# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:15:47 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 4-O-methyl-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)[C@@H](O)[C@@H](O)O[C@@H]1CO
#
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
 B8D  B8D  4-O-methyl-alpha-D-glucopyranose  D-saccharide  27  13  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B8D
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
 B8D  O1    O  OH1   0  -0.660   9.7291  46.8819  41.7823
 B8D  C1    C  CH1   0   0.233   9.2895  47.2878  43.0366
 B8D  C2    C  CH1   0   0.013   8.8130  48.7355  42.9450
 B8D  O2    O  OH1   0  -0.666   7.8378  48.8231  41.9406
 B8D  C3    C  CH1   0  -0.009   9.9939  49.6686  42.7051
 B8D  O3    O  OH1   0  -0.670   9.4944  50.9852  42.7144
 B8D  C4    C  CH1   0   0.025  11.0394  49.4496  43.7937
 B8D  O4    O  O2    0  -0.501  12.1572  50.2612  43.5122
 B8D  C5    C  CH1   0  -0.001  11.4381  47.9708  43.8224
 B8D  O5    O  O2    0  -0.503  10.2805  47.1726  44.0226
 B8D  C6    C  CH2   0  -0.191  12.4393  47.6169  44.8999
 B8D  O6    O  OH1   0  -0.668  11.9399  47.9755  46.1660
 B8D  CJ7   C  CH3   0  -0.409  12.6097  51.0462  44.5909
 B8D  HO1   H  HOH1  0   0.459   9.8516  45.9262  41.7886
 B8D  H1    H  HCH1  0   0.234   8.4694  46.6531  43.3932
 B8D  H2    H  HCH1  0   0.217   8.3869  48.9847  43.9292
 B8D  HO2   H  HOH1  0   0.449   7.4999  49.7244  41.9361
 B8D  H3    H  HCH1  0   0.214  10.4460  49.4324  41.7306
 B8D  HO3   H  HOH1  0   0.453  10.1843  51.5751  42.3947
 B8D  H4    H  HCH1  0   0.222  10.5930  49.7223  44.7599
 B8D  H5    H  HCH1  0   0.224  11.9162  47.7226  42.8644
 B8D  H61   H  HCH2  0   0.219  12.6470  46.5404  44.8353
 B8D  H62   H  HCH2  0   0.209  13.3797  48.1302  44.6663
 B8D  HO6   H  HOH1  0   0.456  12.6279  47.8128  46.8172
 B8D  HJ7   H  HCH3  0   0.231  13.4285  51.6646  44.2250
 B8D  HJ7A  H  HCH3  0   0.210  11.8241  51.7060  44.9737
 B8D  HJ7B  H  HCH3  0   0.210  12.9807  50.4427  45.4247

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
 B8D  O1   C1    single  1.390  0.020  1.390
 B8D  O1   HO1   single  0.850  0.020  0.980
 B8D  C1   C2    single  1.527  0.020  1.527
 B8D  C1   O5    single  1.403  0.020  1.403
 B8D  C1   H1    single  0.970  0.020  1.090
 B8D  O2   C2    single  1.403  0.020  1.403
 B8D  C3   C2    single  1.524  0.020  1.524
 B8D  C2   H2    single  0.970  0.020  1.090
 B8D  O2   HO2   single  0.850  0.020  0.980
 B8D  C3   O3    single  1.408  0.020  1.408
 B8D  C3   C4    single  1.525  0.020  1.525
 B8D  C3   H3    single  0.970  0.020  1.090
 B8D  O3   HO3   single  0.850  0.020  0.980
 B8D  O4   C4    single  1.410  0.020  1.410
 B8D  C4   C5    single  1.532  0.020  1.532
 B8D  C4   H4    single  0.970  0.020  1.090
 B8D  O4   CJ7   single  1.409  0.020  1.409
 B8D  C5   O5    single  1.420  0.020  1.420
 B8D  C5   C6    single  1.513  0.020  1.513
 B8D  C5   H5    single  0.970  0.020  1.090
 B8D  C6   O6    single  1.408  0.020  1.408
 B8D  C6   H61   single  0.970  0.020  1.090
 B8D  C6   H62   single  0.970  0.020  1.090
 B8D  O6   HO6   single  0.850  0.020  0.980
 B8D  CJ7  HJ7   single  0.970  0.020  1.090
 B8D  CJ7  HJ7A  single  0.970  0.020  1.090
 B8D  CJ7  HJ7B  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
 B8D  HO1   O1   C1    108.91  3.000
 B8D  H1    C1   O5    104.61  3.000
 B8D  H1    C1   C2    109.57  3.000
 B8D  O5    C1   C2    109.91  3.000
 B8D  H1    C1   O1    111.16  3.000
 B8D  O5    C1   O1    112.76  3.000
 B8D  C2    C1   O1    108.75  3.000
 B8D  H2    C2   C3    107.58  3.000
 B8D  H2    C2   O2    110.91  3.000
 B8D  C3    C2   O2    112.81  3.000
 B8D  H2    C2   C1    106.36  3.000
 B8D  C3    C2   C1    110.37  3.000
 B8D  O2    C2   C1    108.61  3.000
 B8D  HO2   O2   C2    107.82  3.000
 B8D  H3    C3   C4    108.65  3.000
 B8D  H3    C3   O3    110.64  3.000
 B8D  C4    C3   O3    111.88  3.000
 B8D  H3    C3   C2    109.05  3.000
 B8D  C4    C3   C2    109.32  3.000
 B8D  O3    C3   C2    107.25  3.000
 B8D  HO3   O3   C3    108.45  3.000
 B8D  H4    C4   C5    109.20  3.000
 B8D  H4    C4   O4    110.79  3.000
 B8D  C5    C4   O4    110.68  3.000
 B8D  H4    C4   C3    108.28  3.000
 B8D  C5    C4   C3    109.29  3.000
 B8D  O4    C4   C3    108.56  3.000
 B8D  CJ7   O4   C4    115.00  3.000
 B8D  H5    C5   C6    106.26  3.000
 B8D  H5    C5   O5    110.52  3.000
 B8D  C6    C5   O5    107.91  3.000
 B8D  H5    C5   C4    108.36  3.000
 B8D  C6    C5   C4    114.29  3.000
 B8D  O5    C5   C4    109.46  3.000
 B8D  C5    O5   C1    115.50  3.000
 B8D  H62   C6   H61   106.51  3.000
 B8D  H62   C6   O6    112.13  3.000
 B8D  H61   C6   O6    111.70  3.000
 B8D  H62   C6   C5    107.84  3.000
 B8D  H61   C6   C5    108.22  3.000
 B8D  O6    C6   C5    110.26  3.000
 B8D  HO6   O6   C6    108.20  3.000
 B8D  HJ7B  CJ7  HJ7A  108.01  3.000
 B8D  HJ7B  CJ7  HJ7   108.31  3.000
 B8D  HJ7A  CJ7  HJ7   108.34  3.000
 B8D  HJ7B  CJ7  O4    112.65  3.000
 B8D  HJ7A  CJ7  O4    111.90  3.000
 B8D  HJ7   CJ7  O4    107.49  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
 B8D  Var_01  HJ7  CJ7  O4  C4  -176.52  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
 B8D  chir_01  C1  O1  C2  O5  positiv
 B8D  chir_02  C2  O2  C1  C3  negativ
 B8D  chir_03  C3  O3  C2  C4  positiv
 B8D  chir_04  C4  O4  C5  C3  positiv
 B8D  chir_05  C5  O5  C4  C6  negativ

