# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:27:29 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  39  21  .  2023-02-15  2023-02-15
;
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  OC    -1  -0.582  -6.0466  -0.8413  -0.3853
 SI3  C1   C  C      0   0.348  -5.0443  -0.1209  -0.2891
 SI3  O1B  O  O      0  -0.577  -4.9755   1.1193  -0.2480
 SI3  C2   C  C      0   0.241  -3.6807  -0.8712  -0.2158
 SI3  O2   O  O      0  -0.393  -3.6438  -2.0787  -0.2316
 SI3  C3   C  CH2    0  -0.593  -2.4339  -0.0235  -0.1683
 SI3  C4   C  CH1    0   0.066  -1.1609  -0.8035   0.1159
 SI3  O4   O  OH1    0  -0.670  -1.1570  -1.3283   1.4274
 SI3  C5   C  CH1    0  -0.153   0.0878   0.0504  -0.1540
 SI3  N5   N  NH1    0  -0.638   0.1085   1.2231   0.6923
 SI3  C10  C  C      0   0.514  -0.0866   2.4885   0.2620
 SI3  C11  C  CH3    0  -0.785   0.0383   3.5330   1.3453
 SI3  O10  O  O      0  -0.490  -0.3411   2.7692  -0.8987
 SI3  C6   C  CH1    0   0.047   1.3891  -0.7483   0.0361
 SI3  O6   O  OH1    0  -0.667   1.3690  -1.9365  -0.7247
 SI3  C7   C  CH1    0  -0.022   2.6349   0.0912  -0.2764
 SI3  O7   O  OH1    0  -0.664   2.6170   0.5695  -1.6054
 SI3  C8   C  CH1    0  -0.025   3.9384  -0.6696   0.0267
 SI3  O8   O  OH1    0  -0.660   3.9342  -1.1883   1.3370
 SI3  C9   C  CH2    0  -0.157   5.1516   0.2142  -0.2202
 SI3  O9   O  OH1    0  -0.671   6.3182  -0.5453  -0.0053
 SI3  H2   H  HCH2   0   0.275  -2.3600   0.4913  -1.1329
 SI3  H3   H  HCH2   0   0.261  -2.5751   0.7812   0.5586
 SI3  H4   H  HCH1   0   0.233  -1.1245  -1.6661  -0.5526
 SI3  H5   H  HOH1   0   0.441  -1.4168  -0.6331   2.0412
 SI3  H6   H  HCH1   0   0.260   0.0359   0.4002  -1.1878
 SI3  H7   H  HNH1   0   0.397   0.3313   1.0918   1.6670
 SI3  H8   H  HCH3   0   0.266   1.0573   3.5634   1.7343
 SI3  H9   H  HCH3   0   0.261  -0.2138   4.5153   0.9554
 SI3  H10  H  HCH3   0   0.262  -0.6220   3.3063   2.1830
 SI3  H11  H  HCH1   0   0.235   1.4477  -1.0631   1.0809
 SI3  H12  H  HOH1   0   0.443   1.1463  -1.7236  -1.6374
 SI3  H13  H  HCH1   0   0.232   2.6144   0.9819   0.3618
 SI3  H14  H  HOH1   0   0.444   2.8600  -0.1455  -2.2039
 SI3  H15  H  HCH1   0   0.229   3.9966  -1.5410  -0.6358
 SI3  H16  H  HOH1   0   0.444   3.9502  -0.4523   1.9591
 SI3  H17  H  HCH2   0   0.204   5.1123   0.6103  -1.2404
 SI3  H18  H  HCH2   0   0.190   5.1032   1.0807   0.4580
 SI3  H19  H  HOH1   0   0.455   7.0749   0.0230  -0.1742

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  1.409  0.020  1.409
 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  1.534  0.020  1.534
 SI3  O10  C10  double  1.221  0.020  1.221
 SI3  O6   C6   single  1.411  0.020  1.411
 SI3  C6   C5   single  1.539  0.020  1.539
 SI3  C10  C11  single  1.510  0.020  1.510
 SI3  C10  N5   single  1.351  0.020  1.351
 SI3  C5   N5   single  1.446  0.020  1.446
 SI3  C5   C4   single  1.537  0.020  1.537
 SI3  O1B  C1   deloc   1.243  0.020  1.243
 SI3  C4   C3   single  1.520  0.020  1.520
 SI3  C4   O4   single  1.413  0.020  1.413
 SI3  C1   O1A  deloc   1.238  0.020  1.238
 SI3  C1   C2   single  1.558  0.020  1.558
 SI3  C3   C2   single  1.509  0.020  1.509
 SI3  C2   O2   double  1.208  0.020  1.208
 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  C2   C1   O1B  115.51  3.000
 SI3  C2   C1   O1A  115.59  3.000
 SI3  O1B  C1   O1A  128.91  3.000
 SI3  C3   C2   O2   122.46  3.000
 SI3  O2   C2   C1   120.50  3.000
 SI3  C3   C2   C1   117.01  3.000
 SI3  H3   C3   H2   104.36  3.000
 SI3  H3   C3   C4   111.19  3.000
 SI3  H2   C3   C4   110.44  3.000
 SI3  H3   C3   C2   109.13  3.000
 SI3  H2   C3   C2   106.97  3.000
 SI3  C4   C3   C2   114.20  3.000
 SI3  H4   C4   C5   107.72  3.000
 SI3  H4   C4   O4   105.95  3.000
 SI3  C5   C4   O4   111.55  3.000
 SI3  H4   C4   C3   108.59  3.000
 SI3  O4   C4   C3   111.51  3.000
 SI3  C5   C4   C3   111.26  3.000
 SI3  H5   O4   C4   108.83  3.000
 SI3  H6   C5   C6   108.86  3.000
 SI3  H6   C5   N5   107.14  3.000
 SI3  C6   C5   N5   109.66  3.000
 SI3  H6   C5   C4   107.79  3.000
 SI3  N5   C5   C4   111.06  3.000
 SI3  C6   C5   C4   112.16  3.000
 SI3  H7   N5   C10  117.51  3.000
 SI3  H7   N5   C5   117.59  3.000
 SI3  C10  N5   C5   124.83  3.000
 SI3  O10  C10  C11  122.70  3.000
 SI3  C11  C10  N5   114.05  3.000
 SI3  O10  C10  N5   123.25  3.000
 SI3  H10  C11  H9   108.85  3.000
 SI3  H10  C11  H8   107.30  3.000
 SI3  H9   C11  H8   108.63  3.000
 SI3  H10  C11  C10  110.93  3.000
 SI3  H9   C11  C10  110.40  3.000
 SI3  H8   C11  C10  110.63  3.000
 SI3  H11  C6   C7   107.99  3.000
 SI3  H11  C6   O6   105.88  3.000
 SI3  C7   C6   O6   111.25  3.000
 SI3  H11  C6   C5   108.24  3.000
 SI3  O6   C6   C5   111.00  3.000
 SI3  C7   C6   C5   112.18  3.000
 SI3  H12  O6   C6   109.15  3.000
 SI3  H13  C7   C8   107.63  3.000
 SI3  H13  C7   O7   105.81  3.000
 SI3  C8   C7   O7   111.31  3.000
 SI3  H13  C7   C6   108.11  3.000
 SI3  C8   C7   C6   112.15  3.000
 SI3  O7   C7   C6   111.50  3.000
 SI3  H14  O7   C7   109.26  3.000
 SI3  H15  C8   C9   108.75  3.000
 SI3  H15  C8   O8   105.63  3.000
 SI3  C9   C8   O8   111.54  3.000
 SI3  H15  C8   C7   108.60  3.000
 SI3  O8   C8   C7   111.26  3.000
 SI3  C9   C8   C7   110.87  3.000
 SI3  H16  O8   C8   108.60  3.000
 SI3  H18  C9   H17  106.70  3.000
 SI3  H18  C9   O9   111.51  3.000
 SI3  H17  C9   O9   111.52  3.000
 SI3  H18  C9   C8   108.79  3.000
 SI3  H17  C9   C8   109.44  3.000
 SI3  O9   C9   C8   108.82  3.000
 SI3  H19  O9   C9   107.84  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  Var_01    C3   C2   C1   O1A  177.00  30.0  2
 SI3  Var_02    C4   C3   C2   C1   171.10  30.0  1
 SI3  Var_03    H8   C11  C10  N5    64.65  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

