# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:04:47 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (2R,3R,4R,5R,6S)-5-(acetylamino)-6-[(2S)-2,3-dihydroxypropyl]-2,3-difluoro-4-hydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   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]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
 9SM  9SM  '(2R,3R,4R,5R,6S)-5-(acetylamino)-6-[(2S)-2,3-dihydroxypropyl]-2,3-difluoro-4-hydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  D-saccharide  38  21  .  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_9SM
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
 9SM  OAC  O  OH1   0  -0.578  -1.2572   3.1454  -1.6830
 9SM  CAO  C  C     0   0.457  -0.1876   2.5633  -1.1800
 9SM  OAE  O  O     0  -0.397   0.8827   2.4867  -1.7127
 9SM  CAV  C  CT    0   0.537  -0.4517   2.0188   0.2431
 9SM  FAJ  F  F     0  -0.347  -0.2534   3.1003   1.0629
 9SM  CAS  C  CH1   0   0.092  -1.8646   1.4839   0.4666
 9SM  FAI  F  F     0  -0.369  -1.9978   1.2668   1.8291
 9SM  CAR  C  CH1   0  -0.001  -2.0444   0.1614  -0.2630
 9SM  OAG  O  OH1   0  -0.653  -3.2885  -0.4123   0.0104
 9SM  OAM  O  O2    0  -0.485   0.4918   1.1011   0.6103
 9SM  CAU  C  CH1   0   0.026   0.4322  -0.1725  -0.0356
 9SM  CAQ  C  CH2   0  -0.493   1.5553  -1.0050   0.5482
 9SM  CAP  C  CH1   0  -0.001   2.9461  -0.5391   0.1211
 9SM  CAK  C  CH2   0  -0.157   4.0043  -1.3501   0.8502
 9SM  OAD  O  OH1   0  -0.669   5.2801  -0.8768   0.4929
 9SM  OAF  O  OH1   0  -0.658   3.1064  -0.5893  -1.2788
 9SM  CAT  C  CH1   0  -0.125  -0.9476  -0.8161   0.1661
 9SM  NAL  N  NH1   0  -0.632  -1.0353  -2.0315  -0.5960
 9SM  CAN  C  C     0   0.527  -1.3872  -3.2275  -0.0797
 9SM  OAB  O  O     0  -0.495  -1.6002  -3.4067   1.1097
 9SM  CAA  C  CH3   0  -0.782  -1.5002  -4.3440  -1.0860
 9SM  H1   H  HOH1  0   0.498  -1.0669   3.5205  -2.5580
 9SM  H2   H  HCH1  0   0.272  -2.6242   2.2116   0.1719
 9SM  H3   H  HCH1  0   0.238  -1.9256   0.3550  -1.3403
 9SM  H4   H  HOH1  0   0.463  -3.9523  -0.0050  -0.5546
 9SM  H5   H  HCH1  0   0.244   0.6009  -0.0467  -1.1135
 9SM  H6   H  HCH2  0   0.249   1.4734  -0.9956   1.6389
 9SM  H7   H  HCH2  0   0.252   1.4188  -2.0448   0.2374
 9SM  H8   H  HCH1  0   0.234   3.0730   0.5134   0.3920
 9SM  H9   H  HCH2  0   0.200   3.8257  -1.2624   1.9299
 9SM  H10  H  HCH2  0   0.191   3.8796  -2.4141   0.5973
 9SM  H11  H  HOH1  0   0.455   5.9349  -1.4161   0.9448
 9SM  H12  H  HOH1  0   0.441   3.0287  -1.5073  -1.5619
 9SM  H13  H  HCH1  0   0.279  -1.0822  -1.0716   1.2189
 9SM  H14  H  HNH1  0   0.402  -0.9143  -1.9621  -1.5949
 9SM  H15  H  HCH3  0   0.250  -1.1446  -4.0740  -2.0783
 9SM  H16  H  HCH3  0   0.266  -0.9377  -5.2085  -0.7363
 9SM  H17  H  HCH3  0   0.270  -2.5445  -4.6475  -1.1679

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
 9SM  OAE  CAO  double  1.198  0.020  1.198
 9SM  CAA  CAN  single  1.507  0.020  1.507
 9SM  OAC  CAO  single  1.318  0.020  1.318
 9SM  CAO  CAV  single  1.546  0.020  1.546
 9SM  NAL  CAN  single  1.349  0.020  1.349
 9SM  NAL  CAT  single  1.437  0.020  1.437
 9SM  CAR  OAG  single  1.397  0.020  1.397
 9SM  CAR  CAT  single  1.531  0.020  1.531
 9SM  CAR  CAS  single  1.521  0.020  1.521
 9SM  CAN  OAB  double  1.222  0.020  1.222
 9SM  OAF  CAP  single  1.410  0.020  1.410
 9SM  CAT  CAU  single  1.536  0.020  1.536
 9SM  CAS  CAV  single  1.527  0.020  1.527
 9SM  CAS  FAI  single  1.386  0.020  1.386
 9SM  CAU  OAM  single  1.429  0.020  1.429
 9SM  CAU  CAQ  single  1.515  0.020  1.515
 9SM  CAV  OAM  single  1.366  0.020  1.366
 9SM  CAV  FAJ  single  1.372  0.020  1.372
 9SM  CAP  CAQ  single  1.528  0.020  1.528
 9SM  CAP  CAK  single  1.520  0.020  1.520
 9SM  CAK  OAD  single  1.407  0.020  1.407
 9SM  OAC  H1   single  0.850  0.020  0.980
 9SM  CAS  H2   single  0.970  0.020  1.090
 9SM  CAR  H3   single  0.970  0.020  1.090
 9SM  OAG  H4   single  0.850  0.020  0.980
 9SM  CAU  H5   single  0.970  0.020  1.090
 9SM  CAQ  H6   single  0.970  0.020  1.090
 9SM  CAQ  H7   single  0.970  0.020  1.090
 9SM  CAP  H8   single  0.970  0.020  1.090
 9SM  CAK  H9   single  0.970  0.020  1.090
 9SM  CAK  H10  single  0.970  0.020  1.090
 9SM  OAD  H11  single  0.850  0.020  0.980
 9SM  OAF  H12  single  0.850  0.020  0.980
 9SM  CAT  H13  single  0.970  0.020  1.090
 9SM  NAL  H14  single  0.860  0.020  1.020
 9SM  CAA  H15  single  0.970  0.020  1.090
 9SM  CAA  H16  single  0.970  0.020  1.090
 9SM  CAA  H17  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
 9SM  H1   OAC  CAO  110.83  3.000
 9SM  CAV  CAO  OAE  122.64  3.000
 9SM  CAV  CAO  OAC  111.61  3.000
 9SM  OAE  CAO  OAC  125.71  3.000
 9SM  OAM  CAV  CAS  111.36  3.000
 9SM  OAM  CAV  FAJ  105.62  3.000
 9SM  CAS  CAV  FAJ  108.81  3.000
 9SM  FAJ  CAV  CAO  104.34  3.000
 9SM  OAM  CAV  CAO  111.46  3.000
 9SM  CAS  CAV  CAO  114.58  3.000
 9SM  H2   CAS  CAR  111.57  3.000
 9SM  H2   CAS  FAI  107.62  3.000
 9SM  CAR  CAS  FAI  108.90  3.000
 9SM  H2   CAS  CAV  111.74  3.000
 9SM  FAI  CAS  CAV  106.72  3.000
 9SM  CAR  CAS  CAV  110.10  3.000
 9SM  H3   CAR  CAT  108.02  3.000
 9SM  H3   CAR  OAG  111.09  3.000
 9SM  CAT  CAR  OAG  108.72  3.000
 9SM  H3   CAR  CAS  107.68  3.000
 9SM  CAT  CAR  CAS  109.64  3.000
 9SM  OAG  CAR  CAS  111.62  3.000
 9SM  H4   OAG  CAR  109.00  3.000
 9SM  CAU  OAM  CAV  116.63  3.000
 9SM  H5   CAU  CAT  108.36  3.000
 9SM  H5   CAU  CAQ  109.10  3.000
 9SM  CAT  CAU  CAQ  112.65  3.000
 9SM  H5   CAU  OAM  109.58  3.000
 9SM  CAQ  CAU  OAM  106.54  3.000
 9SM  CAT  CAU  OAM  110.58  3.000
 9SM  H7   CAQ  H6   106.39  3.000
 9SM  H7   CAQ  CAP  108.91  3.000
 9SM  H6   CAQ  CAP  110.14  3.000
 9SM  H7   CAQ  CAU  108.69  3.000
 9SM  H6   CAQ  CAU  108.91  3.000
 9SM  CAP  CAQ  CAU  113.55  3.000
 9SM  H8   CAP  OAF  105.48  3.000
 9SM  H8   CAP  CAK  108.29  3.000
 9SM  OAF  CAP  CAK  112.22  3.000
 9SM  H8   CAP  CAQ  109.25  3.000
 9SM  CAK  CAP  CAQ  109.70  3.000
 9SM  OAF  CAP  CAQ  111.73  3.000
 9SM  H10  CAK  H9   106.54  3.000
 9SM  H10  CAK  OAD  111.69  3.000
 9SM  H9   CAK  OAD  111.74  3.000
 9SM  H10  CAK  CAP  109.07  3.000
 9SM  H9   CAK  CAP  108.42  3.000
 9SM  OAD  CAK  CAP  109.28  3.000
 9SM  H11  OAD  CAK  108.04  3.000
 9SM  H12  OAF  CAP  108.44  3.000
 9SM  H13  CAT  NAL  107.82  3.000
 9SM  H13  CAT  CAU  109.61  3.000
 9SM  NAL  CAT  CAU  109.85  3.000
 9SM  H13  CAT  CAR  109.36  3.000
 9SM  CAU  CAT  CAR  109.83  3.000
 9SM  NAL  CAT  CAR  110.34  3.000
 9SM  H14  NAL  CAN  118.12  3.000
 9SM  H14  NAL  CAT  117.37  3.000
 9SM  CAN  NAL  CAT  124.23  3.000
 9SM  CAA  CAN  OAB  121.89  3.000
 9SM  OAB  CAN  NAL  123.24  3.000
 9SM  CAA  CAN  NAL  114.87  3.000
 9SM  H17  CAA  H16  107.32  3.000
 9SM  H17  CAA  H15  108.27  3.000
 9SM  H16  CAA  H15  108.73  3.000
 9SM  H17  CAA  CAN  109.15  3.000
 9SM  H16  CAA  CAN  109.57  3.000
 9SM  H15  CAA  CAN  113.61  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
 9SM  CONST_01  CAA  CAN  NAL  CAT  180.00   0.0  0
 9SM  CONST_02  OAB  CAN  NAL  CAT    0.00   0.0  0
 9SM  CONST_03  H1   OAC  CAO  CAV  180.00   0.0  0
 9SM  CONST_04  H14  NAL  CAN  OAB  180.00   0.0  0
 9SM  Var_01    H15  CAA  CAN  NAL    8.31  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
 9SM  chir_01  CAV  CAS  OAM  FAJ  positiv
 9SM  chir_02  CAS  FAI  CAV  CAR  negativ
 9SM  chir_03  CAR  OAG  CAS  CAT  negativ
 9SM  chir_04  CAU  OAM  CAT  CAQ  positiv
 9SM  chir_05  CAP  OAF  CAK  CAQ  positiv
 9SM  chir_06  CAT  NAL  CAU  CAR  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
 9SM  plan-1  CAT  0.020
 9SM  plan-1  NAL  0.020
 9SM  plan-1  CAN  0.020
 9SM  plan-1  OAB  0.020
 9SM  plan-1  CAA  0.020
 9SM  plan-1  H14  0.020
 9SM  plan-2  OAC  0.020
 9SM  plan-2  CAO  0.020
 9SM  plan-2  OAE  0.020
 9SM  plan-2  CAV  0.020
 9SM  plan-2  H1   0.020

