# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:20:30 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2S)-2-{[2-(acetylamino)-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[C@@H](CC(O)=O)C(O)=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
 GMT  GMT  '(2S)-2-{[2-(acetylamino)-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid'  D-saccharide  42  23  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GMT
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
 GMT  O16  O  O     0  -0.434   2.9691   1.1643   0.9057
 GMT  C12  C  C     0   0.565   2.8640   1.6842  -0.1759
 GMT  O15  O  OH1   0  -0.589   3.8195   1.6579  -1.0953
 GMT  C11  C  CH2   0  -0.599   1.6662   2.4731  -0.6394
 GMT  C9   C  CH1   0  -0.053   0.3919   1.9951   0.0482
 GMT  C10  C  C     0   0.535  -0.7687   2.8715  -0.3972
 GMT  O14  O  OH1   0  -0.590  -0.7717   4.0209   0.2623
 GMT  O13  O  O     0  -0.422  -1.5488   2.5842  -1.2642
 GMT  O1   O  O2    0  -0.499   0.1716   0.6628  -0.3195
 GMT  C1   C  CH1   0   0.280  -0.1516  -0.2119   0.7222
 GMT  O5   O  O2    0  -0.494  -1.4653  -0.0678   1.1533
 GMT  C5   C  CH1   0  -0.024  -2.4737  -0.4128   0.2126
 GMT  C6   C  CH2   0  -0.165  -3.8061  -0.2146   0.9017
 GMT  O6   O  OH1   0  -0.665  -3.9650   1.1471   1.2160
 GMT  C4   C  CH1   0  -0.004  -2.2862  -1.8585  -0.2556
 GMT  O4   O  OH1   0  -0.674  -3.1943  -2.1848  -1.2856
 GMT  C3   C  CH1   0   0.032  -0.8809  -2.0563  -0.8160
 GMT  O3   O  OH1   0  -0.665  -0.6390  -3.3991  -1.1453
 GMT  C2   C  CH1   0  -0.155   0.1368  -1.6354   0.2343
 GMT  N2   N  NH1   0  -0.628   1.4838  -1.7529  -0.2576
 GMT  C7   C  C     0   0.532   2.5293  -2.0904   0.5196
 GMT  O7   O  O     0  -0.506   2.4117  -2.3917   1.6996
 GMT  C8   C  CH3   0  -0.784   3.8684  -2.0953  -0.1726
 GMT  H1   H  HOH1  0   0.480   4.6031   1.2049  -0.7485
 GMT  H2   H  HCH2  0   0.312   1.8546   3.5257  -0.4071
 GMT  H3   H  HCH2  0   0.293   1.5656   2.4042  -1.7241
 GMT  H4   H  HCH1  0   0.273   0.5088   2.0983   1.1333
 GMT  H5   H  HOH1  0   0.487  -1.4679   4.6029  -0.0785
 GMT  H6   H  HCH1  0   0.252   0.4690   0.0042   1.5991
 GMT  H7   H  HCH1  0   0.239  -2.4228   0.2475  -0.6615
 GMT  H8   H  HCH2  0   0.201  -4.5981  -0.5647   0.2285
 GMT  H9   H  HCH2  0   0.197  -3.8409  -0.8506   1.7976
 GMT  H10  H  HOH1  0   0.455  -4.8113   1.2482   1.6608
 GMT  H11  H  HCH1  0   0.227  -2.4082  -2.5337   0.6037
 GMT  H12  H  HOH1  0   0.463  -3.9783  -2.5864  -0.9017
 GMT  H13  H  HCH1  0   0.218  -0.7771  -1.4120  -1.7044
 GMT  H14  H  HOH1  0   0.451  -1.3026  -3.6648  -1.7910
 GMT  H15  H  HCH1  0   0.279   0.0353  -2.2979   1.0975
 GMT  H16  H  HNH1  0   0.399   1.6644  -1.4605  -1.2042
 GMT  H17  H  HCH3  0   0.247   3.8254  -1.7612  -1.2075
 GMT  H18  H  HCH3  0   0.262   4.5591  -1.4548   0.3744
 GMT  H19  H  HCH3  0   0.270   4.2797  -3.1048  -0.1564

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
 GMT  O6   C6   single  1.407  0.020  1.407
 GMT  C6   C5   single  1.513  0.020  1.513
 GMT  O5   C5   single  1.422  0.020  1.422
 GMT  O5   C1   single  1.390  0.020  1.390
 GMT  C4   C5   single  1.531  0.020  1.531
 GMT  C4   O4   single  1.411  0.020  1.411
 GMT  C4   C3   single  1.526  0.020  1.526
 GMT  O7   C7   double  1.224  0.020  1.224
 GMT  C1   C2   single  1.532  0.020  1.532
 GMT  C1   O1   single  1.398  0.020  1.398
 GMT  C2   C3   single  1.522  0.020  1.522
 GMT  C2   N2   single  1.439  0.020  1.439
 GMT  O3   C3   single  1.404  0.020  1.404
 GMT  O13  C10  double  1.201  0.020  1.201
 GMT  C7   N2   single  1.346  0.020  1.346
 GMT  C7   C8   single  1.507  0.020  1.507
 GMT  C10  C9   single  1.521  0.020  1.521
 GMT  C10  O14  single  1.325  0.020  1.325
 GMT  O1   C9   single  1.399  0.020  1.399
 GMT  C9   C11  single  1.525  0.020  1.525
 GMT  O16  C12  double  1.205  0.020  1.205
 GMT  C11  C12  single  1.507  0.020  1.507
 GMT  C12  O15  single  1.326  0.020  1.326
 GMT  O15  H1   single  0.850  0.020  0.980
 GMT  C11  H2   single  0.970  0.020  1.090
 GMT  C11  H3   single  0.970  0.020  1.090
 GMT  C9   H4   single  0.970  0.020  1.090
 GMT  O14  H5   single  0.850  0.020  0.980
 GMT  C1   H6   single  0.970  0.020  1.090
 GMT  C5   H7   single  0.970  0.020  1.090
 GMT  C6   H8   single  0.970  0.020  1.090
 GMT  C6   H9   single  0.970  0.020  1.090
 GMT  O6   H10  single  0.850  0.020  0.980
 GMT  C4   H11  single  0.970  0.020  1.090
 GMT  O4   H12  single  0.850  0.020  0.980
 GMT  C3   H13  single  0.970  0.020  1.090
 GMT  O3   H14  single  0.850  0.020  0.980
 GMT  C2   H15  single  0.970  0.020  1.090
 GMT  N2   H16  single  0.860  0.020  1.020
 GMT  C8   H17  single  0.970  0.020  1.090
 GMT  C8   H18  single  0.970  0.020  1.090
 GMT  C8   H19  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
 GMT  C11  C12  O15  111.70  3.000
 GMT  O15  C12  O16  123.44  3.000
 GMT  C11  C12  O16  124.84  3.000
 GMT  H1   O15  C12  110.10  3.000
 GMT  H3   C11  H2   106.71  3.000
 GMT  H3   C11  C9   110.56  3.000
 GMT  H2   C11  C9   110.47  3.000
 GMT  H3   C11  C12  110.23  3.000
 GMT  H2   C11  C12  107.54  3.000
 GMT  C9   C11  C12  111.18  3.000
 GMT  H4   C9   O1   111.50  3.000
 GMT  H4   C9   C10  108.48  3.000
 GMT  O1   C9   C10  110.59  3.000
 GMT  H4   C9   C11  109.12  3.000
 GMT  O1   C9   C11  108.15  3.000
 GMT  C10  C9   C11  108.96  3.000
 GMT  O13  C10  O14  124.42  3.000
 GMT  O14  C10  C9   110.85  3.000
 GMT  O13  C10  C9   124.68  3.000
 GMT  H5   O14  C10  110.33  3.000
 GMT  C1   O1   C9   115.86  3.000
 GMT  H6   C1   C2   109.36  3.000
 GMT  H6   C1   O5   105.46  3.000
 GMT  C2   C1   O5   111.90  3.000
 GMT  H6   C1   O1   109.99  3.000
 GMT  C2   C1   O1   107.48  3.000
 GMT  O5   C1   O1   112.63  3.000
 GMT  C5   O5   C1   116.10  3.000
 GMT  H7   C5   C4   108.61  3.000
 GMT  H7   C5   C6   108.97  3.000
 GMT  C4   C5   C6   111.76  3.000
 GMT  H7   C5   O5   110.39  3.000
 GMT  C4   C5   O5   110.16  3.000
 GMT  C6   C5   O5   106.95  3.000
 GMT  H9   C6   H8   107.02  3.000
 GMT  H9   C6   O6   111.99  3.000
 GMT  H8   C6   O6   111.38  3.000
 GMT  H9   C6   C5   108.87  3.000
 GMT  H8   C6   C5   108.33  3.000
 GMT  O6   C6   C5   109.15  3.000
 GMT  H10  O6   C6   107.73  3.000
 GMT  H11  C4   C3   108.04  3.000
 GMT  H11  C4   O4   110.91  3.000
 GMT  C3   C4   O4   107.13  3.000
 GMT  H11  C4   C5   109.10  3.000
 GMT  C3   C4   C5   110.34  3.000
 GMT  O4   C4   C5   111.26  3.000
 GMT  H12  O4   C4   109.27  3.000
 GMT  H13  C3   C2   109.36  3.000
 GMT  H13  C3   O3   110.73  3.000
 GMT  C2   C3   O3   108.14  3.000
 GMT  H13  C3   C4   107.87  3.000
 GMT  O3   C3   C4   111.65  3.000
 GMT  C2   C3   C4   109.06  3.000
 GMT  H14  O3   C3   107.60  3.000
 GMT  H15  C2   N2   107.91  3.000
 GMT  H15  C2   C3   108.38  3.000
 GMT  N2   C2   C3   111.56  3.000
 GMT  H15  C2   C1   107.11  3.000
 GMT  N2   C2   C1   111.16  3.000
 GMT  C3   C2   C1   110.54  3.000
 GMT  H16  N2   C7   118.45  3.000
 GMT  H16  N2   C2   117.75  3.000
 GMT  C7   N2   C2   123.39  3.000
 GMT  C8   C7   O7   121.83  3.000
 GMT  C8   C7   N2   115.20  3.000
 GMT  O7   C7   N2   122.96  3.000
 GMT  H19  C8   H18  107.33  3.000
 GMT  H19  C8   H17  108.26  3.000
 GMT  H18  C8   H17  108.79  3.000
 GMT  H19  C8   C7   109.35  3.000
 GMT  H18  C8   C7   109.31  3.000
 GMT  H17  C8   C7   113.61  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
 GMT  CONST_01  O7   C7   N2   C2     0.00   0.0  0
 GMT  CONST_02  C8   C7   N2   C2   180.00   0.0  0
 GMT  CONST_03  H16  N2   C7   O7   180.00   0.0  0
 GMT  CONST_04  H1   O15  C12  O16    0.00   0.0  0
 GMT  CONST_05  H5   O14  C10  C9   180.00   0.0  0
 GMT  Var_01    C9   C11  C12  O16  -28.33  30.0  2
 GMT  Var_02    H17  C8   C7   N2     3.66  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
 GMT  chir_01  C9  C10  O1  C11  negativ
 GMT  chir_02  C1  O5   O1  C2   positiv
 GMT  chir_03  C5  O5   C4  C6   negativ
 GMT  chir_04  C4  O4   C5  C3   positiv
 GMT  chir_05  C3  O3   C4  C2   negativ
 GMT  chir_06  C2  N2   C3  C1   positiv

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
 GMT  plan-1  C2   0.020
 GMT  plan-1  N2   0.020
 GMT  plan-1  C7   0.020
 GMT  plan-1  O7   0.020
 GMT  plan-1  C8   0.020
 GMT  plan-1  H16  0.020
 GMT  plan-2  O16  0.020
 GMT  plan-2  C12  0.020
 GMT  plan-2  O15  0.020
 GMT  plan-2  C11  0.020
 GMT  plan-2  H1   0.020
 GMT  plan-3  C9   0.020
 GMT  plan-3  C10  0.020
 GMT  plan-3  O14  0.020
 GMT  plan-3  O13  0.020
 GMT  plan-3  H5   0.020

