# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 19:15:42 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-3,5,7-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]1C[C@H](O)CO)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
 9SJ  9SJ  '5-(acetylamino)-2,6-anhydro-3,5,7-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 OK
;

data_comp_9SJ
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
 9SJ  O10  O  O      0  -0.504  -1.4377   3.2404  -1.5102
 9SJ  C10  C  C      0   0.525  -1.2440   3.2964  -0.3037
 9SJ  C11  C  CH3    0  -0.782  -1.2928   4.6059   0.4442
 9SJ  N5   N  NH1    0  -0.629  -0.9679   2.2201   0.4552
 9SJ  C5   C  CH1    0  -0.129  -0.9363   0.8607  -0.0220
 9SJ  C4   C  CH1    0   0.026  -2.0704   0.0550   0.6097
 9SJ  O4   O  OH1    0  -0.662  -3.2915   0.6105   0.2010
 9SJ  C3   C  CH1    0   0.151  -1.9460  -1.4192   0.2638
 9SJ  F1   F  F      0  -0.385  -2.1850  -1.5890  -1.1021
 9SJ  C6   C  CH1    0   0.077   0.4158   0.2012   0.3046
 9SJ  O6   O  O2     0  -0.488   0.4079  -1.1499  -0.0854
 9SJ  C2   C  CH1    0  -0.157  -0.5550  -1.9290   0.5798
 9SJ  C1   C  C      0   0.395  -0.3985  -3.4214   0.2075
 9SJ  O1A  O  O      0  -0.584   0.5523  -3.7390  -0.5194
 9SJ  O1B  O  OC    -1  -0.613  -1.2617  -4.1658   0.7108
 9SJ  C7   C  CH2    0  -0.501   1.5663   0.8834  -0.4137
 9SJ  C8   C  CH1    0   0.003   2.9370   0.3103  -0.0634
 9SJ  O8   O  OH1    0  -0.665   3.1936   0.3518   1.3244
 9SJ  C9   C  CH2    0  -0.154   4.0148   1.0231  -0.8631
 9SJ  O9   O  OH1    0  -0.671   5.2590   0.4122  -0.6154
 9SJ  H1   H  HCH3   0   0.264  -0.6110   5.3169  -0.0216
 9SJ  H2   H  HCH3   0   0.266  -2.2971   5.0241   0.3715
 9SJ  H3   H  HCH3   0   0.247  -1.0345   4.5176   1.4978
 9SJ  H4   H  HNH1   0   0.396  -0.8541   2.3593   1.4474
 9SJ  H5   H  HCH1   0   0.263  -1.0647   0.8832  -1.1063
 9SJ  H6   H  HCH1   0   0.215  -1.9551   0.1175   1.7035
 9SJ  H7   H  HOH1   0   0.455  -3.9851   0.2891   0.7856
 9SJ  H8   H  HCH1   0   0.228  -2.6924  -2.0028   0.8081
 9SJ  H9   H  HCH1   0   0.202   0.5739   0.2759   1.3945
 9SJ  H10  H  HCH1   0   0.222  -0.4244  -1.8461   1.6725
 9SJ  H12  H  HCH2   0   0.237   1.4102   0.8059  -1.4944
 9SJ  H13  H  HCH2   0   0.240   1.5492   1.9518  -0.1770
 9SJ  H14  H  HCH1   0   0.232   2.9576  -0.7502  -0.3312
 9SJ  H15  H  HOH1   0   0.440   3.1503   1.2696   1.6149
 9SJ  H16  H  HCH2   0   0.198   3.7465   0.9762  -1.9265
 9SJ  H17  H  HCH2   0   0.188   4.0233   2.0889  -0.5877
 9SJ  H18  H  HOH1   0   0.454   5.9178   0.8470  -1.1636

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
 9SJ  C11  C10  single  1.509  0.020  1.509
 9SJ  O8   C8   single  1.412  0.020  1.412
 9SJ  N5   C10  single  1.346  0.020  1.346
 9SJ  N5   C5   single  1.441  0.020  1.441
 9SJ  C10  O10  double  1.223  0.020  1.223
 9SJ  O9   C9   single  1.408  0.020  1.408
 9SJ  C4   C5   single  1.528  0.020  1.528
 9SJ  C4   O4   single  1.402  0.020  1.402
 9SJ  C4   C3   single  1.519  0.020  1.519
 9SJ  C6   C5   single  1.539  0.020  1.539
 9SJ  C6   C7   single  1.518  0.020  1.518
 9SJ  C6   O6   single  1.406  0.020  1.406
 9SJ  C8   C7   single  1.526  0.020  1.526
 9SJ  C8   C9   single  1.520  0.020  1.520
 9SJ  C2   C3   single  1.515  0.020  1.515
 9SJ  C2   O6   single  1.406  0.020  1.406
 9SJ  C2   C1   single  1.546  0.020  1.546
 9SJ  C3   F1   single  1.397  0.020  1.397
 9SJ  C1   O1A  deloc   1.238  0.020  1.238
 9SJ  C1   O1B  deloc   1.246  0.020  1.246
 9SJ  C11  H1   single  0.970  0.020  1.090
 9SJ  C11  H2   single  0.970  0.020  1.090
 9SJ  C11  H3   single  0.970  0.020  1.090
 9SJ  N5   H4   single  0.860  0.020  1.020
 9SJ  C5   H5   single  0.970  0.020  1.090
 9SJ  C4   H6   single  0.970  0.020  1.090
 9SJ  O4   H7   single  0.850  0.020  0.980
 9SJ  C3   H8   single  0.970  0.020  1.090
 9SJ  C6   H9   single  0.970  0.020  1.090
 9SJ  C2   H10  single  0.970  0.020  1.090
 9SJ  C7   H12  single  0.970  0.020  1.090
 9SJ  C7   H13  single  0.970  0.020  1.090
 9SJ  C8   H14  single  0.970  0.020  1.090
 9SJ  O8   H15  single  0.850  0.020  0.980
 9SJ  C9   H16  single  0.970  0.020  1.090
 9SJ  C9   H17  single  0.970  0.020  1.090
 9SJ  O9   H18  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
 9SJ  N5   C10  C11  114.92  3.000
 9SJ  N5   C10  O10  123.51  3.000
 9SJ  C11  C10  O10  121.57  3.000
 9SJ  H3   C11  H2   108.32  3.000
 9SJ  H3   C11  H1   108.56  3.000
 9SJ  H2   C11  H1   107.31  3.000
 9SJ  H3   C11  C10  113.69  3.000
 9SJ  H2   C11  C10  109.24  3.000
 9SJ  H1   C11  C10  109.52  3.000
 9SJ  H4   N5   C5   116.98  3.000
 9SJ  H4   N5   C10  117.88  3.000
 9SJ  C5   N5   C10  124.91  3.000
 9SJ  H5   C5   C6   108.83  3.000
 9SJ  H5   C5   C4   109.51  3.000
 9SJ  C6   C5   C4   109.77  3.000
 9SJ  H5   C5   N5   107.87  3.000
 9SJ  C6   C5   N5   110.68  3.000
 9SJ  C4   C5   N5   110.14  3.000
 9SJ  H6   C4   C3   105.81  3.000
 9SJ  H6   C4   O4   110.98  3.000
 9SJ  C3   C4   O4   112.91  3.000
 9SJ  H6   C4   C5   107.63  3.000
 9SJ  C3   C4   C5   110.90  3.000
 9SJ  O4   C4   C5   108.48  3.000
 9SJ  H7   O4   C4   108.56  3.000
 9SJ  H8   C3   C2   110.09  3.000
 9SJ  H8   C3   F1   107.77  3.000
 9SJ  C2   C3   F1   108.67  3.000
 9SJ  H8   C3   C4   110.42  3.000
 9SJ  F1   C3   C4   109.06  3.000
 9SJ  C2   C3   C4   110.75  3.000
 9SJ  H9   C6   C7   109.16  3.000
 9SJ  H9   C6   O6   109.86  3.000
 9SJ  C7   C6   O6   107.74  3.000
 9SJ  H9   C6   C5   107.84  3.000
 9SJ  O6   C6   C5   110.36  3.000
 9SJ  C7   C6   C5   111.88  3.000
 9SJ  C2   O6   C6   113.89  3.000
 9SJ  H10  C2   C1   107.40  3.000
 9SJ  H10  C2   O6   110.23  3.000
 9SJ  C1   C2   O6   110.59  3.000
 9SJ  H10  C2   C3   106.85  3.000
 9SJ  C1   C2   C3   111.57  3.000
 9SJ  O6   C2   C3   110.10  3.000
 9SJ  O1B  C1   O1A  128.01  3.000
 9SJ  O1B  C1   C2   114.16  3.000
 9SJ  O1A  C1   C2   117.81  3.000
 9SJ  H13  C7   H12  106.28  3.000
 9SJ  H13  C7   C8   109.32  3.000
 9SJ  H12  C7   C8   109.15  3.000
 9SJ  H13  C7   C6   108.93  3.000
 9SJ  H12  C7   C6   109.10  3.000
 9SJ  C8   C7   C6   113.78  3.000
 9SJ  H14  C8   C9   108.21  3.000
 9SJ  H14  C8   O8   105.41  3.000
 9SJ  C9   C8   O8   112.00  3.000
 9SJ  H14  C8   C7   108.95  3.000
 9SJ  C9   C8   C7   109.88  3.000
 9SJ  O8   C8   C7   112.19  3.000
 9SJ  H15  O8   C8   108.43  3.000
 9SJ  H17  C9   H16  106.59  3.000
 9SJ  H17  C9   O9   111.67  3.000
 9SJ  H16  C9   O9   111.58  3.000
 9SJ  H17  C9   C8   109.14  3.000
 9SJ  H16  C9   C8   108.44  3.000
 9SJ  O9   C9   C8   109.31  3.000
 9SJ  H18  O9   C9   108.01  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
 9SJ  CONST_01  C5  N5   C10  O10    0.00   0.0  0
 9SJ  CONST_02  C5  N5   C10  C11  180.00   0.0  0
 9SJ  CONST_03  H4  N5   C10  O10  180.00   0.0  0
 9SJ  Var_01    H1  C11  C10  O10  -54.38  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
 9SJ  chir_01  C5  N5  C4  C6  positiv
 9SJ  chir_02  C4  O4  C5  C3  positiv
 9SJ  chir_03  C3  F1  C2  C4  negativ
 9SJ  chir_04  C6  O6  C7  C5  negativ
 9SJ  chir_05  C2  O6  C3  C1  negativ
 9SJ  chir_06  C8  O8  C9  C7  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
 9SJ  plan-1  O10  0.020
 9SJ  plan-1  C10  0.020
 9SJ  plan-1  C11  0.020
 9SJ  plan-1  N5   0.020
 9SJ  plan-1  C5   0.020
 9SJ  plan-1  H4   0.020
 9SJ  plan-2  C2   0.020
 9SJ  plan-2  C1   0.020
 9SJ  plan-2  O1A  0.020
 9SJ  plan-2  O1B  0.020

