# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:33:47 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: 2-(acetylamino)-2,6-dideoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](O)[C@H](NC(C)=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
 Z9W  Z9W  2-(acetylamino)-2,6-dideoxy-beta-D-glucopyranose  D-saccharide  29  14  .  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_Z9W
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
 Z9W  C1   C  CH1   0   0.316  -18.6098  84.0873  -20.6302
 Z9W  C2   C  CH1   0  -0.187  -17.2531  83.4000  -20.4255
 Z9W  C7   C  C     0   0.530  -15.5233  85.1080  -20.0835
 Z9W  C8   C  CH3   0  -0.775  -14.3592  85.8225  -20.7182
 Z9W  C3   C  CH1   0   0.015  -17.2423  82.0631  -21.1574
 Z9W  C4   C  CH1   0   0.018  -18.4486  81.2308  -20.7353
 Z9W  C5   C  CH1   0   0.010  -19.7377  82.0394  -20.9088
 Z9W  C6   C  CH3   0  -0.697  -20.9666  81.2978  -20.4275
 Z9W  O1   O  OH1   0  -0.652  -18.7087  85.2960  -19.9778
 Z9W  N2   N  NH1   0  -0.627  -16.1627  84.2298  -20.8757
 Z9W  O7   O  O     0  -0.511  -15.8418  85.3024  -18.9156
 Z9W  O3   O  OH1   0  -0.663  -16.0287  81.4176  -20.8737
 Z9W  O4   O  OH1   0  -0.674  -18.4451  80.0704  -21.5346
 Z9W  O5   O  O2    0  -0.496  -19.6330  83.2410  -20.1666
 Z9W  H1   H  HCH1  0   0.196  -18.7586  84.2859  -21.7036
 Z9W  HO1  H  HOH1  0   0.453  -18.1956  85.2742  -19.1601
 Z9W  H2   H  HCH1  0   0.273  -17.1257  83.2125  -19.3531
 Z9W  HN2  H  HNH1  0   0.404  -15.8652  84.1419  -21.8345
 Z9W  H81  H  HCH3  0   0.266  -14.4289  86.8902  -20.5158
 Z9W  H82  H  HCH3  0   0.271  -13.4329  85.4644  -20.2673
 Z9W  H83  H  HCH3  0   0.251  -14.2928  85.6735  -21.7941
 Z9W  H3   H  HCH1  0   0.215  -17.3356  82.2594  -22.2400
 Z9W  HO3  H  HOH1  0   0.453  -16.0174  80.5851  -21.3577
 Z9W  H4   H  HCH1  0   0.220  -18.3386  80.9802  -19.6695
 Z9W  HO4  H  HOH1  0   0.462  -18.9472  79.3813  -21.0902
 Z9W  H5   H  HCH1  0   0.215  -19.8572  82.2753  -21.9788
 Z9W  H61  H  HCH3  0   0.236  -21.1369  80.4026  -21.0243
 Z9W  H62  H  HCH3  0   0.231  -20.8669  80.9986  -19.3825
 Z9W  H63  H  HCH3  0   0.247  -21.8549  81.9225  -20.5230

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
 Z9W  C1  H1   single  0.970  0.020  1.090
 Z9W  C1  O1   single  1.377  0.020  1.377
 Z9W  O1  HO1  single  0.850  0.020  0.980
 Z9W  C1  O5   single  1.406  0.020  1.406
 Z9W  C1  C2   single  1.535  0.020  1.535
 Z9W  C2  H2   single  0.970  0.020  1.090
 Z9W  C2  N2   single  1.442  0.020  1.442
 Z9W  N2  HN2  single  0.860  0.020  1.020
 Z9W  N2  C7   single  1.344  0.020  1.344
 Z9W  C7  O7   double  1.226  0.020  1.226
 Z9W  C7  C8   single  1.506  0.020  1.506
 Z9W  C8  H81  single  0.970  0.020  1.090
 Z9W  C8  H82  single  0.970  0.020  1.090
 Z9W  C8  H83  single  0.970  0.020  1.090
 Z9W  C2  C3   single  1.524  0.020  1.524
 Z9W  C3  H3   single  0.970  0.020  1.090
 Z9W  C3  O3   single  1.403  0.020  1.403
 Z9W  O3  HO3  single  0.850  0.020  0.980
 Z9W  C3  C4   single  1.525  0.020  1.525
 Z9W  C4  H4   single  0.970  0.020  1.090
 Z9W  C4  O4   single  1.409  0.020  1.409
 Z9W  O4  HO4  single  0.850  0.020  0.980
 Z9W  C4  C5   single  1.532  0.020  1.532
 Z9W  C5  H5   single  0.970  0.020  1.090
 Z9W  C5  O5   single  1.416  0.020  1.416
 Z9W  C5  C6   single  1.514  0.020  1.514
 Z9W  C6  H61  single  0.970  0.020  1.090
 Z9W  C6  H62  single  0.970  0.020  1.090
 Z9W  C6  H63  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
 Z9W  H1   C1  O5   109.35  3.000
 Z9W  O5   C1  O1   108.65  3.000
 Z9W  H1   C1  O1   107.08  3.000
 Z9W  O5   C1  C2   109.25  3.000
 Z9W  O1   C1  C2   113.17  3.000
 Z9W  H1   C1  C2   109.28  3.000
 Z9W  H2   C2  N2   108.42  3.000
 Z9W  N2   C2  C3   110.45  3.000
 Z9W  H2   C2  C3   108.60  3.000
 Z9W  C3   C2  C1   109.58  3.000
 Z9W  N2   C2  C1   111.66  3.000
 Z9W  H2   C2  C1   108.05  3.000
 Z9W  O7   C7  N2   122.77  3.000
 Z9W  O7   C7  C8   121.80  3.000
 Z9W  N2   C7  C8   115.41  3.000
 Z9W  H83  C8  H82  108.17  3.000
 Z9W  H83  C8  H81  108.78  3.000
 Z9W  H82  C8  H81  107.43  3.000
 Z9W  H83  C8  C7   113.50  3.000
 Z9W  H82  C8  C7   109.05  3.000
 Z9W  H81  C8  C7   109.71  3.000
 Z9W  H3   C3  O3   110.67  3.000
 Z9W  O3   C3  C4   112.15  3.000
 Z9W  H3   C3  C4   107.55  3.000
 Z9W  C4   C3  C2   109.89  3.000
 Z9W  O3   C3  C2   108.21  3.000
 Z9W  H3   C3  C2   108.31  3.000
 Z9W  H4   C4  O4   111.20  3.000
 Z9W  O4   C4  C5   111.88  3.000
 Z9W  H4   C4  C5   108.31  3.000
 Z9W  C5   C4  C3   110.26  3.000
 Z9W  O4   C4  C3   106.89  3.000
 Z9W  H4   C4  C3   108.25  3.000
 Z9W  H5   C5  O5   109.58  3.000
 Z9W  O5   C5  C6   108.00  3.000
 Z9W  H5   C5  C6   108.99  3.000
 Z9W  C6   C5  C4   112.87  3.000
 Z9W  O5   C5  C4   109.05  3.000
 Z9W  H5   C5  C4   108.31  3.000
 Z9W  H63  C6  H62  108.38  3.000
 Z9W  H63  C6  H61  107.20  3.000
 Z9W  H62  C6  H61  108.27  3.000
 Z9W  H63  C6  C5   110.67  3.000
 Z9W  H62  C6  C5   111.38  3.000
 Z9W  H61  C6  C5   110.81  3.000
 Z9W  HO1  O1  C1   110.07  3.000
 Z9W  HN2  N2  C7   118.50  3.000
 Z9W  C7   N2  C2   123.46  3.000
 Z9W  HN2  N2  C2   118.03  3.000
 Z9W  HO3  O3  C3   107.83  3.000
 Z9W  HO4  O4  C4   109.07  3.000
 Z9W  C5   O5  C1   113.06  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
 Z9W  CONST_01  O7   C7  N2  C2    0.00   0.0  0
 Z9W  CONST_02  C8   C7  N2  C2  180.00   0.0  0
 Z9W  CONST_03  HN2  N2  C7  C8    0.00   0.0  0
 Z9W  Var_01    H81  C8  C7  N2  132.53  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
 Z9W  chir_01  C1  O1  O5  C2  positiv
 Z9W  chir_02  C2  N2  C3  C1  positiv
 Z9W  chir_03  C3  O3  C2  C4  positiv
 Z9W  chir_04  C4  O4  C5  C3  positiv
 Z9W  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
 Z9W  plan-1  C2   0.020
 Z9W  plan-1  C7   0.020
 Z9W  plan-1  C8   0.020
 Z9W  plan-1  N2   0.020
 Z9W  plan-1  O7   0.020
 Z9W  plan-1  HN2  0.020

