# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:37:11 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 2-[(2S)-oxiran-2-yl]ethyl alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](OCC[C@H]2CO2)[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
 EBG  EBG  '2-[(2S)-oxiran-2-yl]ethyl alpha-D-glucopyranoside'  D-saccharide  35  17  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EBG
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
 EBG  C1    C  CH1   0   0.250  -0.7016   1.1139  -0.5799
 EBG  O1    O  O2    0  -0.499  -1.0542   0.2100   0.4126
 EBG  C2    C  CH1   0  -0.019  -1.2658   0.6170  -1.9130
 EBG  O2    O  OH1   0  -0.668  -2.6400   0.3355  -1.8432
 EBG  C3    C  CH1   0  -0.010  -0.5401  -0.6498  -2.3501
 EBG  O3    O  OH1   0  -0.675  -0.9182  -1.0451  -3.6489
 EBG  C4    C  CH1   0   0.035   0.9639  -0.4031  -2.3738
 EBG  O4    O  OH1   0  -0.673   1.6773  -1.5843  -2.6440
 EBG  C5    C  CH1   0  -0.015   1.4228   0.1294  -1.0176
 EBG  O5    O  O2    0  -0.504   0.6833   1.2936  -0.6857
 EBG  C6    C  CH2   0  -0.161   2.8866   0.5154  -1.0208
 EBG  O6    O  OH1   0  -0.669   3.2492   0.9166   0.2795
 EBG  C7    C  CH2   0  -0.136  -0.6956   0.6021   1.7237
 EBG  C8    C  CH2   0  -0.509  -1.3849  -0.3288   2.7040
 EBG  C9    C  CH1   0  -0.002  -1.0661   0.0371   4.1255
 EBG  C10   C  CH2   0  -0.248  -0.9112  -0.9737   5.1646
 EBG  O9    O  O2    0  -0.489   0.2211  -0.3221   4.6078
 EBG  H1    H  HCH1  0   0.231  -1.0959   2.1141  -0.3463
 EBG  H2    H  HCH1  0   0.230  -1.0596   1.4007  -2.6556
 EBG  HO2   H  HOH1  0   0.458  -3.1308   1.1588  -1.9213
 EBG  H3    H  HCH1  0   0.219  -0.7468  -1.4507  -1.6249
 EBG  HO3   H  HOH1  0   0.456  -1.8237  -1.3686  -3.6176
 EBG  H4    H  HCH1  0   0.209   1.1708   0.3671  -3.1352
 EBG  HO4   H  HOH1  0   0.454   1.3789  -1.9267  -3.4931
 EBG  H5    H  HCH1  0   0.228   1.2703  -0.6545  -0.2619
 EBG  H61   H  HCH2  0   0.194   3.0457   1.3172  -1.7559
 EBG  H62   H  HCH2  0   0.212   3.4714  -0.3476  -1.3556
 EBG  HO6   H  HOH1  0   0.456   4.1951   1.0873   0.2829
 EBG  H71   H  HCH2  0   0.218   0.3902   0.5554   1.8617
 EBG  H72   H  HCH2  0   0.208  -1.0028   1.6409   1.9072
 EBG  H81   H  HCH2  0   0.243  -2.4685  -0.2719   2.5692
 EBG  H82   H  HCH2  0   0.245  -1.0864  -1.3626   2.5099
 EBG  H9    H  HCH1  0   0.255  -1.3945   1.0295   4.4342
 EBG  H101  H  HCH2  0   0.240  -1.1416  -0.7264   6.1971
 EBG  H102  H  HCH2  0   0.238  -1.0263  -2.0244   4.9104

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
 EBG  C1   O1    single  1.388  0.020  1.388
 EBG  C1   C2    single  1.531  0.020  1.531
 EBG  C1   O5    single  1.401  0.020  1.401
 EBG  C1   H1    single  0.970  0.020  1.090
 EBG  O1   C7    single  1.415  0.020  1.415
 EBG  C2   O2    single  1.404  0.020  1.404
 EBG  C2   C3    single  1.524  0.020  1.524
 EBG  C2   H2    single  0.970  0.020  1.090
 EBG  O2   HO2   single  0.850  0.020  0.980
 EBG  C3   O3    single  1.409  0.020  1.409
 EBG  C3   C4    single  1.524  0.020  1.524
 EBG  C3   H3    single  0.970  0.020  1.090
 EBG  O3   HO3   single  0.850  0.020  0.980
 EBG  C4   O4    single  1.406  0.020  1.406
 EBG  C4   C5    single  1.528  0.020  1.528
 EBG  C4   H4    single  0.970  0.020  1.090
 EBG  O4   HO4   single  0.850  0.020  0.980
 EBG  C5   O5    single  1.419  0.020  1.419
 EBG  C5   C6    single  1.514  0.020  1.514
 EBG  C5   H5    single  0.970  0.020  1.090
 EBG  C6   O6    single  1.408  0.020  1.408
 EBG  C6   H61   single  0.970  0.020  1.090
 EBG  C6   H62   single  0.970  0.020  1.090
 EBG  O6   HO6   single  0.850  0.020  0.980
 EBG  C7   C8    single  1.517  0.020  1.517
 EBG  C7   H71   single  0.970  0.020  1.090
 EBG  C7   H72   single  0.970  0.020  1.090
 EBG  C8   C9    single  1.502  0.020  1.502
 EBG  C8   H81   single  0.970  0.020  1.090
 EBG  C8   H82   single  0.970  0.020  1.090
 EBG  C9   C10   single  1.458  0.020  1.458
 EBG  C9   O9    single  1.421  0.020  1.421
 EBG  C9   H9    single  0.970  0.020  1.090
 EBG  C10  O9    single  1.420  0.020  1.420
 EBG  C10  H101  single  0.970  0.020  1.090
 EBG  C10  H102  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
 EBG  H1    C1   O5    104.70  3.000
 EBG  H1    C1   C2    110.36  3.000
 EBG  O5    C1   C2    109.90  3.000
 EBG  H1    C1   O1    110.44  3.000
 EBG  O5    C1   O1    112.88  3.000
 EBG  C2    C1   O1    108.53  3.000
 EBG  C7    O1   C1    114.70  3.000
 EBG  H2    C2   C3    108.04  3.000
 EBG  H2    C2   O2    111.10  3.000
 EBG  C3    C2   O2    108.28  3.000
 EBG  H2    C2   C1    106.73  3.000
 EBG  C3    C2   C1    110.13  3.000
 EBG  O2    C2   C1    112.48  3.000
 EBG  HO2   O2   C2    108.89  3.000
 EBG  H3    C3   C4    108.27  3.000
 EBG  H3    C3   O3    110.67  3.000
 EBG  C4    C3   O3    107.21  3.000
 EBG  H3    C3   C2    109.07  3.000
 EBG  C4    C3   C2    109.86  3.000
 EBG  O3    C3   C2    111.69  3.000
 EBG  HO3   O3   C3    108.47  3.000
 EBG  H4    C4   C5    108.25  3.000
 EBG  H4    C4   O4    111.03  3.000
 EBG  C5    C4   O4    108.12  3.000
 EBG  H4    C4   C3    108.00  3.000
 EBG  C5    C4   C3    109.82  3.000
 EBG  O4    C4   C3    111.57  3.000
 EBG  HO4   O4   C4    108.11  3.000
 EBG  H5    C5   C6    108.51  3.000
 EBG  H5    C5   O5    110.61  3.000
 EBG  C6    C5   O5    107.18  3.000
 EBG  H5    C5   C4    108.66  3.000
 EBG  C6    C5   C4    112.18  3.000
 EBG  O5    C5   C4    109.70  3.000
 EBG  C5    O5   C1    115.34  3.000
 EBG  H62   C6   H61   107.04  3.000
 EBG  H62   C6   O6    111.67  3.000
 EBG  H61   C6   O6    111.86  3.000
 EBG  H62   C6   C5    108.43  3.000
 EBG  H61   C6   C5    109.11  3.000
 EBG  O6    C6   C5    108.64  3.000
 EBG  HO6   O6   C6    107.90  3.000
 EBG  H72   C7   H71   107.24  3.000
 EBG  H72   C7   C8    110.19  3.000
 EBG  H71   C7   C8    110.05  3.000
 EBG  H72   C7   O1    110.23  3.000
 EBG  H71   C7   O1    110.86  3.000
 EBG  C8    C7   O1    108.27  3.000
 EBG  H82   C8   H81   107.33  3.000
 EBG  H82   C8   C9    109.90  3.000
 EBG  H81   C8   C9    108.32  3.000
 EBG  H82   C8   C7    109.95  3.000
 EBG  H81   C8   C7    109.79  3.000
 EBG  C9    C8   C7    111.44  3.000
 EBG  H9    C9   O9    114.02  3.000
 EBG  H9    C9   C10   117.48  3.000
 EBG  O9    C9   C10    59.10  3.000
 EBG  H9    C9   C8    115.20  3.000
 EBG  O9    C9   C8    116.87  3.000
 EBG  C10   C9   C8    121.89  3.000
 EBG  H102  C10  H101  114.82  3.000
 EBG  H102  C10  O9    115.86  3.000
 EBG  H101  C10  O9    115.93  3.000
 EBG  H102  C10  C9    119.48  3.000
 EBG  H101  C10  C9    119.80  3.000
 EBG  O9    C10  C9     59.15  3.000
 EBG  C10   O9   C9     61.75  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
 EBG  Var_01  O9    C10  C9  C8   104.36  30.0  1
 EBG  Var_02  H101  C10  O9  C9  -110.69  30.0  1
 EBG  Var_03  C10   C9   C8  C7  -144.62  30.0  3
 EBG  Var_04  C8    C7   O1  C1   168.65  30.0  3
 EBG  Var_05  C9    C8   C7  O1  -179.23  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
 EBG  chir_01  C1  O1  C2   O5  positiv
 EBG  chir_02  C2  O2  C1   C3  negativ
 EBG  chir_03  C3  O3  C2   C4  positiv
 EBG  chir_04  C4  O4  C5   C3  positiv
 EBG  chir_05  C5  O5  C4   C6  negativ
 EBG  chir_06  C9  C8  C10  O9  both

