# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 00:13:26 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: hexyl 3-deoxy-beta-D-xylo-hexopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCO[C@@H]1O[C@H](CO)[C@H](O)C[C@H]1O
#
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
 DLG  DLG  'hexyl 3-deoxy-beta-D-xylo-hexopyranoside'  D-saccharide  41  17  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DLG
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
 DLG  C1    C  CH1   0   0.324  17.9573  63.9998  46.0243
 DLG  C2    C  CH1   0   0.021  16.9696  62.9381  45.5577
 DLG  C3    C  CH2   0  -0.524  17.1725  61.6816  46.4029
 DLG  C4    C  CH1   0   0.010  18.6207  61.2135  46.4046
 DLG  C5    C  CH1   0   0.004  19.5099  62.3974  46.7949
 DLG  C6    C  CH2   0  -0.171  20.9882  62.0774  46.7479
 DLG  O1    O  O2    0  -0.496  17.8652  65.1054  45.2112
 DLG  O2    O  OH1   0  -0.668  15.6728  63.4647  45.7042
 DLG  O4    O  OH1   0  -0.670  18.9198  60.7055  45.1215
 DLG  O5    O  O2    0  -0.500  19.2678  63.4975  45.9441
 DLG  O6    O  OH1   0  -0.664  21.7021  63.1490  47.3166
 DLG  C11   C  CH2   0  -0.140  18.5199  66.2674  45.6949
 DLG  C12   C  CH2   0  -0.463  18.1215  67.4428  44.8241
 DLG  C13   C  CH2   0  -0.440  18.6911  68.7726  45.3139
 DLG  C14   C  CH2   0  -0.425  20.2099  68.8811  45.2232
 DLG  C15   C  CH2   0  -0.422  20.7589  70.2332  45.6745
 DLG  C16   C  CH3   0  -0.665  20.3585  71.3994  44.7795
 DLG  H1    H  HCH1  0   0.172  17.7314  64.2629  47.0780
 DLG  H2    H  HCH1  0   0.208  17.1886  62.7111  44.5045
 DLG  H3    H  HCH2  0   0.239  16.8786  61.9009  47.4342
 DLG  H32   H  HCH2  0   0.255  16.5199  60.8776  46.0518
 DLG  H4    H  HCH1  0   0.227  18.7395  60.4364  47.1714
 DLG  H5    H  HCH1  0   0.212  19.2509  62.6586  47.8349
 DLG  H61   H  HCH2  0   0.202  21.1494  61.1425  47.3021
 DLG  H62   H  HCH2  0   0.199  21.2948  61.8953  45.7098
 DLG  HO2   H  HOH1  0   0.451  15.0408  62.7875  45.4429
 DLG  HO4   H  HOH1  0   0.453  19.7185  60.1721  45.1718
 DLG  HO6   H  HOH1  0   0.453  22.6411  62.9597  47.2348
 DLG  H111  H  HCH2  0   0.197  18.2253  66.4575  46.7365
 DLG  H112  H  HCH2  0   0.208  19.6054  66.1281  45.6874
 DLG  H121  H  HCH2  0   0.221  18.4449  67.2642  43.7938
 DLG  H122  H  HCH2  0   0.229  17.0302  67.5087  44.8050
 DLG  H131  H  HCH2  0   0.231  18.2318  69.5710  44.7262
 DLG  H132  H  HCH2  0   0.212  18.3764  68.9431  46.3495
 DLG  H141  H  HCH2  0   0.223  20.6740  68.1000  45.8316
 DLG  H142  H  HCH2  0   0.207  20.5262  68.6895  44.1915
 DLG  H151  H  HCH2  0   0.210  20.4338  70.4284  46.7012
 DLG  H152  H  HCH2  0   0.220  21.8498  70.1736  45.7108
 DLG  H161  H  HCH3  0   0.226  20.8247  72.3278  45.1117
 DLG  H162  H  HCH3  0   0.214  20.6699  71.2265  43.7473
 DLG  H163  H  HCH3  0   0.219  19.2804  71.5635  44.7745

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
 DLG  C1   C2    single  1.523  0.020  1.523
 DLG  C1   O1    single  1.375  0.020  1.375
 DLG  C1   O5    single  1.406  0.020  1.406
 DLG  C1   H1    single  0.970  0.020  1.090
 DLG  C2   C3    single  1.528  0.020  1.528
 DLG  C2   O2    single  1.407  0.020  1.407
 DLG  C2   H2    single  0.970  0.020  1.090
 DLG  C3   C4    single  1.522  0.020  1.522
 DLG  C3   H3    single  0.970  0.020  1.090
 DLG  C3   H32   single  0.970  0.020  1.090
 DLG  C4   C5    single  1.531  0.020  1.531
 DLG  C4   O4    single  1.412  0.020  1.412
 DLG  C4   H4    single  0.970  0.020  1.090
 DLG  C5   C6    single  1.513  0.020  1.513
 DLG  C5   O5    single  1.412  0.020  1.412
 DLG  C5   H5    single  0.970  0.020  1.090
 DLG  C6   O6    single  1.408  0.020  1.408
 DLG  C6   H61   single  0.970  0.020  1.090
 DLG  C6   H62   single  0.970  0.020  1.090
 DLG  O1   C11   single  1.419  0.020  1.419
 DLG  O2   HO2   single  0.850  0.020  0.980
 DLG  O4   HO4   single  0.850  0.020  0.980
 DLG  O6   HO6   single  0.850  0.020  0.980
 DLG  C11  C12   single  1.516  0.020  1.516
 DLG  C11  H111  single  0.970  0.020  1.090
 DLG  C11  H112  single  0.970  0.020  1.090
 DLG  C12  C13   single  1.527  0.020  1.527
 DLG  C12  H121  single  0.970  0.020  1.090
 DLG  C12  H122  single  0.970  0.020  1.090
 DLG  C13  C14   single  1.525  0.020  1.525
 DLG  C13  H131  single  0.970  0.020  1.090
 DLG  C13  H132  single  0.970  0.020  1.090
 DLG  C14  C15   single  1.528  0.020  1.528
 DLG  C14  H141  single  0.970  0.020  1.090
 DLG  C14  H142  single  0.970  0.020  1.090
 DLG  C15  C16   single  1.524  0.020  1.524
 DLG  C15  H151  single  0.970  0.020  1.090
 DLG  C15  H152  single  0.970  0.020  1.090
 DLG  C16  H161  single  0.970  0.020  1.090
 DLG  C16  H162  single  0.970  0.020  1.090
 DLG  C16  H163  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
 DLG  H1    C1   O5    109.19  3.000
 DLG  H1    C1   O1    110.93  3.000
 DLG  O5    C1   O1    108.41  3.000
 DLG  H1    C1   C2    108.92  3.000
 DLG  O5    C1   C2    109.75  3.000
 DLG  O1    C1   C2    109.62  3.000
 DLG  H2    C2   O2    111.13  3.000
 DLG  H2    C2   C3    109.49  3.000
 DLG  O2    C2   C3    111.87  3.000
 DLG  H2    C2   C1    107.96  3.000
 DLG  O2    C2   C1    107.74  3.000
 DLG  C3    C2   C1    108.52  3.000
 DLG  H32   C3   H3    106.83  3.000
 DLG  H32   C3   C4    110.01  3.000
 DLG  H3    C3   C4    108.42  3.000
 DLG  H32   C3   C2    110.35  3.000
 DLG  H3    C3   C2    108.71  3.000
 DLG  C4    C3   C2    112.33  3.000
 DLG  H4    C4   O4    110.91  3.000
 DLG  H4    C4   C5    107.84  3.000
 DLG  O4    C4   C5    112.75  3.000
 DLG  H4    C4   C3    108.75  3.000
 DLG  O4    C4   C3    108.13  3.000
 DLG  C5    C4   C3    108.36  3.000
 DLG  H5    C5   O5    110.09  3.000
 DLG  H5    C5   C6    107.98  3.000
 DLG  O5    C5   C6    108.28  3.000
 DLG  H5    C5   C4    106.68  3.000
 DLG  O5    C5   C4    110.45  3.000
 DLG  C6    C5   C4    113.32  3.000
 DLG  H62   C6   H61   107.15  3.000
 DLG  H62   C6   O6    111.51  3.000
 DLG  H61   C6   O6    111.69  3.000
 DLG  H62   C6   C5    109.71  3.000
 DLG  H61   C6   C5    107.92  3.000
 DLG  O6    C6   C5    108.78  3.000
 DLG  C11   O1   C1    115.20  3.000
 DLG  HO2   O2   C2    108.27  3.000
 DLG  HO4   O4   C4    109.15  3.000
 DLG  C5    O5   C1    113.82  3.000
 DLG  HO6   O6   C6    108.13  3.000
 DLG  H112  C11  H111  107.12  3.000
 DLG  H112  C11  C12   110.81  3.000
 DLG  H111  C11  C12   109.87  3.000
 DLG  H112  C11  O1    110.56  3.000
 DLG  H111  C11  O1    109.94  3.000
 DLG  C12   C11  O1    108.54  3.000
 DLG  H122  C12  H121  106.75  3.000
 DLG  H122  C12  C13   108.99  3.000
 DLG  H121  C12  C13   109.50  3.000
 DLG  H122  C12  C11   108.60  3.000
 DLG  H121  C12  C11   109.66  3.000
 DLG  C13   C12  C11   113.13  3.000
 DLG  H132  C13  H131  105.89  3.000
 DLG  H132  C13  C14   109.33  3.000
 DLG  H131  C13  C14   109.55  3.000
 DLG  H132  C13  C12   109.36  3.000
 DLG  H131  C13  C12   107.88  3.000
 DLG  C14   C13  C12   114.47  3.000
 DLG  H142  C14  H141  106.05  3.000
 DLG  H142  C14  C15   109.22  3.000
 DLG  H141  C14  C15   108.39  3.000
 DLG  H142  C14  C13   109.32  3.000
 DLG  H141  C14  C13   109.80  3.000
 DLG  C15   C14  C13   113.78  3.000
 DLG  H152  C15  H151  105.96  3.000
 DLG  H152  C15  C16   108.88  3.000
 DLG  H151  C15  C16   109.66  3.000
 DLG  H152  C15  C14   108.67  3.000
 DLG  H151  C15  C14   109.16  3.000
 DLG  C16   C15  C14   114.18  3.000
 DLG  H163  C16  H162  107.54  3.000
 DLG  H163  C16  H161  107.21  3.000
 DLG  H162  C16  H161  107.51  3.000
 DLG  H163  C16  C15   112.19  3.000
 DLG  H162  C16  C15   111.05  3.000
 DLG  H161  C16  C15   111.12  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
 DLG  Var_01  C12   C11  O1   C1   -170.03  30.0  3
 DLG  Var_02  C13   C12  C11  O1    175.89  30.0  3
 DLG  Var_03  C14   C13  C12  C11    66.40  30.0  3
 DLG  Var_04  C15   C14  C13  C12   178.13  30.0  3
 DLG  Var_05  C16   C15  C14  C13   -66.16  30.0  3
 DLG  Var_06  H161  C16  C15  C14  -176.59  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
 DLG  chir_01  C1  C2  O1  O5  positiv
 DLG  chir_02  C2  O2  C1  C3  negativ
 DLG  chir_03  C4  O4  C3  C5  positiv
 DLG  chir_04  C5  O5  C4  C6  negativ

