# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:16:32 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (2S,5S)-hexane-2,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)CC[C@H](C)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
 DYD  DYD  '(2S,5S)-hexane-2,5-diol  '  ligand  22  8  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DYD
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
 DYD  C01  C  CH3   0  -0.686  -3.0674   0.8034  -0.4106
 DYD  C02  C  CH1   0   0.047  -1.9320  -0.2058  -0.3197
 DYD  C03  C  CH2   0  -0.429  -0.5769   0.4814  -0.2500
 DYD  C04  C  CH2   0  -0.429   0.6026  -0.4851  -0.2460
 DYD  C05  C  CH1   0   0.047   1.9571   0.2017  -0.3309
 DYD  C06  C  CH3   0  -0.687   3.0929  -0.8086  -0.4049
 DYD  O07  O  OH1   0  -0.677   2.0882   1.0394   0.8053
 DYD  O08  O  OH1   0  -0.677  -2.0618  -1.0212   0.8331
 DYD  H1   H  HCH3  0   0.230  -4.0381   0.3043  -0.4509
 DYD  H2   H  HCH3  0   0.221  -3.0650   1.4720   0.4524
 DYD  H3   H  HCH3  0   0.224  -2.9756   1.4119  -1.3111
 DYD  H4   H  HCH1  0   0.188  -1.9527  -0.8305  -1.2264
 DYD  H5   H  HCH2  0   0.216  -0.4941   1.1456  -1.1165
 DYD  H6   H  HCH2  0   0.220  -0.5483   1.1254   0.6343
 DYD  H7   H  HCH2  0   0.220   0.5779  -1.1171   0.6472
 DYD  H8   H  HCH2  0   0.216   0.5165  -1.1603  -1.1034
 DYD  H9   H  HCH1  0   0.188   1.9753   0.8087  -1.2496
 DYD  H10  H  HCH3  0   0.224   2.9997  -1.4327  -1.2944
 DYD  H11  H  HCH3  0   0.230   4.0634  -0.3101  -0.4551
 DYD  H12  H  HCH3  0   0.221   3.0911  -1.4620   0.4697
 DYD  H13  H  HOH1  0   0.446   2.9374   1.4880   0.7513
 DYD  H14  H  HOH1  0   0.446  -2.9058  -1.4801   0.7829

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
 DYD  O08  C02  single  1.418  0.020  1.418
 DYD  C02  C01  single  1.522  0.020  1.522
 DYD  C02  C03  single  1.521  0.020  1.521
 DYD  C04  C03  single  1.525  0.020  1.525
 DYD  C04  C05  single  1.521  0.020  1.521
 DYD  O07  C05  single  1.418  0.020  1.418
 DYD  C06  C05  single  1.522  0.020  1.522
 DYD  C01  H1   single  0.970  0.020  1.090
 DYD  C01  H2   single  0.970  0.020  1.090
 DYD  C01  H3   single  0.970  0.020  1.090
 DYD  C02  H4   single  0.970  0.020  1.090
 DYD  C03  H5   single  0.970  0.020  1.090
 DYD  C03  H6   single  0.970  0.020  1.090
 DYD  C04  H7   single  0.970  0.020  1.090
 DYD  C04  H8   single  0.970  0.020  1.090
 DYD  C05  H9   single  0.970  0.020  1.090
 DYD  C06  H10  single  0.970  0.020  1.090
 DYD  C06  H11  single  0.970  0.020  1.090
 DYD  C06  H12  single  0.970  0.020  1.090
 DYD  O07  H13  single  0.850  0.020  0.980
 DYD  O08  H14  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
 DYD  H3   C01  H2   108.11  3.000
 DYD  H3   C01  H1   107.41  3.000
 DYD  H2   C01  H1   108.12  3.000
 DYD  H3   C01  C02  110.89  3.000
 DYD  H2   C01  C02  110.93  3.000
 DYD  H1   C01  C02  111.24  3.000
 DYD  H4   C02  O08  109.97  3.000
 DYD  H4   C02  C03  108.10  3.000
 DYD  O08  C02  C03  107.71  3.000
 DYD  H4   C02  C01  108.24  3.000
 DYD  C03  C02  C01  111.58  3.000
 DYD  O08  C02  C01  111.20  3.000
 DYD  H6   C03  H5   106.30  3.000
 DYD  H6   C03  C04  110.53  3.000
 DYD  H5   C03  C04  109.15  3.000
 DYD  H6   C03  C02  109.03  3.000
 DYD  H5   C03  C02  107.77  3.000
 DYD  C04  C03  C02  113.76  3.000
 DYD  H8   C04  H7   106.34  3.000
 DYD  H8   C04  C05  107.75  3.000
 DYD  H7   C04  C05  109.05  3.000
 DYD  H8   C04  C03  109.15  3.000
 DYD  H7   C04  C03  110.53  3.000
 DYD  C05  C04  C03  113.73  3.000
 DYD  H9   C05  O07  109.96  3.000
 DYD  H9   C05  C06  108.24  3.000
 DYD  O07  C05  C06  111.24  3.000
 DYD  H9   C05  C04  108.07  3.000
 DYD  C06  C05  C04  111.56  3.000
 DYD  O07  C05  C04  107.72  3.000
 DYD  H12  C06  H11  108.14  3.000
 DYD  H12  C06  H10  108.11  3.000
 DYD  H11  C06  H10  107.44  3.000
 DYD  H12  C06  C05  110.92  3.000
 DYD  H11  C06  C05  111.25  3.000
 DYD  H10  C06  C05  110.85  3.000
 DYD  H13  O07  C05  108.19  3.000
 DYD  H14  O08  C02  108.19  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
 DYD  Var_01  C05  C04  C03  C02  173.64  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
 DYD  chir_01  C02  O08  C01  C03  negativ
 DYD  chir_02  C05  O07  C04  C06  positiv

