# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:08:14 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-beta-D-allopyranose
#   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
 NAA  NAA  2-(acetylamino)-2-deoxy-beta-D-allopyranose  D-saccharide  30  15  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NAA
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
 NAA  C1   C  CH1   0   0.314  12.0336  47.2307  19.6443
 NAA  C2   C  CH1   0  -0.150  10.7214  47.6834  20.2956
 NAA  C3   C  CH1   0  -0.014   9.5524  47.4848  19.3320
 NAA  C4   C  CH1   0   0.027   9.8671  48.1407  17.9884
 NAA  C5   C  CH1   0  -0.002  11.2179  47.6363  17.4671
 NAA  C6   C  CH2   0  -0.197  11.6359  48.2469  16.1471
 NAA  C7   C  C     0   0.493  10.6825  47.4567  22.7914
 NAA  C8   C  CH3   0  -0.811  11.1253  48.8907  22.9437
 NAA  N2   N  NH1   0  -0.615  10.4718  46.9996  21.5371
 NAA  O1   O  OH1   0  -0.650  13.0737  47.5526  20.4888
 NAA  O3   O  OH1   0  -0.668   9.3428  46.0975  19.2007
 NAA  O4   O  OH1   0  -0.674   8.8094  47.8226  17.1164
 NAA  O5   O  O2    0  -0.501  12.2126  47.9229  18.4321
 NAA  O6   O  OH1   0  -0.667  11.6360  49.6508  16.2476
 NAA  O7   O  O     0  -0.490  10.4958  46.7379  23.7627
 NAA  H1   H  HCH1  0   0.190  11.9980  46.1468  19.4459
 NAA  H2   H  HCH1  0   0.284  10.8027  48.7563  20.4829
 NAA  H3   H  HCH1  0   0.242   8.6662  47.9722  19.7617
 NAA  H4   H  HCH1  0   0.226   9.9357  49.2227  18.1592
 NAA  H5   H  HCH1  0   0.223  11.1482  46.5505  17.3010
 NAA  H61  H  HCH2  0   0.219  12.6263  47.8541  15.8829
 NAA  H62  H  HCH2  0   0.206  10.9440  47.8891  15.3743
 NAA  H81  H  HCH3  0   0.265  11.2298  49.1219  24.0004
 NAA  H82  H  HCH3  0   0.266  12.0793  49.0724  22.4502
 NAA  H83  H  HCH3  0   0.263  10.3979  49.5789  22.5105
 NAA  HN2  H  HNH1  0   0.386  10.1761  46.0355  21.4684
 NAA  HO1  H  HOH1  0   0.463  13.8500  47.0313  20.2585
 NAA  HO3  H  HOH1  0   0.457   8.5781  45.9552  18.6335
 NAA  HO4  H  HOH1  0   0.460   8.8093  48.4367  16.3764
 NAA  HO6  H  HOH1  0   0.457  11.8578  50.0149  15.3861

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
 NAA  C1  C2   single  1.533  0.020  1.533
 NAA  C1  O1   single  1.378  0.020  1.378
 NAA  C1  O5   single  1.407  0.020  1.407
 NAA  C1  H1   single  0.970  0.020  1.090
 NAA  C2  C3   single  1.528  0.020  1.528
 NAA  C2  N2   single  1.439  0.020  1.439
 NAA  C2  H2   single  0.970  0.020  1.090
 NAA  C3  C4   single  1.528  0.020  1.528
 NAA  C3  O3   single  1.409  0.020  1.409
 NAA  C3  H3   single  0.970  0.020  1.090
 NAA  C4  C5   single  1.533  0.020  1.533
 NAA  C4  O4   single  1.407  0.020  1.407
 NAA  C4  H4   single  0.970  0.020  1.090
 NAA  C5  C6   single  1.513  0.020  1.513
 NAA  C5  O5   single  1.415  0.020  1.415
 NAA  C5  H5   single  0.970  0.020  1.090
 NAA  C6  O6   single  1.408  0.020  1.408
 NAA  C6  H61  single  0.970  0.020  1.090
 NAA  C6  H62  single  0.970  0.020  1.090
 NAA  C7  C8   single  1.508  0.020  1.508
 NAA  C7  N2   single  1.352  0.020  1.352
 NAA  C7  O7   double  1.223  0.020  1.223
 NAA  C8  H81  single  0.970  0.020  1.090
 NAA  C8  H82  single  0.970  0.020  1.090
 NAA  C8  H83  single  0.970  0.020  1.090
 NAA  N2  HN2  single  0.860  0.020  1.020
 NAA  O1  HO1  single  0.850  0.020  0.980
 NAA  O3  HO3  single  0.850  0.020  0.980
 NAA  O4  HO4  single  0.850  0.020  0.980
 NAA  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
 NAA  H1   C1  O5   109.43  3.000
 NAA  H1   C1  O1   111.37  3.000
 NAA  O5   C1  O1   108.48  3.000
 NAA  H1   C1  C2   109.82  3.000
 NAA  O5   C1  C2   109.24  3.000
 NAA  O1   C1  C2   108.46  3.000
 NAA  H2   C2  N2   109.37  3.000
 NAA  H2   C2  C3   107.03  3.000
 NAA  N2   C2  C3   110.46  3.000
 NAA  H2   C2  C1   107.40  3.000
 NAA  N2   C2  C1   112.00  3.000
 NAA  C3   C2  C1   110.40  3.000
 NAA  H3   C3  O3   110.68  3.000
 NAA  H3   C3  C4   108.64  3.000
 NAA  O3   C3  C4   111.80  3.000
 NAA  H3   C3  C2   108.22  3.000
 NAA  O3   C3  C2   107.49  3.000
 NAA  C4   C3  C2   109.95  3.000
 NAA  H4   C4  O4   111.48  3.000
 NAA  H4   C4  C5   108.79  3.000
 NAA  O4   C4  C5   112.15  3.000
 NAA  H4   C4  C3   107.42  3.000
 NAA  O4   C4  C3   107.04  3.000
 NAA  C5   C4  C3   109.83  3.000
 NAA  H5   C5  O5   110.32  3.000
 NAA  H5   C5  C6   106.49  3.000
 NAA  O5   C5  C6   108.60  3.000
 NAA  H5   C5  C4   108.67  3.000
 NAA  O5   C5  C4   108.71  3.000
 NAA  C6   C5  C4   114.03  3.000
 NAA  H62  C6  H61  106.42  3.000
 NAA  H62  C6  O6   112.06  3.000
 NAA  H61  C6  O6   111.97  3.000
 NAA  H62  C6  C5   107.97  3.000
 NAA  H61  C6  C5   108.35  3.000
 NAA  O6   C6  C5   109.89  3.000
 NAA  O7   C7  N2   120.97  3.000
 NAA  O7   C7  C8   121.57  3.000
 NAA  N2   C7  C8   117.45  3.000
 NAA  H83  C8  H82  107.39  3.000
 NAA  H83  C8  H81  108.42  3.000
 NAA  H82  C8  H81  108.71  3.000
 NAA  H83  C8  C7   111.34  3.000
 NAA  H82  C8  C7   111.71  3.000
 NAA  H81  C8  C7   109.19  3.000
 NAA  HN2  N2  C7   115.55  3.000
 NAA  HN2  N2  C2   116.45  3.000
 NAA  C7   N2  C2   127.79  3.000
 NAA  HO1  O1  C1   109.60  3.000
 NAA  HO3  O3  C3   108.58  3.000
 NAA  HO4  O4  C4   109.43  3.000
 NAA  C5   O5  C1   113.47  3.000
 NAA  HO6  O6  C6   108.29  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
 NAA  CONST_01  C8   C7  N2  C2    0.00   0.0  0
 NAA  CONST_02  O7   C7  N2  C2  180.00   0.0  0
 NAA  CONST_03  HN2  N2  C7  C8  180.00   0.0  0
 NAA  Var_01    H81  C8  C7  N2  178.59  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
 NAA  chir_01  C1  C2  O1  O5  positiv
 NAA  chir_02  C2  N2  C3  C1  positiv
 NAA  chir_03  C3  O3  C2  C4  negativ
 NAA  chir_04  C4  O4  C3  C5  negativ
 NAA  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
 NAA  plan-1  C2   0.020
 NAA  plan-1  C7   0.020
 NAA  plan-1  C8   0.020
 NAA  plan-1  N2   0.020
 NAA  plan-1  O7   0.020
 NAA  plan-1  HN2  0.020

