# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 05:11:27 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-(hydroxymethyl)phenyl beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2ccccc2CO)[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
 SA0  SA0  '2-(hydroxymethyl)phenyl beta-D-glucopyranoside'  D-saccharide  38  20  .  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_SA0
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
 SA0  C1    C  CH1   0   0.272   0.4202   0.2769  -0.0914
 SA0  O1    O  O2    0  -0.505  -0.8567   0.4630   0.4267
 SA0  C2    C  CH1   0  -0.026   1.2169   1.5564   0.1482
 SA0  O2    O  OH1   0  -0.665   0.6942   2.6378  -0.5796
 SA0  C3    C  CH1   0  -0.011   2.6520   1.3278  -0.3116
 SA0  O3    O  OH1   0  -0.671   3.4887   2.4067   0.0268
 SA0  C4    C  CH1   0   0.040   3.2372   0.0733   0.3323
 SA0  O4    O  OH1   0  -0.670   4.4905  -0.2453  -0.2165
 SA0  C5    C  CH1   0  -0.022   2.2980  -1.1099   0.0936
 SA0  O5    O  O2    0  -0.494   1.0141  -0.7869   0.5914
 SA0  C6    C  CH2   0  -0.155   2.7584  -2.3728   0.7877
 SA0  O6    O  OH1   0  -0.666   1.8897  -3.4199   0.4271
 SA0  OAA   O  OH1   0  -0.667  -4.6062   2.1103   0.6461
 SA0  CAF   C  CR16  0  -0.260  -4.1191  -1.6585  -0.9594
 SA0  CAG   C  CR16  0  -0.260  -2.8604  -2.2234  -1.0737
 SA0  CAH   C  CR16  0  -0.296  -4.2612  -0.3995  -0.3864
 SA0  CAI   C  CR16  0  -0.347  -1.7402  -1.5400  -0.6149
 SA0  CAN   C  CR6   0  -0.060  -3.1575   0.3101   0.0668
 SA0  CAO   C  CR6   0   0.340  -1.8942  -0.2786  -0.0548
 SA0  H1    H  HCH1  0   0.213   0.3678   0.0622  -1.1731
 SA0  H2    H  HCH1  0   0.231   1.2189   1.7597   1.2292
 SA0  HO2   H  HOH1  0   0.458  -0.1016   2.9516  -0.1398
 SA0  H3    H  HCH1  0   0.220   2.6440   1.1686  -1.4020
 SA0  HO3   H  HOH1  0   0.458   3.2643   3.1572  -0.5320
 SA0  H4    H  HCH1  0   0.215   3.3109   0.2408   1.4187
 SA0  HO4   H  HOH1  0   0.456   5.0899   0.4895  -0.0496
 SA0  H5    H  HCH1  0   0.228   2.2423  -1.2996  -0.9909
 SA0  H6    H  HCH2  0   0.213   3.7905  -2.5776   0.4853
 SA0  H6A   H  HCH2  0   0.200   2.7660  -2.2018   1.8730
 SA0  HO6   H  HOH1  0   0.457   2.1733  -4.2127   0.8909
 SA0  HOAA  H  HOH1  0   0.463  -4.6584   2.9468   1.1168
 SA0  HAG   H  HCR6  0   0.258  -2.7371  -3.2054  -1.5112
 SA0  HAH   H  HCR6  0   0.257  -5.2481   0.0335  -0.3002
 SA0  HAI   H  HCR6  0   0.283  -0.7687  -2.0117  -0.6767
 SA0  HAJ   H  HCH2  0   0.210  -2.6144   2.3715   0.1322
 SA0  HAJA  H  HCH2  0   0.220  -2.8872   1.6467   1.7076
 SA0  HAF   H  HCR6  0   0.252  -4.9931  -2.1935  -1.3069
 SA0  CAJ   C  CH2   0  -0.169  -3.2706   1.6802   0.6793

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
 SA0  C1   O1    single    1.390  0.020  1.390
 SA0  C1   C2    single    1.526  0.020  1.526
 SA0  C1   O5    single    1.397  0.020  1.397
 SA0  O1   CAO   single    1.363  0.020  1.363
 SA0  C2   O2    single    1.404  0.020  1.404
 SA0  C2   C3    single    1.524  0.020  1.524
 SA0  C3   O3    single    1.407  0.020  1.407
 SA0  C3   C4    single    1.527  0.020  1.527
 SA0  C4   O4    single    1.405  0.020  1.405
 SA0  C4   C5    single    1.529  0.020  1.529
 SA0  C5   O5    single    1.414  0.020  1.414
 SA0  C5   C6    single    1.513  0.020  1.513
 SA0  C6   O6    single    1.408  0.020  1.408
 SA0  OAA  CAJ   single    1.404  0.020  1.404
 SA0  CAF  CAG   aromatic  1.384  0.020  1.384
 SA0  CAF  CAH   aromatic  1.391  0.020  1.391
 SA0  CAG  CAI   aromatic  1.390  0.020  1.390
 SA0  CAH  CAN   aromatic  1.388  0.020  1.388
 SA0  CAI  CAO   aromatic  1.389  0.020  1.389
 SA0  CAJ  CAN   single    1.505  0.020  1.505
 SA0  CAN  CAO   aromatic  1.399  0.020  1.399
 SA0  C1   H1    single    0.970  0.020  1.090
 SA0  C2   H2    single    0.970  0.020  1.090
 SA0  O2   HO2   single    0.850  0.020  0.980
 SA0  C3   H3    single    0.970  0.020  1.090
 SA0  O3   HO3   single    0.850  0.020  0.980
 SA0  C4   H4    single    0.970  0.020  1.090
 SA0  O4   HO4   single    0.850  0.020  0.980
 SA0  C5   H5    single    0.970  0.020  1.090
 SA0  C6   H6    single    0.970  0.020  1.090
 SA0  C6   H6A   single    0.970  0.020  1.090
 SA0  O6   HO6   single    0.850  0.020  0.980
 SA0  OAA  HOAA  single    0.850  0.020  0.980
 SA0  CAF  HAF   single    0.930  0.020  1.080
 SA0  CAG  HAG   single    0.930  0.020  1.080
 SA0  CAH  HAH   single    0.930  0.020  1.080
 SA0  CAI  HAI   single    0.930  0.020  1.080
 SA0  CAJ  HAJ   single    0.970  0.020  1.090
 SA0  CAJ  HAJA  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
 SA0  H1    C1   O5   110.55  3.000
 SA0  H1    C1   C2   109.97  3.000
 SA0  O5    C1   C2   109.87  3.000
 SA0  H1    C1   O1   110.33  3.000
 SA0  O5    C1   O1   108.08  3.000
 SA0  C2    C1   O1   107.98  3.000
 SA0  CAO   O1   C1   119.64  3.000
 SA0  H2    C2   C3   108.81  3.000
 SA0  H2    C2   O2   111.57  3.000
 SA0  C3    C2   O2   108.04  3.000
 SA0  H2    C2   C1   108.07  3.000
 SA0  C3    C2   C1   108.57  3.000
 SA0  O2    C2   C1   111.71  3.000
 SA0  HO2   O2   C2   108.79  3.000
 SA0  H3    C3   C4   107.55  3.000
 SA0  H3    C3   O3   110.68  3.000
 SA0  C4    C3   O3   107.51  3.000
 SA0  H3    C3   C2   108.26  3.000
 SA0  C4    C3   C2   110.91  3.000
 SA0  O3    C3   C2   111.86  3.000
 SA0  HO3   O3   C3   108.65  3.000
 SA0  H4    C4   C5   108.22  3.000
 SA0  H4    C4   O4   111.10  3.000
 SA0  C5    C4   O4   108.15  3.000
 SA0  H4    C4   C3   108.46  3.000
 SA0  C5    C4   C3   109.54  3.000
 SA0  O4    C4   C3   111.31  3.000
 SA0  HO4   O4   C4   108.34  3.000
 SA0  H5    C5   C6   108.85  3.000
 SA0  H5    C5   O5   109.86  3.000
 SA0  C6    C5   O5   107.79  3.000
 SA0  H5    C5   C4   108.53  3.000
 SA0  C6    C5   C4   112.78  3.000
 SA0  O5    C5   C4   109.02  3.000
 SA0  C5    O5   C1   112.82  3.000
 SA0  H6A   C6   H6   107.19  3.000
 SA0  H6A   C6   O6   111.90  3.000
 SA0  H6    C6   O6   111.83  3.000
 SA0  H6A   C6   C5   108.99  3.000
 SA0  H6    C6   C5   108.44  3.000
 SA0  O6    C6   C5   108.40  3.000
 SA0  HO6   O6   C6   107.93  3.000
 SA0  HOAA  OAA  CAJ  107.86  3.000
 SA0  HAF   CAF  CAH  119.83  3.000
 SA0  HAF   CAF  CAG  120.41  3.000
 SA0  CAH   CAF  CAG  119.76  3.000
 SA0  HAG   CAG  CAI  119.19  3.000
 SA0  HAG   CAG  CAF  120.48  3.000
 SA0  CAI   CAG  CAF  120.32  3.000
 SA0  HAH   CAH  CAN  119.67  3.000
 SA0  HAH   CAH  CAF  119.26  3.000
 SA0  CAN   CAH  CAF  121.07  3.000
 SA0  HAI   CAI  CAO  121.25  3.000
 SA0  HAI   CAI  CAG  119.37  3.000
 SA0  CAO   CAI  CAG  119.36  3.000
 SA0  CAO   CAN  CAJ  119.10  3.000
 SA0  CAO   CAN  CAH  118.32  3.000
 SA0  CAJ   CAN  CAH  122.58  3.000
 SA0  CAN   CAO  CAI  121.16  3.000
 SA0  CAN   CAO  O1   115.32  3.000
 SA0  CAI   CAO  O1   123.52  3.000
 SA0  HAJA  CAJ  HAJ  106.08  3.000
 SA0  HAJA  CAJ  CAN  109.10  3.000
 SA0  HAJ   CAJ  CAN  108.97  3.000
 SA0  HAJA  CAJ  OAA  111.34  3.000
 SA0  HAJ   CAJ  OAA  111.32  3.000
 SA0  CAN   CAJ  OAA  109.93  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
 SA0  CONST_01  CAO  CAI  CAG  CAF    0.00   0.0  0
 SA0  CONST_02  CAO  CAN  CAH  CAF    0.00   0.0  0
 SA0  CONST_03  CAN  CAH  CAF  CAG    0.00   0.0  0
 SA0  CONST_04  CAN  CAO  CAI  CAG    0.00   0.0  0
 SA0  CONST_05  CAI  CAG  CAF  CAH    0.00   0.0  0
 SA0  CONST_06  CAI  CAO  CAN  CAH    0.00   0.0  0
 SA0  CONST_07  CAG  CAI  CAO  O1   180.00   0.0  0
 SA0  CONST_08  CAH  CAN  CAO  O1   180.00   0.0  0
 SA0  CONST_09  CAJ  CAN  CAH  CAF  180.00   0.0  0
 SA0  CONST_10  CAJ  CAN  CAO  CAI  180.00   0.0  0
 SA0  CONST_11  HAI  CAI  CAG  CAF  180.00   0.0  0
 SA0  CONST_12  HAH  CAH  CAF  CAG  180.00   0.0  0
 SA0  CONST_13  HAG  CAG  CAF  CAH  180.00   0.0  0
 SA0  CONST_14  HAF  CAF  CAG  CAI  180.00   0.0  0
 SA0  Var_01    CAI  CAO  O1   C1    26.81  30.0  2
 SA0  Var_02    CAH  CAN  CAJ  OAA   -2.89  30.0  2

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
 SA0  chir_01  C1  O1  C2  O5  negativ
 SA0  chir_02  C2  O2  C1  C3  negativ
 SA0  chir_03  C3  O3  C2  C4  positiv
 SA0  chir_04  C4  O4  C5  C3  positiv
 SA0  chir_05  C5  O5  C4  C6  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 SA0  plan-1  O1   0.020
 SA0  plan-1  CAF  0.020
 SA0  plan-1  CAG  0.020
 SA0  plan-1  CAH  0.020
 SA0  plan-1  CAI  0.020
 SA0  plan-1  CAN  0.020
 SA0  plan-1  CAO  0.020
 SA0  plan-1  HAG  0.020
 SA0  plan-1  HAH  0.020
 SA0  plan-1  HAI  0.020
 SA0  plan-1  HAF  0.020
 SA0  plan-1  CAJ  0.020

