# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:36:14 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: N-acetyl-2-(acetylamino)-2-deoxy-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1NC(C)=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
 TVD  TVD  N-acetyl-2-(acetylamino)-2-deoxy-beta-D-glucopyranosylamine  D-saccharide  36  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 OK
;

data_comp_TVD
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
 TVD  O7   O  O     0  -0.492  26.9342   -9.6216   1.6307
 TVD  C7   C  C     0   0.513  26.2741  -10.5928   1.9669
 TVD  C8   C  CH3   0  -0.783  26.6443  -11.4702   3.1366
 TVD  N2   N  NH1   0  -0.633  25.1454  -10.9719   1.3267
 TVD  C2   C  CH1   0  -0.177  24.6278  -10.3352   0.1426
 TVD  C1   C  CH1   0   0.265  25.0058  -11.1111  -1.1245
 TVD  N1   N  NH1   0  -0.667  26.4187  -11.1429  -1.2819
 TVD  C9   C  C     0   0.518  27.0768  -12.1359  -1.9288
 TVD  C10  C  CH3   0  -0.787  28.5649  -11.9252  -2.0371
 TVD  O9   O  O     0  -0.484  26.5080  -13.1086  -2.3936
 TVD  C3   C  CH1   0   0.008  23.1067  -10.2080   0.2396
 TVD  O3   O  OH1   0  -0.665  22.7250   -9.3490   1.2850
 TVD  C4   C  CH1   0   0.046  22.5315   -9.6457  -1.0545
 TVD  C5   C  CH1   0  -0.009  23.0198  -10.4899  -2.2318
 TVD  C6   C  CH2   0  -0.180  22.5261  -10.0093  -3.5792
 TVD  O6   O  OH1   0  -0.672  22.9102   -8.6704  -3.7775
 TVD  O5   O  O2    0  -0.491  24.4330  -10.4920  -2.2528
 TVD  O4   O  OH1   0  -0.673  21.1269   -9.6812  -1.0502
 TVD  H81  H  HCH3  0   0.263  27.5266  -11.0818   3.6380
 TVD  H82  H  HCH3  0   0.266  25.8266  -11.5293   3.8555
 TVD  H83  H  HCH3  0   0.268  26.8538  -12.4861   2.7984
 TVD  HN2  H  HNH1  0   0.405  24.7108  -11.8376   1.6110
 TVD  H2   H  HCH1  0   0.277  25.0545   -9.3310   0.0751
 TVD  H1   H  HCH1  0   0.224  24.6404  -12.1436  -1.0403
 TVD  HN1  H  HNH1  0   0.402  26.9463  -10.3459  -0.9594
 TVD  H11  H  HCH3  0   0.265  29.0591  -12.8527  -2.3140
 TVD  H12  H  HCH3  0   0.275  28.7738  -11.1818  -2.8087
 TVD  H13  H  HCH3  0   0.259  28.9940  -11.5577  -1.1052
 TVD  H3   H  HCH1  0   0.217  22.6817  -11.2144   0.3886
 TVD  HO3  H  HOH1  0   0.456  22.9033   -9.7832   2.1253
 TVD  H4   H  HCH1  0   0.218  22.9035   -8.6184  -1.1800
 TVD  H5   H  HCH1  0   0.227  22.6446  -11.5186  -2.1027
 TVD  H61  H  HCH2  0   0.214  21.4387  -10.1353  -3.6086
 TVD  H62  H  HCH2  0   0.214  22.9417  -10.6704  -4.3516
 TVD  HO6  H  HOH1  0   0.459  22.4579   -8.3415  -4.5589
 TVD  HO4  H  HOH1  0   0.454  20.8147   -9.1574  -0.3052

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
 TVD  O6   C6   single  1.407  0.020  1.407
 TVD  C6   C5   single  1.513  0.020  1.513
 TVD  O9   C9   double  1.219  0.020  1.219
 TVD  C5   O5   single  1.413  0.020  1.413
 TVD  C5   C4   single  1.529  0.020  1.529
 TVD  O5   C1   single  1.409  0.020  1.409
 TVD  C9   C10  single  1.507  0.020  1.507
 TVD  C9   N1   single  1.356  0.020  1.356
 TVD  N1   C1   single  1.422  0.020  1.422
 TVD  C1   C2   single  1.533  0.020  1.533
 TVD  C4   O4   single  1.405  0.020  1.405
 TVD  C4   C3   single  1.524  0.020  1.524
 TVD  C2   C3   single  1.530  0.020  1.530
 TVD  C2   N2   single  1.441  0.020  1.441
 TVD  C3   O3   single  1.406  0.020  1.406
 TVD  N2   C7   single  1.352  0.020  1.352
 TVD  O7   C7   double  1.221  0.020  1.221
 TVD  C7   C8   single  1.508  0.020  1.508
 TVD  C8   H81  single  0.970  0.020  1.090
 TVD  C8   H82  single  0.970  0.020  1.090
 TVD  C8   H83  single  0.970  0.020  1.090
 TVD  N2   HN2  single  0.860  0.020  1.020
 TVD  C2   H2   single  0.970  0.020  1.090
 TVD  C1   H1   single  0.970  0.020  1.090
 TVD  N1   HN1  single  0.860  0.020  1.020
 TVD  C10  H11  single  0.970  0.020  1.090
 TVD  C10  H12  single  0.970  0.020  1.090
 TVD  C10  H13  single  0.970  0.020  1.090
 TVD  C3   H3   single  0.970  0.020  1.090
 TVD  O3   HO3  single  0.850  0.020  0.980
 TVD  C4   H4   single  0.970  0.020  1.090
 TVD  C5   H5   single  0.970  0.020  1.090
 TVD  C6   H61  single  0.970  0.020  1.090
 TVD  C6   H62  single  0.970  0.020  1.090
 TVD  O6   HO6  single  0.850  0.020  0.980
 TVD  O4   HO4  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
 TVD  N2   C7   C8   114.15  3.000
 TVD  C8   C7   O7   122.91  3.000
 TVD  N2   C7   O7   122.94  3.000
 TVD  H83  C8   H82  107.33  3.000
 TVD  H83  C8   H81  108.66  3.000
 TVD  H82  C8   H81  108.91  3.000
 TVD  H83  C8   C7   110.39  3.000
 TVD  H82  C8   C7   111.02  3.000
 TVD  H81  C8   C7   110.44  3.000
 TVD  HN2  N2   C2   117.12  3.000
 TVD  HN2  N2   C7   117.81  3.000
 TVD  C2   N2   C7   124.42  3.000
 TVD  H2   C2   C3   108.40  3.000
 TVD  H2   C2   C1   108.52  3.000
 TVD  C3   C2   C1   109.86  3.000
 TVD  H2   C2   N2   108.45  3.000
 TVD  C3   C2   N2   109.99  3.000
 TVD  C1   C2   N2   111.53  3.000
 TVD  H1   C1   O5   109.83  3.000
 TVD  H1   C1   N1   108.54  3.000
 TVD  O5   C1   N1   108.98  3.000
 TVD  H1   C1   C2   109.29  3.000
 TVD  N1   C1   C2   110.35  3.000
 TVD  O5   C1   C2   109.83  3.000
 TVD  HN1  N1   C9   118.52  3.000
 TVD  HN1  N1   C1   117.81  3.000
 TVD  C9   N1   C1   123.48  3.000
 TVD  O9   C9   C10  123.03  3.000
 TVD  C10  C9   N1   114.29  3.000
 TVD  O9   C9   N1   122.68  3.000
 TVD  H13  C10  H12  107.43  3.000
 TVD  H13  C10  H11  109.06  3.000
 TVD  H12  C10  H11  108.31  3.000
 TVD  H13  C10  C9   111.99  3.000
 TVD  H12  C10  C9   109.57  3.000
 TVD  H11  C10  C9   110.37  3.000
 TVD  H3   C3   C4   107.83  3.000
 TVD  H3   C3   O3   110.65  3.000
 TVD  C4   C3   O3   107.67  3.000
 TVD  H3   C3   C2   108.42  3.000
 TVD  O3   C3   C2   111.59  3.000
 TVD  C4   C3   C2   110.62  3.000
 TVD  HO3  O3   C3   108.86  3.000
 TVD  H4   C4   O4   111.22  3.000
 TVD  H4   C4   C5   108.66  3.000
 TVD  O4   C4   C5   107.92  3.000
 TVD  H4   C4   C3   108.30  3.000
 TVD  O4   C4   C3   111.44  3.000
 TVD  C5   C4   C3   109.25  3.000
 TVD  H5   C5   O5   109.91  3.000
 TVD  H5   C5   C6   106.83  3.000
 TVD  O5   C5   C6   108.27  3.000
 TVD  H5   C5   C4   108.44  3.000
 TVD  O5   C5   C4   109.37  3.000
 TVD  C6   C5   C4   113.96  3.000
 TVD  H62  C6   H61  106.71  3.000
 TVD  H62  C6   O6   111.73  3.000
 TVD  H61  C6   O6   112.14  3.000
 TVD  H62  C6   C5   108.15  3.000
 TVD  H61  C6   C5   108.14  3.000
 TVD  O6   C6   C5   109.79  3.000
 TVD  HO6  O6   C6   108.17  3.000
 TVD  C5   O5   C1   113.29  3.000
 TVD  HO4  O4   C4   108.23  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
 TVD  CONST_01  C2   N2   C7  O7     0.00   0.0  0
 TVD  CONST_02  C2   N2   C7  C8   180.00   0.0  0
 TVD  CONST_03  O9   C9   N1  C1     0.00   0.0  0
 TVD  CONST_04  C10  C9   N1  C1   180.00   0.0  0
 TVD  CONST_05  HN2  N2   C7  O7   180.00   0.0  0
 TVD  CONST_06  HN1  N1   C9  C10    0.00   0.0  0
 TVD  Var_01    H81  C8   C7  O7     2.80  30.0  3
 TVD  Var_02    H11  C10  C9  N1   164.73  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
 TVD  chir_01  C2  C1  C3  N2  negativ
 TVD  chir_02  C1  O5  N1  C2  negativ
 TVD  chir_03  C3  O3  C2  C4  positiv
 TVD  chir_04  C4  O4  C5  C3  positiv
 TVD  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
 TVD  plan-1  O7   0.020
 TVD  plan-1  C7   0.020
 TVD  plan-1  C8   0.020
 TVD  plan-1  N2   0.020
 TVD  plan-1  C2   0.020
 TVD  plan-1  HN2  0.020
 TVD  plan-2  C1   0.020
 TVD  plan-2  N1   0.020
 TVD  plan-2  C9   0.020
 TVD  plan-2  C10  0.020
 TVD  plan-2  O9   0.020
 TVD  plan-2  HN1  0.020

