# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 17:29:12 2020
#   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  37  20  .  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_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  -0.580  -3.4497   1.5504  -0.6112
 9S7  C1   C  C      0   0.394  -2.6785   2.2106   0.0967
 9S7  O1A  O  OC    -1  -0.614  -2.8239   3.3761   0.5132
 9S7  C2   C  CH1    0  -0.152  -1.3713   1.5324   0.5695
 9S7  C3   C  CH1    0   0.147  -0.1565   2.3768   0.2441
 9S7  F1   F  F      0  -0.384  -0.1161   2.5984  -1.1346
 9S7  O6   O  O2     0  -0.489  -1.2462   0.2508   0.0038
 9S7  C6   C  CH1    0   0.033  -0.1324  -0.4744   0.4588
 9S7  C7   C  CH1    0   0.010  -0.2212  -1.8715  -0.1518
 9S7  C8   C  CH2    0  -0.479  -1.4566  -2.6162   0.3486
 9S7  C9   C  CH2    0  -0.139  -1.4469  -4.0785  -0.0545
 9S7  O9   O  OH1    0  -0.676  -2.5888  -4.7034   0.4947
 9S7  O7   O  OH1    0  -0.665  -0.1542  -1.8267  -1.5600
 9S7  C5   C  CH1    0  -0.117   1.1698   0.2577   0.0967
 9S7  C4   C  CH1    0   0.030   1.1223   1.6733   0.6681
 9S7  O4   O  OH1    0  -0.661   2.2798   2.3563   0.2683
 9S7  N5   N  NH1    0  -0.633   2.3112  -0.4596   0.6039
 9S7  C10  C  C      0   0.526   3.4031  -0.7647  -0.1222
 9S7  O10  O  O      0  -0.502   3.5167  -0.5067  -1.3118
 9S7  C11  C  CH3    0  -0.783   4.5015  -1.4621   0.6422
 9S7  H2   H  HCH1   0   0.223  -1.4222   1.4559   1.6691
 9S7  H3   H  HCH1   0   0.229  -0.2404   3.3493   0.7350
 9S7  H4   H  HCH1   0   0.209  -0.1695  -0.5851   1.5577
 9S7  H5   H  HCH1   0   0.236   0.6659  -2.4240   0.1730
 9S7  H6   H  HCH2   0   0.227  -1.4853  -2.5490   1.4406
 9S7  H7   H  HCH2   0   0.235  -2.3652  -2.1326  -0.0229
 9S7  H8   H  HCH2   0   0.193  -1.4338  -4.1625  -1.1475
 9S7  H9   H  HCH2   0   0.187  -0.5227  -4.5472   0.3116
 9S7  H10  H  HOH1   0   0.452  -2.5798  -5.6276   0.2313
 9S7  H11  H  HOH1   0   0.441  -0.8933  -1.2936  -1.8739
 9S7  H12  H  HCH1   0   0.265   1.2640   0.3041  -0.9889
 9S7  H13  H  HCH1   0   0.212   1.0726   1.5903   1.7656
 9S7  H14  H  HOH1   0   0.454   2.3456   3.1693   0.7791
 9S7  H15  H  HNH1   0   0.396   2.3257  -0.6728   1.5890
 9S7  H16  H  HCH3   0   0.247   4.2208  -1.7399   1.6564
 9S7  H17  H  HCH3   0   0.264   4.8017  -2.3615   0.1064
 9S7  H18  H  HCH3   0   0.267   5.3731  -0.8090   0.6957

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  1.509  0.020  1.509
 9S7  O9   C9   single  1.413  0.020  1.413
 9S7  N5   C10  single  1.346  0.020  1.346
 9S7  N5   C5   single  1.440  0.020  1.440
 9S7  C10  O10  double  1.223  0.020  1.223
 9S7  C8   C9   single  1.517  0.020  1.517
 9S7  C8   C7   single  1.527  0.020  1.527
 9S7  C7   C6   single  1.527  0.020  1.527
 9S7  C7   O7   single  1.410  0.020  1.410
 9S7  C6   C5   single  1.537  0.020  1.537
 9S7  C6   O6   single  1.405  0.020  1.405
 9S7  C4   C5   single  1.527  0.020  1.527
 9S7  C4   O4   single  1.402  0.020  1.402
 9S7  C4   C3   single  1.520  0.020  1.520
 9S7  O6   C2   single  1.406  0.020  1.406
 9S7  C3   C2   single  1.515  0.020  1.515
 9S7  C3   F1   single  1.397  0.020  1.397
 9S7  C2   C1   single  1.547  0.020  1.547
 9S7  C1   O1B  deloc   1.238  0.020  1.238
 9S7  C1   O1A  deloc   1.246  0.020  1.246
 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  113.99  3.000
 9S7  O1A  C1   O1B  128.12  3.000
 9S7  C2   C1   O1B  117.88  3.000
 9S7  H2   C2   O6   109.98  3.000
 9S7  H2   C2   C3   106.84  3.000
 9S7  O6   C2   C3   110.50  3.000
 9S7  H2   C2   C1   107.22  3.000
 9S7  C3   C2   C1   111.57  3.000
 9S7  O6   C2   C1   110.60  3.000
 9S7  H3   C3   C4   110.56  3.000
 9S7  H3   C3   F1   107.72  3.000
 9S7  C4   C3   F1   108.93  3.000
 9S7  H3   C3   C2   109.76  3.000
 9S7  F1   C3   C2   108.88  3.000
 9S7  C4   C3   C2   110.91  3.000
 9S7  C6   O6   C2   114.25  3.000
 9S7  H4   C6   C5   108.08  3.000
 9S7  H4   C6   C7   107.70  3.000
 9S7  C5   C6   C7   113.01  3.000
 9S7  H4   C6   O6   110.31  3.000
 9S7  C5   C6   O6   110.46  3.000
 9S7  C7   C6   O6   107.26  3.000
 9S7  H5   C7   O7   105.89  3.000
 9S7  H5   C7   C8   108.20  3.000
 9S7  O7   C7   C8   112.41  3.000
 9S7  H5   C7   C6   107.22  3.000
 9S7  O7   C7   C6   111.55  3.000
 9S7  C8   C7   C6   111.24  3.000
 9S7  H7   C8   H6   106.85  3.000
 9S7  H7   C8   C9   109.95  3.000
 9S7  H6   C8   C9   108.93  3.000
 9S7  H7   C8   C7   110.18  3.000
 9S7  H6   C8   C7   108.56  3.000
 9S7  C9   C8   C7   112.21  3.000
 9S7  H9   C9   H8   106.82  3.000
 9S7  H9   C9   O9   111.20  3.000
 9S7  H8   C9   O9   111.31  3.000
 9S7  H9   C9   C8   109.14  3.000
 9S7  H8   C9   C8   109.81  3.000
 9S7  O9   C9   C8   108.54  3.000
 9S7  H10  O9   C9   108.13  3.000
 9S7  H11  O7   C7   107.83  3.000
 9S7  H12  C5   N5   107.65  3.000
 9S7  H12  C5   C4   109.61  3.000
 9S7  N5   C5   C4   110.76  3.000
 9S7  H12  C5   C6   109.14  3.000
 9S7  C4   C5   C6   109.09  3.000
 9S7  N5   C5   C6   110.56  3.000
 9S7  H13  C4   O4   110.98  3.000
 9S7  H13  C4   C5   107.71  3.000
 9S7  O4   C4   C5   108.61  3.000
 9S7  H13  C4   C3   105.95  3.000
 9S7  O4   C4   C3   112.93  3.000
 9S7  C5   C4   C3   110.54  3.000
 9S7  H14  O4   C4   108.45  3.000
 9S7  H15  N5   C10  117.87  3.000
 9S7  H15  N5   C5   117.44  3.000
 9S7  C10  N5   C5   124.45  3.000
 9S7  C11  C10  O10  121.52  3.000
 9S7  O10  C10  N5   123.52  3.000
 9S7  C11  C10  N5   114.96  3.000
 9S7  H18  C11  H17  107.36  3.000
 9S7  H18  C11  H16  108.26  3.000
 9S7  H17  C11  H16  108.59  3.000
 9S7  H18  C11  C10  109.26  3.000
 9S7  H17  C11  C10  109.46  3.000
 9S7  H16  C11  C10  113.72  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  H15  N5   C10  O10  180.00   0.0  0
 9S7  Var_01    O9   C9   C8   C7   177.49  30.0  3
 9S7  Var_02    H16  C11  C10  N5     7.15  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

