# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 02:03:18 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[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
 NDG  NDG  2-(acetylamino)-2-deoxy-alpha-D-glucopyranose  D-saccharide  30  15  .  2012-04-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NDG
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
 NDG  C1   C  CH1   0   0.264  72.5196  19.2559  10.6351
 NDG  C2   C  CH1   0  -0.172  72.8988  20.0425  11.8863
 NDG  C3   C  CH1   0   0.031  72.7982  19.1885  13.1602
 NDG  C4   C  CH1   0  -0.055  71.8814  17.9589  12.9676
 NDG  C5   C  CH1   0  -0.040  70.7582  18.2388  11.9693
 NDG  C6   C  CH2   0  -0.166  69.6932  19.1725  12.5383
 NDG  C7   C  C     0   0.519  74.4265  21.9627  11.6218
 NDG  C8   C  CH3   0  -0.777  75.8762  22.3516  11.4693
 NDG  O5   O  O2    0  -0.501  71.2304  18.7364  10.7152
 NDG  O3   O  OH1   0  -0.661  72.3417  20.0530  14.1741
 NDG  O4   O  OH1   0  -0.680  72.6142  16.8053  12.6304
 NDG  O6   O  OH1   0  -0.658  68.5979  19.3391  11.6708
 NDG  O7   O  O     0  -0.492  73.5352  22.7987  11.6270
 NDG  N2   N  NH1   0  -0.633  74.2024  20.6390  11.7490
 NDG  O1   O  OH1   0  -0.674  73.4922  18.2567  10.4492
 NDG  H1   H  HCH1  0   0.251  72.5131  19.9291   9.7721
 NDG  H2   H  HCH1  0   0.286  72.1788  20.8592  11.9642
 NDG  H3   H  HCH1  0   0.236  73.7939  18.7959  13.4074
 NDG  H4   H  HCH1  0   0.257  71.4147  17.7346  13.9324
 NDG  H5   H  HCH1  0   0.244  70.2718  17.2797  11.7510
 NDG  H61  H  HCH2  0   0.202  69.3795  18.7754  13.5125
 NDG  H62  H  HCH2  0   0.228  70.0979  20.1691  12.7197
 NDG  H81  H  HCH3  0   0.265  76.0128  22.8640  10.5170
 NDG  H82  H  HCH3  0   0.265  76.1457  23.0551  12.2568
 NDG  H83  H  HCH3  0   0.249  76.5639  21.5091  11.5081
 NDG  HO3  H  HOH1  0   0.454  72.3944  19.5915  15.0179
 NDG  HO4  H  HOH1  0   0.443  73.0811  16.9872  11.8011
 NDG  HO6  H  HOH1  0   0.445  68.1450  18.4937  11.5890
 NDG  HN2  H  HNH1  0   0.400  74.9925  20.0147  11.7091
 NDG  HO1  H  HOH1  0   0.473  73.4234  17.9019   9.5550

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
 NDG  C1  C2   single  1.526  0.020  1.526
 NDG  C1  O5   single  1.392  0.020  1.392
 NDG  C1  O1   single  1.407  0.020  1.407
 NDG  C1  H1   single  0.970  0.020  1.090
 NDG  C2  C3   single  1.537  0.020  1.537
 NDG  C2  N2   single  1.440  0.020  1.440
 NDG  C2  H2   single  0.970  0.020  1.090
 NDG  C3  C4   single  1.546  0.020  1.546
 NDG  C3  O3   single  1.408  0.020  1.408
 NDG  C3  H3   single  0.970  0.020  1.090
 NDG  C4  C5   single  1.529  0.020  1.529
 NDG  C4  O4   single  1.408  0.020  1.408
 NDG  C4  H4   single  0.970  0.020  1.090
 NDG  C5  C6   single  1.526  0.020  1.526
 NDG  C5  O5   single  1.429  0.020  1.429
 NDG  C5  H5   single  0.970  0.020  1.090
 NDG  C6  O6   single  1.407  0.020  1.407
 NDG  C6  H61  single  0.970  0.020  1.090
 NDG  C6  H62  single  0.970  0.020  1.090
 NDG  C7  C8   single  1.509  0.020  1.509
 NDG  C7  O7   double  1.222  0.020  1.222
 NDG  C7  N2   single  1.349  0.020  1.349
 NDG  C8  H81  single  0.970  0.020  1.090
 NDG  C8  H82  single  0.970  0.020  1.090
 NDG  C8  H83  single  0.970  0.020  1.090
 NDG  O3  HO3  single  0.850  0.020  0.980
 NDG  O4  HO4  single  0.850  0.020  0.980
 NDG  O6  HO6  single  0.850  0.020  0.980
 NDG  N2  HN2  single  0.860  0.020  1.020
 NDG  O1  HO1  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
 NDG  H1   C1  O1   109.68  3.000
 NDG  H1   C1  O5   105.63  3.000
 NDG  O1   C1  O5   112.50  3.000
 NDG  H1   C1  C2   109.33  3.000
 NDG  O1   C1  C2   107.62  3.000
 NDG  O5   C1  C2   112.04  3.000
 NDG  H2   C2  N2   107.09  3.000
 NDG  H2   C2  C3   108.26  3.000
 NDG  N2   C2  C3   111.62  3.000
 NDG  H2   C2  C1   106.28  3.000
 NDG  N2   C2  C1   111.12  3.000
 NDG  C3   C2  C1   112.15  3.000
 NDG  H3   C3  O3   110.56  3.000
 NDG  H3   C3  C4   106.34  3.000
 NDG  O3   C3  C4   112.69  3.000
 NDG  H3   C3  C2   109.01  3.000
 NDG  O3   C3  C2   106.07  3.000
 NDG  C4   C3  C2   112.17  3.000
 NDG  H4   C4  O4   105.37  3.000
 NDG  H4   C4  C5   107.44  3.000
 NDG  O4   C4  C5   112.10  3.000
 NDG  H4   C4  C3   107.81  3.000
 NDG  O4   C4  C3   111.90  3.000
 NDG  C5   C4  C3   111.81  3.000
 NDG  H5   C5  O5   106.03  3.000
 NDG  H5   C5  C6   107.43  3.000
 NDG  O5   C5  C6   110.16  3.000
 NDG  H5   C5  C4   107.19  3.000
 NDG  O5   C5  C4   113.20  3.000
 NDG  C6   C5  C4   112.41  3.000
 NDG  H62  C6  H61  106.79  3.000
 NDG  H62  C6  O6   106.45  3.000
 NDG  H61  C6  O6   111.56  3.000
 NDG  H62  C6  C5   111.22  3.000
 NDG  H61  C6  C5   108.00  3.000
 NDG  O6   C6  C5   112.69  3.000
 NDG  N2   C7  O7   123.36  3.000
 NDG  N2   C7  C8   114.97  3.000
 NDG  O7   C7  C8   121.67  3.000
 NDG  H83  C8  H82  108.53  3.000
 NDG  H83  C8  H81  108.42  3.000
 NDG  H82  C8  H81  107.27  3.000
 NDG  H83  C8  C7   113.83  3.000
 NDG  H82  C8  C7   109.33  3.000
 NDG  H81  C8  C7   109.26  3.000
 NDG  C5   O5  C1   119.10  3.000
 NDG  HO3  O3  C3   108.59  3.000
 NDG  HO4  O4  C4   107.58  3.000
 NDG  HO6  O6  C6   108.34  3.000
 NDG  HN2  N2  C7   118.30  3.000
 NDG  HN2  N2  C2   117.19  3.000
 NDG  C7   N2  C2   124.47  3.000
 NDG  HO1  O1  C1   109.54  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
 NDG  CONST_01  C8   C7  N2  C2  180.00   0.0  0
 NDG  CONST_02  O7   C7  N2  C2    0.00   0.0  0
 NDG  CONST_03  HN2  N2  C7  C8    0.00   0.0  0
 NDG  Var_01    H81  C8  C7  O7  -60.17  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
 NDG  chir_01  C1  C2  O5  O1  positiv
 NDG  chir_02  C2  N2  C3  C1  positiv
 NDG  chir_03  C3  O3  C2  C4  positiv
 NDG  chir_04  C4  O4  C5  C3  positiv
 NDG  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
 NDG  plan-1  C2   0.020
 NDG  plan-1  C7   0.020
 NDG  plan-1  C8   0.020
 NDG  plan-1  O7   0.020
 NDG  plan-1  N2   0.020
 NDG  plan-1  HN2  0.020

