# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 17:21:25 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: N-[(1R,2S,3R,4R,5R)-2,3-dihydroxy-6,8-dioxabicyclo[3.2.1]oct-4-yl]acetamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@H]2CO[C@@H]1O2
#
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
 Z4S  Z4S  'N-[(1R,2S,3R,4R,5R)-2,3-dihydroxy-6,8-dioxabicyclo[3.2.1]oct-4-yl]acetamide (non-preferred name)'  D-saccharide  27  14  .  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_Z4S
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
 Z4S  O4   O  OH1   0  -0.668  31.2609  15.8903  12.2751
 Z4S  C4   C  CH1   0   0.043  30.8067  14.9913  13.2578
 Z4S  C5   C  CH1   0  -0.124  30.4585  13.6572  12.5730
 Z4S  O5   O  O2    0  -0.478  29.0479  13.4942  12.4975
 Z4S  C6   C  CH2   0  -0.172  30.8452  12.4331  13.4075
 Z4S  O6   O  O2    0  -0.495  29.6842  12.1926  14.1918
 Z4S  C1   C  CH1   0   0.256  28.7306  13.1553  13.8168
 Z4S  C2   C  CH1   0  -0.150  28.8274  14.4102  14.7228
 Z4S  N2   N  NH1   0  -0.637  27.5323  14.8816  15.1459
 Z4S  C7   C  C     0   0.505  27.0897  14.8607  16.4238
 Z4S  C8   C  CH3   0  -0.784  25.6869  15.3920  16.5982
 Z4S  O7   O  O     0  -0.483  27.7633  14.4527  17.3562
 Z4S  C3   C  CH1   0   0.026  29.5715  15.5272  13.9788
 Z4S  O3   O  OH1   0  -0.663  29.9885  16.5542  14.8439
 Z4S  HO3  H  HOH1  0   0.454  29.2185  17.0707  15.1015
 Z4S  H4   H  HCH1  0   0.226  31.5929  14.8147  14.0064
 Z4S  H5   H  HCH1  0   0.277  30.8743  13.6268  11.5655
 Z4S  H61  H  HCH2  0   0.239  31.0518  11.5667  12.7741
 Z4S  H62  H  HCH2  0   0.234  31.7141  12.6104  14.0446
 Z4S  H1   H  HCH1  0   0.258  27.7306  12.7153  13.8504
 Z4S  H2   H  HCH1  0   0.276  29.3808  14.1434  15.6244
 Z4S  HN2  H  HNH1  0   0.403  26.9031  15.2192  14.4323
 Z4S  H81  H  HCH3  0   0.260  25.3878  15.3359  17.6413
 Z4S  H82  H  HCH3  0   0.264  25.6222  16.4303  16.2699
 Z4S  H83  H  HCH3  0   0.263  24.9791  14.8183  15.9984
 Z4S  H3   H  HCH1  0   0.223  28.8946  15.9229  13.2080
 Z4S  HO4  H  HOH1  0   0.449  31.4895  16.7196  12.7078

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
 Z4S  O4   C4   single  1.407  0.020  1.407
 Z4S  C4   C5   single  1.540  0.020  1.540
 Z4S  C4   C3   single  1.527  0.020  1.527
 Z4S  C4   H4   single  0.970  0.020  1.090
 Z4S  C5   O5   single  1.422  0.020  1.422
 Z4S  C5   C6   single  1.531  0.020  1.531
 Z4S  C5   H5   single  0.970  0.020  1.090
 Z4S  O5   C1   single  1.399  0.020  1.399
 Z4S  C6   O6   single  1.422  0.020  1.422
 Z4S  C6   H61  single  0.970  0.020  1.090
 Z4S  C6   H62  single  0.970  0.020  1.090
 Z4S  O6   C1   single  1.406  0.020  1.406
 Z4S  C1   C2   single  1.551  0.020  1.551
 Z4S  C1   H1   single  0.970  0.020  1.090
 Z4S  C2   N2   single  1.442  0.020  1.442
 Z4S  C2   C3   single  1.535  0.020  1.535
 Z4S  C2   H2   single  0.970  0.020  1.090
 Z4S  N2   C7   single  1.353  0.020  1.353
 Z4S  N2   HN2  single  0.860  0.020  1.020
 Z4S  C7   C8   single  1.510  0.020  1.510
 Z4S  C7   O7   double  1.220  0.020  1.220
 Z4S  C8   H81  single  0.970  0.020  1.090
 Z4S  C8   H82  single  0.970  0.020  1.090
 Z4S  C8   H83  single  0.970  0.020  1.090
 Z4S  C3   O3   single  1.406  0.020  1.406
 Z4S  C3   H3   single  0.970  0.020  1.090
 Z4S  HO3  O3   single  0.850  0.020  0.980
 Z4S  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
 Z4S  HO4  O4  C4   108.24  3.000
 Z4S  H4   C4  C3   108.24  3.000
 Z4S  H4   C4  C5   108.98  3.000
 Z4S  C3   C4  C5   109.33  3.000
 Z4S  H4   C4  O4   110.32  3.000
 Z4S  C3   C4  O4   111.50  3.000
 Z4S  C5   C4  O4   108.42  3.000
 Z4S  H5   C5  C6   112.64  3.000
 Z4S  H5   C5  O5   109.03  3.000
 Z4S  C6   C5  O5   100.83  3.000
 Z4S  H5   C5  C4   110.42  3.000
 Z4S  C6   C5  C4   113.15  3.000
 Z4S  O5   C5  C4   110.33  3.000
 Z4S  C1   O5  C5   101.70  3.000
 Z4S  H62  C6  H61  108.44  3.000
 Z4S  H62  C6  O6   110.83  3.000
 Z4S  H61  C6  O6   109.87  3.000
 Z4S  H62  C6  C5   112.91  3.000
 Z4S  H61  C6  C5   111.44  3.000
 Z4S  O6   C6  C5   103.28  3.000
 Z4S  C1   O6  C6   106.91  3.000
 Z4S  H1   C1  C2   111.40  3.000
 Z4S  H1   C1  O6   109.67  3.000
 Z4S  C2   C1  O6   110.86  3.000
 Z4S  H1   C1  O5   109.52  3.000
 Z4S  C2   C1  O5   109.93  3.000
 Z4S  O6   C1  O5   105.29  3.000
 Z4S  H2   C2  C3   109.44  3.000
 Z4S  H2   C2  N2   107.04  3.000
 Z4S  C3   C2  N2   109.87  3.000
 Z4S  H2   C2  C1   108.45  3.000
 Z4S  C3   C2  C1   109.64  3.000
 Z4S  N2   C2  C1   112.33  3.000
 Z4S  HN2  N2  C7   117.98  3.000
 Z4S  HN2  N2  C2   117.50  3.000
 Z4S  C7   N2  C2   124.48  3.000
 Z4S  O7   C7  C8   122.83  3.000
 Z4S  O7   C7  N2   123.12  3.000
 Z4S  C8   C7  N2   114.05  3.000
 Z4S  H83  C8  H82  107.25  3.000
 Z4S  H83  C8  H81  108.78  3.000
 Z4S  H82  C8  H81  108.76  3.000
 Z4S  H83  C8  C7   110.75  3.000
 Z4S  H82  C8  C7   110.81  3.000
 Z4S  H81  C8  C7   110.39  3.000
 Z4S  H3   C3  O3   110.55  3.000
 Z4S  H3   C3  C2   107.66  3.000
 Z4S  O3   C3  C2   112.16  3.000
 Z4S  H3   C3  C4   107.05  3.000
 Z4S  O3   C3  C4   107.87  3.000
 Z4S  C2   C3  C4   111.45  3.000
 Z4S  HO3  O3  C3   108.64  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
 Z4S  CONST_01  C8   C7  N2  C2   180.00   0.0  0
 Z4S  CONST_02  O7   C7  N2  C2     0.00   0.0  0
 Z4S  CONST_03  HN2  N2  C7  C8     0.00   0.0  0
 Z4S  Var_01    H61  C6  O6  C1  -117.65  30.0  3
 Z4S  Var_02    H81  C8  C7  N2   179.26  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
 Z4S  chir_01  C4  O4  C5  C3  positiv
 Z4S  chir_02  C5  O5  C4  C6  negativ
 Z4S  chir_03  C1  O6  O5  C2  positiv
 Z4S  chir_04  C2  N2  C3  C1  positiv
 Z4S  chir_05  C3  O3  C2  C4  positiv

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
 Z4S  plan-1  C2   0.020
 Z4S  plan-1  N2   0.020
 Z4S  plan-1  C7   0.020
 Z4S  plan-1  C8   0.020
 Z4S  plan-1  O7   0.020
 Z4S  plan-1  HN2  0.020

