# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:54:47 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 5-hydroxypentyl alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[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
 E5G  E5G  '5-hydroxypentyl alpha-D-glucopyranoside'  D-saccharide  40  18  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_E5G
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
 E5G  O6   O  OH1   0  -0.665   5.2948  -14.0075  -0.2221
 E5G  C6   C  CH2   0  -0.161   4.4865  -12.8682  -0.3929
 E5G  C5   C  CH1   0  -0.018   5.3593  -11.6869  -0.7600
 E5G  O5   O  O2    0  -0.503   5.9515  -11.9760  -2.0175
 E5G  C4   C  CH1   0  -0.003   4.5506  -10.3870  -0.8481
 E5G  O4   O  OH1   0  -0.669   4.0704   -9.9856   0.4164
 E5G  C3   C  CH1   0  -0.004   5.4350   -9.2609  -1.3715
 E5G  O3   O  OH1   0  -0.670   4.6957   -8.0876  -1.6140
 E5G  C2   C  CH1   0   0.008   6.0750   -9.6752  -2.6890
 E5G  O2   O  OH1   0  -0.665   6.9766   -8.7196  -3.1821
 E5G  C1   C  CH1   0   0.264   6.8191  -10.9972  -2.5174
 E5G  O1   O  O2    0  -0.494   7.9177  -10.7799  -1.7038
 E5G  C15  C  CH2   0  -0.148   8.8880  -11.8111  -1.6840
 E5G  C14  C  CH2   0  -0.468  10.1966  -11.2410  -1.1729
 E5G  C13  C  CH2   0  -0.435  10.7871  -10.1706  -2.0872
 E5G  C12  C  CH2   0  -0.459  12.0130   -9.4664  -1.5142
 E5G  C11  C  CH2   0  -0.139  13.2041  -10.3866  -1.3267
 E5G  O11  O  OH1   0  -0.671  14.3125   -9.6184  -0.9052
 E5G  HO6  H  HOH1  0   0.454   4.7239  -14.7460   0.0079
 E5G  H61  H  HCH2  0   0.200   3.9442  -12.6215   0.5278
 E5G  H62  H  HCH2  0   0.197   3.7345  -13.0121  -1.1815
 E5G  H5   H  HCH1  0   0.223   6.1308  -11.5621   0.0132
 E5G  H4   H  HCH1  0   0.221   3.7239  -10.5340  -1.5586
 E5G  HO4  H  HOH1  0   0.459   3.1943  -10.3542   0.5585
 E5G  H3   H  HCH1  0   0.213   6.2274   -9.0747  -0.6308
 E5G  HO3  H  HOH1  0   0.451   4.3597   -7.7645  -0.7716
 E5G  H2   H  HCH1  0   0.219   5.2671   -9.8632  -3.4130
 E5G  HO2  H  HOH1  0   0.451   6.4918   -7.9009  -3.3272
 E5G  H1   H  HCH1  0   0.234   7.1358  -11.3776  -3.4988
 E5G  H12  H  HCH2  0   0.219   8.5612  -12.6382  -1.0434
 E5G  H13  H  HCH2  0   0.202   9.0259  -12.2197  -2.6945
 E5G  H14  H  HCH2  0   0.223  10.0467  -10.8335  -0.1674
 E5G  H15  H  HCH2  0   0.230  10.8936  -12.0754  -1.0616
 E5G  H16  H  HCH2  0   0.213  11.0438  -10.6226  -3.0514
 E5G  H17  H  HCH2  0   0.230  10.0250   -9.4180  -2.2979
 E5G  H18  H  HCH2  0   0.226  12.3021   -8.6556  -2.1895
 E5G  H19  H  HCH2  0   0.217  11.7549   -9.0006  -0.5577
 E5G  H20  H  HCH2  0   0.183  13.4115  -10.9003  -2.2765
 E5G  H21  H  HCH2  0   0.192  12.9658  -11.1675  -0.5933
 E5G  H22  H  HOH1  0   0.447  15.0444  -10.2175  -0.7339

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
 E5G  O2   C2   single  1.403  0.020  1.403
 E5G  C2   C1   single  1.527  0.020  1.527
 E5G  C2   C3   single  1.522  0.020  1.522
 E5G  C1   O5   single  1.400  0.020  1.400
 E5G  C1   O1   single  1.384  0.020  1.384
 E5G  O3   C3   single  1.408  0.020  1.408
 E5G  O5   C5   single  1.420  0.020  1.420
 E5G  O1   C15  single  1.416  0.020  1.416
 E5G  C15  C14  single  1.516  0.020  1.516
 E5G  C3   C4   single  1.525  0.020  1.525
 E5G  C13  C14  single  1.527  0.020  1.527
 E5G  C13  C12  single  1.525  0.020  1.525
 E5G  C11  O11  single  1.413  0.020  1.413
 E5G  C11  C12  single  1.517  0.020  1.517
 E5G  C4   C5   single  1.534  0.020  1.534
 E5G  C4   O4   single  1.411  0.020  1.411
 E5G  C5   C6   single  1.514  0.020  1.514
 E5G  C6   O6   single  1.407  0.020  1.407
 E5G  O6   HO6  single  0.850  0.020  0.980
 E5G  C6   H61  single  0.970  0.020  1.090
 E5G  C6   H62  single  0.970  0.020  1.090
 E5G  C5   H5   single  0.970  0.020  1.090
 E5G  C4   H4   single  0.970  0.020  1.090
 E5G  O4   HO4  single  0.850  0.020  0.980
 E5G  C3   H3   single  0.970  0.020  1.090
 E5G  O3   HO3  single  0.850  0.020  0.980
 E5G  C2   H2   single  0.970  0.020  1.090
 E5G  O2   HO2  single  0.850  0.020  0.980
 E5G  C1   H1   single  0.970  0.020  1.090
 E5G  C15  H12  single  0.970  0.020  1.090
 E5G  C15  H13  single  0.970  0.020  1.090
 E5G  C14  H14  single  0.970  0.020  1.090
 E5G  C14  H15  single  0.970  0.020  1.090
 E5G  C13  H16  single  0.970  0.020  1.090
 E5G  C13  H17  single  0.970  0.020  1.090
 E5G  C12  H18  single  0.970  0.020  1.090
 E5G  C12  H19  single  0.970  0.020  1.090
 E5G  C11  H20  single  0.970  0.020  1.090
 E5G  C11  H21  single  0.970  0.020  1.090
 E5G  O11  H22  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
 E5G  HO6  O6   C6   108.05  3.000
 E5G  H62  C6   H61  107.07  3.000
 E5G  H62  C6   C5   108.82  3.000
 E5G  H61  C6   C5   108.25  3.000
 E5G  H62  C6   O6   111.97  3.000
 E5G  H61  C6   O6   111.36  3.000
 E5G  C5   C6   O6   109.26  3.000
 E5G  H5   C5   C4   108.32  3.000
 E5G  H5   C5   O5   110.69  3.000
 E5G  C4   C5   O5   109.98  3.000
 E5G  H5   C5   C6   108.83  3.000
 E5G  C4   C5   C6   111.79  3.000
 E5G  O5   C5   C6   107.24  3.000
 E5G  C1   O5   C5   115.61  3.000
 E5G  H4   C4   C3   108.24  3.000
 E5G  H4   C4   O4   111.18  3.000
 E5G  C3   C4   O4   107.15  3.000
 E5G  H4   C4   C5   108.68  3.000
 E5G  O4   C4   C5   111.66  3.000
 E5G  C3   C4   C5   109.87  3.000
 E5G  HO4  O4   C4   109.49  3.000
 E5G  H3   C3   C2   109.02  3.000
 E5G  H3   C3   O3   110.67  3.000
 E5G  C2   C3   O3   107.37  3.000
 E5G  H3   C3   C4   108.16  3.000
 E5G  O3   C3   C4   111.72  3.000
 E5G  C2   C3   C4   109.88  3.000
 E5G  HO3  O3   C3   108.20  3.000
 E5G  H2   C2   C1   106.48  3.000
 E5G  H2   C2   O2   110.90  3.000
 E5G  C1   C2   O2   108.42  3.000
 E5G  H2   C2   C3   107.89  3.000
 E5G  C1   C2   C3   110.08  3.000
 E5G  O2   C2   C3   112.89  3.000
 E5G  HO2  O2   C2   107.98  3.000
 E5G  H1   C1   O1   110.51  3.000
 E5G  H1   C1   C2   109.86  3.000
 E5G  O1   C1   C2   108.48  3.000
 E5G  H1   C1   O5   104.79  3.000
 E5G  O1   C1   O5   113.06  3.000
 E5G  C2   C1   O5   110.09  3.000
 E5G  C15  O1   C1   115.96  3.000
 E5G  H13  C15  H12  107.11  3.000
 E5G  H13  C15  C14  109.97  3.000
 E5G  H12  C15  C14  110.13  3.000
 E5G  H13  C15  O1   110.11  3.000
 E5G  H12  C15  O1   110.70  3.000
 E5G  C14  C15  O1   108.80  3.000
 E5G  H15  C14  H14  106.12  3.000
 E5G  H15  C14  C13  110.47  3.000
 E5G  H14  C14  C13  109.99  3.000
 E5G  H15  C14  C15  107.32  3.000
 E5G  H14  C14  C15  109.35  3.000
 E5G  C13  C14  C15  113.31  3.000
 E5G  H17  C13  H16  106.15  3.000
 E5G  H17  C13  C12  108.38  3.000
 E5G  H16  C13  C12  109.44  3.000
 E5G  H17  C13  C14  109.20  3.000
 E5G  H16  C13  C14  109.18  3.000
 E5G  C12  C13  C14  114.18  3.000
 E5G  H19  C12  H18  106.63  3.000
 E5G  H19  C12  C11  109.59  3.000
 E5G  H18  C12  C11  108.57  3.000
 E5G  H19  C12  C13  109.58  3.000
 E5G  H18  C12  C13  108.82  3.000
 E5G  C11  C12  C13  113.42  3.000
 E5G  H21  C11  H20  106.60  3.000
 E5G  H21  C11  O11  110.97  3.000
 E5G  H20  C11  O11  111.33  3.000
 E5G  H21  C11  C12  110.10  3.000
 E5G  H20  C11  C12  108.95  3.000
 E5G  O11  C11  C12  108.85  3.000
 E5G  H22  O11  C11  108.15  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
 E5G  Var_01  C14  C15  O1   C1   160.26  30.0  3
 E5G  Var_02  C13  C14  C15  O1   -63.97  30.0  3
 E5G  Var_03  C12  C13  C14  C15  173.11  30.0  1
 E5G  Var_04  C11  C12  C13  C14   64.64  30.0  3
 E5G  Var_05  O11  C11  C12  C13  174.96  30.0  2

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
 E5G  chir_01  C5  O5  C4  C6  negativ
 E5G  chir_02  C4  O4  C5  C3  positiv
 E5G  chir_03  C3  O3  C2  C4  positiv
 E5G  chir_04  C2  O2  C3  C1  positiv
 E5G  chir_05  C1  O5  O1  C2  positiv

