# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:24:20 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: octyl beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCO[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
 BOG  BOG  'octyl beta-D-glucopyranoside'  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 PERFECT
;

data_comp_BOG
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
 BOG  C1    C  CH1   0   0.311  -22.4213  -89.0340  58.9866
 BOG  O1    O  O2    0  -0.495  -23.1662  -88.1688  58.2255
 BOG  C2    C  CH1   0   0.005  -22.3565  -88.5202  60.4199
 BOG  O2    O  OH1   0  -0.663  -21.7149  -87.2724  60.4196
 BOG  C3    C  CH1   0  -0.021  -21.6013  -89.5411  61.2610
 BOG  O3    O  OH1   0  -0.669  -21.5883  -89.0633  62.5853
 BOG  C4    C  CH1   0   0.031  -22.2415  -90.9191  61.1465
 BOG  O4    O  OH1   0  -0.683  -21.4398  -91.8141  61.8751
 BOG  C5    C  CH1   0  -0.030  -22.3583  -91.2986  59.6638
 BOG  O5    O  O2    0  -0.500  -23.0591  -90.2911  58.9689
 BOG  C6    C  CH2   0  -0.178  -23.1496  -92.5788  59.4370
 BOG  O6    O  OH1   0  -0.671  -22.4886  -93.6408  60.0978
 BOG  C1'   C  CH2   0  -0.191  -22.9600  -88.2213  56.8181
 BOG  C2'   C  CH2   0  -0.434  -22.1490  -87.0382  56.3204
 BOG  C3'   C  CH2   0  -0.429  -20.7000  -87.0220  56.7926
 BOG  C4'   C  CH2   0  -0.407  -19.8944  -85.8665  56.2128
 BOG  C5'   C  CH2   0  -0.409  -18.4415  -85.8732  56.6710
 BOG  C6'   C  CH2   0  -0.405  -17.6198  -84.7225  56.1056
 BOG  C7'   C  CH2   0  -0.417  -16.1636  -84.7471  56.5533
 BOG  C8'   C  CH3   0  -0.659  -15.3481  -83.5933  55.9867
 BOG  H1    H  HCH1  0   0.189  -21.3941  -89.1463  58.5940
 BOG  H2    H  HCH1  0   0.212  -23.3878  -88.4399  60.8006
 BOG  HO2   H  HOH1  0   0.450  -21.5183  -87.0403  61.3339
 BOG  H3    H  HCH1  0   0.212  -20.5747  -89.6148  60.8659
 BOG  HO3   H  HOH1  0   0.455  -20.9469  -89.5732  63.0897
 BOG  H4    H  HCH1  0   0.198  -23.2626  -90.8661  61.5606
 BOG  HO4   H  HOH1  0   0.449  -21.7237  -92.7087  61.6403
 BOG  H5    H  HCH1  0   0.224  -21.3424  -91.4187  59.2507
 BOG  H61   H  HCH2  0   0.215  -24.1663  -92.4382  59.8231
 BOG  H62   H  HCH2  0   0.223  -23.2274  -92.7686  58.3599
 BOG  HO6   H  HOH1  0   0.469  -23.0931  -94.3856  60.1689
 BOG  H1'1  H  HCH2  0   0.214  -22.4737  -89.1592  56.5279
 BOG  H1'2  H  HCH2  0   0.233  -23.9470  -88.2169  56.3496
 BOG  H2'1  H  HCH2  0   0.218  -22.1734  -87.0673  55.2262
 BOG  H2'2  H  HCH2  0   0.221  -22.6487  -86.1081  56.6098
 BOG  H3'1  H  HCH2  0   0.217  -20.6615  -86.9646  57.8838
 BOG  H3'2  H  HCH2  0   0.207  -20.2212  -87.9685  56.5172
 BOG  H4'1  H  HCH2  0   0.206  -19.9318  -85.9078  55.1188
 BOG  H4'2  H  HCH2  0   0.207  -20.3630  -84.9179  56.4971
 BOG  H5'1  H  HCH2  0   0.206  -18.4065  -85.8389  57.7656
 BOG  H5'2  H  HCH2  0   0.205  -17.9775  -86.8235  56.3847
 BOG  H6'1  H  HCH2  0   0.205  -17.6626  -84.7488  55.0110
 BOG  H6'2  H  HCH2  0   0.205  -18.0743  -83.7707  56.4026
 BOG  H7'1  H  HCH2  0   0.209  -16.1212  -84.7231  57.6467
 BOG  H7'2  H  HCH2  0   0.209  -15.7097  -85.6972  56.2549
 BOG  H8'1  H  HCH3  0   0.224  -14.3102  -83.6339  56.3192
 BOG  H8'2  H  HCH3  0   0.215  -15.3460  -83.6105  54.8953
 BOG  H8'3  H  HCH3  0   0.215  -15.7571  -82.6306  56.2989

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
 BOG  C1   O1    single  1.372  0.020  1.372
 BOG  C1   C2    single  1.524  0.020  1.524
 BOG  C1   O5    single  1.410  0.020  1.410
 BOG  C1   H1    single  0.970  0.020  1.090
 BOG  O1   C1'   single  1.423  0.020  1.423
 BOG  C2   O2    single  1.403  0.020  1.403
 BOG  C2   C3    single  1.523  0.020  1.523
 BOG  C2   H2    single  0.970  0.020  1.090
 BOG  O2   HO2   single  0.850  0.020  0.980
 BOG  C3   O3    single  1.408  0.020  1.408
 BOG  C3   C4    single  1.524  0.020  1.524
 BOG  C3   H3    single  0.970  0.020  1.090
 BOG  O3   HO3   single  0.850  0.020  0.980
 BOG  C4   O4    single  1.405  0.020  1.405
 BOG  C4   C5    single  1.535  0.020  1.535
 BOG  C4   H4    single  0.970  0.020  1.090
 BOG  O4   HO4   single  0.850  0.020  0.980
 BOG  C5   O5    single  1.410  0.020  1.410
 BOG  C5   C6    single  1.522  0.020  1.522
 BOG  C5   H5    single  0.970  0.020  1.090
 BOG  C6   O6    single  1.415  0.020  1.415
 BOG  C6   H61   single  0.970  0.020  1.090
 BOG  C6   H62   single  0.970  0.020  1.090
 BOG  O6   HO6   single  0.850  0.020  0.980
 BOG  C1'  C2'   single  1.518  0.020  1.518
 BOG  C1'  H1'1  single  0.970  0.020  1.090
 BOG  C1'  H1'2  single  0.970  0.020  1.090
 BOG  C2'  C3'   single  1.524  0.020  1.524
 BOG  C2'  H2'1  single  0.970  0.020  1.090
 BOG  C2'  H2'2  single  0.970  0.020  1.090
 BOG  C3'  C4'   single  1.523  0.020  1.523
 BOG  C3'  H3'1  single  0.970  0.020  1.090
 BOG  C3'  H3'2  single  0.970  0.020  1.090
 BOG  C4'  C5'   single  1.523  0.020  1.523
 BOG  C4'  H4'1  single  0.970  0.020  1.090
 BOG  C4'  H4'2  single  0.970  0.020  1.090
 BOG  C5'  C6'   single  1.523  0.020  1.523
 BOG  C5'  H5'1  single  0.970  0.020  1.090
 BOG  C5'  H5'2  single  0.970  0.020  1.090
 BOG  C6'  C7'   single  1.524  0.020  1.524
 BOG  C6'  H6'1  single  0.970  0.020  1.090
 BOG  C6'  H6'2  single  0.970  0.020  1.090
 BOG  C7'  C8'   single  1.522  0.020  1.522
 BOG  C7'  H7'1  single  0.970  0.020  1.090
 BOG  C7'  H7'2  single  0.970  0.020  1.090
 BOG  C8'  H8'1  single  0.970  0.020  1.090
 BOG  C8'  H8'2  single  0.970  0.020  1.090
 BOG  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
 BOG  H1    C1   O5    108.99  3.000
 BOG  H1    C1   C2    109.20  3.000
 BOG  O5    C1   C2    109.37  3.000
 BOG  H1    C1   O1    111.81  3.000
 BOG  O5    C1   O1    108.04  3.000
 BOG  C2    C1   O1    109.40  3.000
 BOG  C1'   O1   C1    116.52  3.000
 BOG  H2    C2   C3    108.79  3.000
 BOG  H2    C2   O2    111.29  3.000
 BOG  C3    C2   O2    111.69  3.000
 BOG  H2    C2   C1    108.03  3.000
 BOG  C3    C2   C1    108.33  3.000
 BOG  O2    C2   C1    108.61  3.000
 BOG  HO2   O2   C2    107.90  3.000
 BOG  H3    C3   C4    107.69  3.000
 BOG  H3    C3   O3    110.56  3.000
 BOG  C4    C3   O3    112.42  3.000
 BOG  H3    C3   C2    107.97  3.000
 BOG  C4    C3   C2    110.88  3.000
 BOG  O3    C3   C2    107.25  3.000
 BOG  HO3   O3   C3    108.63  3.000
 BOG  H4    C4   C5    107.71  3.000
 BOG  H4    C4   O4    111.35  3.000
 BOG  C5    C4   O4    112.75  3.000
 BOG  H4    C4   C3    108.50  3.000
 BOG  C5    C4   C3    109.15  3.000
 BOG  O4    C4   C3    107.30  3.000
 BOG  HO4   O4   C4    107.20  3.000
 BOG  H5    C5   C6    109.35  3.000
 BOG  H5    C5   O5    110.54  3.000
 BOG  C6    C5   O5    105.61  3.000
 BOG  H5    C5   C4    108.58  3.000
 BOG  C6    C5   C4    113.05  3.000
 BOG  O5    C5   C4    109.70  3.000
 BOG  C5    O5   C1    113.95  3.000
 BOG  H62   C6   H61   107.60  3.000
 BOG  H62   C6   O6    111.23  3.000
 BOG  H61   C6   O6    111.40  3.000
 BOG  H62   C6   C5    109.20  3.000
 BOG  H61   C6   C5    108.77  3.000
 BOG  O6    C6   C5    108.59  3.000
 BOG  HO6   O6   C6    108.79  3.000
 BOG  H1'2  C1'  H1'1  106.91  3.000
 BOG  H1'2  C1'  C2'   109.81  3.000
 BOG  H1'1  C1'  C2'   110.07  3.000
 BOG  H1'2  C1'  O1    107.03  3.000
 BOG  H1'1  C1'  O1    110.96  3.000
 BOG  C2'   C1'  O1    111.88  3.000
 BOG  H2'2  C2'  H2'1  106.06  3.000
 BOG  H2'2  C2'  C3'   110.06  3.000
 BOG  H2'1  C2'  C3'   109.33  3.000
 BOG  H2'2  C2'  C1'   109.36  3.000
 BOG  H2'1  C2'  C1'   107.15  3.000
 BOG  C3'   C2'  C1'   114.49  3.000
 BOG  H3'2  C3'  H3'1  106.30  3.000
 BOG  H3'2  C3'  C4'   109.17  3.000
 BOG  H3'1  C3'  C4'   108.75  3.000
 BOG  H3'2  C3'  C2'   109.17  3.000
 BOG  H3'1  C3'  C2'   110.08  3.000
 BOG  C4'   C3'  C2'   113.14  3.000
 BOG  H4'2  C4'  H4'1  106.09  3.000
 BOG  H4'2  C4'  C5'   109.49  3.000
 BOG  H4'1  C4'  C5'   109.44  3.000
 BOG  H4'2  C4'  C3'   109.38  3.000
 BOG  H4'1  C4'  C3'   109.48  3.000
 BOG  C5'   C4'  C3'   112.74  3.000
 BOG  H5'2  C5'  H5'1  105.95  3.000
 BOG  H5'2  C5'  C6'   109.26  3.000
 BOG  H5'1  C5'  C6'   109.27  3.000
 BOG  H5'2  C5'  C4'   109.21  3.000
 BOG  H5'1  C5'  C4'   109.31  3.000
 BOG  C6'   C5'  C4'   113.55  3.000
 BOG  H6'2  C6'  H6'1  105.99  3.000
 BOG  H6'2  C6'  C7'   109.31  3.000
 BOG  H6'1  C6'  C7'   109.30  3.000
 BOG  H6'2  C6'  C5'   109.39  3.000
 BOG  H6'1  C6'  C5'   109.37  3.000
 BOG  C7'   C6'  C5'   113.22  3.000
 BOG  H7'2  C7'  H7'1  105.98  3.000
 BOG  H7'2  C7'  C8'   109.53  3.000
 BOG  H7'1  C7'  C8'   109.54  3.000
 BOG  H7'2  C7'  C6'   109.28  3.000
 BOG  H7'1  C7'  C6'   109.29  3.000
 BOG  C8'   C7'  C6'   112.98  3.000
 BOG  H8'3  C8'  H8'2  107.49  3.000
 BOG  H8'3  C8'  H8'1  107.59  3.000
 BOG  H8'2  C8'  H8'1  107.60  3.000
 BOG  H8'3  C8'  C7'   111.18  3.000
 BOG  H8'2  C8'  C7'   111.18  3.000
 BOG  H8'1  C8'  C7'   111.60  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
 BOG  Var_01  C2'   C1'  O1   C1   -105.13  30.0  3
 BOG  Var_02  C3'   C2'  C1'  O1     67.48  30.0  3
 BOG  Var_03  C4'   C3'  C2'  C1'   176.75  30.0  3
 BOG  Var_04  C5'   C4'  C3'  C2'  -178.98  30.0  3
 BOG  Var_05  C6'   C5'  C4'  C3'  -179.81  30.0  3
 BOG  Var_06  C7'   C6'  C5'  C4'  -179.22  30.0  3
 BOG  Var_07  C8'   C7'  C6'  C5'  -179.91  30.0  3
 BOG  Var_08  H8'1  C8'  C7'  C6'  -179.87  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
 BOG  chir_01  C1  O1  C2  O5  negativ
 BOG  chir_02  C2  O2  C1  C3  negativ
 BOG  chir_03  C3  O3  C2  C4  positiv
 BOG  chir_04  C4  O4  C5  C3  positiv
 BOG  chir_05  C5  O5  C4  C6  negativ

