# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:09:17 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: nonyl beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCO[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
 BNG  BNG  'nonyl beta-D-glucopyranoside'  D-saccharide  51  21  .  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_BNG
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
 BNG  C1    C  CH1   0   0.315  98.2862  10.4638  31.7097
 BNG  C2    C  CH1   0   0.002  98.1997   9.3954  32.7914
 BNG  C3    C  CH1   0  -0.010  98.0940   8.0321  32.1178
 BNG  C4    C  CH1   0   0.002  96.9502   7.9944  31.1102
 BNG  C5    C  CH1   0  -0.021  97.0957   9.1691  30.1355
 BNG  C6    C  CH2   0  -0.159  95.9297   9.2744  29.1769
 BNG  C2'   C  CH2   0  -0.461  98.4724  14.0872  32.0713
 BNG  C3'   C  CH2   0  -0.411  96.9786  14.3941  32.0925
 BNG  C4'   C  CH2   0  -0.411  96.6740  15.8029  32.5850
 BNG  C5'   C  CH2   0  -0.409  95.1872  16.1365  32.5743
 BNG  C6'   C  CH2   0  -0.409  94.8873  17.5550  33.0418
 BNG  C7'   C  CH2   0  -0.404  93.4044  17.9030  33.0075
 BNG  C8'   C  CH2   0  -0.417  93.1076  19.3248  33.4682
 BNG  C9'   C  CH3   0  -0.659  91.6253  19.6687  33.4175
 BNG  O1    O  O2    0  -0.492  98.2857  11.7109  32.2859
 BNG  O2    O  OH1   0  -0.666  99.3463   9.4896  33.5962
 BNG  O3    O  OH1   0  -0.668  97.9361   7.0727  33.1346
 BNG  O4    O  OH1   0  -0.668  97.0194   6.7477  30.4548
 BNG  O5    O  O2    0  -0.496  97.1603  10.3722  30.8722
 BNG  O6    O  OH1   0  -0.664  96.1830  10.3170  28.2668
 BNG  H1    H  HCH1  0   0.181  99.2038  10.2992  31.1122
 BNG  H2    H  HCH1  0   0.212  97.2821   9.5712  33.3763
 BNG  H3    H  HCH1  0   0.210  99.0317   7.8586  31.5631
 BNG  H4    H  HCH1  0   0.223  96.0003   8.1044  31.6535
 BNG  H5    H  HCH1  0   0.218  98.0221   9.0276  29.5533
 BNG  H61   H  HCH2  0   0.201  95.8144   8.3117  28.6648
 BNG  H62   H  HCH2  0   0.199  95.0097   9.4466  29.7526
 BNG  H1'1  H  HCH2  0   0.208  98.3984  12.6853  30.4514
 BNG  H1'2  H  HCH2  0   0.220  99.9001  12.6256  31.3794
 BNG  H2'1  H  HCH2  0   0.223  98.8864  14.1538  33.0821
 BNG  H2'2  H  HCH2  0   0.225  98.9901  14.8485  31.4799
 BNG  H3'1  H  HCH2  0   0.207  96.5751  14.2694  31.0814
 BNG  H3'2  H  HCH2  0   0.215  96.4554  13.6686  32.7217
 BNG  H4'1  H  HCH2  0   0.208  97.0666  15.9291  33.5999
 BNG  H4'2  H  HCH2  0   0.206  97.2102  16.5271  31.9618
 BNG  H5'1  H  HCH2  0   0.205  94.7947  15.9976  31.5609
 BNG  H5'2  H  HCH2  0   0.206  94.6487  15.4228  33.2074
 BNG  H6'1  H  HCH2  0   0.205  95.2679  17.6906  34.0601
 BNG  H6'2  H  HCH2  0   0.205  95.4395  18.2652  32.4164
 BNG  H7'1  H  HCH2  0   0.204  93.0242  17.7656  31.9891
 BNG  H7'2  H  HCH2  0   0.205  92.8495  17.1961  33.6343
 BNG  H8'1  H  HCH2  0   0.209  93.4807  19.4599  34.4882
 BNG  H8'2  H  HCH2  0   0.209  93.6679  20.0297  32.8463
 BNG  H9'1  H  HCH3  0   0.224  91.4382  20.6899  33.7514
 BNG  H9'2  H  HCH3  0   0.214  91.2347  19.5765  32.4025
 BNG  H9'3  H  HCH3  0   0.214  91.0428  19.0010  34.0552
 BNG  HO2   H  HOH1  0   0.450  99.3432   8.7432  34.2048
 BNG  HO3   H  HOH1  0   0.452  97.9934   6.1980  32.7364
 BNG  HO4   H  HOH1  0   0.459  96.1354   6.4770  30.1924
 BNG  HO6   H  HOH1  0   0.454  95.4350  10.3779  27.6662
 BNG  C1'   C  CH2   0  -0.166  98.8127  12.7435  31.4643

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
 BNG  C1   C2    single  1.523  0.020  1.523
 BNG  C1   O1    single  1.374  0.020  1.374
 BNG  C1   O5    single  1.406  0.020  1.406
 BNG  C1   H1    single  0.970  0.020  1.090
 BNG  C2   C3    single  1.524  0.020  1.524
 BNG  C2   O2    single  1.404  0.020  1.404
 BNG  C2   H2    single  0.970  0.020  1.090
 BNG  C3   C4    single  1.525  0.020  1.525
 BNG  C3   O3    single  1.407  0.020  1.407
 BNG  C3   H3    single  0.970  0.020  1.090
 BNG  C4   C5    single  1.533  0.020  1.533
 BNG  C4   O4    single  1.410  0.020  1.410
 BNG  C4   H4    single  0.970  0.020  1.090
 BNG  C5   C6    single  1.513  0.020  1.513
 BNG  C5   O5    single  1.412  0.020  1.412
 BNG  C5   H5    single  0.970  0.020  1.090
 BNG  C6   O6    single  1.407  0.020  1.407
 BNG  C6   H61   single  0.970  0.020  1.090
 BNG  C6   H62   single  0.970  0.020  1.090
 BNG  C1'  C2'   single  1.513  0.020  1.513
 BNG  C1'  O1    single  1.421  0.020  1.421
 BNG  C1'  H1'1  single  0.970  0.020  1.090
 BNG  C1'  H1'2  single  0.970  0.020  1.090
 BNG  C2'  C3'   single  1.525  0.020  1.525
 BNG  C2'  H2'1  single  0.970  0.020  1.090
 BNG  C2'  H2'2  single  0.970  0.020  1.090
 BNG  C3'  C4'   single  1.523  0.020  1.523
 BNG  C3'  H3'1  single  0.970  0.020  1.090
 BNG  C3'  H3'2  single  0.970  0.020  1.090
 BNG  C4'  C5'   single  1.524  0.020  1.524
 BNG  C4'  H4'1  single  0.970  0.020  1.090
 BNG  C4'  H4'2  single  0.970  0.020  1.090
 BNG  C5'  C6'   single  1.523  0.020  1.523
 BNG  C5'  H5'1  single  0.970  0.020  1.090
 BNG  C5'  H5'2  single  0.970  0.020  1.090
 BNG  C6'  C7'   single  1.523  0.020  1.523
 BNG  C6'  H6'1  single  0.970  0.020  1.090
 BNG  C6'  H6'2  single  0.970  0.020  1.090
 BNG  C7'  C8'   single  1.524  0.020  1.524
 BNG  C7'  H7'1  single  0.970  0.020  1.090
 BNG  C7'  H7'2  single  0.970  0.020  1.090
 BNG  C8'  C9'   single  1.522  0.020  1.522
 BNG  C8'  H8'1  single  0.970  0.020  1.090
 BNG  C8'  H8'2  single  0.970  0.020  1.090
 BNG  C9'  H9'1  single  0.970  0.020  1.090
 BNG  C9'  H9'2  single  0.970  0.020  1.090
 BNG  C9'  H9'3  single  0.970  0.020  1.090
 BNG  O2   HO2   single  0.850  0.020  0.980
 BNG  O3   HO3   single  0.850  0.020  0.980
 BNG  O4   HO4   single  0.850  0.020  0.980
 BNG  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
 BNG  H1    C1   O5    109.42  3.000
 BNG  H1    C1   O1    111.19  3.000
 BNG  O5    C1   O1    107.98  3.000
 BNG  H1    C1   C2    109.03  3.000
 BNG  O5    C1   C2    109.38  3.000
 BNG  O1    C1   C2    109.82  3.000
 BNG  H2    C2   O2    111.40  3.000
 BNG  H2    C2   C3    108.63  3.000
 BNG  O2    C2   C3    111.71  3.000
 BNG  H2    C2   C1    108.20  3.000
 BNG  O2    C2   C1    108.28  3.000
 BNG  C3    C2   C1    108.52  3.000
 BNG  H3    C3   O3    110.58  3.000
 BNG  H3    C3   C4    107.55  3.000
 BNG  O3    C3   C4    112.12  3.000
 BNG  H3    C3   C2    107.69  3.000
 BNG  O3    C3   C2    107.35  3.000
 BNG  C4    C3   C2    111.48  3.000
 BNG  H4    C4   O4    111.13  3.000
 BNG  H4    C4   C5    108.62  3.000
 BNG  O4    C4   C5    112.15  3.000
 BNG  H4    C4   C3    108.61  3.000
 BNG  O4    C4   C3    106.99  3.000
 BNG  C5    C4   C3    109.26  3.000
 BNG  H5    C5   O5    110.25  3.000
 BNG  H5    C5   C6    108.77  3.000
 BNG  O5    C5   C6    107.85  3.000
 BNG  H5    C5   C4    108.47  3.000
 BNG  O5    C5   C4    108.99  3.000
 BNG  C6    C5   C4    112.52  3.000
 BNG  H62   C6   H61   107.11  3.000
 BNG  H62   C6   O6    111.93  3.000
 BNG  H61   C6   O6    111.56  3.000
 BNG  H62   C6   C5    108.91  3.000
 BNG  H61   C6   C5    108.41  3.000
 BNG  O6    C6   C5    108.82  3.000
 BNG  H2'2  C2'  H2'1  106.13  3.000
 BNG  H2'2  C2'  C3'   109.33  3.000
 BNG  H2'1  C2'  C3'   110.21  3.000
 BNG  H2'2  C2'  C1'   107.14  3.000
 BNG  H2'1  C2'  C1'   109.85  3.000
 BNG  C3'   C2'  C1'   113.86  3.000
 BNG  H3'2  C3'  H3'1  106.22  3.000
 BNG  H3'2  C3'  C4'   109.38  3.000
 BNG  H3'1  C3'  C4'   109.26  3.000
 BNG  H3'2  C3'  C2'   110.07  3.000
 BNG  H3'1  C3'  C2'   108.96  3.000
 BNG  C4'   C3'  C2'   112.74  3.000
 BNG  H4'2  C4'  H4'1  105.98  3.000
 BNG  H4'2  C4'  C5'   109.20  3.000
 BNG  H4'1  C4'  C5'   109.33  3.000
 BNG  H4'2  C4'  C3'   109.24  3.000
 BNG  H4'1  C4'  C3'   109.54  3.000
 BNG  C5'   C4'  C3'   113.29  3.000
 BNG  H5'2  C5'  H5'1  106.02  3.000
 BNG  H5'2  C5'  C6'   109.42  3.000
 BNG  H5'1  C5'  C6'   109.35  3.000
 BNG  H5'2  C5'  C4'   109.45  3.000
 BNG  H5'1  C5'  C4'   109.16  3.000
 BNG  C6'   C5'  C4'   113.19  3.000
 BNG  H6'2  C6'  H6'1  105.97  3.000
 BNG  H6'2  C6'  C7'   109.25  3.000
 BNG  H6'1  C6'  C7'   109.32  3.000
 BNG  H6'2  C6'  C5'   109.22  3.000
 BNG  H6'1  C6'  C5'   109.39  3.000
 BNG  C7'   C6'  C5'   113.42  3.000
 BNG  H7'2  C7'  H7'1  105.97  3.000
 BNG  H7'2  C7'  C8'   109.29  3.000
 BNG  H7'1  C7'  C8'   109.29  3.000
 BNG  H7'2  C7'  C6'   109.44  3.000
 BNG  H7'1  C7'  C6'   109.27  3.000
 BNG  C8'   C7'  C6'   113.33  3.000
 BNG  H8'2  C8'  H8'1  105.99  3.000
 BNG  H8'2  C8'  C9'   109.52  3.000
 BNG  H8'1  C8'  C9'   109.58  3.000
 BNG  H8'2  C8'  C7'   109.24  3.000
 BNG  H8'1  C8'  C7'   109.29  3.000
 BNG  C9'   C8'  C7'   112.98  3.000
 BNG  H9'3  C9'  H9'2  107.49  3.000
 BNG  H9'3  C9'  H9'1  107.60  3.000
 BNG  H9'2  C9'  H9'1  107.60  3.000
 BNG  H9'3  C9'  C8'   111.22  3.000
 BNG  H9'2  C9'  C8'   111.12  3.000
 BNG  H9'1  C9'  C8'   111.62  3.000
 BNG  C1'   O1   C1    114.65  3.000
 BNG  HO2   O2   C2    107.92  3.000
 BNG  HO3   O3   C3    108.29  3.000
 BNG  HO4   O4   C4    109.31  3.000
 BNG  C5    O5   C1    113.76  3.000
 BNG  HO6   O6   C6    108.12  3.000
 BNG  H1'2  C1'  H1'1  107.31  3.000
 BNG  H1'2  C1'  O1    109.53  3.000
 BNG  H1'1  C1'  O1    110.84  3.000
 BNG  H1'2  C1'  C2'   110.45  3.000
 BNG  H1'1  C1'  C2'   109.45  3.000
 BNG  O1    C1'  C2'   109.27  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
 BNG  Var_01  C2'   C1'  O1   C1    167.25  30.0  1
 BNG  Var_02  C4'   C3'  C2'  C1'  -174.54  30.0  3
 BNG  Var_03  C5'   C4'  C3'  C2'   178.38  30.0  3
 BNG  Var_04  O1    C1'  C2'  C3'   -65.46  30.0  2
 BNG  Var_05  C6'   C5'  C4'  C3'  -178.89  30.0  3
 BNG  Var_06  C7'   C6'  C5'  C4'   178.89  30.0  3
 BNG  Var_07  C8'   C7'  C6'  C5'  -179.68  30.0  3
 BNG  Var_08  C9'   C8'  C7'  C6'   179.42  30.0  3
 BNG  Var_09  H9'1  C9'  C8'  C7'   180.00  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
 BNG  chir_01  C1  C2  O1  O5  positiv
 BNG  chir_02  C2  O2  C1  C3  negativ
 BNG  chir_03  C3  O3  C2  C4  positiv
 BNG  chir_04  C4  O4  C3  C5  negativ
 BNG  chir_05  C5  O5  C4  C6  negativ

