# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:21:33 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: octyl 1-thio-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCS[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
 SOG  SOG  'octyl 1-thio-beta-D-glucopyranoside'  D-saccharide  48  20  .  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_SOG
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
 SOG  C1    C  CH1   0  -0.132  -0.3519   0.0201  -1.9494
 SOG  C2    C  CH1   0   0.017  -1.3615   0.0687  -3.1002
 SOG  C3    C  CH1   0  -0.001  -0.7352  -0.5835  -4.3268
 SOG  C4    C  CH1   0   0.032   0.6250   0.0321  -4.6360
 SOG  C5    C  CH1   0  -0.012   1.5074  -0.0181  -3.3888
 SOG  C6    C  CH2   0  -0.156   2.8377   0.6714  -3.6031
 SOG  C2'   C  CH2   0  -0.425  -0.6726   0.5428   2.1763
 SOG  C3'   C  CH2   0  -0.411   0.0309  -0.1528   3.3362
 SOG  C4'   C  CH2   0  -0.414  -0.4549   0.3250   4.6986
 SOG  C5'   C  CH2   0  -0.413   0.2393  -0.3780   5.8580
 SOG  C6'   C  CH2   0  -0.407  -0.2417   0.0941   7.2242
 SOG  C7'   C  CH2   0  -0.420   0.4536  -0.6092   8.3833
 SOG  C8'   C  CH3   0  -0.662  -0.0330  -0.1316   9.7445
 SOG  S1    S  S2    0  -0.015  -1.0389   0.8806  -0.5211
 SOG  O2    O  OH1   0  -0.662  -2.5328  -0.6432  -2.7996
 SOG  O3    O  OH1   0  -0.671  -1.5359  -0.4303  -5.4739
 SOG  O4    O  OH1   0  -0.671   1.2790  -0.6683  -5.6646
 SOG  O5    O  O2    0  -0.471   0.8506   0.6377  -2.3198
 SOG  O6    O  OH1   0  -0.669   3.6257   0.5045  -2.4486
 SOG  H1    H  HCH1  0   0.253  -0.1829  -1.0291  -1.6616
 SOG  H2    H  HCH1  0   0.225  -1.5748   1.1241  -3.3307
 SOG  H3    H  HCH1  0   0.217  -0.5796  -1.6500  -4.0972
 SOG  H4    H  HCH1  0   0.213   0.4752   1.0888  -4.9100
 SOG  H5    H  HCH1  0   0.222   1.6877  -1.0745  -3.1295
 SOG  H61   H  HCH2  0   0.214   3.3156   0.2349  -4.4861
 SOG  H62   H  HCH2  0   0.196   2.6586   1.7328  -3.8262
 SOG  H1'1  H  HCH2  0   0.267   0.9053   0.2277   0.7342
 SOG  H1'2  H  HCH2  0   0.266  -0.3310  -1.0345   0.7393
 SOG  H2'1  H  HCH2  0   0.230  -1.7511   0.3743   2.2480
 SOG  H2'2  H  HCH2  0   0.231  -0.5185   1.6234   2.2497
 SOG  H3'1  H  HCH2  0   0.216   1.1108   0.0101   3.2565
 SOG  H3'2  H  HCH2  0   0.215  -0.1207  -1.2344   3.2555
 SOG  H4'1  H  HCH2  0   0.210  -1.5366   0.1690   4.7741
 SOG  H4'2  H  HCH2  0   0.210  -0.2985   1.4060   4.7820
 SOG  H5'1  H  HCH2  0   0.208   1.3211  -0.2228   5.7806
 SOG  H5'2  H  HCH2  0   0.208   0.0830  -1.4590   5.7721
 SOG  H6'1  H  HCH2  0   0.206  -1.3236  -0.0621   7.3023
 SOG  H6'2  H  HCH2  0   0.206  -0.0863   1.1753   7.3105
 SOG  H7'1  H  HCH2  0   0.210   1.5340  -0.4531   8.3043
 SOG  H7'2  H  HCH2  0   0.210   0.2976  -1.6890   8.2961
 SOG  H8'1  H  HCH3  0   0.225   0.4780  -0.6477  10.5582
 SOG  H8'2  H  HCH3  0   0.216   0.1404   0.9388   9.8714
 SOG  H8'3  H  HCH3  0   0.216  -1.1040  -0.3058   9.8633
 SOG  HO2   H  HOH1  0   0.450  -2.9685  -0.2173  -2.0527
 SOG  HO3   H  HOH1  0   0.458  -2.3148  -0.9879  -5.3831
 SOG  HO4   H  HOH1  0   0.455   0.7259  -0.6308  -6.4521
 SOG  HO6   H  HOH1  0   0.456   4.4950   0.8725  -2.6295
 SOG  C1'   C  CH2   0  -0.547  -0.1645   0.0402   0.8341

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
 SOG  C1   C2    single  1.532  0.020  1.532
 SOG  C1   S1    single  1.803  0.020  1.803
 SOG  C1   O5    single  1.402  0.020  1.402
 SOG  C1   H1    single  0.970  0.020  1.090
 SOG  C2   C3    single  1.524  0.020  1.524
 SOG  C2   O2    single  1.403  0.020  1.403
 SOG  C2   H2    single  0.970  0.020  1.090
 SOG  C3   C4    single  1.525  0.020  1.525
 SOG  C3   O3    single  1.407  0.020  1.407
 SOG  C3   H3    single  0.970  0.020  1.090
 SOG  C4   C5    single  1.529  0.020  1.529
 SOG  C4   O4    single  1.406  0.020  1.406
 SOG  C4   H4    single  0.970  0.020  1.090
 SOG  C5   C6    single  1.514  0.020  1.514
 SOG  C5   O5    single  1.416  0.020  1.416
 SOG  C5   H5    single  0.970  0.020  1.090
 SOG  C6   O6    single  1.408  0.020  1.408
 SOG  C6   H61   single  0.970  0.020  1.090
 SOG  C6   H62   single  0.970  0.020  1.090
 SOG  C1'  C2'   single  1.521  0.020  1.521
 SOG  C1'  S1    single  1.819  0.020  1.819
 SOG  C1'  H1'1  single  0.970  0.020  1.090
 SOG  C1'  H1'2  single  0.970  0.020  1.090
 SOG  C2'  C3'   single  1.525  0.020  1.525
 SOG  C2'  H2'1  single  0.970  0.020  1.090
 SOG  C2'  H2'2  single  0.970  0.020  1.090
 SOG  C3'  C4'   single  1.523  0.020  1.523
 SOG  C3'  H3'1  single  0.970  0.020  1.090
 SOG  C3'  H3'2  single  0.970  0.020  1.090
 SOG  C4'  C5'   single  1.523  0.020  1.523
 SOG  C4'  H4'1  single  0.970  0.020  1.090
 SOG  C4'  H4'2  single  0.970  0.020  1.090
 SOG  C5'  C6'   single  1.523  0.020  1.523
 SOG  C5'  H5'1  single  0.970  0.020  1.090
 SOG  C5'  H5'2  single  0.970  0.020  1.090
 SOG  C6'  C7'   single  1.524  0.020  1.524
 SOG  C6'  H6'1  single  0.970  0.020  1.090
 SOG  C6'  H6'2  single  0.970  0.020  1.090
 SOG  C7'  C8'   single  1.522  0.020  1.522
 SOG  C7'  H7'1  single  0.970  0.020  1.090
 SOG  C7'  H7'2  single  0.970  0.020  1.090
 SOG  C8'  H8'1  single  0.970  0.020  1.090
 SOG  C8'  H8'2  single  0.970  0.020  1.090
 SOG  C8'  H8'3  single  0.970  0.020  1.090
 SOG  O2   HO2   single  0.850  0.020  0.980
 SOG  O3   HO3   single  0.850  0.020  0.980
 SOG  O4   HO4   single  0.850  0.020  0.980
 SOG  O6   HO6   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
 SOG  H1    C1   O5    110.93  3.000
 SOG  H1    C1   S1    107.82  3.000
 SOG  O5    C1   S1    109.02  3.000
 SOG  H1    C1   C2    109.14  3.000
 SOG  O5    C1   C2    110.67  3.000
 SOG  S1    C1   C2    109.20  3.000
 SOG  H2    C2   O2    111.68  3.000
 SOG  H2    C2   C3    108.74  3.000
 SOG  O2    C2   C3    107.36  3.000
 SOG  H2    C2   C1    108.39  3.000
 SOG  O2    C2   C1    111.91  3.000
 SOG  C3    C2   C1    108.68  3.000
 SOG  H3    C3   O3    110.82  3.000
 SOG  H3    C3   C4    107.88  3.000
 SOG  O3    C3   C4    107.36  3.000
 SOG  H3    C3   C2    107.73  3.000
 SOG  O3    C3   C2    112.07  3.000
 SOG  C4    C3   C2    110.92  3.000
 SOG  H4    C4   O4    111.05  3.000
 SOG  H4    C4   C5    108.23  3.000
 SOG  O4    C4   C5    108.19  3.000
 SOG  H4    C4   C3    108.44  3.000
 SOG  O4    C4   C3    111.24  3.000
 SOG  C5    C4   C3    109.65  3.000
 SOG  H5    C5   O5    110.01  3.000
 SOG  H5    C5   C6    109.03  3.000
 SOG  O5    C5   C6    107.68  3.000
 SOG  H5    C5   C4    108.52  3.000
 SOG  O5    C5   C4    109.46  3.000
 SOG  C6    C5   C4    112.14  3.000
 SOG  H62   C6   H61   107.00  3.000
 SOG  H62   C6   O6    111.85  3.000
 SOG  H61   C6   O6    111.71  3.000
 SOG  H62   C6   C5    108.98  3.000
 SOG  H61   C6   C5    108.43  3.000
 SOG  O6    C6   C5    108.77  3.000
 SOG  H2'2  C2'  H2'1  106.66  3.000
 SOG  H2'2  C2'  C3'   109.55  3.000
 SOG  H2'1  C2'  C3'   109.55  3.000
 SOG  H2'2  C2'  C1'   109.80  3.000
 SOG  H2'1  C2'  C1'   109.66  3.000
 SOG  C3'   C2'  C1'   111.50  3.000
 SOG  H3'2  C3'  H3'1  106.15  3.000
 SOG  H3'2  C3'  C4'   109.37  3.000
 SOG  H3'1  C3'  C4'   109.45  3.000
 SOG  H3'2  C3'  C2'   109.31  3.000
 SOG  H3'1  C3'  C2'   109.38  3.000
 SOG  C4'   C3'  C2'   112.97  3.000
 SOG  H4'2  C4'  H4'1  106.04  3.000
 SOG  H4'2  C4'  C5'   109.42  3.000
 SOG  H4'1  C4'  C5'   109.37  3.000
 SOG  H4'2  C4'  C3'   109.40  3.000
 SOG  H4'1  C4'  C3'   109.38  3.000
 SOG  C5'   C4'  C3'   113.00  3.000
 SOG  H5'2  C5'  H5'1  105.96  3.000
 SOG  H5'2  C5'  C6'   109.33  3.000
 SOG  H5'1  C5'  C6'   109.34  3.000
 SOG  H5'2  C5'  C4'   109.31  3.000
 SOG  H5'1  C5'  C4'   109.32  3.000
 SOG  C6'   C5'  C4'   113.31  3.000
 SOG  H6'2  C6'  H6'1  105.96  3.000
 SOG  H6'2  C6'  C7'   109.32  3.000
 SOG  H6'1  C6'  C7'   109.30  3.000
 SOG  H6'2  C6'  C5'   109.36  3.000
 SOG  H6'1  C6'  C5'   109.35  3.000
 SOG  C7'   C6'  C5'   113.28  3.000
 SOG  H7'2  C7'  H7'1  106.00  3.000
 SOG  H7'2  C7'  C8'   109.58  3.000
 SOG  H7'1  C7'  C8'   109.59  3.000
 SOG  H7'2  C7'  C6'   109.25  3.000
 SOG  H7'1  C7'  C6'   109.25  3.000
 SOG  C8'   C7'  C6'   112.93  3.000
 SOG  H8'3  C8'  H8'2  107.44  3.000
 SOG  H8'3  C8'  H8'1  107.64  3.000
 SOG  H8'2  C8'  H8'1  107.63  3.000
 SOG  H8'3  C8'  C7'   111.15  3.000
 SOG  H8'2  C8'  C7'   111.14  3.000
 SOG  H8'1  C8'  C7'   111.65  3.000
 SOG  C1'   S1   C1    100.75  3.000
 SOG  HO2   O2   C2    108.61  3.000
 SOG  HO3   O3   C3    108.70  3.000
 SOG  HO4   O4   C4    108.16  3.000
 SOG  C5    O5   C1    113.17  3.000
 SOG  HO6   O6   C6    107.85  3.000
 SOG  H1'2  C1'  H1'1  108.11  3.000
 SOG  H1'2  C1'  S1    108.48  3.000
 SOG  H1'1  C1'  S1    108.90  3.000
 SOG  H1'2  C1'  C2'   110.56  3.000
 SOG  H1'1  C1'  C2'   110.59  3.000
 SOG  S1    C1'  C2'   110.14  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
 SOG  Var_01  C2'   C1'  S1   C1   -175.74  30.0  1
 SOG  Var_02  C4'   C3'  C2'  C1'  -179.92  30.0  3
 SOG  Var_03  C5'   C4'  C3'  C2'   179.52  30.0  3
 SOG  Var_04  S1    C1'  C2'  C3'   179.42  30.0  1
 SOG  Var_05  C6'   C5'  C4'  C3'  -179.97  30.0  3
 SOG  Var_06  C7'   C6'  C5'  C4'  -179.98  30.0  3
 SOG  Var_07  C8'   C7'  C6'  C5'  -180.00  30.0  3
 SOG  Var_08  H8'1  C8'  C7'  C6'  -179.98  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
 SOG  chir_01  C1  C2  S1  O5  positiv
 SOG  chir_02  C2  O2  C1  C3  negativ
 SOG  chir_03  C3  O3  C2  C4  positiv
 SOG  chir_04  C4  O4  C5  C3  positiv
 SOG  chir_05  C5  O5  C4  C6  negativ

