# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:52:30 2021
#   Inital geometry file: a 91 line input string
#   Ligand name: a 3 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)[C@@](F)(O[C@H]1[C@H](O)[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
 SFJ  SFJ  '(2R,3R,4R,5R,6R)-5-(acetylamino)-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxy lic acid (non-preferred name)'  D-saccharide  39  22  .  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_SFJ
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
 SFJ  C11   C  CH3   0  -0.772  50.4237   96.9692  10.3071
 SFJ  C9    C  CH2   0  -0.155  44.6201   95.4159   8.4096
 SFJ  C10   C  C     0   0.551  49.0730   97.6223  10.3917
 SFJ  C1    C  C     0   0.479  44.3956   96.9867  14.1326
 SFJ  C7    C  CH1   0  -0.020  45.8226   96.8297  10.0777
 SFJ  C4    C  CH1   0  -0.020  47.1389   98.4626  13.3426
 SFJ  C3    C  CH1   0   0.095  45.8039   99.1164  13.6767
 SFJ  C5    C  CH1   0  -0.134  47.1614   98.0935  11.8596
 SFJ  C6    C  CH1   0  -0.010  45.9486   97.2014  11.5544
 SFJ  C2    C  CT    0   0.538  44.6397   98.2272  13.2410
 SFJ  N5    N  NH1   0  -0.625  48.4020   97.4333  11.5400
 SFJ  O10   O  O     0  -0.517  48.6277   98.2979   9.4652
 SFJ  O9    O  OH1   0  -0.673  43.3748   94.8459   8.0810
 SFJ  O1A   O  O     0  -0.410  43.9670   95.9527  13.6968
 SFJ  O8    O  OH1   0  -0.680  44.3182   95.0173  10.7191
 SFJ  O7    O  OH1   0  -0.690  45.8439   97.9602   9.2486
 SFJ  O4    O  OH1   0  -0.653  48.2071   99.3202  13.6121
 SFJ  O6    O  O2    0  -0.489  44.7459   97.8756  11.9246
 SFJ  FAI   F  F     0  -0.366  45.6902  100.2923  12.9545
 SFJ  O1B   O  OH1   0  -0.569  44.6580   97.2340  15.3946
 SFJ  C8    C  CH1   0   0.008  44.5278   96.0496   9.7848
 SFJ  H111  H  HCH3  0   0.270  50.5360   96.4846   9.3391
 SFJ  H113  H  HCH3  0   0.277  51.1941   97.7376  10.3827
 SFJ  H112  H  HCH3  0   0.256  50.5968   96.2359  11.0919
 SFJ  H91   H  HCH2  0   0.207  44.9148   96.1859   7.6888
 SFJ  H7    H  HCH1  0   0.226  46.6654   96.1555   9.8655
 SFJ  H4    H  HCH1  0   0.248  47.2127   97.5362  13.9327
 SFJ  H32   H  HCH1  0   0.278  45.7442   99.3707  14.7370
 SFJ  H5    H  HCH1  0   0.287  47.1006   99.0107  11.2695
 SFJ  H6    H  HCH1  0   0.254  46.0582   96.2708  12.1271
 SFJ  HN5   H  HNH1  0   0.412  48.8221   96.8475  12.2452
 SFJ  HO9   H  HOH1  0   0.454  43.4361   94.4961   7.1879
 SFJ  HO8   H  HOH1  0   0.451  43.9771   95.3945  11.5382
 SFJ  HO7   H  HOH1  0   0.460  46.7699   98.2485   9.1814
 SFJ  HO4   H  HOH1  0   0.466  48.3974   99.2987  14.5555
 SFJ  HO1B  H  HOH1  0   0.502  44.4476   96.4694  15.9556
 SFJ  H8    H  HCH1  0   0.217  43.6897   96.7599   9.7815
 SFJ  FAJ   F  F     0  -0.343  43.4773   98.9447  13.3433
 SFJ  H92   H  HCH2  0   0.191  45.4206   94.6617   8.4204

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
 SFJ  O9   C9    single  1.408  0.020  1.408
 SFJ  C9   C8    single  1.517  0.020  1.517
 SFJ  O7   C7    single  1.402  0.020  1.402
 SFJ  O10  C10   double  1.230  0.020  1.230
 SFJ  C8   C7    single  1.540  0.020  1.540
 SFJ  C8   O8    single  1.408  0.020  1.408
 SFJ  C7   C6    single  1.528  0.020  1.528
 SFJ  C10  C11   single  1.503  0.020  1.503
 SFJ  C10  N5    single  1.343  0.020  1.343
 SFJ  C6   C5    single  1.536  0.020  1.536
 SFJ  C6   O6    single  1.428  0.020  1.428
 SFJ  N5   C5    single  1.441  0.020  1.441
 SFJ  C5   C4    single  1.528  0.020  1.528
 SFJ  O6   C2    single  1.367  0.020  1.367
 SFJ  FAI  C3    single  1.385  0.020  1.385
 SFJ  FAJ  C2    single  1.370  0.020  1.370
 SFJ  C2   C3    single  1.528  0.020  1.528
 SFJ  C2   C1    single  1.547  0.020  1.547
 SFJ  C4   C3    single  1.524  0.020  1.524
 SFJ  C4   O4    single  1.396  0.020  1.396
 SFJ  O1A  C1    double  1.201  0.020  1.201
 SFJ  C1   O1B   single  1.312  0.020  1.312
 SFJ  C11  H111  single  0.970  0.020  1.090
 SFJ  C11  H113  single  0.970  0.020  1.090
 SFJ  C11  H112  single  0.970  0.020  1.090
 SFJ  C9   H92   single  0.970  0.020  1.090
 SFJ  C9   H91   single  0.970  0.020  1.090
 SFJ  C7   H7    single  0.970  0.020  1.090
 SFJ  C4   H4    single  0.970  0.020  1.090
 SFJ  C3   H32   single  0.970  0.020  1.090
 SFJ  C5   H5    single  0.970  0.020  1.090
 SFJ  C6   H6    single  0.970  0.020  1.090
 SFJ  N5   HN5   single  0.860  0.020  1.020
 SFJ  O9   HO9   single  0.850  0.020  0.980
 SFJ  O8   HO8   single  0.850  0.020  0.980
 SFJ  O7   HO7   single  0.850  0.020  0.980
 SFJ  O4   HO4   single  0.850  0.020  0.980
 SFJ  O1B  HO1B  single  0.850  0.020  0.980
 SFJ  C8   H8    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
 SFJ  H112  C11  H113  108.21  3.000
 SFJ  H112  C11  H111  108.97  3.000
 SFJ  H113  C11  H111  107.60  3.000
 SFJ  H112  C11  C10   113.29  3.000
 SFJ  H113  C11  C10   108.95  3.000
 SFJ  H111  C11  C10   109.66  3.000
 SFJ  H91   C9   H92   107.02  3.000
 SFJ  H91   C9   C8    108.62  3.000
 SFJ  H92   C9   C8    108.78  3.000
 SFJ  H91   C9   O9    111.65  3.000
 SFJ  H92   C9   O9    111.61  3.000
 SFJ  C8    C9   O9    109.07  3.000
 SFJ  O10   C10  N5    122.70  3.000
 SFJ  N5    C10  C11   115.85  3.000
 SFJ  O10   C10  C11   121.45  3.000
 SFJ  O1B   C1   O1A   125.62  3.000
 SFJ  O1B   C1   C2    111.81  3.000
 SFJ  O1A   C1   C2    122.51  3.000
 SFJ  H7    C7   C8    107.28  3.000
 SFJ  H7    C7   O7    111.62  3.000
 SFJ  C8    C7   O7    107.99  3.000
 SFJ  H7    C7   C6    105.80  3.000
 SFJ  C8    C7   C6    112.12  3.000
 SFJ  O7    C7   C6    111.97  3.000
 SFJ  H4    C4   O4    111.23  3.000
 SFJ  H4    C4   C5    108.42  3.000
 SFJ  O4    C4   C5    108.93  3.000
 SFJ  H4    C4   C3    107.59  3.000
 SFJ  O4    C4   C3    111.38  3.000
 SFJ  C5    C4   C3    109.23  3.000
 SFJ  H32   C3   FAI   107.71  3.000
 SFJ  H32   C3   C2    111.76  3.000
 SFJ  FAI   C3   C2    106.43  3.000
 SFJ  H32   C3   C4    111.14  3.000
 SFJ  C2    C3   C4    110.81  3.000
 SFJ  FAI   C3   C4    108.78  3.000
 SFJ  H5    C5   N5    108.22  3.000
 SFJ  H5    C5   C6    109.65  3.000
 SFJ  N5    C5   C6    111.68  3.000
 SFJ  H5    C5   C4    108.70  3.000
 SFJ  N5    C5   C4    109.78  3.000
 SFJ  C6    C5   C4    108.75  3.000
 SFJ  H6    C6   O6    110.43  3.000
 SFJ  H6    C6   C5    108.04  3.000
 SFJ  O6    C6   C5    109.84  3.000
 SFJ  H6    C6   C7    107.82  3.000
 SFJ  O6    C6   C7    107.22  3.000
 SFJ  C5    C6   C7    113.48  3.000
 SFJ  FAJ   C2   O6    105.82  3.000
 SFJ  FAJ   C2   C3    108.68  3.000
 SFJ  O6    C2   C3    111.41  3.000
 SFJ  C3    C2   C1    114.99  3.000
 SFJ  FAJ   C2   C1    104.07  3.000
 SFJ  O6    C2   C1    111.17  3.000
 SFJ  HN5   N5   C5    118.01  3.000
 SFJ  HN5   N5   C10   118.12  3.000
 SFJ  C5    N5   C10   123.72  3.000
 SFJ  HO9   O9   C9    107.92  3.000
 SFJ  HO8   O8   C8    109.24  3.000
 SFJ  HO7   O7   C7    107.13  3.000
 SFJ  HO4   O4   C4    109.08  3.000
 SFJ  C2    O6   C6    115.90  3.000
 SFJ  HO1B  O1B  C1    111.32  3.000
 SFJ  H8    C8   O8    111.25  3.000
 SFJ  H8    C8   C7    108.33  3.000
 SFJ  O8    C8   C7    111.74  3.000
 SFJ  H8    C8   C9    108.29  3.000
 SFJ  O8    C8   C9    107.72  3.000
 SFJ  C7    C8   C9    109.44  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
 SFJ  CONST_01  C5    N5   C10  C11  180.00   0.0  0
 SFJ  CONST_02  O10   C10  N5   C5     0.00   0.0  0
 SFJ  CONST_03  HO1B  O1B  C1   C2   180.00   0.0  0
 SFJ  CONST_04  HN5   N5   C10  C11    0.00   0.0  0
 SFJ  Var_01    H111  C11  C10  N5   135.31  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
 SFJ  chir_01  C7  O7   C8  C6  positiv
 SFJ  chir_02  C4  O4   C5  C3  positiv
 SFJ  chir_03  C3  FAI  C2  C4  negativ
 SFJ  chir_04  C5  N5   C4  C6  positiv
 SFJ  chir_05  C6  O6   C7  C5  negativ
 SFJ  chir_06  C2  O6   C3  C1  positiv
 SFJ  chir_07  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
 SFJ  plan-1  C11   0.020
 SFJ  plan-1  C10   0.020
 SFJ  plan-1  C5    0.020
 SFJ  plan-1  N5    0.020
 SFJ  plan-1  O10   0.020
 SFJ  plan-1  HN5   0.020
 SFJ  plan-2  C1    0.020
 SFJ  plan-2  C2    0.020
 SFJ  plan-2  O1A   0.020
 SFJ  plan-2  O1B   0.020
 SFJ  plan-2  HO1B  0.020

