# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 08:03:25 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-hydroxyethyl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCO[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
 8LR  8LR  '2-hydroxyethyl alpha-D-mannopyranoside'  D-saccharide  31  15  .  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_8LR
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
 8LR  OAF   O  OH1   0  -0.669   3.3903  -0.4854  -1.6478
 8LR  CAG   C  CH2   0  -0.185   3.5967  -1.0949  -0.3947
 8LR  CAH   C  CH2   0  -0.174   2.5499  -0.6126   0.5754
 8LR  O1    O  O2    0  -0.500   1.2814  -1.0882   0.1690
 8LR  C1    C  CH1   0   0.248   0.2475  -0.8257   1.0601
 8LR  O5    O  O2    0  -0.499  -0.0056   0.5404   1.2120
 8LR  C5    C  CH1   0  -0.011  -0.4193   1.2182   0.0369
 8LR  C6    C  CH2   0  -0.159  -0.5983   2.6763   0.4010
 8LR  O6    O  OH1   0  -0.669   0.6492   3.2019   0.7892
 8LR  C4    C  CH1   0   0.034  -1.7093   0.5965  -0.5000
 8LR  O4    O  OH1   0  -0.677  -2.0341   1.2457  -1.7063
 8LR  C3    C  CH1   0   0.001  -1.4926  -0.8967  -0.7219
 8LR  O3    O  OH1   0  -0.674  -2.7089  -1.4399  -1.1798
 8LR  C2    C  CH1   0  -0.029  -0.9959  -1.5664   0.5562
 8LR  O2    O  OH1   0  -0.669  -2.0216  -1.5102   1.5146
 8LR  HAG1  H  HCH2  0   0.201   3.5564  -2.1899  -0.4598
 8LR  HAG2  H  HCH2  0   0.202   4.5757  -0.8377   0.0292
 8LR  HAH1  H  HCH2  0   0.213   2.7997  -0.9923   1.5745
 8LR  HAH2  H  HCH2  0   0.218   2.5682   0.4820   0.6276
 8LR  H1    H  HCH1  0   0.230   0.5104  -1.1763   2.0701
 8LR  H2    H  HCH1  0   0.230  -0.7136  -2.6054   0.3353
 8LR  H5    H  HCH1  0   0.224   0.3518   1.1419  -0.7433
 8LR  H61C  H  HCH2  0   0.210  -1.0054   3.2038  -0.4680
 8LR  H62C  H  HCH2  0   0.194  -1.3430   2.7562   1.2055
 8LR  H4    H  HCH1  0   0.210  -2.5052   0.7382   0.2467
 8LR  H6    H  HOH1  0   0.455   0.5339   4.1404   0.9616
 8LR  HA    H  HOH1  0   0.451  -2.8009   0.7999  -2.0815
 8LR  H3    H  HCH1  0   0.229  -0.7084  -1.0096  -1.4828
 8LR  HB    H  HOH1  0   0.457  -2.5246  -2.2622  -1.6434
 8LR  HC    H  HOH1  0   0.455  -1.7601  -2.0389   2.2748
 8LR  HAF   H  HOH1  0   0.455   4.0418  -0.8372  -2.2606

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
 8LR  OAF  CAG   single  1.409  0.020  1.409
 8LR  CAG  CAH   single  1.506  0.020  1.506
 8LR  CAH  O1    single  1.414  0.020  1.414
 8LR  O1   C1    single  1.390  0.020  1.390
 8LR  C1   O5    single  1.398  0.020  1.398
 8LR  C1   C2    single  1.532  0.020  1.532
 8LR  O5   C5    single  1.418  0.020  1.418
 8LR  C5   C6    single  1.513  0.020  1.513
 8LR  C5   C4    single  1.529  0.020  1.529
 8LR  C6   O6    single  1.408  0.020  1.408
 8LR  C4   O4    single  1.408  0.020  1.408
 8LR  C4   C3    single  1.525  0.020  1.525
 8LR  C3   O3    single  1.409  0.020  1.409
 8LR  C3   C2    single  1.526  0.020  1.526
 8LR  C2   O2    single  1.405  0.020  1.405
 8LR  CAG  HAG1  single  0.970  0.020  1.090
 8LR  CAG  HAG2  single  0.970  0.020  1.090
 8LR  CAH  HAH1  single  0.970  0.020  1.090
 8LR  CAH  HAH2  single  0.970  0.020  1.090
 8LR  C1   H1    single  0.970  0.020  1.090
 8LR  C2   H2    single  0.970  0.020  1.090
 8LR  C5   H5    single  0.970  0.020  1.090
 8LR  C6   H61C  single  0.970  0.020  1.090
 8LR  C6   H62C  single  0.970  0.020  1.090
 8LR  C4   H4    single  0.970  0.020  1.090
 8LR  O6   H6    single  0.850  0.020  0.980
 8LR  O4   HA    single  0.850  0.020  0.980
 8LR  C3   H3    single  0.970  0.020  1.090
 8LR  O3   HB    single  0.850  0.020  0.980
 8LR  O2   HC    single  0.850  0.020  0.980
 8LR  OAF  HAF   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
 8LR  HAF   OAF  CAG   108.03  3.000
 8LR  HAG2  CAG  HAG1  106.82  3.000
 8LR  HAG2  CAG  CAH   107.23  3.000
 8LR  HAG1  CAG  CAH   109.40  3.000
 8LR  HAG2  CAG  OAF   111.90  3.000
 8LR  HAG1  CAG  OAF   111.93  3.000
 8LR  CAH   CAG  OAF   109.42  3.000
 8LR  HAH2  CAH  HAH1  107.36  3.000
 8LR  HAH2  CAH  O1    111.38  3.000
 8LR  HAH1  CAH  O1    110.44  3.000
 8LR  HAH2  CAH  CAG   109.81  3.000
 8LR  HAH1  CAH  CAG   108.50  3.000
 8LR  O1    CAH  CAG   109.30  3.000
 8LR  C1    O1   CAH   114.80  3.000
 8LR  H1    C1   C2    109.97  3.000
 8LR  H1    C1   O5    104.77  3.000
 8LR  C2    C1   O5    111.18  3.000
 8LR  H1    C1   O1    110.51  3.000
 8LR  C2    C1   O1    107.54  3.000
 8LR  O5    C1   O1    112.89  3.000
 8LR  C5    O5   C1    115.47  3.000
 8LR  H5    C5   C4    108.31  3.000
 8LR  H5    C5   C6    108.69  3.000
 8LR  C4    C5   C6    112.11  3.000
 8LR  H5    C5   O5    110.50  3.000
 8LR  C4    C5   O5    110.04  3.000
 8LR  C6    C5   O5    107.19  3.000
 8LR  H62C  C6   H61C  107.10  3.000
 8LR  H62C  C6   O6    111.79  3.000
 8LR  H61C  C6   O6    111.60  3.000
 8LR  H62C  C6   C5    109.05  3.000
 8LR  H61C  C6   C5    108.49  3.000
 8LR  O6    C6   C5    108.73  3.000
 8LR  H6    O6   C6    107.91  3.000
 8LR  H4    C4   C3    109.12  3.000
 8LR  H4    C4   O4    110.81  3.000
 8LR  C3    C4   O4    111.07  3.000
 8LR  H4    C4   C5    108.63  3.000
 8LR  C3    C4   C5    109.22  3.000
 8LR  O4    C4   C5    107.93  3.000
 8LR  HA    O4   C4    107.70  3.000
 8LR  H3    C3   C2    107.62  3.000
 8LR  H3    C3   O3    110.59  3.000
 8LR  C2    C3   O3    112.59  3.000
 8LR  H3    C3   C4    107.63  3.000
 8LR  C2    C3   C4    110.73  3.000
 8LR  O3    C3   C4    107.59  3.000
 8LR  HB    O3   C3    108.71  3.000
 8LR  H2    C2   O2    111.25  3.000
 8LR  H2    C2   C3    109.28  3.000
 8LR  O2    C2   C3    108.43  3.000
 8LR  H2    C2   C1    108.34  3.000
 8LR  O2    C2   C1    110.41  3.000
 8LR  C3    C2   C1    109.11  3.000
 8LR  HC    O2   C2    108.58  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
 8LR  Var_01  HAH1  CAH  O1   C1   54.38  30.0  1
 8LR  Var_02  O1    CAH  CAG  OAF  66.75  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
 8LR  chir_01  C1  O1  O5  C2  negativ
 8LR  chir_02  C5  O5  C6  C4  positiv
 8LR  chir_03  C4  O4  C5  C3  positiv
 8LR  chir_04  C3  O3  C2  C4  positiv
 8LR  chir_05  C2  O2  C1  C3  positiv

