# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:03:00 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-carboxamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[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
 GLG  GLG  '(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-carboxamide (non-preferred name)'  D-saccharide  27  14  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GLG
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
 GLG  C1   C  CH1   0  -0.148  -1.1104  -0.6895   0.4614
 GLG  C2   C  CH1   0   0.015   0.0193  -0.7989   1.4961
 GLG  C3   C  CH1   0  -0.007   1.1288   0.1914   1.1704
 GLG  C4   C  CH1   0   0.039   1.6066  -0.0381  -0.2603
 GLG  C5   C  CH1   0  -0.026   0.4169   0.0201  -1.2152
 GLG  C6   C  CH2   0  -0.155   0.7892  -0.3093  -2.6442
 GLG  O2   O  OH1   0  -0.664  -0.3930  -0.6102   2.8224
 GLG  O3   O  OH1   0  -0.675   2.2449   0.0199   2.0112
 GLG  O4   O  OH1   0  -0.671   2.5307   0.9413  -0.6638
 GLG  O5   O  O2    0  -0.490  -0.5741  -0.9160  -0.8210
 GLG  O6   O  OH1   0  -0.669  -0.3507  -0.1147  -3.4487
 GLG  C7   C  C     0   0.481  -1.9596   0.5911   0.4969
 GLG  O7   O  O     0  -0.470  -2.0921   1.2735   1.4989
 GLG  H1   H  HCH1  0   0.295  -1.8132  -1.5127   0.6383
 GLG  H2   H  HCH1  0   0.237   0.4355  -1.8091   1.3673
 GLG  H3   H  HCH1  0   0.217   0.7378   1.2179   1.2489
 GLG  H4   H  HCH1  0   0.212   2.0481  -1.0463  -0.3137
 GLG  H5   H  HCH1  0   0.227   0.0125   1.0440  -1.1924
 GLG  H61  H  HCH2  0   0.215   1.6167   0.3387  -2.9498
 GLG  H62  H  HCH2  0   0.199   1.1535  -1.3449  -2.6924
 GLG  HO2  H  HOH1  0   0.458  -0.7468  -1.4397   3.1558
 GLG  HO3  H  HOH1  0   0.455   1.9841   0.2421   2.9106
 GLG  HO4  H  HOH1  0   0.455   3.2854   0.9064  -0.0671
 GLG  HO6  H  HOH1  0   0.458  -0.1013  -0.2700  -4.3639
 GLG  HN1  H  HNH2  0   0.401  -3.1756   1.6664  -0.7380
 GLG  HN2  H  HNH2  0   0.406  -2.4186   0.3133  -1.4904
 GLG  N    N  NH2   0  -0.795  -2.5979   0.8456  -0.6554

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
 GLG  C1  C2   single  1.536  0.020  1.536
 GLG  C1  O5   single  1.408  0.020  1.408
 GLG  C1  C7   single  1.537  0.020  1.537
 GLG  C1  H1   single  0.970  0.020  1.090
 GLG  C2  C3   single  1.522  0.020  1.522
 GLG  C2  O2   single  1.402  0.020  1.402
 GLG  C2  H2   single  0.970  0.020  1.090
 GLG  C3  C4   single  1.526  0.020  1.526
 GLG  C3  O3   single  1.408  0.020  1.408
 GLG  C3  H3   single  0.970  0.020  1.090
 GLG  C4  C5   single  1.527  0.020  1.527
 GLG  C4  O4   single  1.406  0.020  1.406
 GLG  C4  H4   single  0.970  0.020  1.090
 GLG  C5  C6   single  1.513  0.020  1.513
 GLG  C5  O5   single  1.419  0.020  1.419
 GLG  C5  H5   single  0.970  0.020  1.090
 GLG  C6  O6   single  1.409  0.020  1.409
 GLG  C6  H61  single  0.970  0.020  1.090
 GLG  C6  H62  single  0.970  0.020  1.090
 GLG  O2  HO2  single  0.850  0.020  0.980
 GLG  O3  HO3  single  0.850  0.020  0.980
 GLG  O4  HO4  single  0.850  0.020  0.980
 GLG  O6  HO6  single  0.850  0.020  0.980
 GLG  N   C7   single  1.342  0.020  1.342
 GLG  N   HN1  single  0.860  0.020  1.020
 GLG  N   HN2  single  0.860  0.020  1.020
 GLG  C7  O7   double  1.220  0.020  1.220

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
 GLG  H1   C1  C7   105.52  3.000
 GLG  H1   C1  O5   105.67  3.000
 GLG  C7   C1  O5   111.43  3.000
 GLG  H1   C1  C2   108.01  3.000
 GLG  C7   C1  C2   116.76  3.000
 GLG  O5   C1  C2   108.78  3.000
 GLG  H2   C2  O2   110.23  3.000
 GLG  H2   C2  C3   107.24  3.000
 GLG  O2   C2  C3   109.22  3.000
 GLG  H2   C2  C1   105.35  3.000
 GLG  O2   C2  C1   114.30  3.000
 GLG  C3   C2  C1   110.22  3.000
 GLG  H3   C3  O3   110.64  3.000
 GLG  H3   C3  C4   108.55  3.000
 GLG  O3   C3  C4   107.07  3.000
 GLG  H3   C3  C2   109.41  3.000
 GLG  O3   C3  C2   111.76  3.000
 GLG  C4   C3  C2   109.33  3.000
 GLG  H4   C4  O4   111.11  3.000
 GLG  H4   C4  C5   108.47  3.000
 GLG  O4   C4  C5   107.83  3.000
 GLG  H4   C4  C3   107.97  3.000
 GLG  O4   C4  C3   111.73  3.000
 GLG  C5   C4  C3   109.68  3.000
 GLG  H5   C5  O5   110.56  3.000
 GLG  H5   C5  C6   108.20  3.000
 GLG  O5   C5  C6   106.89  3.000
 GLG  H5   C5  C4   107.98  3.000
 GLG  O5   C5  C4   110.20  3.000
 GLG  C6   C5  C4   113.00  3.000
 GLG  H62  C6  H61  107.16  3.000
 GLG  H62  C6  O6   111.92  3.000
 GLG  H61  C6  O6   111.74  3.000
 GLG  H62  C6  C5   109.16  3.000
 GLG  H61  C6  C5   108.72  3.000
 GLG  O6   C6  C5   108.07  3.000
 GLG  HO2  O2  C2   108.67  3.000
 GLG  HO3  O3  C3   108.36  3.000
 GLG  HO4  O4  C4   108.19  3.000
 GLG  C5   O5  C1   114.38  3.000
 GLG  HO6  O6  C6   108.15  3.000
 GLG  O7   C7  N    123.22  3.000
 GLG  O7   C7  C1   123.04  3.000
 GLG  N    C7  C1   113.65  3.000
 GLG  HN2  N   HN1  117.73  3.000
 GLG  HN2  N   C7   121.84  3.000
 GLG  HN1  N   C7   119.87  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
 GLG  CONST_01  HN1  N  C7  C1  180.00  0.0  0
 GLG  CONST_02  HN2  N  C7  C1    0.00  0.0  0

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
 GLG  chir_01  C1  C2  O5  C7  positiv
 GLG  chir_02  C2  O2  C1  C3  negativ
 GLG  chir_03  C3  O3  C2  C4  positiv
 GLG  chir_04  C4  O4  C5  C3  positiv
 GLG  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
 GLG  plan-1  C1   0.020
 GLG  plan-1  C7   0.020
 GLG  plan-1  O7   0.020
 GLG  plan-1  HN1  0.020
 GLG  plan-1  HN2  0.020
 GLG  plan-1  N    0.020

