# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:03:10 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-3,5,8-trideoxy-3-fluoro-D-threo-L-galacto-nononic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)[C@H](O[C@H]1[C@H](O)CCO)C(O)=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
 9S7  9S7  '5-(acetylamino)-2,6-anhydro-3,5,8-trideoxy-3-fluoro-D-threo-L-galacto-nononic acid'  D-saccharide  38  20  .  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_9S7
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
 9S7  O1B  O  O     0  -0.414  24.1809  20.5206  65.2411
 9S7  C1   C  C     0   0.517  23.4737  19.9456  64.4611
 9S7  O1A  O  OH1   0  -0.591  22.1551  20.0548  64.4168
 9S7  C2   C  CH1   0  -0.120  23.9707  19.0028  63.3812
 9S7  C3   C  CH1   0   0.147  23.3993  17.6031  63.5565
 9S7  F1   F  F     0  -0.371  23.6873  17.1748  64.8478
 9S7  O6   O  O2    0  -0.485  25.3617  18.9865  63.4522
 9S7  C6   C  CH1   0   0.049  25.9646  18.2219  62.4308
 9S7  C7   C  CH1   0   0.015  27.4773  18.4442  62.4867
 9S7  C8   C  CH2   0  -0.471  27.8171  19.9280  62.4108
 9S7  C9   C  CH2   0  -0.162  29.2985  20.2080  62.2503
 9S7  O9   O  OH1   0  -0.677  29.7505  19.6554  61.0310
 9S7  O7   O  OH1   0  -0.699  28.0515  17.9053  63.6524
 9S7  C5   C  CH1   0  -0.137  25.5534  16.7478  62.5942
 9S7  C4   C  CH1   0  -0.003  24.0291  16.6485  62.5508
 9S7  O4   O  OH1   0  -0.656  23.6608  15.3204  62.7882
 9S7  N5   N  NH1   0  -0.621  26.1147  15.9042  61.5662
 9S7  C10  C  C     0   0.539  27.2276  15.1689  61.7160
 9S7  O10  O  O     0  -0.517  27.9400  15.2344  62.7163
 9S7  C11  C  CH3   0  -0.774  27.5324  14.2247  60.5847
 9S7  H1   H  HOH1  0   0.492  21.8424  20.6535  65.1122
 9S7  H2   H  HCH1  0   0.282  23.6179  19.3867  62.4092
 9S7  H3   H  HCH1  0   0.259  22.3129  17.6088  63.4359
 9S7  H4   H  HCH1  0   0.224  25.6181  18.5710  61.4426
 9S7  H5   H  HCH1  0   0.218  27.8860  17.9619  61.5892
 9S7  H6   H  HCH2  0   0.238  27.4731  20.4365  63.3144
 9S7  H7   H  HCH2  0   0.229  27.2698  20.3766  61.5760
 9S7  H8   H  HCH2  0   0.197  29.8458  19.7938  63.1050
 9S7  H9   H  HCH2  0   0.202  29.4512  21.2948  62.2735
 9S7  H10  H  HOH1  0   0.453  30.7040  19.7662  60.9865
 9S7  H11  H  HOH1  0   0.454  28.0937  16.9426  63.5325
 9S7  H12  H  HCH1  0   0.276  25.8973  16.3853  63.5668
 9S7  H13  H  HCH1  0   0.238  23.6921  16.9883  61.5584
 9S7  H14  H  HOH1  0   0.461  22.7459  15.1951  62.5164
 9S7  H15  H  HNH1  0   0.408  25.5984  15.8095  60.7051
 9S7  H16  H  HCH3  0   0.266  28.6013  14.0343  60.5316
 9S7  H17  H  HCH3  0   0.276  27.0291  13.2736  60.7683
 9S7  H18  H  HCH3  0   0.259  27.1880  14.6013  59.6230

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
 9S7  C11  C10  single  1.505  0.020  1.505
 9S7  O9   C9   single  1.413  0.020  1.413
 9S7  N5   C10  single  1.342  0.020  1.342
 9S7  N5   C5   single  1.443  0.020  1.443
 9S7  C10  O10  double  1.230  0.020  1.230
 9S7  C8   C9   single  1.516  0.020  1.516
 9S7  C8   C7   single  1.524  0.020  1.524
 9S7  C7   C6   single  1.530  0.020  1.530
 9S7  C7   O7   single  1.407  0.020  1.407
 9S7  C6   C5   single  1.539  0.020  1.539
 9S7  C6   O6   single  1.411  0.020  1.411
 9S7  C4   C5   single  1.528  0.020  1.528
 9S7  C4   O4   single  1.399  0.020  1.399
 9S7  C4   C3   single  1.523  0.020  1.523
 9S7  O6   C2   single  1.393  0.020  1.393
 9S7  C3   C2   single  1.522  0.020  1.522
 9S7  C3   F1   single  1.391  0.020  1.391
 9S7  C2   C1   single  1.517  0.020  1.517
 9S7  C1   O1B  double  1.200  0.020  1.200
 9S7  C1   O1A  single  1.324  0.020  1.324
 9S7  O1A  H1   single  0.850  0.020  0.980
 9S7  C2   H2   single  0.970  0.020  1.090
 9S7  C3   H3   single  0.970  0.020  1.090
 9S7  C6   H4   single  0.970  0.020  1.090
 9S7  C7   H5   single  0.970  0.020  1.090
 9S7  C8   H6   single  0.970  0.020  1.090
 9S7  C8   H7   single  0.970  0.020  1.090
 9S7  C9   H8   single  0.970  0.020  1.090
 9S7  C9   H9   single  0.970  0.020  1.090
 9S7  O9   H10  single  0.850  0.020  0.980
 9S7  O7   H11  single  0.850  0.020  0.980
 9S7  C5   H12  single  0.970  0.020  1.090
 9S7  C4   H13  single  0.970  0.020  1.090
 9S7  O4   H14  single  0.850  0.020  0.980
 9S7  N5   H15  single  0.860  0.020  1.020
 9S7  C11  H16  single  0.970  0.020  1.090
 9S7  C11  H17  single  0.970  0.020  1.090
 9S7  C11  H18  single  0.970  0.020  1.090

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
 9S7  C2   C1   O1A  110.71  3.000
 9S7  O1A  C1   O1B  124.71  3.000
 9S7  C2   C1   O1B  124.58  3.000
 9S7  H1   O1A  C1   110.37  3.000
 9S7  H2   C2   O6   111.61  3.000
 9S7  H2   C2   C3   107.55  3.000
 9S7  O6   C2   C3   110.99  3.000
 9S7  H2   C2   C1   107.84  3.000
 9S7  C3   C2   C1   111.50  3.000
 9S7  O6   C2   C1   107.34  3.000
 9S7  H3   C3   C4   109.96  3.000
 9S7  H3   C3   F1   108.05  3.000
 9S7  C4   C3   F1   109.54  3.000
 9S7  H3   C3   C2   110.83  3.000
 9S7  F1   C3   C2   108.21  3.000
 9S7  C4   C3   C2   110.19  3.000
 9S7  C6   O6   C2   113.34  3.000
 9S7  H4   C6   C5   108.30  3.000
 9S7  H4   C6   C7   107.28  3.000
 9S7  C5   C6   C7   113.54  3.000
 9S7  H4   C6   O6   110.03  3.000
 9S7  C5   C6   O6   109.15  3.000
 9S7  C7   C6   O6   108.50  3.000
 9S7  H5   C7   O7   110.93  3.000
 9S7  H5   C7   C8   107.70  3.000
 9S7  O7   C7   C8   108.85  3.000
 9S7  H5   C7   C6   105.93  3.000
 9S7  O7   C7   C6   112.22  3.000
 9S7  C8   C7   C6   111.11  3.000
 9S7  H7   C8   H6   106.41  3.000
 9S7  H7   C8   C9   109.40  3.000
 9S7  H6   C8   C9   108.02  3.000
 9S7  H7   C8   C7   109.00  3.000
 9S7  H6   C8   C7   109.99  3.000
 9S7  C9   C8   C7   113.76  3.000
 9S7  H9   C9   H8   106.74  3.000
 9S7  H9   C9   O9   111.16  3.000
 9S7  H8   C9   O9   111.43  3.000
 9S7  H9   C9   C8   108.45  3.000
 9S7  H8   C9   C8   109.60  3.000
 9S7  O9   C9   C8   109.38  3.000
 9S7  H10  O9   C9   108.20  3.000
 9S7  H11  O7   C7   107.17  3.000
 9S7  H12  C5   N5   108.51  3.000
 9S7  H12  C5   C4   108.51  3.000
 9S7  N5   C5   C4   109.25  3.000
 9S7  H12  C5   C6   109.15  3.000
 9S7  C4   C5   C6   109.01  3.000
 9S7  N5   C5   C6   112.35  3.000
 9S7  H13  C4   O4   111.42  3.000
 9S7  H13  C4   C5   108.10  3.000
 9S7  O4   C4   C5   108.64  3.000
 9S7  H13  C4   C3   105.97  3.000
 9S7  O4   C4   C3   111.98  3.000
 9S7  C5   C4   C3   110.67  3.000
 9S7  H14  O4   C4   109.02  3.000
 9S7  H15  N5   C10  117.93  3.000
 9S7  H15  N5   C5   117.64  3.000
 9S7  C10  N5   C5   124.27  3.000
 9S7  C11  C10  O10  121.84  3.000
 9S7  O10  C10  N5   122.81  3.000
 9S7  C11  C10  N5   115.33  3.000
 9S7  H18  C11  H17  107.70  3.000
 9S7  H18  C11  H16  109.17  3.000
 9S7  H17  C11  H16  107.99  3.000
 9S7  H18  C11  C10  112.52  3.000
 9S7  H17  C11  C10  109.08  3.000
 9S7  H16  C11  C10  110.23  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
 9S7  CONST_01  C11  C10  N5   C5   180.00   0.0  0
 9S7  CONST_02  O10  C10  N5   C5     0.00   0.0  0
 9S7  CONST_03  H1   O1A  C1   C2   180.00   0.0  0
 9S7  CONST_04  H15  N5   C10  O10  180.00   0.0  0
 9S7  Var_01    O9   C9   C8   C7    62.39  30.0  3
 9S7  Var_02    H16  C11  C10  N5   153.33  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
 9S7  chir_01  C2  O6  C3  C1  negativ
 9S7  chir_02  C3  F1  C2  C4  negativ
 9S7  chir_03  C6  O6  C5  C7  positiv
 9S7  chir_04  C7  O7  C6  C8  negativ
 9S7  chir_05  C5  N5  C6  C4  negativ
 9S7  chir_06  C4  O4  C5  C3  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
 9S7  plan-1  C5   0.020
 9S7  plan-1  N5   0.020
 9S7  plan-1  C10  0.020
 9S7  plan-1  O10  0.020
 9S7  plan-1  C11  0.020
 9S7  plan-1  H15  0.020
 9S7  plan-2  O1B  0.020
 9S7  plan-2  C1   0.020
 9S7  plan-2  O1A  0.020
 9S7  plan-2  C2   0.020
 9S7  plan-2  H1   0.020

