# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 19:14:58 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: ~{N}-[(2~{S},3~{R},4~{S},6~{S})-6-(hydroxymethyl)-2,4-bis(oxidanyl)oxan-3-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)C[C@@H](CO)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
 8B9  8B9  ~{N}-[(2~{S},3~{R},4~{S},6~{S})-6-(hydroxymethyl)-2,4-bis(oxidanyl)oxan-3-yl]ethanamide  D-saccharide  29  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_8B9
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
 8B9  C1   C  CH1   0   0.264  23.4892  10.8733  12.9891
 8B9  C2   C  CH1   0  -0.142  24.8180  11.4377  13.5034
 8B9  C3   C  CH1   0   0.067  25.9146  10.3774  13.4479
 8B9  C4   C  CH2   0  -0.493  25.4304   9.1238  14.1693
 8B9  C5   C  CH1   0   0.015  24.0978   8.6552  13.6078
 8B9  C6   C  CH2   0  -0.176  23.4891   7.5026  14.3886
 8B9  C7   C  C     0   0.515  25.4432  13.8186  13.3408
 8B9  C8   C  CH3   0  -0.778  25.8563  14.9044  12.3765
 8B9  O3   O  OH1   0  -0.662  27.0658  10.9270  14.0429
 8B9  O6   O  OH1   0  -0.667  24.3648   6.4041  14.3031
 8B9  O7   O  O     0  -0.496  25.3740  14.0247  14.5441
 8B9  N2   N  NH1   0  -0.627  25.1675  12.6291  12.7728
 8B9  O5   O  O2    0  -0.502  23.1386   9.7026  13.6670
 8B9  O1   O  OH1   0  -0.665  23.6163  10.6778  11.6151
 8B9  H1   H  HCH1  0   0.237  22.6863  11.5841  13.2151
 8B9  H2   H  HCH1  0   0.268  24.6691  11.7219  14.5476
 8B9  H3   H  HCH1  0   0.205  26.1094  10.1236  12.3956
 8B9  H4   H  HCH2  0   0.250  26.1730   8.3285  14.0709
 8B9  H5A  H  HCH2  0   0.227  25.3210   9.3422  15.2377
 8B9  H5   H  HCH1  0   0.218  24.2365   8.3315  12.5673
 8B9  H61  H  HCH2  0   0.195  23.3301   7.8195  15.4284
 8B9  H62  H  HCH2  0   0.210  22.5037   7.2703  13.9638
 8B9  H81  H  HCH3  0   0.261  25.2616  15.7988  12.5570
 8B9  H82  H  HCH3  0   0.265  26.8991  15.1667  12.5587
 8B9  H83  H  HCH3  0   0.247  25.7544  14.6237  11.3300
 8B9  HO3  H  HOH1  0   0.450  27.7946  10.3126  13.9097
 8B9  HO6  H  HOH1  0   0.457  23.9932   5.6832  14.8188
 8B9  HN2  H  HNH1  0   0.395  25.2622  12.5419  11.7732
 8B9  HO1  H  HOH1  0   0.463  22.7428  10.5566  11.2274

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
 8B9  C8  C7   single  1.510  0.020  1.510
 8B9  N2  C7   single  1.347  0.020  1.347
 8B9  N2  C2   single  1.441  0.020  1.441
 8B9  C1  C2   single  1.533  0.020  1.533
 8B9  C1  O5   single  1.397  0.020  1.397
 8B9  C7  O7   double  1.223  0.020  1.223
 8B9  C3  C2   single  1.526  0.020  1.526
 8B9  C3  O3   single  1.408  0.020  1.408
 8B9  C3  C4   single  1.525  0.020  1.525
 8B9  C5  O5   single  1.421  0.020  1.421
 8B9  C5  C4   single  1.520  0.020  1.520
 8B9  C5  C6   single  1.519  0.020  1.519
 8B9  C6  O6   single  1.407  0.020  1.407
 8B9  C1  O1   single  1.394  0.020  1.394
 8B9  C1  H1   single  0.970  0.020  1.090
 8B9  C2  H2   single  0.970  0.020  1.090
 8B9  C3  H3   single  0.970  0.020  1.090
 8B9  C4  H4   single  0.970  0.020  1.090
 8B9  C4  H5A  single  0.970  0.020  1.090
 8B9  C5  H5   single  0.970  0.020  1.090
 8B9  C6  H61  single  0.970  0.020  1.090
 8B9  C6  H62  single  0.970  0.020  1.090
 8B9  C8  H81  single  0.970  0.020  1.090
 8B9  C8  H82  single  0.970  0.020  1.090
 8B9  C8  H83  single  0.970  0.020  1.090
 8B9  O3  HO3  single  0.850  0.020  0.980
 8B9  O6  HO6  single  0.850  0.020  0.980
 8B9  N2  HN2  single  0.860  0.020  1.020
 8B9  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
 8B9  H1   C1  O1   111.17  3.000
 8B9  H1   C1  O5   105.04  3.000
 8B9  O1   C1  O5   112.56  3.000
 8B9  H1   C1  C2   109.10  3.000
 8B9  O1   C1  C2   107.67  3.000
 8B9  O5   C1  C2   111.30  3.000
 8B9  H2   C2  N2   107.62  3.000
 8B9  H2   C2  C3   108.26  3.000
 8B9  N2   C2  C3   112.44  3.000
 8B9  H2   C2  C1   107.36  3.000
 8B9  C3   C2  C1   110.79  3.000
 8B9  N2   C2  C1   110.16  3.000
 8B9  H3   C3  O3   110.47  3.000
 8B9  H3   C3  C4   108.61  3.000
 8B9  O3   C3  C4   112.37  3.000
 8B9  H3   C3  C2   108.80  3.000
 8B9  C4   C3  C2   109.00  3.000
 8B9  O3   C3  C2   107.52  3.000
 8B9  H5A  C4  H4   107.50  3.000
 8B9  H5A  C4  C5   109.52  3.000
 8B9  H4   C4  C5   109.77  3.000
 8B9  H5A  C4  C3   109.21  3.000
 8B9  H4   C4  C3   109.87  3.000
 8B9  C5   C4  C3   110.92  3.000
 8B9  H5   C5  O5   109.98  3.000
 8B9  H5   C5  C6   108.29  3.000
 8B9  O5   C5  C6   105.50  3.000
 8B9  H5   C5  C4   109.27  3.000
 8B9  C6   C5  C4   113.28  3.000
 8B9  O5   C5  C4   110.42  3.000
 8B9  H62  C6  H61  107.30  3.000
 8B9  H62  C6  O6   111.70  3.000
 8B9  H61  C6  O6   111.88  3.000
 8B9  H62  C6  C5   108.74  3.000
 8B9  H61  C6  C5   109.00  3.000
 8B9  O6   C6  C5   108.15  3.000
 8B9  N2   C7  O7   123.53  3.000
 8B9  O7   C7  C8   121.52  3.000
 8B9  N2   C7  C8   114.95  3.000
 8B9  H83  C8  H82  108.19  3.000
 8B9  H83  C8  H81  108.66  3.000
 8B9  H82  C8  H81  107.27  3.000
 8B9  H83  C8  C7   113.77  3.000
 8B9  H82  C8  C7   109.14  3.000
 8B9  H81  C8  C7   109.59  3.000
 8B9  HO3  O3  C3   108.15  3.000
 8B9  HO6  O6  C6   108.20  3.000
 8B9  HN2  N2  C7   118.39  3.000
 8B9  HN2  N2  C2   117.02  3.000
 8B9  C7   N2  C2   124.49  3.000
 8B9  C5   O5  C1   115.33  3.000
 8B9  HO1  O1  C1   109.38  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
 8B9  CONST_01  C8   C7  N2  C2  180.00   0.0  0
 8B9  CONST_02  O7   C7  N2  C2    0.00   0.0  0
 8B9  CONST_03  HN2  N2  C7  C8    0.00   0.0  0
 8B9  Var_01    H81  C8  C7  O7  -50.78  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
 8B9  chir_01  C1  C2  O5  O1  positiv
 8B9  chir_02  C2  N2  C3  C1  positiv
 8B9  chir_03  C3  O3  C2  C4  positiv
 8B9  chir_04  C5  O5  C6  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
 8B9  plan-1  C2   0.020
 8B9  plan-1  C7   0.020
 8B9  plan-1  C8   0.020
 8B9  plan-1  O7   0.020
 8B9  plan-1  N2   0.020
 8B9  plan-1  HN2  0.020

