# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:35:34 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  40  23  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.645   3.3326   1.8167   0.7126
 GMT  C12  C  C      0   0.415   2.8133   1.6500  -0.4055
 GMT  O15  O  OC    -1  -0.595   3.1625   0.8094  -1.2693
 GMT  C11  C  CH2    0  -0.585   1.6077   2.5413  -0.7432
 GMT  C9   C  CH1    0  -0.055   0.3815   2.0996   0.0538
 GMT  C10  C  C      0   0.362  -0.8232   2.9941  -0.2950
 GMT  O14  O  OC    -1  -0.685  -0.9129   4.0438   0.3756
 GMT  O13  O  O      0  -0.450  -1.5529   2.6420  -1.2379
 GMT  O1   O  O2     0  -0.560   0.1631   0.7328  -0.2557
 GMT  C1   C  CH1    0   0.290  -0.1245  -0.1190   0.7937
 GMT  O5   O  O2     0  -0.519  -1.4529  -0.0397   1.2227
 GMT  C5   C  CH1    0  -0.001  -2.4246  -0.3637   0.2398
 GMT  C6   C  CH2    0  -0.175  -3.7812  -0.2494   0.9016
 GMT  O6   O  OH1    0  -0.706  -4.0103   1.0854   1.2818
 GMT  C4   C  CH1    0  -0.047  -2.1890  -1.7835  -0.2903
 GMT  O4   O  OH1    0  -0.703  -3.0372  -2.0718  -1.3837
 GMT  C3   C  CH1    0   0.026  -0.7533  -1.9523  -0.7798
 GMT  O3   O  OH1    0  -0.660  -0.4798  -3.2861  -1.1269
 GMT  C2   C  CH1    0  -0.097   0.2108  -1.5375   0.3275
 GMT  N2   N  NH1    0  -0.672   1.5918  -1.6123  -0.0749
 GMT  C7   C  C      0   0.467   2.4292  -2.5845   0.3270
 GMT  O7   O  O      0  -0.388   2.0915  -3.5162   1.0478
 GMT  C8   C  CH3    0  -0.761   3.8404  -2.4547  -0.1919
 GMT  H2   H  HCH2   0   0.259   1.8205   3.5831  -0.4903
 GMT  H3   H  HCH2   0   0.202   1.3762   2.4996  -1.8111
 GMT  H4   H  HCH1   0   0.153   0.6067   2.2053   1.1226
 GMT  H6   H  HCH1   0   0.266   0.4779   0.1301   1.6781
 GMT  H7   H  HCH1   0   0.282  -2.3648   0.3459  -0.5940
 GMT  H8   H  HCH2   0   0.232  -4.5434  -0.5967   0.1923
 GMT  H9   H  HCH2   0   0.185  -3.8140  -0.9312   1.7637
 GMT  H10  H  HOH1   0   0.441  -4.8699   1.1235   1.7108
 GMT  H11  H  HCH1   0   0.212  -2.3512  -2.5011   0.5283
 GMT  H12  H  HOH1   0   0.447  -3.8642  -2.4356  -1.0562
 GMT  H13  H  HCH1   0   0.215  -0.6081  -1.2887  -1.6457
 GMT  H14  H  HOH1   0   0.445  -1.0732  -3.5296  -1.8450
 GMT  H15  H  HCH1   0   0.243   0.0744  -2.2103   1.1777
 GMT  H16  H  HNH1   0   0.359   1.9736  -0.8428  -0.6170
 GMT  H17  H  HCH3   0   0.255   3.9921  -3.1660  -1.0058
 GMT  H18  H  HCH3   0   0.251   4.0621  -1.4552  -0.5612
 GMT  H19  H  HCH3   0   0.294   4.5454  -2.7099   0.5980

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  1.514  0.020  1.514
 GMT  O5   C5   single  1.420  0.020  1.420
 GMT  O5   C1   single  1.398  0.020  1.398
 GMT  C4   C5   single  1.534  0.020  1.534
 GMT  C4   O4   single  1.413  0.020  1.413
 GMT  C4   C3   single  1.526  0.020  1.526
 GMT  O7   C7   double  1.226  0.020  1.226
 GMT  C1   C2   single  1.530  0.020  1.530
 GMT  C1   O1   single  1.382  0.020  1.382
 GMT  C2   C3   single  1.526  0.020  1.526
 GMT  C2   N2   single  1.440  0.020  1.440
 GMT  O3   C3   single  1.405  0.020  1.405
 GMT  O13  C10  deloc   1.243  0.020  1.243
 GMT  C7   N2   single  1.345  0.020  1.345
 GMT  C7   C8   single  1.509  0.020  1.509
 GMT  C10  C9   single  1.540  0.020  1.540
 GMT  C10  O14  deloc   1.249  0.020  1.249
 GMT  O1   C9   single  1.418  0.020  1.418
 GMT  C9   C11  single  1.528  0.020  1.528
 GMT  O16  C12  deloc   1.244  0.020  1.244
 GMT  C11  C12  single  1.537  0.020  1.537
 GMT  C12  O15  deloc   1.255  0.020  1.255
 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  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  117.10  3.000
 GMT  O15  C12  O16  126.32  3.000
 GMT  C11  C12  O16  116.57  3.000
 GMT  H3   C11  H2   107.67  3.000
 GMT  H3   C11  C9   109.18  3.000
 GMT  H2   C11  C9   108.13  3.000
 GMT  H3   C11  C12  111.01  3.000
 GMT  H2   C11  C12  110.43  3.000
 GMT  C9   C11  C12  110.33  3.000
 GMT  H4   C9   O1   109.69  3.000
 GMT  H4   C9   C10  108.97  3.000
 GMT  O1   C9   C10  112.94  3.000
 GMT  H4   C9   C11  108.40  3.000
 GMT  O1   C9   C11  106.76  3.000
 GMT  C10  C9   C11  109.98  3.000
 GMT  O13  C10  O14  127.10  3.000
 GMT  O14  C10  C9   115.00  3.000
 GMT  O13  C10  C9   117.79  3.000
 GMT  C1   O1   C9   117.41  3.000
 GMT  H6   C1   C2   109.59  3.000
 GMT  H6   C1   O5   105.13  3.000
 GMT  C2   C1   O5   110.75  3.000
 GMT  H6   C1   O1   110.94  3.000
 GMT  C2   C1   O1   107.12  3.000
 GMT  O5   C1   O1   113.31  3.000
 GMT  C5   O5   C1   115.14  3.000
 GMT  H7   C5   C4   109.14  3.000
 GMT  H7   C5   C6   109.42  3.000
 GMT  C4   C5   C6   111.02  3.000
 GMT  H7   C5   O5   109.97  3.000
 GMT  C4   C5   O5   110.21  3.000
 GMT  C6   C5   O5   107.06  3.000
 GMT  H9   C6   H8   106.84  3.000
 GMT  H9   C6   O6   111.81  3.000
 GMT  H8   C6   O6   111.22  3.000
 GMT  H9   C6   C5   108.83  3.000
 GMT  H8   C6   C5   108.42  3.000
 GMT  O6   C6   C5   109.62  3.000
 GMT  H10  O6   C6   107.69  3.000
 GMT  H11  C4   C3   107.76  3.000
 GMT  H11  C4   O4   110.73  3.000
 GMT  C3   C4   O4   107.09  3.000
 GMT  H11  C4   C5   108.90  3.000
 GMT  C3   C4   C5   110.96  3.000
 GMT  O4   C4   C5   111.34  3.000
 GMT  H12  O4   C4   109.27  3.000
 GMT  H13  C3   C2   108.89  3.000
 GMT  H13  C3   O3   110.63  3.000
 GMT  C2   C3   O3   108.32  3.000
 GMT  H13  C3   C4   108.04  3.000
 GMT  O3   C3   C4   111.54  3.000
 GMT  C2   C3   C4   109.37  3.000
 GMT  H14  O3   C3   107.72  3.000
 GMT  H15  C2   N2   107.76  3.000
 GMT  H15  C2   C3   108.57  3.000
 GMT  N2   C2   C3   112.89  3.000
 GMT  H15  C2   C1   107.83  3.000
 GMT  N2   C2   C1   110.07  3.000
 GMT  C3   C2   C1   109.55  3.000
 GMT  H16  N2   C7   118.23  3.000
 GMT  H16  N2   C2   118.05  3.000
 GMT  C7   N2   C2   123.45  3.000
 GMT  C8   C7   O7   121.69  3.000
 GMT  C8   C7   N2   114.68  3.000
 GMT  O7   C7   N2   123.63  3.000
 GMT  H19  C8   H18  109.23  3.000
 GMT  H19  C8   H17  107.35  3.000
 GMT  H18  C8   H17  108.49  3.000
 GMT  H19  C8   C7   109.62  3.000
 GMT  H18  C8   C7   112.71  3.000
 GMT  H17  C8   C7   109.29  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  Var_01    C9   C11  C12  O16   -72.62  30.0  3
 GMT  Var_02    H17  C8   C7   N2   -103.27  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-3  C9   0.020
 GMT  plan-3  C10  0.020
 GMT  plan-3  O14  0.020
 GMT  plan-3  O13  0.020

