# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 22:30:49 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: N-acetyl-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]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
 NBG  NBG  N-acetyl-beta-D-glucopyranosylamine  D-saccharide  30  15  .  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_NBG
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
 NBG  C1   C  CH1   0   0.215   0.2709   0.1602   0.7222
 NBG  C2   C  CH1   0  -0.031   1.5366  -0.2250  -0.0480
 NBG  C3   C  CH1   0  -0.004   1.4242   0.2770  -1.4806
 NBG  C4   C  CH1   0   0.034   0.1234  -0.1949  -2.1207
 NBG  C5   C  CH1   0  -0.014  -1.0571   0.1862  -1.2264
 NBG  C6   C  CH2   0  -0.156  -2.3695  -0.3473  -1.7609
 NBG  C8   C  CH3   0  -0.781  -0.0333  -0.4890   4.4250
 NBG  N1   N  NH1   0  -0.676   0.3089  -0.3693   2.0434
 NBG  O3   O  OH1   0  -0.672   2.4827  -0.1838  -2.2858
 NBG  O2   O  OH1   0  -0.664   2.6800   0.3615   0.5200
 NBG  O4   O  OH1   0  -0.672  -0.0691   0.3998  -3.3800
 NBG  O5   O  O2    0  -0.489  -0.8661  -0.3514   0.0651
 NBG  O6   O  OH1   0  -0.670  -3.4135   0.1112  -0.9356
 NBG  O7   O  O     0  -0.483  -0.6417   1.4010   3.0857
 NBG  H1   H  HCH1  0   0.231   0.2120   1.2539   0.7900
 NBG  H2   H  HCH1  0   0.227   1.6143  -1.3233  -0.0643
 NBG  H3   H  HCH1  0   0.216   1.4054   1.3787  -1.4549
 NBG  H4   H  HCH1  0   0.213   0.1536  -1.2934  -2.2007
 NBG  H5   H  HCH1  0   0.221  -1.1153   1.2861  -1.1722
 NBG  H61  H  HCH2  0   0.213  -2.4881  -0.0035  -2.7934
 NBG  H62  H  HCH2  0   0.196  -2.3229  -1.4449  -1.7887
 NBG  H81  H  HCH3  0   0.265  -0.7969  -0.1750   5.1325
 NBG  H82  H  HCH3  0   0.255  -0.0984  -1.5670   4.2846
 NBG  H83  H  HCH3  0   0.275   0.9419  -0.2710   4.8645
 NBG  HN1  H  HNH1  0   0.404   0.5998  -1.3296   2.1526
 NBG  HO3  H  HOH1  0   0.457   3.2931   0.2542  -2.0079
 NBG  HO2  H  HOH1  0   0.457   2.9091  -0.1132   1.3251
 NBG  HO4  H  HOH1  0   0.455   0.6547   0.1285  -3.9540
 NBG  HO6  H  HOH1  0   0.457  -4.2443  -0.1871  -1.3159
 NBG  C7   C  C     0   0.521  -0.1747   0.2767   3.1349

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
 NBG  C1  C2   single  1.531  0.020  1.531
 NBG  C1  N1   single  1.424  0.020  1.424
 NBG  C1  O5   single  1.409  0.020  1.409
 NBG  C1  H1   single  0.970  0.020  1.090
 NBG  C2  C3   single  1.522  0.020  1.522
 NBG  C2  O2   single  1.405  0.020  1.405
 NBG  C2  H2   single  0.970  0.020  1.090
 NBG  C3  C4   single  1.525  0.020  1.525
 NBG  C3  O3   single  1.407  0.020  1.407
 NBG  C3  H3   single  0.970  0.020  1.090
 NBG  C4  C5   single  1.529  0.020  1.529
 NBG  C4  O4   single  1.406  0.020  1.406
 NBG  C4  H4   single  0.970  0.020  1.090
 NBG  C5  C6   single  1.514  0.020  1.514
 NBG  C5  O5   single  1.412  0.020  1.412
 NBG  C5  H5   single  0.970  0.020  1.090
 NBG  C6  O6   single  1.408  0.020  1.408
 NBG  C6  H61  single  0.970  0.020  1.090
 NBG  C6  H62  single  0.970  0.020  1.090
 NBG  C7  C8   single  1.507  0.020  1.507
 NBG  C7  N1   single  1.357  0.020  1.357
 NBG  C7  O7   double  1.218  0.020  1.218
 NBG  C8  H81  single  0.970  0.020  1.090
 NBG  C8  H82  single  0.970  0.020  1.090
 NBG  C8  H83  single  0.970  0.020  1.090
 NBG  N1  HN1  single  0.860  0.020  1.020
 NBG  O3  HO3  single  0.850  0.020  0.980
 NBG  O2  HO2  single  0.850  0.020  0.980
 NBG  O4  HO4  single  0.850  0.020  0.980
 NBG  O6  HO6  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
 NBG  H1   C1  O5   110.32  3.000
 NBG  H1   C1  N1   108.34  3.000
 NBG  O5   C1  N1   108.61  3.000
 NBG  H1   C1  C2   109.04  3.000
 NBG  O5   C1  C2   109.95  3.000
 NBG  N1   C1  C2   110.56  3.000
 NBG  H2   C2  O2   111.40  3.000
 NBG  H2   C2  C3   108.67  3.000
 NBG  O2   C2  C3   107.63  3.000
 NBG  H2   C2  C1   108.47  3.000
 NBG  O2   C2  C1   111.38  3.000
 NBG  C3   C2  C1   109.24  3.000
 NBG  H3   C3  O3   110.70  3.000
 NBG  H3   C3  C4   107.73  3.000
 NBG  O3   C3  C4   107.46  3.000
 NBG  H3   C3  C2   108.00  3.000
 NBG  O3   C3  C2   112.02  3.000
 NBG  C4   C3  C2   110.86  3.000
 NBG  H4   C4  O4   111.12  3.000
 NBG  H4   C4  C5   108.18  3.000
 NBG  O4   C4  C5   108.22  3.000
 NBG  H4   C4  C3   108.40  3.000
 NBG  O4   C4  C3   111.22  3.000
 NBG  C5   C4  C3   109.64  3.000
 NBG  H5   C5  O5   109.99  3.000
 NBG  H5   C5  C6   108.85  3.000
 NBG  O5   C5  C6   107.82  3.000
 NBG  H5   C5  C4   108.54  3.000
 NBG  O5   C5  C4   109.61  3.000
 NBG  C6   C5  C4   112.02  3.000
 NBG  H62  C6  H61  107.12  3.000
 NBG  H62  C6  O6   111.81  3.000
 NBG  H61  C6  O6   111.74  3.000
 NBG  H62  C6  C5   108.91  3.000
 NBG  H61  C6  C5   108.44  3.000
 NBG  O6   C6  C5   108.73  3.000
 NBG  H83  C8  H82  107.64  3.000
 NBG  H83  C8  H81  107.92  3.000
 NBG  H82  C8  H81  109.13  3.000
 NBG  H83  C8  C7   109.09  3.000
 NBG  H82  C8  C7   112.76  3.000
 NBG  H81  C8  C7   110.15  3.000
 NBG  HN1  N1  C7   117.93  3.000
 NBG  HN1  N1  C1   117.51  3.000
 NBG  C7   N1  C1   124.03  3.000
 NBG  HO3  O3  C3   108.61  3.000
 NBG  HO2  O2  C2   109.03  3.000
 NBG  HO4  O4  C4   108.18  3.000
 NBG  C5   O5  C1   113.42  3.000
 NBG  HO6  O6  C6   107.94  3.000
 NBG  O7   C7  N1   122.91  3.000
 NBG  O7   C7  C8   122.64  3.000
 NBG  N1   C7  C8   114.41  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
 NBG  CONST_01  C8   C7  N1  C1   180.00   0.0  0
 NBG  CONST_02  O7   C7  N1  C1     0.00   0.0  0
 NBG  CONST_03  HN1  N1  C7  C8     0.00   0.0  0
 NBG  Var_01    H81  C8  C7  N1  -154.01  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
 NBG  chir_01  C1  C2  N1  O5  positiv
 NBG  chir_02  C2  O2  C1  C3  negativ
 NBG  chir_03  C3  O3  C2  C4  positiv
 NBG  chir_04  C4  O4  C5  C3  positiv
 NBG  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
 NBG  plan-1  C1   0.020
 NBG  plan-1  C8   0.020
 NBG  plan-1  N1   0.020
 NBG  plan-1  O7   0.020
 NBG  plan-1  HN1  0.020
 NBG  plan-1  C7   0.020

