# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:38:32 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R,3R,4R,5R,6R)-5-(acetylamino)-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-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]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-carboxylic acid (non-preferred name)'  D-saccharide  38  22  .  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_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  CAA  C  CH3    0  -0.781  -1.6750   4.1436   1.4832
 SFJ  CAK  C  CH2    0  -0.160   3.9909   1.2695  -0.4501
 SFJ  CAN  C  C      0   0.526  -1.5450   3.1310   0.3730
 SFJ  CAO  C  C      0   0.335  -0.3613  -2.6853   1.0474
 SFJ  CAQ  C  CH1    0  -0.012   1.4809   0.9931  -0.3793
 SFJ  CAR  C  CH1    0   0.000  -2.1503  -0.2533   0.1697
 SFJ  CAS  C  CH1    0   0.107  -1.9140  -1.5135  -0.6477
 SFJ  CAT  C  CH1    0  -0.123  -1.0423   0.7640  -0.1083
 SFJ  CAU  C  CH1    0   0.013   0.3303   0.1043   0.0918
 SFJ  CAV  C  CT     0   0.477  -0.5198  -2.0542  -0.3726
 SFJ  NAL  N  NH1    0  -0.633  -1.1680   1.8992   0.7677
 SFJ  OAB  O  O      0  -0.500  -1.7637   3.4268  -0.7927
 SFJ  OAD  O  OH1    0  -0.670   5.1975   0.7625   0.0712
 SFJ  OAE  O  O      0  -0.568   0.7892  -2.7125   1.4998
 SFJ  OAF  O  OH1    0  -0.658   2.8507   0.5054   1.5531
 SFJ  OAG  O  OH1    0  -0.661   1.4595   1.1540  -1.7761
 SFJ  OAH  O  OH1    0  -0.661  -3.3844   0.3419  -0.1248
 SFJ  OAM  O  O2     0  -0.510   0.4275  -1.0889  -0.6630
 SFJ  FAI  F  F      0  -0.383  -1.9974  -1.1869  -1.9999
 SFJ  OAC  O  OC    -1  -0.581  -1.4103  -3.1255   1.5492
 SFJ  CAP  C  CH1    0  -0.025   2.8355   0.4789   0.1440
 SFJ  H1   H  HCH3   0   0.248  -1.3587   3.7725   2.4561
 SFJ  H2   H  HCH3   0   0.265  -1.0845   5.0260   1.2382
 SFJ  H3   H  HCH3   0   0.267  -2.7151   4.4619   1.5590
 SFJ  H6   H  HCH1   0   0.242   1.3256   1.9938   0.0391
 SFJ  H7   H  HCH1   0   0.231  -2.0940  -0.5414   1.2283
 SFJ  H8   H  HCH1   0   0.245  -2.6746  -2.2681  -0.4407
 SFJ  H9   H  HCH1   0   0.270  -1.1287   1.1228  -1.1348
 SFJ  H10  H  HCH1   0   0.243   0.4676  -0.1083   1.1602
 SFJ  H11  H  HNH1   0   0.399  -1.0455   1.7360   1.7552
 SFJ  H12  H  HOH1   0   0.454   5.9203   1.2520  -0.3305
 SFJ  H13  H  HOH1   0   0.442   2.8403   1.4243   1.8435
 SFJ  H14  H  HOH1   0   0.447   1.4908   0.2803  -2.1820
 SFJ  H15  H  HOH1   0   0.458  -4.0737  -0.1262   0.3559
 SFJ  H17  H  HCH1   0   0.234   2.9528  -0.5749  -0.1308
 SFJ  H4   H  HCH2   0   0.187   3.8616   2.3360  -0.2070
 SFJ  FAJ  F  F      0  -0.371  -0.2589  -3.0653  -1.2760
 SFJ  H5   H  HCH2   0   0.206   3.9592   1.1894  -1.5413

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  OAD  CAK  single  1.409  0.020  1.409
 SFJ  CAK  CAP  single  1.521  0.020  1.521
 SFJ  OAG  CAQ  single  1.406  0.020  1.406
 SFJ  OAB  CAN  double  1.222  0.020  1.222
 SFJ  CAP  CAQ  single  1.540  0.020  1.540
 SFJ  CAP  OAF  single  1.409  0.020  1.409
 SFJ  CAQ  CAU  single  1.528  0.020  1.528
 SFJ  CAN  CAA  single  1.508  0.020  1.508
 SFJ  CAN  NAL  single  1.347  0.020  1.347
 SFJ  CAU  CAT  single  1.536  0.020  1.536
 SFJ  CAU  OAM  single  1.415  0.020  1.415
 SFJ  NAL  CAT  single  1.439  0.020  1.439
 SFJ  CAT  CAR  single  1.530  0.020  1.530
 SFJ  OAM  CAV  single  1.383  0.020  1.383
 SFJ  FAI  CAS  single  1.394  0.020  1.394
 SFJ  FAJ  CAV  single  1.381  0.020  1.381
 SFJ  CAV  CAS  single  1.520  0.020  1.520
 SFJ  CAV  CAO  single  1.562  0.020  1.562
 SFJ  CAR  CAS  single  1.521  0.020  1.521
 SFJ  CAR  OAH  single  1.401  0.020  1.401
 SFJ  OAE  CAO  deloc   1.237  0.020  1.237
 SFJ  CAO  OAC  deloc   1.243  0.020  1.243
 SFJ  CAA  H1   single  0.970  0.020  1.090
 SFJ  CAA  H2   single  0.970  0.020  1.090
 SFJ  CAA  H3   single  0.970  0.020  1.090
 SFJ  CAK  H4   single  0.970  0.020  1.090
 SFJ  CAK  H5   single  0.970  0.020  1.090
 SFJ  CAQ  H6   single  0.970  0.020  1.090
 SFJ  CAR  H7   single  0.970  0.020  1.090
 SFJ  CAS  H8   single  0.970  0.020  1.090
 SFJ  CAT  H9   single  0.970  0.020  1.090
 SFJ  CAU  H10  single  0.970  0.020  1.090
 SFJ  NAL  H11  single  0.860  0.020  1.020
 SFJ  OAD  H12  single  0.850  0.020  0.980
 SFJ  OAF  H13  single  0.850  0.020  0.980
 SFJ  OAG  H14  single  0.850  0.020  0.980
 SFJ  OAH  H15  single  0.850  0.020  0.980
 SFJ  CAP  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
 SFJ  H3   CAA  H2   107.23  3.000
 SFJ  H3   CAA  H1   108.34  3.000
 SFJ  H2   CAA  H1   108.64  3.000
 SFJ  H3   CAA  CAN  109.23  3.000
 SFJ  H2   CAA  CAN  109.36  3.000
 SFJ  H1   CAA  CAN  113.83  3.000
 SFJ  H5   CAK  H4   106.70  3.000
 SFJ  H5   CAK  CAP  109.24  3.000
 SFJ  H4   CAK  CAP  109.15  3.000
 SFJ  H5   CAK  OAD  111.55  3.000
 SFJ  H4   CAK  OAD  111.55  3.000
 SFJ  CAP  CAK  OAD  108.60  3.000
 SFJ  OAB  CAN  NAL  123.42  3.000
 SFJ  NAL  CAN  CAA  114.98  3.000
 SFJ  OAB  CAN  CAA  121.60  3.000
 SFJ  OAC  CAO  OAE  129.01  3.000
 SFJ  OAC  CAO  CAV  115.11  3.000
 SFJ  OAE  CAO  CAV  115.85  3.000
 SFJ  H6   CAQ  CAP  107.45  3.000
 SFJ  H6   CAQ  OAG  105.82  3.000
 SFJ  CAP  CAQ  OAG  112.89  3.000
 SFJ  H6   CAQ  CAU  107.86  3.000
 SFJ  CAP  CAQ  CAU  111.30  3.000
 SFJ  OAG  CAQ  CAU  111.17  3.000
 SFJ  H7   CAR  OAH  111.04  3.000
 SFJ  H7   CAR  CAT  108.20  3.000
 SFJ  OAH  CAR  CAT  108.50  3.000
 SFJ  H7   CAR  CAS  107.02  3.000
 SFJ  OAH  CAR  CAS  112.08  3.000
 SFJ  CAT  CAR  CAS  109.93  3.000
 SFJ  H8   CAS  FAI  107.72  3.000
 SFJ  H8   CAS  CAV  111.03  3.000
 SFJ  FAI  CAS  CAV  108.29  3.000
 SFJ  H8   CAS  CAR  111.28  3.000
 SFJ  CAV  CAS  CAR  109.88  3.000
 SFJ  FAI  CAS  CAR  108.55  3.000
 SFJ  H9   CAT  NAL  107.84  3.000
 SFJ  H9   CAT  CAU  109.55  3.000
 SFJ  NAL  CAT  CAU  109.72  3.000
 SFJ  H9   CAT  CAR  109.41  3.000
 SFJ  NAL  CAT  CAR  110.53  3.000
 SFJ  CAU  CAT  CAR  109.76  3.000
 SFJ  H10  CAU  OAM  110.31  3.000
 SFJ  H10  CAU  CAT  108.76  3.000
 SFJ  OAM  CAU  CAT  110.74  3.000
 SFJ  H10  CAU  CAQ  108.56  3.000
 SFJ  OAM  CAU  CAQ  105.91  3.000
 SFJ  CAT  CAU  CAQ  112.51  3.000
 SFJ  FAJ  CAV  OAM  104.13  3.000
 SFJ  FAJ  CAV  CAS  108.38  3.000
 SFJ  OAM  CAV  CAS  109.98  3.000
 SFJ  CAS  CAV  CAO  113.66  3.000
 SFJ  FAJ  CAV  CAO  106.25  3.000
 SFJ  OAM  CAV  CAO  113.78  3.000
 SFJ  H11  NAL  CAT  117.24  3.000
 SFJ  H11  NAL  CAN  117.96  3.000
 SFJ  CAT  NAL  CAN  124.55  3.000
 SFJ  H12  OAD  CAK  107.83  3.000
 SFJ  H13  OAF  CAP  108.61  3.000
 SFJ  H14  OAG  CAQ  108.31  3.000
 SFJ  H15  OAH  CAR  108.63  3.000
 SFJ  CAV  OAM  CAU  115.42  3.000
 SFJ  H17  CAP  OAF  105.53  3.000
 SFJ  H17  CAP  CAQ  109.27  3.000
 SFJ  OAF  CAP  CAQ  110.05  3.000
 SFJ  H17  CAP  CAK  108.71  3.000
 SFJ  OAF  CAP  CAK  111.88  3.000
 SFJ  CAQ  CAP  CAK  111.21  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  CAT  NAL  CAN  CAA  180.00   0.0  0
 SFJ  CONST_02  OAB  CAN  NAL  CAT    0.00   0.0  0
 SFJ  CONST_03  H11  NAL  CAN  CAA    0.00   0.0  0
 SFJ  Var_01    H1   CAA  CAN  NAL    5.28  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  CAQ  OAG  CAP  CAU  positiv
 SFJ  chir_02  CAR  OAH  CAT  CAS  positiv
 SFJ  chir_03  CAS  FAI  CAV  CAR  negativ
 SFJ  chir_04  CAT  NAL  CAR  CAU  positiv
 SFJ  chir_05  CAU  OAM  CAQ  CAT  negativ
 SFJ  chir_06  CAV  OAM  CAS  CAO  positiv
 SFJ  chir_07  CAP  OAF  CAK  CAQ  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  CAA  0.020
 SFJ  plan-1  CAN  0.020
 SFJ  plan-1  CAT  0.020
 SFJ  plan-1  NAL  0.020
 SFJ  plan-1  OAB  0.020
 SFJ  plan-1  H11  0.020
 SFJ  plan-2  CAO  0.020
 SFJ  plan-2  CAV  0.020
 SFJ  plan-2  OAE  0.020
 SFJ  plan-2  OAC  0.020

