# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:20:14 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-alpha-D-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[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
 A2G  A2G  2-(acetylamino)-2-deoxy-alpha-D-galactopyranose  D-saccharide  30  15  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A2G
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
 A2G  O5   O  O2    0  -0.495  -5.2519  11.7070  77.5272
 A2G  C1   C  CH1   0   0.271  -5.5582  10.4251  77.1026
 A2G  O1   O  OH1   0  -0.662  -6.9465  10.3382  76.9356
 A2G  C2   C  CH1   0  -0.143  -5.0264   9.3657  78.0860
 A2G  N2   N  NH1   0  -0.650  -5.4240   8.0415  77.6714
 A2G  C3   C  CH1   0   0.040  -5.5056   9.6709  79.4997
 A2G  O3   O  OH1   0  -0.661  -4.9659   8.7072  80.3644
 A2G  C4   C  CH1   0  -0.024  -5.1112  11.1001  79.8759
 A2G  O4   O  OH1   0  -0.671  -3.7084  11.1740  79.9516
 A2G  C5   C  CH1   0   0.000  -5.6912  12.0548  78.8314
 A2G  C6   C  CH2   0  -0.196  -5.2731  13.5043  79.0209
 A2G  O6   O  OH1   0  -0.667  -5.6489  13.8978  80.3185
 A2G  C7   C  C     0   0.523  -4.6534   7.2438  76.9031
 A2G  O7   O  O     0  -0.492  -3.5716   7.5972  76.4573
 A2G  C8   C  CH3   0  -0.777  -5.2181   5.8731  76.6279
 A2G  H1   H  HCH1  0   0.228  -5.0443  10.2984  76.1410
 A2G  HO1  H  HOH1  0   0.454  -7.1604   9.4805  76.5523
 A2G  H2   H  HCH1  0   0.266  -3.9356   9.4134  78.0598
 A2G  HN2  H  HNH1  0   0.403  -6.2864   7.6659  78.0346
 A2G  H3   H  HCH1  0   0.220  -6.6054   9.6316  79.5131
 A2G  HO3  H  HOH1  0   0.451  -5.3731   8.8132  81.2302
 A2G  H4   H  HCH1  0   0.239  -5.5739  11.3336  80.8444
 A2G  HO4  H  HOH1  0   0.456  -3.4689  11.9347  80.4888
 A2G  H5   H  HCH1  0   0.227  -6.7859  11.9981  78.9004
 A2G  H61  H  HCH2  0   0.202  -4.1916  13.5968  78.8591
 A2G  H81  H  HCH3  0   0.265  -5.2697   5.7123  75.5515
 A2G  H82  H  HCH3  0   0.266  -4.5448   5.1189  77.0358
 A2G  H83  H  HCH3  0   0.249  -6.2089   5.7139  77.0490
 A2G  H62  H  HCH2  0   0.220  -5.7644  14.1133  78.2517
 A2G  HO6  H  HOH1  0   0.459  -5.3571  14.8028  80.4581

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
 A2G  O5  C5   single  1.419  0.020  1.419
 A2G  C1  O5   single  1.385  0.020  1.385
 A2G  C1  C2   single  1.540  0.020  1.540
 A2G  C1  H1   single  0.970  0.020  1.090
 A2G  O1  C1   single  1.401  0.020  1.401
 A2G  O1  HO1  single  0.850  0.020  0.980
 A2G  C2  C3   single  1.524  0.020  1.524
 A2G  C2  H2   single  0.970  0.020  1.090
 A2G  N2  C2   single  1.443  0.020  1.443
 A2G  N2  HN2  single  0.860  0.020  1.020
 A2G  C3  C4   single  1.530  0.020  1.530
 A2G  C3  O3   single  1.403  0.020  1.403
 A2G  C3  H3   single  0.970  0.020  1.090
 A2G  O3  HO3  single  0.850  0.020  0.980
 A2G  C4  O4   single  1.407  0.020  1.407
 A2G  C4  H4   single  0.970  0.020  1.090
 A2G  O4  HO4  single  0.850  0.020  0.980
 A2G  C5  C4   single  1.529  0.020  1.529
 A2G  C5  C6   single  1.520  0.020  1.520
 A2G  C5  H5   single  0.970  0.020  1.090
 A2G  C6  O6   single  1.407  0.020  1.407
 A2G  C6  H61  single  0.970  0.020  1.090
 A2G  C7  N2   single  1.349  0.020  1.349
 A2G  O7  C7   double  1.222  0.020  1.222
 A2G  C8  C7   single  1.508  0.020  1.508
 A2G  C8  H81  single  0.970  0.020  1.090
 A2G  C8  H82  single  0.970  0.020  1.090
 A2G  C8  H83  single  0.970  0.020  1.090
 A2G  C6  H62  single  0.970  0.020  1.090
 A2G  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
 A2G  C5   O5  C1   116.11  3.000
 A2G  H1   C1  C2   108.56  3.000
 A2G  H1   C1  O1   110.63  3.000
 A2G  C2   C1  O1   112.06  3.000
 A2G  O1   C1  O5   108.25  3.000
 A2G  H1   C1  O5   105.78  3.000
 A2G  C2   C1  O5   111.38  3.000
 A2G  HO1  O1  C1   108.82  3.000
 A2G  H2   C2  C3   109.12  3.000
 A2G  H2   C2  N2   107.96  3.000
 A2G  C3   C2  N2   111.32  3.000
 A2G  N2   C2  C1   110.64  3.000
 A2G  H2   C2  C1   107.43  3.000
 A2G  C3   C2  C1   110.25  3.000
 A2G  HN2  N2  C7   118.26  3.000
 A2G  C7   N2  C2   123.27  3.000
 A2G  HN2  N2  C2   118.29  3.000
 A2G  H3   C3  C4   106.74  3.000
 A2G  H3   C3  O3   110.64  3.000
 A2G  C4   C3  O3   113.03  3.000
 A2G  H3   C3  C2   108.57  3.000
 A2G  O3   C3  C2   108.26  3.000
 A2G  C4   C3  C2   109.53  3.000
 A2G  HO3  O3  C3   108.43  3.000
 A2G  H4   C4  C5   108.04  3.000
 A2G  C5   C4  O4   112.47  3.000
 A2G  H4   C4  O4   111.19  3.000
 A2G  C5   C4  C3   108.51  3.000
 A2G  H4   C4  C3   107.87  3.000
 A2G  O4   C4  C3   108.63  3.000
 A2G  HO4  O4  C4   108.66  3.000
 A2G  H5   C5  C6   108.39  3.000
 A2G  H5   C5  C4   107.63  3.000
 A2G  C6   C5  C4   113.93  3.000
 A2G  H5   C5  O5   110.71  3.000
 A2G  C6   C5  O5   105.25  3.000
 A2G  C4   C5  O5   110.93  3.000
 A2G  H62  C6  H61  106.93  3.000
 A2G  H62  C6  O6   111.82  3.000
 A2G  H61  C6  O6   112.06  3.000
 A2G  H62  C6  C5   108.58  3.000
 A2G  H61  C6  C5   109.44  3.000
 A2G  O6   C6  C5   107.95  3.000
 A2G  HO6  O6  C6   108.44  3.000
 A2G  C8   C7  O7   121.85  3.000
 A2G  C8   C7  N2   115.31  3.000
 A2G  O7   C7  N2   122.84  3.000
 A2G  H83  C8  H82  108.44  3.000
 A2G  H83  C8  H81  108.51  3.000
 A2G  H82  C8  H81  107.27  3.000
 A2G  H83  C8  C7   113.78  3.000
 A2G  H82  C8  C7   109.23  3.000
 A2G  H81  C8  C7   109.40  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
 A2G  CONST_01  O7   C7  N2  C2    0.00   0.0  0
 A2G  CONST_02  C8   C7  N2  C2  180.00   0.0  0
 A2G  CONST_03  HN2  N2  C7  O7  180.00   0.0  0
 A2G  Var_01    H81  C8  C7  N2  124.32  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
 A2G  chir_01  C1  O5  C2  O1  negativ
 A2G  chir_02  C2  N2  C3  C1  positiv
 A2G  chir_03  C3  O3  C2  C4  positiv
 A2G  chir_04  C4  O4  C5  C3  negativ
 A2G  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
 A2G  plan-1  C2   0.020
 A2G  plan-1  N2   0.020
 A2G  plan-1  C7   0.020
 A2G  plan-1  O7   0.020
 A2G  plan-1  C8   0.020
 A2G  plan-1  HN2  0.020

