# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:48:46 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: (2S)-pentane-1,2,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCC[C@H](O)CO
#
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
 XXD  XXD  '(2S)-pentane-1,2,5-triol '  ligand  20  8  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XXD
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
 XXD  O1    O  OH1   0  -0.669   3.4625   0.2095  -0.3609
 XXD  O5    O  OH1   0  -0.675  -3.8379  -0.2057  -0.2524
 XXD  O7    O  OH1   0  -0.660   1.2197  -1.4565   0.1072
 XXD  C10   C  CH2   0  -0.135  -2.7165   0.4913   0.2472
 XXD  C11   C  CH2   0  -0.154   2.2886   0.7248   0.2202
 XXD  C13   C  CH1   0   0.009   1.0956  -0.0948  -0.2422
 XXD  C14   C  CH2   0  -0.460  -0.2040   0.5182   0.2697
 XXD  C15   C  CH2   0  -0.440  -1.4525  -0.1906  -0.2375
 XXD  HO1   H  HOH1  0   0.453   4.1968   0.7683  -0.0919
 XXD  HO5   H  HOH1  0   0.452  -4.6301   0.2564   0.0353
 XXD  HO7   H  HOH1  0   0.439   1.2289  -1.5237   1.0684
 XXD  H10   H  HCH2  0   0.188  -2.7135   1.5372  -0.0886
 XXD  H10A  H  HCH2  0   0.188  -2.7167   0.5150   1.3456
 XXD  H11   H  HCH2  0   0.186   2.3362   0.7029   1.3199
 XXD  H11A  H  HCH2  0   0.201   2.1205   1.7712  -0.0655
 XXD  H13   H  HCH1  0   0.213   1.0777  -0.0757  -1.3375
 XXD  H14   H  HCH2  0   0.214  -0.1989   0.5231   1.3666
 XXD  H14A  H  HCH2  0   0.217  -0.2358   1.5695  -0.0334
 XXD  H15   H  HCH2  0   0.222  -1.4491  -1.2331   0.0894
 XXD  H15A  H  HCH2  0   0.211  -1.4457  -0.2016  -1.3323

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
 XXD  O1   C11   single  1.407  0.020  1.407
 XXD  O5   C10   single  1.412  0.020  1.412
 XXD  O7   C13   single  1.411  0.020  1.411
 XXD  C10  C15   single  1.516  0.020  1.516
 XXD  C11  C13   single  1.519  0.020  1.519
 XXD  C13  C14   single  1.525  0.020  1.525
 XXD  C14  C15   single  1.523  0.020  1.523
 XXD  O1   HO1   single  0.850  0.020  0.980
 XXD  O5   HO5   single  0.850  0.020  0.980
 XXD  O7   HO7   single  0.850  0.020  0.980
 XXD  C10  H10   single  0.970  0.020  1.090
 XXD  C10  H10A  single  0.970  0.020  1.090
 XXD  C11  H11   single  0.970  0.020  1.090
 XXD  C11  H11A  single  0.970  0.020  1.090
 XXD  C13  H13   single  0.970  0.020  1.090
 XXD  C14  H14   single  0.970  0.020  1.090
 XXD  C14  H14A  single  0.970  0.020  1.090
 XXD  C15  H15   single  0.970  0.020  1.090
 XXD  C15  H15A  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
 XXD  HO1   O1   C11  107.99  3.000
 XXD  HO5   O5   C10  108.15  3.000
 XXD  HO7   O7   C13  108.36  3.000
 XXD  H10A  C10  H10  106.56  3.000
 XXD  H10A  C10  C15  109.25  3.000
 XXD  H10   C10  C15  109.17  3.000
 XXD  H10A  C10  O5   111.37  3.000
 XXD  H10   C10  O5   111.34  3.000
 XXD  C15   C10  O5   109.10  3.000
 XXD  H11A  C11  H11  106.59  3.000
 XXD  H11A  C11  C13  108.35  3.000
 XXD  H11   C11  C13  109.09  3.000
 XXD  H11A  C11  O1   111.67  3.000
 XXD  H11   C11  O1   111.66  3.000
 XXD  C13   C11  O1   109.37  3.000
 XXD  H13   C13  C14  108.33  3.000
 XXD  H13   C13  C11  107.92  3.000
 XXD  C14   C13  C11  110.49  3.000
 XXD  H13   C13  O7   105.41  3.000
 XXD  C14   C13  O7   112.31  3.000
 XXD  C11   C13  O7   112.09  3.000
 XXD  H14A  C14  H14  105.83  3.000
 XXD  H14A  C14  C15  109.33  3.000
 XXD  H14   C14  C15  109.82  3.000
 XXD  H14A  C14  C13  108.53  3.000
 XXD  H14   C14  C13  109.47  3.000
 XXD  C15   C14  C13  113.56  3.000
 XXD  H15A  C15  H15  106.83  3.000
 XXD  H15A  C15  C14  109.43  3.000
 XXD  H15   C15  C14  110.00  3.000
 XXD  H15A  C15  C10  109.24  3.000
 XXD  H15   C15  C10  109.64  3.000
 XXD  C14   C15  C10  111.58  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
 XXD  Var_01  C14  C15  C10  O5    179.96  30.0  3
 XXD  Var_02  C13  C14  C15  C10  -177.46  30.0  1

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
 XXD  chir_01  C13  O7  C11  C14  positiv

