.000
 HIT  H93   C9   H92   106.74  3.000
 HIT  H93   C9   H91   107.62  3.000
 HIT  H92   C9   H91   108.09  3.000
 HIT  H93   C9   C3    110.37  3.000
 HIT  H92   C9   C3    112.20  3.000
 HIT  H91   C9   C3    111.60  3.000
 HIT  CA2   C13  O14   122.92  3.000
 HIT  CA2   C13  CA1   115.93  3.000
 HIT  O14   C13  CA1   121.13  3.000
 HIT  HA2   CA2  C21   108.31  3.000
 HIT  HA2   CA2  C17   109.21  3.000
 HIT  C21   CA2  C17   108.77  3.000
 HIT  HA2   CA2  C13   108.69  3.000
 HIT  C21   CA2  C13   110.58  3.000
 HIT  C17   CA2  C13   111.22  3.000
 HIT  H173  C17  H172  107.56  3.000
 HIT  H173  C17  H171  108.17  3.000
 HIT  H172  C17  H171  108.04  3.000
 HIT  H173  C17  CA2   111.66  3.000
 HIT  H172  C17  CA2   110.21  3.000
 HIT  H171  C17  CA2   111.05  3.000
 HIT  O1    C21  O22   127.58  3.000
 HIT  O1    C21  CA2   115.88  3.000
 HIT  O22   C21  CA2   116.50  3.000
 HIT  HO2   O25  CA1   108.08  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
 HIT  Var_01  H51  C5  C3  CA1   61.79  30.0  3
 HIT  Var_02  H91  C9  C3  CA1  -53.86  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
 HIT  chir_01  CA1  C3   C13  O25  negativ
 HIT  chir_02  CA2  C13  C17  C21  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
 HIT  plan-1  CA1  0.020
 HIT  plan-1  C13  0.020
 HIT  plan-1  O14  0.020
 HIT  plan-1  CA2  0.020
 HIT  plan-2  CA2  0.020
 HIT  plan-2  C21  0.020
 HIT  plan-2  O22  0.020
 HIT  plan-2  O1   0.020

