# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 22:38:11 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-alpha-D-idopyranose
#   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
 LXZ  LXZ  2-(acetylamino)-2-deoxy-alpha-D-idopyranose  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_LXZ
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
 LXZ  O1   O  OH1   0  -0.680  32.7707  -97.2814  -84.9907
 LXZ  C1   C  CH1   0   0.254  31.4858  -96.8181  -84.7936
 LXZ  C2   C  CH1   0  -0.181  31.2038  -95.7281  -85.8280
 LXZ  C3   C  CH1   0   0.045  29.8254  -95.1090  -85.5705
 LXZ  C4   C  CH1   0   0.011  29.7395  -94.6088  -84.1277
 LXZ  C5   C  CH1   0  -0.070  30.1704  -95.6974  -83.1325
 LXZ  C6   C  CH2   0  -0.224  29.1115  -96.7845  -82.8780
 LXZ  C8   C  CH3   0  -0.724  30.9926  -97.3510  -89.2601
 LXZ  N2   N  NH1   0  -0.729  31.3825  -96.1678  -87.1950
 LXZ  O3   O  OH1   0  -0.687  29.5263  -94.0988  -86.4974
 LXZ  O4   O  OH1   0  -0.626  28.4364  -94.1296  -83.8883
 LXZ  O5   O  O2    0  -0.497  31.4174  -96.2443  -83.5032
 LXZ  O6   O  OH1   0  -0.681  28.0318  -96.2673  -82.1205
 LXZ  O7   O  O     0  -0.286  29.6884  -97.6607  -87.2765
 LXZ  HO1  H  HOH1  0   0.399  32.9069  -98.0757  -84.4610
 LXZ  H1   H  HCH1  0   0.239  30.7583  -97.6350  -84.8830
 LXZ  H2   H  HCH1  0   0.255  31.9567  -94.9468  -85.6691
 LXZ  H3   H  HCH1  0   0.267  29.0520  -95.8679  -85.7124
 LXZ  H4   H  HCH1  0   0.177  30.4586  -93.7795  -84.0184
 LXZ  H5   H  HCH1  0   0.265  30.3585  -95.2205  -82.1640
 LXZ  H61  H  HCH2  0   0.250  28.6855  -97.1757  -83.8043
 LXZ  H62  H  HCH2  0   0.270  29.5972  -97.6223  -82.3671
 LXZ  H81  H  HCH3  0   0.267  30.2165  -96.9550  -89.9157
 LXZ  H82  H  HCH3  0   0.277  31.9409  -96.8997  -89.5446
 LXZ  H83  H  HCH3  0   0.261  31.0523  -98.4257  -89.4229
 LXZ  HN2  H  HNH1  0   0.368  32.1106  -95.7149  -87.7191
 LXZ  HO3  H  HOH1  0   0.442  30.1584  -93.3787  -86.3905
 LXZ  HO4  H  HOH1  0   0.469  28.0887  -94.5396  -83.0861
 LXZ  HO6  H  HOH1  0   0.466  28.3087  -96.2028  -81.2003
 LXZ  C7   C  C     0   0.405  30.6206  -97.0829  -87.8202

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
 LXZ  O1  C1   single  1.380  0.020  1.380
 LXZ  O1  HO1  single  0.850  0.020  0.980
 LXZ  C2  C1   single  1.529  0.020  1.529
 LXZ  C1  O5   single  1.414  0.020  1.414
 LXZ  C1  H1   single  0.970  0.020  1.090
 LXZ  N2  C2   single  1.447  0.020  1.447
 LXZ  C2  C3   single  1.533  0.020  1.533
 LXZ  C2  H2   single  0.970  0.020  1.090
 LXZ  O3  C3   single  1.403  0.020  1.403
 LXZ  C3  C4   single  1.529  0.020  1.529
 LXZ  C3  H3   single  0.970  0.020  1.090
 LXZ  C4  O4   single  1.409  0.020  1.409
 LXZ  C4  C5   single  1.537  0.020  1.537
 LXZ  C4  H4   single  0.970  0.020  1.090
 LXZ  O5  C5   single  1.411  0.020  1.411
 LXZ  C5  C6   single  1.539  0.020  1.539
 LXZ  C5  H5   single  0.970  0.020  1.090
 LXZ  C6  O6   single  1.417  0.020  1.417
 LXZ  C6  H61  single  0.970  0.020  1.090
 LXZ  C6  H62  single  0.970  0.020  1.090
 LXZ  C8  C7   single  1.511  0.020  1.511
 LXZ  C7  O7   double  1.224  0.020  1.224
 LXZ  C7  N2   single  1.345  0.020  1.345
 LXZ  C8  H81  single  0.970  0.020  1.090
 LXZ  C8  H82  single  0.970  0.020  1.090
 LXZ  C8  H83  single  0.970  0.020  1.090
 LXZ  N2  HN2  single  0.860  0.020  1.020
 LXZ  O3  HO3  single  0.850  0.020  0.980
 LXZ  O4  HO4  single  0.850  0.020  0.980
 LXZ  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
 LXZ  HO1  O1  C1   109.24  3.000
 LXZ  H1   C1  O5   110.15  3.000
 LXZ  H1   C1  C2   110.68  3.000
 LXZ  O5   C1  C2   108.61  3.000
 LXZ  H1   C1  O1   110.83  3.000
 LXZ  O5   C1  O1   108.16  3.000
 LXZ  C2   C1  O1   108.32  3.000
 LXZ  H2   C2  N2   105.58  3.000
 LXZ  H2   C2  C3   107.78  3.000
 LXZ  N2   C2  C3   113.10  3.000
 LXZ  H2   C2  C1   106.45  3.000
 LXZ  C3   C2  C1   109.89  3.000
 LXZ  N2   C2  C1   113.56  3.000
 LXZ  H3   C3  O3   105.27  3.000
 LXZ  H3   C3  C4   108.05  3.000
 LXZ  O3   C3  C4   112.07  3.000
 LXZ  H3   C3  C2   109.52  3.000
 LXZ  C4   C3  C2   109.94  3.000
 LXZ  O3   C3  C2   111.81  3.000
 LXZ  H4   C4  O4   109.29  3.000
 LXZ  H4   C4  C5   106.60  3.000
 LXZ  O4   C4  C5   112.97  3.000
 LXZ  H4   C4  C3   107.62  3.000
 LXZ  C5   C4  C3   111.32  3.000
 LXZ  O4   C4  C3   108.87  3.000
 LXZ  H5   C5  O5   104.43  3.000
 LXZ  H5   C5  C6   106.23  3.000
 LXZ  O5   C5  C6   112.19  3.000
 LXZ  H5   C5  C4   108.19  3.000
 LXZ  C6   C5  C4   114.50  3.000
 LXZ  O5   C5  C4   110.62  3.000
 LXZ  H62  C6  H61  107.14  3.000
 LXZ  H62  C6  O6   111.59  3.000
 LXZ  H61  C6  O6   106.68  3.000
 LXZ  H62  C6  C5   108.21  3.000
 LXZ  H61  C6  C5   112.41  3.000
 LXZ  O6   C6  C5   110.79  3.000
 LXZ  H83  C8  H82  108.82  3.000
 LXZ  H83  C8  H81  107.92  3.000
 LXZ  H82  C8  H81  108.21  3.000
 LXZ  H83  C8  C7   109.33  3.000
 LXZ  H82  C8  C7   112.96  3.000
 LXZ  H81  C8  C7   109.47  3.000
 LXZ  HN2  N2  C7   118.34  3.000
 LXZ  HN2  N2  C2   116.43  3.000
 LXZ  C7   N2  C2   125.17  3.000
 LXZ  HO3  O3  C3   108.95  3.000
 LXZ  HO4  O4  C4   109.26  3.000
 LXZ  C5   O5  C1   116.09  3.000
 LXZ  HO6  O6  C6   108.43  3.000
 LXZ  O7   C7  N2   123.11  3.000
 LXZ  N2   C7  C8   115.10  3.000
 LXZ  O7   C7  C8   121.80  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
 LXZ  CONST_01  C8   C7  N2  C2   180.00   0.0  0
 LXZ  CONST_02  O7   C7  N2  C2     0.00   0.0  0
 LXZ  CONST_03  HN2  N2  C7  C8     0.00   0.0  0
 LXZ  Var_01    H81  C8  C7  N2  -110.16  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
 LXZ  chir_01  C1  O1  C2  O5  positiv
 LXZ  chir_02  C2  N2  C3  C1  negativ
 LXZ  chir_03  C3  O3  C2  C4  negativ
 LXZ  chir_04  C4  O4  C5  C3  negativ
 LXZ  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
 LXZ  plan-1  C2   0.020
 LXZ  plan-1  C8   0.020
 LXZ  plan-1  N2   0.020
 LXZ  plan-1  O7   0.020
 LXZ  plan-1  HN2  0.020
 LXZ  plan-1  C7   0.020

