# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 08:41:17 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]([C@@H](O)CC(=O)C(O)=O)[C@@H](O)[C@H](O)[C@H](O)CO
#
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
 SI3  SI3  '5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid'  D-saccharide  40  21  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SI3
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
 SI3  O1A  O  OH1   0  -0.570  -6.0221  -0.9179  -0.2759
 SI3  C1   C  C     0   0.485  -4.9875  -0.1082  -0.2706
 SI3  O1B  O  O     0  -0.403  -5.0320   1.0913  -0.3308
 SI3  C2   C  C     0   0.301  -3.6607  -0.8831  -0.1814
 SI3  O2   O  O     0  -0.341  -3.6791  -2.0836  -0.1519
 SI3  C3   C  CH2   0  -0.604  -2.4269  -0.0336  -0.1736
 SI3  C4   C  CH1   0   0.062  -1.1528  -0.8171   0.1072
 SI3  O4   O  OH1   0  -0.663  -1.1534  -1.3483   1.4121
 SI3  C5   C  CH1   0  -0.164   0.0901   0.0447  -0.1655
 SI3  N5   N  NH1   0  -0.647   0.1100   1.2160   0.6831
 SI3  C10  C  C     0   0.530  -0.1451   2.4725   0.2607
 SI3  C11  C  CH3   0  -0.778  -0.0321   3.5378   1.3220
 SI3  O10  O  O     0  -0.494  -0.4622   2.7402  -0.8884
 SI3  C6   C  CH1   0   0.048   1.3948  -0.7493   0.0226
 SI3  O6   O  OH1   0  -0.665   1.3684  -1.9474  -0.7196
 SI3  C7   C  CH1   0  -0.024   2.6337   0.0923  -0.3137
 SI3  O7   O  OH1   0  -0.664   2.5973   0.5558  -1.6475
 SI3  C8   C  CH1   0  -0.026   3.9432  -0.6601  -0.0165
 SI3  O8   O  OH1   0  -0.659   3.9532  -1.1693   1.2973
 SI3  C9   C  CH2   0  -0.156   5.1497   0.2282  -0.2802
 SI3  O9   O  OH1   0  -0.671   6.3215  -0.5254  -0.0732
 SI3  H1   H  HOH1  0   0.494  -6.8478  -0.4119  -0.3305
 SI3  H2   H  HCH2  0   0.302  -2.3697   0.4634  -1.1488
 SI3  H3   H  HCH2  0   0.283  -2.5578   0.7795   0.5471
 SI3  H4   H  HCH1  0   0.248  -1.1165  -1.6748  -0.5671
 SI3  H5   H  HOH1  0   0.443  -1.3366  -0.6417   2.0410
 SI3  H6   H  HCH1  0   0.265   0.0335   0.3936  -1.1993
 SI3  H7   H  HNH1  0   0.398   0.3806   1.0931   1.6462
 SI3  H8   H  HCH3  0   0.250   0.3897   3.1806   2.2595
 SI3  H9   H  HCH3  0   0.266   0.5867   4.3540   0.9510
 SI3  H10  H  HCH3  0   0.270  -1.0221   3.9482   1.5242
 SI3  H11  H  HCH1  0   0.238   1.4661  -1.0492   1.0711
 SI3  H12  H  HOH1  0   0.444   1.1703  -1.7460  -1.6408
 SI3  H13  H  HCH1  0   0.234   2.6166   0.9897   0.3149
 SI3  H14  H  HOH1  0   0.445   2.8568  -0.1573  -2.2413
 SI3  H15  H  HCH1  0   0.231   4.0003  -1.5358  -0.6734
 SI3  H16  H  HOH1  0   0.445   3.9596  -0.4287   1.9142
 SI3  H17  H  HCH2  0   0.204   5.0989   0.6192  -1.3019
 SI3  H18  H  HCH2  0   0.191   5.1039   1.0976   0.3943
 SI3  H19  H  HOH1  0   0.455   7.0742   0.0465  -0.2469

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
 SI3  C9   O9   single  1.408  0.020  1.408
 SI3  C9   C8   single  1.521  0.020  1.521
 SI3  O7   C7   single  1.413  0.020  1.413
 SI3  C8   C7   single  1.539  0.020  1.539
 SI3  C8   O8   single  1.409  0.020  1.409
 SI3  C7   C6   single  1.535  0.020  1.535
 SI3  O10  C10  double  1.222  0.020  1.222
 SI3  O6   C6   single  1.410  0.020  1.410
 SI3  C6   C5   single  1.539  0.020  1.539
 SI3  C10  C11  single  1.508  0.020  1.508
 SI3  C10  N5   single  1.350  0.020  1.350
 SI3  C5   N5   single  1.447  0.020  1.447
 SI3  C5   C4   single  1.537  0.020  1.537
 SI3  O1B  C1   double  1.202  0.020  1.202
 SI3  C4   C3   single  1.522  0.020  1.522
 SI3  C4   O4   single  1.409  0.020  1.409
 SI3  C1   O1A  single  1.314  0.020  1.314
 SI3  C1   C2   single  1.539  0.020  1.539
 SI3  C3   C2   single  1.498  0.020  1.498
 SI3  C2   O2   double  1.201  0.020  1.201
 SI3  O1A  H1   single  0.850  0.020  0.980
 SI3  C3   H2   single  0.970  0.020  1.090
 SI3  C3   H3   single  0.970  0.020  1.090
 SI3  C4   H4   single  0.970  0.020  1.090
 SI3  O4   H5   single  0.850  0.020  0.980
 SI3  C5   H6   single  0.970  0.020  1.090
 SI3  N5   H7   single  0.860  0.020  1.020
 SI3  C11  H8   single  0.970  0.020  1.090
 SI3  C11  H9   single  0.970  0.020  1.090
 SI3  C11  H10  single  0.970  0.020  1.090
 SI3  C6   H11  single  0.970  0.020  1.090
 SI3  O6   H12  single  0.850  0.020  0.980
 SI3  C7   H13  single  0.970  0.020  1.090
 SI3  O7   H14  single  0.850  0.020  0.980
 SI3  C8   H15  single  0.970  0.020  1.090
 SI3  O8   H16  single  0.850  0.020  0.980
 SI3  C9   H17  single  0.970  0.020  1.090
 SI3  C9   H18  single  0.970  0.020  1.090
 SI3  O9   H19  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
 SI3  H1   O1A  C1   110.43  3.000
 SI3  C2   C1   O1B  122.50  3.000
 SI3  C2   C1   O1A  111.64  3.000
 SI3  O1B  C1   O1A  125.86  3.000
 SI3  C3   C2   O2   125.40  3.000
 SI3  O2   C2   C1   119.44  3.000
 SI3  C3   C2   C1   115.14  3.000
 SI3  H3   C3   H2   104.79  3.000
 SI3  H3   C3   C4   111.17  3.000
 SI3  H2   C3   C4   110.73  3.000
 SI3  H3   C3   C2   109.04  3.000
 SI3  H2   C3   C2   107.19  3.000
 SI3  C4   C3   C2   113.49  3.000
 SI3  H4   C4   C5   107.70  3.000
 SI3  H4   C4   O4   106.01  3.000
 SI3  C5   C4   O4   112.09  3.000
 SI3  H4   C4   C3   108.57  3.000
 SI3  O4   C4   C3   111.39  3.000
 SI3  C5   C4   C3   110.83  3.000
 SI3  H5   O4   C4   109.15  3.000
 SI3  H6   C5   C6   108.92  3.000
 SI3  H6   C5   N5   107.29  3.000
 SI3  C6   C5   N5   109.54  3.000
 SI3  H6   C5   C4   107.76  3.000
 SI3  N5   C5   C4   111.17  3.000
 SI3  C6   C5   C4   112.00  3.000
 SI3  H7   N5   C10  117.60  3.000
 SI3  H7   N5   C5   117.74  3.000
 SI3  C10  N5   C5   124.58  3.000
 SI3  O10  C10  C11  121.78  3.000
 SI3  C11  C10  N5   115.03  3.000
 SI3  O10  C10  N5   123.19  3.000
 SI3  H10  C11  H9   107.27  3.000
 SI3  H10  C11  H8   108.40  3.000
 SI3  H9   C11  H8   108.60  3.000
 SI3  H10  C11  C10  109.17  3.000
 SI3  H9   C11  C10  109.40  3.000
 SI3  H8   C11  C10  113.80  3.000
 SI3  H11  C6   C7   107.94  3.000
 SI3  H11  C6   O6   105.85  3.000
 SI3  C7   C6   O6   111.46  3.000
 SI3  H11  C6   C5   108.31  3.000
 SI3  O6   C6   C5   111.00  3.000
 SI3  C7   C6   C5   112.00  3.000
 SI3  H12  O6   C6   109.25  3.000
 SI3  H13  C7   C8   107.62  3.000
 SI3  H13  C7   O7   105.82  3.000
 SI3  C8   C7   O7   111.39  3.000
 SI3  H13  C7   C6   108.10  3.000
 SI3  C8   C7   C6   112.11  3.000
 SI3  O7   C7   C6   111.47  3.000
 SI3  H14  O7   C7   109.40  3.000
 SI3  H15  C8   C9   108.75  3.000
 SI3  H15  C8   O8   105.64  3.000
 SI3  C9   C8   O8   111.53  3.000
 SI3  H15  C8   C7   108.61  3.000
 SI3  O8   C8   C7   111.27  3.000
 SI3  C9   C8   C7   110.85  3.000
 SI3  H16  O8   C8   108.61  3.000
 SI3  H18  C9   H17  106.72  3.000
 SI3  H18  C9   O9   111.53  3.000
 SI3  H17  C9   O9   111.51  3.000
 SI3  H18  C9   C8   108.77  3.000
 SI3  H17  C9   C8   109.47  3.000
 SI3  O9   C9   C8   108.78  3.000
 SI3  H19  O9   C9   107.86  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
 SI3  CONST_01  O10  C10  N5   C5     0.00   0.0  0
 SI3  CONST_02  C11  C10  N5   C5   180.00   0.0  0
 SI3  CONST_03  H7   N5   C10  C11    0.00   0.0  0
 SI3  CONST_04  H1   O1A  C1   O1B    0.00   0.0  0
 SI3  Var_01    C3   C2   C1   O1A  179.84  30.0  2
 SI3  Var_02    C4   C3   C2   C1   172.05  30.0  1
 SI3  Var_03    H8   C11  C10  N5     8.92  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
 SI3  chir_01  C4  C5  C3  O4  positiv
 SI3  chir_02  C5  N5  C6  C4  negativ
 SI3  chir_03  C6  O6  C5  C7  positiv
 SI3  chir_04  C7  O7  C6  C8  negativ
 SI3  chir_05  C8  O8  C7  C9  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
 SI3  plan-1  C5   0.020
 SI3  plan-1  N5   0.020
 SI3  plan-1  C10  0.020
 SI3  plan-1  C11  0.020
 SI3  plan-1  O10  0.020
 SI3  plan-1  H7   0.020
 SI3  plan-2  C1   0.020
 SI3  plan-2  C2   0.020
 SI3  plan-2  O2   0.020
 SI3  plan-2  C3   0.020
 SI3  plan-3  O1A  0.020
 SI3  plan-3  C1   0.020
 SI3  plan-3  O1B  0.020
 SI3  plan-3  C2   0.020
 SI3  plan-3  H1   0.020

