# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 06:49:44 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: methyl 2-(acetylamino)-2-deoxy-alpha-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1NC(C)=O
#
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
 MGC  MGC  'methyl 2-(acetylamino)-2-deoxy-alpha-D-galactopyranoside'  D-saccharide  33  16  .  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_MGC
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
 MGC  O6   O  OH1   0  -0.667  -4.0973   0.9915   0.1191
 MGC  C6   C  CH2   0  -0.172  -3.4356  -0.2376   0.2988
 MGC  C5   C  CH1   0  -0.006  -2.0119  -0.0996  -0.1923
 MGC  O5   O  O2    0  -0.498  -1.3425   0.8072   0.6703
 MGC  C1   C  CH1   0   0.296  -0.0335   1.1148   0.3005
 MGC  O1   O  O2    0  -0.501   0.0341   1.7700  -0.9267
 MGC  CM   C  CH3   0  -0.407  -0.5735   3.0457  -0.9405
 MGC  C2   C  CH1   0  -0.154   0.8283  -0.1484   0.2026
 MGC  N2   N  NH1   0  -0.628   2.1586   0.1810  -0.2367
 MGC  C7   C  C     0   0.522   3.2809  -0.1741   0.4153
 MGC  O7   O  O     0  -0.506   3.2816  -0.7752   1.4810
 MGC  C8   C  CH3   0  -0.779   4.5665   0.2471  -0.2526
 MGC  C3   C  CH1   0   0.058   0.1619  -1.1772  -0.7110
 MGC  O3   O  OH1   0  -0.661   0.9543  -2.3330  -0.7082
 MGC  C4   C  CH1   0  -0.039  -1.2709  -1.4352  -0.2396
 MGC  O4   O  OH1   0  -0.673  -1.2231  -2.0652   1.0188
 MGC  HO6  H  HOH1  0   0.456  -4.9813   0.9102   0.4880
 MGC  H61  H  HCH2  0   0.203  -3.9127  -1.0427  -0.2767
 MGC  H62  H  HCH2  0   0.202  -3.4374  -0.5469   1.3513
 MGC  H5   H  HCH1  0   0.227  -2.0487   0.2958  -1.2174
 MGC  H1   H  HCH1  0   0.237   0.3513   1.7612   1.1014
 MGC  HM1  H  HCH3  0   0.213  -0.1813   3.6849  -0.1421
 MGC  HM2  H  HCH3  0   0.237  -0.3417   3.5061  -1.8990
 MGC  HM3  H  HCH3  0   0.220  -1.6597   2.9870  -0.8349
 MGC  H2   H  HCH1  0   0.277   0.9100  -0.5667   1.2070
 MGC  HN2  H  HNH1  0   0.397   2.2483   0.6660  -1.1153
 MGC  H81  H  HCH3  0   0.247   4.4232   0.7104  -1.2270
 MGC  H82  H  HCH3  0   0.266   5.0906   0.9540   0.3909
 MGC  H83  H  HCH3  0   0.264   5.2127  -0.6217  -0.3737
 MGC  H3   H  HCH1  0   0.218   0.0917  -0.7536  -1.7236
 MGC  HO3  H  HOH1  0   0.452   0.6021  -2.9437  -1.3632
 MGC  H4   H  HCH1  0   0.241  -1.7699  -2.0740  -0.9829
 MGC  HO4  H  HOH1  0   0.458  -2.0372  -2.5583   1.1521

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
 MGC  O6  C6   single  1.408  0.020  1.408
 MGC  O6  HO6  single  0.850  0.020  0.980
 MGC  C6  C5   single  1.512  0.020  1.512
 MGC  C6  H61  single  0.970  0.020  1.090
 MGC  C6  H62  single  0.970  0.020  1.090
 MGC  C5  O5   single  1.419  0.020  1.419
 MGC  C5  C4   single  1.528  0.020  1.528
 MGC  C5  H5   single  0.970  0.020  1.090
 MGC  O5  C1   single  1.395  0.020  1.395
 MGC  C1  O1   single  1.393  0.020  1.393
 MGC  C1  C2   single  1.532  0.020  1.532
 MGC  C1  H1   single  0.970  0.020  1.090
 MGC  O1  CM   single  1.413  0.020  1.413
 MGC  CM  HM1  single  0.970  0.020  1.090
 MGC  CM  HM2  single  0.970  0.020  1.090
 MGC  CM  HM3  single  0.970  0.020  1.090
 MGC  C2  N2   single  1.439  0.020  1.439
 MGC  C2  C3   single  1.529  0.020  1.529
 MGC  C2  H2   single  0.970  0.020  1.090
 MGC  N2  C7   single  1.346  0.020  1.346
 MGC  N2  HN2  single  0.860  0.020  1.020
 MGC  C7  O7   double  1.223  0.020  1.223
 MGC  C7  C8   single  1.509  0.020  1.509
 MGC  C8  H81  single  0.970  0.020  1.090
 MGC  C8  H82  single  0.970  0.020  1.090
 MGC  C8  H83  single  0.970  0.020  1.090
 MGC  C3  O3   single  1.401  0.020  1.401
 MGC  C3  C4   single  1.530  0.020  1.530
 MGC  C3  H3   single  0.970  0.020  1.090
 MGC  O3  HO3  single  0.850  0.020  0.980
 MGC  C4  O4   single  1.408  0.020  1.408
 MGC  C4  H4   single  0.970  0.020  1.090
 MGC  O4  HO4  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
 MGC  HO6  O6  C6   108.03  3.000
 MGC  H62  C6  H61  107.18  3.000
 MGC  H62  C6  C5   109.81  3.000
 MGC  H61  C6  C5   107.80  3.000
 MGC  H62  C6  O6   111.58  3.000
 MGC  H61  C6  O6   111.65  3.000
 MGC  C5   C6  O6   108.75  3.000
 MGC  H5   C5  C4   107.56  3.000
 MGC  H5   C5  O5   110.65  3.000
 MGC  C4   C5  O5   110.39  3.000
 MGC  H5   C5  C6   107.71  3.000
 MGC  C4   C5  C6   112.75  3.000
 MGC  O5   C5  C6   107.76  3.000
 MGC  C1   O5  C5   115.00  3.000
 MGC  H1   C1  C2   109.55  3.000
 MGC  H1   C1  O1   110.40  3.000
 MGC  C2   C1  O1   107.71  3.000
 MGC  H1   C1  O5   105.38  3.000
 MGC  C2   C1  O5   111.28  3.000
 MGC  O1   C1  O5   112.52  3.000
 MGC  CM   O1  C1   114.36  3.000
 MGC  HM3  CM  HM2  108.63  3.000
 MGC  HM3  CM  HM1  108.47  3.000
 MGC  HM2  CM  HM1  108.59  3.000
 MGC  HM3  CM  O1   112.21  3.000
 MGC  HM2  CM  O1   107.39  3.000
 MGC  HM1  CM  O1   111.46  3.000
 MGC  H2   C2  C3   108.95  3.000
 MGC  H2   C2  N2   107.43  3.000
 MGC  C3   C2  N2   112.00  3.000
 MGC  H2   C2  C1   107.42  3.000
 MGC  C3   C2  C1   110.36  3.000
 MGC  N2   C2  C1   110.53  3.000
 MGC  HN2  N2  C7   118.38  3.000
 MGC  HN2  N2  C2   117.30  3.000
 MGC  C7   N2  C2   124.24  3.000
 MGC  C8   C7  O7   121.49  3.000
 MGC  C8   C7  N2   114.99  3.000
 MGC  O7   C7  N2   123.51  3.000
 MGC  H83  C8  H82  107.31  3.000
 MGC  H83  C8  H81  108.55  3.000
 MGC  H82  C8  H81  108.41  3.000
 MGC  H83  C8  C7   109.38  3.000
 MGC  H82  C8  C7   109.23  3.000
 MGC  H81  C8  C7   113.77  3.000
 MGC  H3   C3  C4   106.79  3.000
 MGC  H3   C3  O3   110.83  3.000
 MGC  C4   C3  O3   112.94  3.000
 MGC  H3   C3  C2   108.59  3.000
 MGC  C4   C3  C2   109.72  3.000
 MGC  O3   C3  C2   107.90  3.000
 MGC  HO3  O3  C3   108.37  3.000
 MGC  H4   C4  O4   111.07  3.000
 MGC  H4   C4  C3   108.33  3.000
 MGC  O4   C4  C3   108.60  3.000
 MGC  H4   C4  C5   107.97  3.000
 MGC  O4   C4  C5   112.32  3.000
 MGC  C3   C4  C5   108.44  3.000
 MGC  HO4  O4  C4   108.95  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
 MGC  CONST_01  O7   C7  N2  C2    0.00   0.0  0
 MGC  CONST_02  C8   C7  N2  C2  180.00   0.0  0
 MGC  CONST_03  HN2  N2  C7  O7  180.00   0.0  0
 MGC  Var_01    HM1  CM  O1  C1   53.77  30.0  3
 MGC  Var_02    H81  C8  C7  N2   -5.15  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
 MGC  chir_01  C5  C6  O5  C4  negativ
 MGC  chir_02  C1  O5  O1  C2  positiv
 MGC  chir_03  C2  N2  C3  C1  positiv
 MGC  chir_04  C3  O3  C2  C4  positiv
 MGC  chir_05  C4  O4  C5  C3  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
 MGC  plan-1  C2   0.020
 MGC  plan-1  N2   0.020
 MGC  plan-1  C7   0.020
 MGC  plan-1  O7   0.020
 MGC  plan-1  C8   0.020
 MGC  plan-1  HN2  0.020

