# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 23:59:25 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: (2R)-2,3-dihydroxypropyl beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)CO[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
 RGG  RGG  '(2R)-2,3-dihydroxypropyl beta-D-galactopyranoside'  D-saccharide  35  17  .  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_RGG
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
 RGG  O3'   O  OH1   0  -0.666  -1.2193  -5.2828  -2.6796
 RGG  C3'   C  CH2   0  -0.184  -0.2405  -4.2709  -2.6587
 RGG  C2'   C  CH1   0  -0.024   0.5592  -4.3776  -1.3631
 RGG  O2'   O  OH1   0  -0.667   1.6057  -3.4328  -1.3634
 RGG  C1'   C  CH2   0  -0.150  -0.3188  -4.0898  -0.1650
 RGG  O1    O  O2    0  -0.499   0.4154  -4.3350   1.0218
 RGG  C1    C  CH1   0   0.298  -0.3013  -4.1512   2.1834
 RGG  C2    C  CH1   0  -0.030   0.4540  -4.8119   3.3376
 RGG  O2    O  OH1   0  -0.659   0.5044  -6.2053   3.1770
 RGG  C3    C  CH1   0   0.011  -0.2685  -4.5085   4.6529
 RGG  O3    O  OH1   0  -0.659   0.4224  -5.0094   5.7670
 RGG  C4    C  CH1   0  -0.033  -0.5535  -3.0075   4.7965
 RGG  O4    O  OH1   0  -0.663   0.6227  -2.2881   5.1062
 RGG  C5    C  CH1   0  -0.059  -1.2453  -2.4941   3.5384
 RGG  O5    O  O2    0  -0.495  -0.4382  -2.7709   2.4109
 RGG  C6    C  CH2   0  -0.156  -1.5279  -1.0018   3.5789
 RGG  O6    O  OH1   0  -0.656  -2.2678  -0.5534   2.4709
 RGG  HO3'  H  HOH1  0   0.457  -1.7655  -5.1599  -3.4608
 RGG  H3'   H  HCH2  0   0.209   0.4567  -4.3671  -3.5031
 RGG  H3'A  H  HCH2  0   0.198  -0.6837  -3.2677  -2.7221
 RGG  H2'   H  HCH1  0   0.210   0.9494  -5.4025  -1.2788
 RGG  HO2'  H  HOH1  0   0.451   2.2487  -3.6872  -2.0329
 RGG  H1'   H  HCH2  0   0.213  -0.6601  -3.0486  -0.2105
 RGG  H1'A  H  HCH2  0   0.221  -1.2069  -4.7302  -0.1970
 RGG  H1    H  HCH1  0   0.183  -1.3070  -4.6090   2.1031
 RGG  H2    H  HCH1  0   0.213   1.4674  -4.3792   3.3717
 RGG  HO2   H  HOH1  0   0.450   1.0457  -6.4005   2.4054
 RGG  H3    H  HCH1  0   0.238  -1.2340  -5.0280   4.6282
 RGG  HO3   H  HOH1  0   0.439   1.1785  -4.4312   5.9242
 RGG  H4    H  HCH1  0   0.256  -1.2262  -2.8662   5.6481
 RGG  HO4   H  HOH1  0   0.447   1.1588  -2.1964   4.3101
 RGG  H5    H  HCH1  0   0.229  -2.2077  -3.0276   3.4532
 RGG  H61   H  HCH2  0   0.208  -2.0319  -0.7784   4.5278
 RGG  H62   H  HCH2  0   0.224  -0.5907  -0.4423   3.5754
 RGG  HO6   H  HOH1  0   0.446  -3.1471  -0.9420   2.5144

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
 RGG  O3'  C3'   single  1.408  0.020  1.408
 RGG  C3'  C2'   single  1.526  0.020  1.526
 RGG  C2'  O2'   single  1.410  0.020  1.410
 RGG  C2'  C1'   single  1.513  0.020  1.513
 RGG  C1'  O1    single  1.417  0.020  1.417
 RGG  O1   C1    single  1.377  0.020  1.377
 RGG  C1   C2    single  1.529  0.020  1.529
 RGG  C1   O5    single  1.406  0.020  1.406
 RGG  C2   O2    single  1.404  0.020  1.404
 RGG  C2   C3    single  1.531  0.020  1.531
 RGG  C3   O3    single  1.403  0.020  1.403
 RGG  C3   C4    single  1.535  0.020  1.535
 RGG  C4   O4    single  1.413  0.020  1.413
 RGG  C4   C5    single  1.525  0.020  1.525
 RGG  C5   O5    single  1.414  0.020  1.414
 RGG  C5   C6    single  1.519  0.020  1.519
 RGG  C6   O6    single  1.406  0.020  1.406
 RGG  O3'  HO3'  single  0.850  0.020  0.980
 RGG  C3'  H3'   single  0.970  0.020  1.090
 RGG  C3'  H3'A  single  0.970  0.020  1.090
 RGG  C2'  H2'   single  0.970  0.020  1.090
 RGG  O2'  HO2'  single  0.850  0.020  0.980
 RGG  C1'  H1'   single  0.970  0.020  1.090
 RGG  C1'  H1'A  single  0.970  0.020  1.090
 RGG  C1   H1    single  0.970  0.020  1.090
 RGG  C2   H2    single  0.970  0.020  1.090
 RGG  O2   HO2   single  0.850  0.020  0.980
 RGG  C3   H3    single  0.970  0.020  1.090
 RGG  O3   HO3   single  0.850  0.020  0.980
 RGG  C4   H4    single  0.970  0.020  1.090
 RGG  O4   HO4   single  0.850  0.020  0.980
 RGG  C5   H5    single  0.970  0.020  1.090
 RGG  C6   H61   single  0.970  0.020  1.090
 RGG  C6   H62   single  0.970  0.020  1.090
 RGG  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
 RGG  HO3'  O3'  C3'  108.38  3.000
 RGG  H3'A  C3'  H3'  106.94  3.000
 RGG  H3'A  C3'  C2'  108.92  3.000
 RGG  H3'   C3'  C2'  108.28  3.000
 RGG  H3'A  C3'  O3'  112.02  3.000
 RGG  H3'   C3'  O3'  111.51  3.000
 RGG  C2'   C3'  O3'  109.06  3.000
 RGG  H2'   C2'  C1'  108.81  3.000
 RGG  H2'   C2'  O2'  111.17  3.000
 RGG  C1'   C2'  O2'  107.66  3.000
 RGG  H2'   C2'  C3'  108.43  3.000
 RGG  C1'   C2'  C3'  110.78  3.000
 RGG  O2'   C2'  C3'  109.99  3.000
 RGG  HO2'  O2'  C2'  108.60  3.000
 RGG  H1'A  C1'  H1'  107.55  3.000
 RGG  H1'A  C1'  O1   110.08  3.000
 RGG  H1'   C1'  O1   111.12  3.000
 RGG  H1'A  C1'  C2'  109.65  3.000
 RGG  H1'   C1'  C2'  109.17  3.000
 RGG  O1    C1'  C2'  109.25  3.000
 RGG  C1    O1   C1'  114.44  3.000
 RGG  H1    C1   O5   109.21  3.000
 RGG  H1    C1   C2   108.93  3.000
 RGG  O5    C1   C2   110.49  3.000
 RGG  H1    C1   O1   110.87  3.000
 RGG  O5    C1   O1   108.56  3.000
 RGG  C2    C1   O1   108.78  3.000
 RGG  H2    C2   C3   109.24  3.000
 RGG  H2    C2   O2   111.11  3.000
 RGG  C3    C2   O2   108.18  3.000
 RGG  H2    C2   C1   107.92  3.000
 RGG  C3    C2   C1   109.25  3.000
 RGG  O2    C2   C1   111.11  3.000
 RGG  HO2   O2   C2   108.25  3.000
 RGG  H3    C3   C4   107.58  3.000
 RGG  H3    C3   O3   106.39  3.000
 RGG  C4    C3   O3   111.49  3.000
 RGG  H3    C3   C2   107.59  3.000
 RGG  C4    C3   C2   111.21  3.000
 RGG  O3    C3   C2   112.27  3.000
 RGG  HO3   O3   C3   107.53  3.000
 RGG  H4    C4   C5   108.65  3.000
 RGG  H4    C4   O4   105.98  3.000
 RGG  C5    C4   O4   112.78  3.000
 RGG  H4    C4   C3   108.25  3.000
 RGG  C5    C4   C3   109.66  3.000
 RGG  O4    C4   C3   111.33  3.000
 RGG  HO4   O4   C4   109.29  3.000
 RGG  H5    C5   C6   108.34  3.000
 RGG  H5    C5   O5   109.98  3.000
 RGG  C6    C5   O5   108.65  3.000
 RGG  H5    C5   C4   107.25  3.000
 RGG  C6    C5   C4   113.14  3.000
 RGG  O5    C5   C4   109.45  3.000
 RGG  C5    O5   C1   112.14  3.000
 RGG  H62   C6   H61  107.03  3.000
 RGG  H62   C6   O6   106.61  3.000
 RGG  H61   C6   O6   112.01  3.000
 RGG  H62   C6   C5   110.10  3.000
 RGG  H61   C6   C5   107.97  3.000
 RGG  O6    C6   C5   112.96  3.000
 RGG  HO6   O6   C6   108.45  3.000

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
 RGG  chir_01  C2'  C3'  O2'  C1'  negativ
 RGG  chir_02  C1   O1   O5   C2   positiv
 RGG  chir_03  C2   O2   C1   C3   negativ
 RGG  chir_04  C3   O3   C2   C4   positiv
 RGG  chir_05  C4   O4   C3   C5   positiv
 RGG  chir_06  C5   O5   C4   C6   negativ

