# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:18:06 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-(azidoacetyl)-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)CN=[N+]=[N-])[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
 DL6  DL6  N-(azidoacetyl)-beta-D-glucopyranosylamine  D-saccharide  32  18  .  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_DL6
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
 DL6  O6   O  OH1    0  -0.670  -1.2646   3.4874   0.0681
 DL6  C6   C  CH2    0  -0.156  -2.2751   2.5833   0.4459
 DL6  C5   C  CH1    0  -0.015  -1.9446   1.2180  -0.1192
 DL6  C4   C  CH1    0   0.035  -3.0546   0.2031   0.1566
 DL6  O4   O  OH1    0  -0.671  -4.2158   0.6339  -0.5083
 DL6  C3   C  CH1    0  -0.006  -2.6217  -1.1752  -0.3278
 DL6  O3   O  OH1    0  -0.671  -3.6302  -2.0869   0.0347
 DL6  C2   C  CH1    0  -0.028  -1.2708  -1.5564   0.2617
 DL6  O2   O  OH1    0  -0.663  -0.8735  -2.7676  -0.3280
 DL6  C1   C  CH1    0   0.209  -0.2672  -0.4392  -0.0307
 DL6  N1   N  NH1    0  -0.684   0.9913  -0.7228   0.5800
 DL6  C7   C  C      0   0.547   2.1829  -0.4516   0.0051
 DL6  C8   C  CH2    0  -0.444   3.3757  -0.6712   0.9264
 DL6  N2   N  N      0  -0.350   4.6107  -0.8486   0.1891
 DL6  N3   N  N      1   0.365   5.0290   0.1222  -0.4202
 DL6  N4   N  N     -1  -0.211   5.5242   0.9430  -1.0041
 DL6  O7   O  O      0  -0.464   2.3235  -0.0473  -1.1312
 DL6  O5   O  O2     0  -0.488  -0.7403   0.7839   0.4795
 DL6  HO6  H  HOH1   0   0.457  -1.5217   4.3623   0.3719
 DL6  H61  H  HCH2   0   0.197  -2.3652   2.5032   1.5385
 DL6  H62  H  HCH2   0   0.214  -3.2541   2.8883   0.0629
 DL6  H5   H  HCH1   0   0.225  -1.8139   1.3040  -1.2106
 DL6  H4   H  HCH1   0   0.213  -3.2162   0.1549   1.2455
 DL6  HO4  H  HOH1   0   0.455  -4.9142  -0.0073  -0.3393
 DL6  H3   H  HCH1   0   0.218  -2.5116  -1.1271  -1.4233
 DL6  HO3  H  HOH1   0   0.457  -3.4714  -2.9182  -0.4231
 DL6  H2   H  HCH1   0   0.229  -1.3758  -1.6555   1.3530
 DL6  HO2  H  HOH1   0   0.458  -0.1552  -3.1461   0.1884
 DL6  H1   H  HCH1   0   0.237  -0.1140  -0.3711  -1.1148
 DL6  HN1  H  HNH1   0   0.412   0.9833  -1.0086   1.5493
 DL6  H81  H  HCH2   0   0.300   3.4293   0.1770   1.6184
 DL6  H82  H  HCH2   0   0.296   3.2419  -1.5666   1.5307

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
 DL6  O6  C6   single  1.408  0.020  1.408
 DL6  O6  HO6  single  0.850  0.020  0.980
 DL6  C6  C5   single  1.514  0.020  1.514
 DL6  C6  H61  single  0.970  0.020  1.090
 DL6  C6  H62  single  0.970  0.020  1.090
 DL6  C5  C4   single  1.529  0.020  1.529
 DL6  C5  O5   single  1.413  0.020  1.413
 DL6  C5  H5   single  0.970  0.020  1.090
 DL6  C4  O4   single  1.406  0.020  1.406
 DL6  C4  C3   single  1.524  0.020  1.524
 DL6  C4  H4   single  0.970  0.020  1.090
 DL6  O4  HO4  single  0.850  0.020  0.980
 DL6  C3  O3   single  1.407  0.020  1.407
 DL6  C3  C2   single  1.522  0.020  1.522
 DL6  C3  H3   single  0.970  0.020  1.090
 DL6  O3  HO3  single  0.850  0.020  0.980
 DL6  C2  O2   single  1.405  0.020  1.405
 DL6  C2  C1   single  1.530  0.020  1.530
 DL6  C2  H2   single  0.970  0.020  1.090
 DL6  O2  HO2  single  0.850  0.020  0.980
 DL6  C1  N1   single  1.427  0.020  1.427
 DL6  C1  O5   single  1.407  0.020  1.407
 DL6  C1  H1   single  0.970  0.020  1.090
 DL6  N1  C7   single  1.351  0.020  1.351
 DL6  N1  HN1  single  0.860  0.020  1.020
 DL6  C7  C8   single  1.523  0.020  1.523
 DL6  C7  O7   double  1.214  0.020  1.214
 DL6  C8  N2   single  1.449  0.020  1.449
 DL6  C8  H81  single  0.970  0.020  1.090
 DL6  C8  H82  single  0.970  0.020  1.090
 DL6  N2  N3   double  1.220  0.020  1.220
 DL6  N3  N4   double  1.122  0.020  1.122

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
 DL6  HO6  O6  C6   107.93  3.000
 DL6  H62  C6  H61  107.15  3.000
 DL6  H62  C6  C5   108.41  3.000
 DL6  H61  C6  C5   108.85  3.000
 DL6  H62  C6  O6   111.67  3.000
 DL6  H61  C6  O6   111.87  3.000
 DL6  C5   C6  O6   108.80  3.000
 DL6  H5   C5  O5   110.02  3.000
 DL6  H5   C5  C4   108.44  3.000
 DL6  O5   C5  C4   109.77  3.000
 DL6  H5   C5  C6   108.96  3.000
 DL6  O5   C5  C6   107.75  3.000
 DL6  C4   C5  C6   111.88  3.000
 DL6  H4   C4  C3   108.44  3.000
 DL6  H4   C4  O4   111.08  3.000
 DL6  C3   C4  O4   111.20  3.000
 DL6  H4   C4  C5   108.28  3.000
 DL6  C3   C4  C5   109.68  3.000
 DL6  O4   C4  C5   108.11  3.000
 DL6  HO4  O4  C4   108.17  3.000
 DL6  H3   C3  C2   107.89  3.000
 DL6  H3   C3  O3   110.85  3.000
 DL6  C2   C3  O3   111.96  3.000
 DL6  H3   C3  C4   107.75  3.000
 DL6  C2   C3  C4   110.83  3.000
 DL6  O3   C3  C4   107.49  3.000
 DL6  HO3  O3  C3   108.59  3.000
 DL6  H2   C2  C1   108.53  3.000
 DL6  H2   C2  O2   111.45  3.000
 DL6  C1   C2  O2   111.34  3.000
 DL6  H2   C2  C3   108.77  3.000
 DL6  C1   C2  C3   108.98  3.000
 DL6  O2   C2  C3   107.72  3.000
 DL6  HO2  O2  C2   108.96  3.000
 DL6  H1   C1  O5   110.57  3.000
 DL6  H1   C1  N1   108.19  3.000
 DL6  O5   C1  N1   108.30  3.000
 DL6  H1   C1  C2   109.01  3.000
 DL6  O5   C1  C2   110.17  3.000
 DL6  N1   C1  C2   110.58  3.000
 DL6  HN1  N1  C7   118.17  3.000
 DL6  HN1  N1  C1   117.36  3.000
 DL6  C7   N1  C1   123.77  3.000
 DL6  O7   C7  C8   121.56  3.000
 DL6  O7   C7  N1   124.57  3.000
 DL6  C8   C7  N1   113.86  3.000
 DL6  H82  C8  H81  106.98  3.000
 DL6  H82  C8  N2   106.65  3.000
 DL6  H81  C8  N2   111.98  3.000
 DL6  H82  C8  C7   110.99  3.000
 DL6  H81  C8  C7   107.98  3.000
 DL6  N2   C8  C7   112.17  3.000
 DL6  N3   N2  C8   116.67  3.000
 DL6  N4   N3  N2   173.15  3.000
 DL6  C1   O5  C5   113.57  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
 DL6  CONST_01  C8   C7  N1  C1  180.00   0.0  0
 DL6  CONST_02  O7   C7  N1  C1    0.00   0.0  0
 DL6  CONST_03  HN1  N1  C7  C8    0.00   0.0  0
 DL6  Var_01    N2   C8  C7  N1  159.10  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
 DL6  chir_01  C5  C6  C4  O5  positiv
 DL6  chir_02  C4  O4  C5  C3  positiv
 DL6  chir_03  C3  O3  C4  C2  negativ
 DL6  chir_04  C2  O2  C3  C1  positiv
 DL6  chir_05  C1  O5  N1  C2  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
 DL6  plan-1  C1   0.020
 DL6  plan-1  N1   0.020
 DL6  plan-1  C7   0.020
 DL6  plan-1  C8   0.020
 DL6  plan-1  O7   0.020
 DL6  plan-1  HN1  0.020
 DL6  plan-2  C8   0.020
 DL6  plan-2  N2   0.020
 DL6  plan-2  N3   0.020
 DL6  plan-2  N4   0.020

