# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:40:31 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-O-octyl-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCO[C@H]1[C@H](O)O[C@H](CO)[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
 BGL  BGL  2-O-octyl-beta-D-glucopyranose  D-saccharide  48  20  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BGL
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
 BGL  C1    C  CH1   0   0.274  -22.8875  56.5979  56.6684
 BGL  O1    O  OH1   0  -0.650  -21.9120  56.4991  55.6998
 BGL  C2    C  CH1   0   0.010  -23.3165  58.0621  56.7858
 BGL  O2    O  O2    0  -0.500  -22.2803  58.8434  57.3165
 BGL  C3    C  CH1   0   0.010  -24.5136  58.1797  57.7211
 BGL  O3    O  OH1   0  -0.664  -24.9636  59.5092  57.6892
 BGL  C4    C  CH1   0   0.006  -25.6104  57.2011  57.3187
 BGL  O4    O  OH1   0  -0.673  -26.6282  57.2941  58.2905
 BGL  C5    C  CH1   0  -0.012  -25.0189  55.7908  57.2418
 BGL  O5    O  O2    0  -0.498  -23.9777  55.7927  56.2862
 BGL  C6    C  CH2   0  -0.192  -26.0202  54.7170  56.8788
 BGL  O6    O  OH1   0  -0.667  -26.6614  55.0458  55.6698
 BGL  C1'   C  CH2   0  -0.126  -21.4707  59.5568  56.4053
 BGL  C2'   C  CH2   0  -0.454  -20.8631  60.7495  57.1183
 BGL  C3'   C  CH2   0  -0.429  -19.9206  61.5357  56.2156
 BGL  C4'   C  CH2   0  -0.418  -19.3249  62.7537  56.9136
 BGL  C5'   C  CH2   0  -0.420  -18.3689  63.5667  56.0449
 BGL  C6'   C  CH2   0  -0.410  -17.0745  62.8401  55.6981
 BGL  C7'   C  CH2   0  -0.415  -16.1197  63.6797  54.8588
 BGL  C8'   C  CH3   0  -0.659  -14.8279  62.9455  54.5265
 BGL  H1    H  HCH1  0   0.183  -22.5174  56.2603  57.6535
 BGL  HO1   H  HOH1  0   0.462  -21.4266  55.6751  55.8146
 BGL  H2    H  HCH1  0   0.223  -23.6132  58.4172  55.7862
 BGL  H3    H  HCH1  0   0.203  -24.1775  57.9019  58.7354
 BGL  HO3   H  HOH1  0   0.446  -25.7386  59.5693  58.2578
 BGL  H4    H  HCH1  0   0.225  -25.9851  57.4843  56.3265
 BGL  HO4   H  HOH1  0   0.459  -27.4665  57.0488  57.8884
 BGL  H5    H  HCH1  0   0.221  -24.6219  55.5247  58.2360
 BGL  H61   H  HCH2  0   0.217  -25.4903  53.7576  56.8145
 BGL  H62   H  HCH2  0   0.207  -26.7305  54.6246  57.7096
 BGL  HO6   H  HOH1  0   0.457  -27.3396  54.3860  55.4997
 BGL  H1'1  H  HCH2  0   0.195  -20.6757  58.9200  55.9999
 BGL  H1'2  H  HCH2  0   0.196  -22.0667  59.9037  55.5509
 BGL  H2'1  H  HCH2  0   0.216  -21.6645  61.4028  57.4773
 BGL  H2'2  H  HCH2  0   0.219  -20.3159  60.4072  58.0023
 BGL  H3'1  H  HCH2  0   0.218  -19.1241  60.8721  55.8662
 BGL  H3'2  H  HCH2  0   0.211  -20.4571  61.8637  55.3185
 BGL  H4'1  H  HCH2  0   0.217  -20.1427  63.4000  57.2475
 BGL  H4'2  H  HCH2  0   0.207  -18.8034  62.4341  57.8226
 BGL  H5'1  H  HCH2  0   0.205  -18.8805  63.8642  55.1228
 BGL  H5'2  H  HCH2  0   0.216  -18.1202  64.4969  56.5655
 BGL  H6'1  H  HCH2  0   0.204  -16.5727  62.5406  56.6253
 BGL  H6'2  H  HCH2  0   0.211  -17.2961  61.9125  55.1615
 BGL  H7'1  H  HCH2  0   0.209  -16.6201  63.9789  53.9327
 BGL  H7'2  H  HCH2  0   0.209  -15.8875  64.6075  55.3910
 BGL  H8'1  H  HCH3  0   0.224  -14.1576  63.5614  53.9257
 BGL  H8'2  H  HCH3  0   0.215  -14.2912  62.6624  55.4339
 BGL  H8'3  H  HCH3  0   0.214  -15.0284  62.0311  53.9652

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
 BGL  C1   O1    single  1.378  0.020  1.378
 BGL  C1   C2    single  1.530  0.020  1.530
 BGL  C1   O5    single  1.408  0.020  1.408
 BGL  C1   H1    single  0.970  0.020  1.090
 BGL  O1   HO1   single  0.850  0.020  0.980
 BGL  C2   O2    single  1.402  0.020  1.402
 BGL  C2   C3    single  1.524  0.020  1.524
 BGL  C2   H2    single  0.970  0.020  1.090
 BGL  O2   C1'   single  1.412  0.020  1.412
 BGL  C3   O3    single  1.404  0.020  1.404
 BGL  C3   C4    single  1.524  0.020  1.524
 BGL  C3   H3    single  0.970  0.020  1.090
 BGL  O3   HO3   single  0.850  0.020  0.980
 BGL  C4   O4    single  1.410  0.020  1.410
 BGL  C4   C5    single  1.531  0.020  1.531
 BGL  C4   H4    single  0.970  0.020  1.090
 BGL  O4   HO4   single  0.850  0.020  0.980
 BGL  C5   O5    single  1.413  0.020  1.413
 BGL  C5   C6    single  1.512  0.020  1.512
 BGL  C5   H5    single  0.970  0.020  1.090
 BGL  C6   O6    single  1.407  0.020  1.407
 BGL  C6   H61   single  0.970  0.020  1.090
 BGL  C6   H62   single  0.970  0.020  1.090
 BGL  O6   HO6   single  0.850  0.020  0.980
 BGL  C1'  C2'   single  1.517  0.020  1.517
 BGL  C1'  H1'1  single  0.970  0.020  1.090
 BGL  C1'  H1'2  single  0.970  0.020  1.090
 BGL  C2'  C3'   single  1.524  0.020  1.524
 BGL  C2'  H2'1  single  0.970  0.020  1.090
 BGL  C2'  H2'2  single  0.970  0.020  1.090
 BGL  C3'  C4'   single  1.525  0.020  1.525
 BGL  C3'  H3'1  single  0.970  0.020  1.090
 BGL  C3'  H3'2  single  0.970  0.020  1.090
 BGL  C4'  C5'   single  1.526  0.020  1.526
 BGL  C4'  H4'1  single  0.970  0.020  1.090
 BGL  C4'  H4'2  single  0.970  0.020  1.090
 BGL  C5'  C6'   single  1.524  0.020  1.524
 BGL  C5'  H5'1  single  0.970  0.020  1.090
 BGL  C5'  H5'2  single  0.970  0.020  1.090
 BGL  C6'  C7'   single  1.523  0.020  1.523
 BGL  C6'  H6'1  single  0.970  0.020  1.090
 BGL  C6'  H6'2  single  0.970  0.020  1.090
 BGL  C7'  C8'   single  1.523  0.020  1.523
 BGL  C7'  H7'1  single  0.970  0.020  1.090
 BGL  C7'  H7'2  single  0.970  0.020  1.090
 BGL  C8'  H8'1  single  0.970  0.020  1.090
 BGL  C8'  H8'2  single  0.970  0.020  1.090
 BGL  C8'  H8'3  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
 BGL  H1    C1   O5    109.06  3.000
 BGL  H1    C1   C2    108.53  3.000
 BGL  O5    C1   C2    110.54  3.000
 BGL  H1    C1   O1    111.56  3.000
 BGL  O5    C1   O1    108.43  3.000
 BGL  C2    C1   O1    108.72  3.000
 BGL  HO1   O1   C1    109.52  3.000
 BGL  H2    C2   C3    108.69  3.000
 BGL  H2    C2   O2    111.28  3.000
 BGL  C3    C2   O2    107.78  3.000
 BGL  H2    C2   C1    108.32  3.000
 BGL  C3    C2   C1    109.95  3.000
 BGL  O2    C2   C1    110.80  3.000
 BGL  C1'   O2   C2    117.45  3.000
 BGL  H3    C3   C4    107.47  3.000
 BGL  H3    C3   O3    110.90  3.000
 BGL  C4    C3   O3    111.80  3.000
 BGL  H3    C3   C2    107.77  3.000
 BGL  C4    C3   C2    110.72  3.000
 BGL  O3    C3   C2    108.12  3.000
 BGL  HO3   O3   C3    107.67  3.000
 BGL  H4    C4   C5    108.91  3.000
 BGL  H4    C4   O4    111.06  3.000
 BGL  C5    C4   O4    111.97  3.000
 BGL  H4    C4   C3    108.58  3.000
 BGL  C5    C4   C3    109.07  3.000
 BGL  O4    C4   C3    107.16  3.000
 BGL  HO4   O4   C4    108.92  3.000
 BGL  H5    C5   C6    106.46  3.000
 BGL  H5    C5   O5    110.16  3.000
 BGL  C6    C5   O5    109.05  3.000
 BGL  H5    C5   C4    108.41  3.000
 BGL  C6    C5   C4    114.22  3.000
 BGL  O5    C5   C4    108.50  3.000
 BGL  C5    O5   C1    112.81  3.000
 BGL  H62   C6   H61   106.45  3.000
 BGL  H62   C6   O6    112.04  3.000
 BGL  H61   C6   O6    111.95  3.000
 BGL  H62   C6   C5    107.86  3.000
 BGL  H61   C6   C5    108.36  3.000
 BGL  O6    C6   C5    110.00  3.000
 BGL  HO6   O6   C6    108.25  3.000
 BGL  H1'2  C1'  H1'1  106.82  3.000
 BGL  H1'2  C1'  C2'   109.56  3.000
 BGL  H1'1  C1'  C2'   109.88  3.000
 BGL  H1'2  C1'  O2    110.52  3.000
 BGL  H1'1  C1'  O2    111.15  3.000
 BGL  C2'   C1'  O2    108.88  3.000
 BGL  H2'2  C2'  H2'1  106.73  3.000
 BGL  H2'2  C2'  C3'   109.31  3.000
 BGL  H2'1  C2'  C3'   109.84  3.000
 BGL  H2'2  C2'  C1'   109.51  3.000
 BGL  H2'1  C2'  C1'   109.28  3.000
 BGL  C3'   C2'  C1'   112.03  3.000
 BGL  H3'2  C3'  H3'1  106.06  3.000
 BGL  H3'2  C3'  C4'   109.09  3.000
 BGL  H3'1  C3'  C4'   110.26  3.000
 BGL  H3'2  C3'  C2'   109.68  3.000
 BGL  H3'1  C3'  C2'   109.06  3.000
 BGL  C4'   C3'  C2'   112.50  3.000
 BGL  H4'2  C4'  H4'1  105.94  3.000
 BGL  H4'2  C4'  C5'   109.24  3.000
 BGL  H4'1  C4'  C5'   109.09  3.000
 BGL  H4'2  C4'  C3'   109.43  3.000
 BGL  H4'1  C4'  C3'   108.62  3.000
 BGL  C5'   C4'  C3'   114.18  3.000
 BGL  H5'2  C5'  H5'1  106.00  3.000
 BGL  H5'2  C5'  C6'   108.68  3.000
 BGL  H5'1  C5'  C6'   109.54  3.000
 BGL  H5'2  C5'  C4'   108.93  3.000
 BGL  H5'1  C5'  C4'   109.34  3.000
 BGL  C6'   C5'  C4'   114.04  3.000
 BGL  H6'2  C6'  H6'1  106.02  3.000
 BGL  H6'2  C6'  C7'   108.90  3.000
 BGL  H6'1  C6'  C7'   109.25  3.000
 BGL  H6'2  C6'  C5'   110.10  3.000
 BGL  H6'1  C6'  C5'   109.06  3.000
 BGL  C7'   C6'  C5'   113.25  3.000
 BGL  H7'2  C7'  H7'1  106.06  3.000
 BGL  H7'2  C7'  C8'   109.56  3.000
 BGL  H7'1  C7'  C8'   109.57  3.000
 BGL  H7'2  C7'  C6'   109.41  3.000
 BGL  H7'1  C7'  C6'   109.29  3.000
 BGL  C8'   C7'  C6'   112.72  3.000
 BGL  H8'3  C8'  H8'2  107.49  3.000
 BGL  H8'3  C8'  H8'1  107.62  3.000
 BGL  H8'2  C8'  H8'1  107.59  3.000
 BGL  H8'3  C8'  C7'   111.12  3.000
 BGL  H8'2  C8'  C7'   111.14  3.000
 BGL  H8'1  C8'  C7'   111.68  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
 BGL  Var_01  C2'   C1'  O2   C2    155.34  30.0  3
 BGL  Var_02  C3'   C2'  C1'  O2    177.31  30.0  3
 BGL  Var_03  C4'   C3'  C2'  C1'   178.86  30.0  3
 BGL  Var_04  C5'   C4'  C3'  C2'   179.74  30.0  3
 BGL  Var_05  C6'   C5'  C4'  C3'   -67.41  30.0  3
 BGL  Var_06  C7'   C6'  C5'  C4'  -178.63  30.0  3
 BGL  Var_07  C8'   C7'  C6'  C5'   179.66  30.0  3
 BGL  Var_08  H8'1  C8'  C7'  C6'   179.99  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
 BGL  chir_01  C1  O1  C2  O5  negativ
 BGL  chir_02  C2  O2  C3  C1  positiv
 BGL  chir_03  C3  O3  C2  C4  positiv
 BGL  chir_04  C4  O4  C3  C5  negativ
 BGL  chir_05  C5  O5  C4  C6  negativ

