# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 07:31:14 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-O-acetyl-5-(acetylamino)-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@H](C[C@@](O)(O[C@H]1[C@H](O)[C@@H](O)CO)C(O)=O)OC(C)=O
#
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
 79J  79J  '4-O-acetyl-5-(acetylamino)-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulopyranosonic acid'  D-saccharide  45  24  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_79J
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
 79J  C1   C  C     0   0.525   0.4486   2.9335  -0.6379
 79J  C10  C  C     0   0.528  -1.2781  -2.9885  -0.1902
 79J  C11  C  CH3   0  -0.782  -1.5717  -4.0009  -1.2681
 79J  O1B  O  O     0  -0.432   1.2147   3.8616  -0.6455
 79J  C2   C  CT    0   0.421   0.1270   2.1531   0.6540
 79J  C3   C  CH2   0  -0.550  -1.3225   1.6961   0.7972
 79J  C4   C  CH1   0   0.051  -1.6644   0.4453   0.0021
 79J  O4   O  O2    0  -0.460  -2.8996  -0.0974   0.4744
 79J  C5   C  CH1   0  -0.134  -0.6194  -0.6444   0.2071
 79J  C6   C  CH1   0   0.023   0.7801  -0.0875  -0.0867
 79J  C7   C  CH1   0  -0.023   1.8847  -1.0879   0.2771
 79J  C8   C  CH1   0  -0.017   3.1883  -0.8173  -0.4869
 79J  C9   C  CH2   0  -0.159   4.2789  -1.7794  -0.0412
 79J  O10  O  O     0  -0.493  -1.3554  -3.2685   0.9958
 79J  N5   N  NH1   0  -0.638  -0.9039  -1.7718  -0.6405
 79J  C    C  C     0   0.568  -4.0469   0.3373  -0.0464
 79J  O    O  O     0  -0.449  -4.1133   1.1965  -0.8882
 79J  CH3  C  CH3   0  -0.772  -5.2163  -0.3830   0.5538
 79J  O1A  O  OH1   0  -0.576  -0.1560   2.4524  -1.7038
 79J  O2   O  OH1   0  -0.646   0.4080   2.9576   1.7284
 79J  O6   O  O2    0  -0.510   1.0231   1.0628   0.6997
 79J  O7   O  OH1   0  -0.666   2.0502  -1.1722   1.6731
 79J  O8   O  OH1   0  -0.656   3.6182   0.5234  -0.4578
 79J  O9   O  OH1   0  -0.672   5.3648  -1.6702  -0.9321
 79J  H1   H  HCH3  0   0.270  -0.8196  -4.7897  -1.2340
 79J  H2   H  HCH3  0   0.266  -2.5384  -4.4650  -1.0775
 79J  H3   H  HCH3  0   0.250  -1.5809  -3.5812  -2.2721
 79J  H4   H  HCH2  0   0.280  -1.4738   1.4758   1.8579
 79J  H5   H  HCH2  0   0.284  -1.9971   2.5150   0.5386
 79J  H6   H  HCH1  0   0.261  -1.7520   0.6676  -1.0629
 79J  H7   H  HCH1  0   0.278  -0.6496  -0.9845   1.2447
 79J  H8   H  HCH1  0   0.244   0.8572   0.1327  -1.1602
 79J  H9   H  HCH1  0   0.253   1.5503  -2.0769  -0.0506
 79J  H10  H  HCH1  0   0.233   2.9672  -1.0254  -1.5404
 79J  H11  H  HCH2  0   0.199   4.5781  -1.5453   0.9887
 79J  H12  H  HCH2  0   0.195   3.8687  -2.7986  -0.0282
 79J  H13  H  HNH1  0   0.402  -0.8933  -1.6177  -1.6371
 79J  H14  H  HCH3  0   0.274  -5.2268  -0.2549   1.6364
 79J  H15  H  HCH3  0   0.263  -6.1479  -0.0076   0.1409
 79J  H16  H  HCH3  0   0.273  -5.1443  -1.4531   0.3569
 79J  H17  H  HOH1  0   0.496   0.1144   2.9344  -2.5021
 79J  H18  H  HOH1  0   0.459   1.1716   3.5166   1.5271
 79J  H19  H  HOH1  0   0.446   2.0596  -0.2784   2.0342
 79J  H20  H  HOH1  0   0.439   3.8014   0.7787   0.4520
 79J  H21  H  HOH1  0   0.454   6.0798  -2.2183  -0.5979

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
 79J  O8   C8   single  1.408  0.020  1.408
 79J  O9   C9   single  1.409  0.020  1.409
 79J  C8   C9   single  1.521  0.020  1.521
 79J  C8   C7   single  1.535  0.020  1.535
 79J  O7   C7   single  1.408  0.020  1.408
 79J  C7   C6   single  1.534  0.020  1.534
 79J  C6   O6   single  1.414  0.020  1.414
 79J  C6   C5   single  1.535  0.020  1.535
 79J  O6   C2   single  1.412  0.020  1.412
 79J  C11  C10  single  1.508  0.020  1.508
 79J  C10  N5   single  1.350  0.020  1.350
 79J  C10  O10  double  1.221  0.020  1.221
 79J  N5   C5   single  1.439  0.020  1.439
 79J  C5   C4   single  1.524  0.020  1.524
 79J  O2   C2   single  1.371  0.020  1.371
 79J  C2   C1   single  1.543  0.020  1.543
 79J  C2   C3   single  1.527  0.020  1.527
 79J  O1B  C1   double  1.203  0.020  1.203
 79J  C1   O1A  single  1.317  0.020  1.317
 79J  C4   C3   single  1.521  0.020  1.521
 79J  C4   O4   single  1.429  0.020  1.429
 79J  O4   C    single  1.333  0.020  1.333
 79J  O    C    double  1.205  0.020  1.205
 79J  C    CH3  single  1.499  0.020  1.499
 79J  C11  H1   single  0.970  0.020  1.090
 79J  C11  H2   single  0.970  0.020  1.090
 79J  C11  H3   single  0.970  0.020  1.090
 79J  C3   H4   single  0.970  0.020  1.090
 79J  C3   H5   single  0.970  0.020  1.090
 79J  C4   H6   single  0.970  0.020  1.090
 79J  C5   H7   single  0.970  0.020  1.090
 79J  C6   H8   single  0.970  0.020  1.090
 79J  C7   H9   single  0.970  0.020  1.090
 79J  C8   H10  single  0.970  0.020  1.090
 79J  C9   H11  single  0.970  0.020  1.090
 79J  C9   H12  single  0.970  0.020  1.090
 79J  N5   H13  single  0.860  0.020  1.020
 79J  CH3  H14  single  0.970  0.020  1.090
 79J  CH3  H15  single  0.970  0.020  1.090
 79J  CH3  H16  single  0.970  0.020  1.090
 79J  O1A  H17  single  0.850  0.020  0.980
 79J  O2   H18  single  0.850  0.020  0.980
 79J  O7   H19  single  0.850  0.020  0.980
 79J  O8   H20  single  0.850  0.020  0.980
 79J  O9   H21  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
 79J  O1A  C1   C2   113.41  3.000
 79J  O1A  C1   O1B  124.69  3.000
 79J  C2   C1   O1B  121.87  3.000
 79J  N5   C10  O10  123.23  3.000
 79J  O10  C10  C11  121.88  3.000
 79J  N5   C10  C11  114.88  3.000
 79J  H3   C11  H2   108.57  3.000
 79J  H3   C11  H1   108.28  3.000
 79J  H2   C11  H1   107.37  3.000
 79J  H3   C11  C10  113.72  3.000
 79J  H2   C11  C10  109.50  3.000
 79J  H1   C11  C10  109.21  3.000
 79J  O6   C2   O2   107.31  3.000
 79J  O2   C2   C3   107.27  3.000
 79J  O6   C2   C3   111.62  3.000
 79J  C3   C2   C1   115.33  3.000
 79J  O2   C2   C1   108.45  3.000
 79J  O6   C2   C1   106.57  3.000
 79J  H5   C3   H4   107.17  3.000
 79J  H5   C3   C4   110.74  3.000
 79J  H4   C3   C4   108.07  3.000
 79J  H5   C3   C2   109.87  3.000
 79J  H4   C3   C2   106.41  3.000
 79J  C4   C3   C2   114.24  3.000
 79J  H6   C4   C5   109.39  3.000
 79J  H6   C4   O4   109.29  3.000
 79J  C5   C4   O4   106.06  3.000
 79J  H6   C4   C3   111.14  3.000
 79J  O4   C4   C3   109.49  3.000
 79J  C5   C4   C3   111.32  3.000
 79J  C    O4   C4   119.40  3.000
 79J  H7   C5   N5   108.07  3.000
 79J  H7   C5   C6   108.67  3.000
 79J  N5   C5   C6   110.60  3.000
 79J  H7   C5   C4   109.36  3.000
 79J  N5   C5   C4   110.21  3.000
 79J  C6   C5   C4   109.89  3.000
 79J  H8   C6   O6   111.61  3.000
 79J  H8   C6   C7   108.18  3.000
 79J  O6   C6   C7   105.95  3.000
 79J  H8   C6   C5   108.89  3.000
 79J  O6   C6   C5   110.20  3.000
 79J  C7   C6   C5   112.00  3.000
 79J  H9   C7   O7   106.18  3.000
 79J  H9   C7   C8   105.66  3.000
 79J  O7   C7   C8   113.84  3.000
 79J  H9   C7   C6   107.36  3.000
 79J  O7   C7   C6   111.02  3.000
 79J  C8   C7   C6   112.24  3.000
 79J  H10  C8   O8   105.19  3.000
 79J  H10  C8   C9   107.82  3.000
 79J  O8   C8   C9   112.16  3.000
 79J  H10  C8   C7   105.87  3.000
 79J  C9   C8   C7   110.58  3.000
 79J  O8   C8   C7   114.64  3.000
 79J  H12  C9   H11  106.76  3.000
 79J  H12  C9   O9   111.54  3.000
 79J  H11  C9   O9   111.51  3.000
 79J  H12  C9   C8   108.81  3.000
 79J  H11  C9   C8   109.60  3.000
 79J  O9   C9   C8   108.56  3.000
 79J  H13  N5   C5   117.41  3.000
 79J  H13  N5   C10  118.04  3.000
 79J  C5   N5   C10  124.36  3.000
 79J  CH3  C    O    125.42  3.000
 79J  CH3  C    O4   111.00  3.000
 79J  O    C    O4   123.58  3.000
 79J  H16  CH3  H15  109.10  3.000
 79J  H16  CH3  H14  107.17  3.000
 79J  H15  CH3  H14  109.19  3.000
 79J  H16  CH3  C    110.35  3.000
 79J  H15  CH3  C    110.55  3.000
 79J  H14  CH3  C    110.41  3.000
 79J  H17  O1A  C1   110.88  3.000
 79J  H18  O2   C2   109.74  3.000
 79J  C6   O6   C2   120.06  3.000
 79J  H19  O7   C7   108.48  3.000
 79J  H20  O8   C8   109.28  3.000
 79J  H21  O9   C9   108.02  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
 79J  CONST_01  C5   N5   C10  C11  180.00   0.0  0
 79J  CONST_02  O10  C10  N5   C5     0.00   0.0  0
 79J  CONST_03  H17  O1A  C1   C2   180.00   0.0  0
 79J  CONST_04  H13  N5   C10  C11    0.00   0.0  0
 79J  Var_01    O    C    O4   C4    -1.63  30.0  3
 79J  Var_02    H14  CH3  C    O4    57.79  30.0  3
 79J  Var_03    H1   C11  C10  O10  -65.98  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
 79J  chir_01  C2  O6  C1  C3  negativ
 79J  chir_02  C4  O4  C5  C3  positiv
 79J  chir_03  C5  N5  C6  C4  negativ
 79J  chir_04  C6  O6  C7  C5  negativ
 79J  chir_05  C7  O7  C6  C8  negativ
 79J  chir_06  C8  O8  C7  C9  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
 79J  plan-1  C10  0.020
 79J  plan-1  C11  0.020
 79J  plan-1  C5   0.020
 79J  plan-1  O10  0.020
 79J  plan-1  N5   0.020
 79J  plan-1  H13  0.020
 79J  plan-2  C1   0.020
 79J  plan-2  O1B  0.020
 79J  plan-2  C2   0.020
 79J  plan-2  O1A  0.020
 79J  plan-2  H17  0.020
 79J  plan-3  O4   0.020
 79J  plan-3  C    0.020
 79J  plan-3  O    0.020
 79J  plan-3  CH3  0.020

