# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 21:15:54 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (2R,3R,4R,5R,6R)-5-(acetylamino)-6-[(1R,2R)-1,2-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: C[C@@H](O)[C@@H](O)[C@@H]1O[C@](F)([C@H](F)[C@H](O)[C@H]1NC(C)=O)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
 9T7  9T7  '(2R,3R,4R,5R,6R)-5-(acetylamino)-6-[(1R,2R)-1,2-dihydroxypropyl]-2,3-difluoro-4-hydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  D-saccharide  37  21  .  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_9T7
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
 9T7  OAC  O  OC    -1  -0.580   2.3149   2.3232  -1.5728
 9T7  CAO  C  C      0   0.335   2.3577   1.1866  -1.0705
 9T7  OAE  O  O      0  -0.570   2.8514   0.1508  -1.5322
 9T7  CAV  C  CT     0   0.476   1.7444   1.0727   0.3612
 9T7  FAJ  F  F      0  -0.372   2.7908   1.2641   1.2426
 9T7  CAS  C  CH1    0   0.106   0.6771   2.1150   0.6521
 9T7  FAI  F  F      0  -0.383   0.3630   2.0493   2.0079
 9T7  CAR  C  CH1    0  -0.003  -0.5774   1.8074  -0.1506
 9T7  OAD  O  OH1    0  -0.660  -1.6319   2.6742   0.1687
 9T7  OAM  O  O2     0  -0.509   1.2687  -0.1881   0.6700
 9T7  CAU  C  CH1    0   0.017   0.1346  -0.6061  -0.0688
 9T7  CAQ  C  CH1    0  -0.002  -0.2063  -2.0094   0.4336
 9T7  CAP  C  CH1    0   0.006   0.8475  -3.0487   0.0087
 9T7  CAK  C  CH3    0  -0.684   0.5669  -4.4176   0.6099
 9T7  OAF  O  OH1    0  -0.662   0.9246  -3.1109  -1.4015
 9T7  OAG  O  OH1    0  -0.662  -0.4263  -2.0115   1.8227
 9T7  CAT  C  CH1    0  -0.123  -1.0345   0.3742   0.1217
 9T7  NAL  N  NH1    0  -0.633  -2.1158   0.0179  -0.7598
 9T7  CAN  C  C      0   0.526  -3.3834  -0.2147  -0.3665
 9T7  OAB  O  O      0  -0.499  -3.7396  -0.2059   0.8025
 9T7  CAA  C  CH3    0  -0.782  -4.3515  -0.5037  -1.4872
 9T7  H2   H  HCH1   0   0.244   1.0421   3.1222   0.4428
 9T7  H3   H  HCH1   0   0.230  -0.3094   1.8911  -1.2128
 9T7  H4   H  HOH1   0   0.457  -1.4786   3.5176  -0.2683
 9T7  H5   H  HCH1   0   0.239   0.3802  -0.6645  -1.1364
 9T7  H6   H  HCH1   0   0.237  -1.1577  -2.3055  -0.0239
 9T7  H7   H  HCH1   0   0.228   1.8350  -2.7117   0.3385
 9T7  H8   H  HCH3   0   0.218  -0.4303  -4.7740   0.3361
 9T7  H9   H  HCH3   0   0.235   1.2955  -5.1436   0.2472
 9T7  H10  H  HCH3   0   0.233   0.6269  -4.4035   1.6966
 9T7  H11  H  HOH1   0   0.441   0.1049  -3.4969  -1.7299
 9T7  H12  H  HOH1   0   0.445   0.3721  -1.6912   2.2575
 9T7  H13  H  HCH1   0   0.271  -1.4001   0.3009   1.1469
 9T7  H14  H  HNH1   0   0.398  -1.9269   0.0351  -1.7501
 9T7  H15  H  HCH3   0   0.265  -4.8451  -1.4571  -1.3022
 9T7  H16  H  HCH3   0   0.267  -5.1245   0.2648  -1.5036
 9T7  H17  H  HCH3   0   0.248  -3.8853  -0.5421  -2.4701

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
 9T7  OAE  CAO  deloc   1.237  0.020  1.237
 9T7  CAA  CAN  single  1.509  0.020  1.509
 9T7  OAC  CAO  deloc   1.243  0.020  1.243
 9T7  CAO  CAV  single  1.562  0.020  1.562
 9T7  NAL  CAN  single  1.347  0.020  1.347
 9T7  NAL  CAT  single  1.440  0.020  1.440
 9T7  CAR  OAD  single  1.402  0.020  1.402
 9T7  CAR  CAS  single  1.521  0.020  1.521
 9T7  CAR  CAT  single  1.529  0.020  1.529
 9T7  CAN  OAB  double  1.222  0.020  1.222
 9T7  CAS  CAV  single  1.520  0.020  1.520
 9T7  CAS  FAI  single  1.393  0.020  1.393
 9T7  CAT  CAU  single  1.538  0.020  1.538
 9T7  CAU  OAM  single  1.417  0.020  1.417
 9T7  CAU  CAQ  single  1.529  0.020  1.529
 9T7  CAV  OAM  single  1.383  0.020  1.383
 9T7  CAV  FAJ  single  1.381  0.020  1.381
 9T7  OAF  CAP  single  1.414  0.020  1.414
 9T7  CAQ  CAP  single  1.540  0.020  1.540
 9T7  CAQ  OAG  single  1.406  0.020  1.406
 9T7  CAP  CAK  single  1.521  0.020  1.521
 9T7  CAS  H2   single  0.970  0.020  1.090
 9T7  CAR  H3   single  0.970  0.020  1.090
 9T7  OAD  H4   single  0.850  0.020  0.980
 9T7  CAU  H5   single  0.970  0.020  1.090
 9T7  CAQ  H6   single  0.970  0.020  1.090
 9T7  CAP  H7   single  0.970  0.020  1.090
 9T7  CAK  H8   single  0.970  0.020  1.090
 9T7  CAK  H9   single  0.970  0.020  1.090
 9T7  CAK  H10  single  0.970  0.020  1.090
 9T7  OAF  H11  single  0.850  0.020  0.980
 9T7  OAG  H12  single  0.850  0.020  0.980
 9T7  CAT  H13  single  0.970  0.020  1.090
 9T7  NAL  H14  single  0.860  0.020  1.020
 9T7  CAA  H15  single  0.970  0.020  1.090
 9T7  CAA  H16  single  0.970  0.020  1.090
 9T7  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
 9T7  CAV  CAO  OAE  115.97  3.000
 9T7  CAV  CAO  OAC  115.06  3.000
 9T7  OAE  CAO  OAC  128.94  3.000
 9T7  OAM  CAV  CAS  109.94  3.000
 9T7  OAM  CAV  FAJ  104.15  3.000
 9T7  CAS  CAV  FAJ  108.34  3.000
 9T7  FAJ  CAV  CAO  106.10  3.000
 9T7  OAM  CAV  CAO  113.98  3.000
 9T7  CAS  CAV  CAO  113.66  3.000
 9T7  H2   CAS  CAR  111.17  3.000
 9T7  H2   CAS  FAI  107.79  3.000
 9T7  CAR  CAS  FAI  108.55  3.000
 9T7  H2   CAS  CAV  111.18  3.000
 9T7  FAI  CAS  CAV  108.20  3.000
 9T7  CAR  CAS  CAV  109.85  3.000
 9T7  H3   CAR  CAT  108.45  3.000
 9T7  H3   CAR  OAD  110.89  3.000
 9T7  CAT  CAR  OAD  108.31  3.000
 9T7  H3   CAR  CAS  107.08  3.000
 9T7  CAT  CAR  CAS  110.01  3.000
 9T7  OAD  CAR  CAS  112.04  3.000
 9T7  H4   OAD  CAR  108.59  3.000
 9T7  CAU  OAM  CAV  115.34  3.000
 9T7  H5   CAU  CAT  108.95  3.000
 9T7  H5   CAU  CAQ  108.71  3.000
 9T7  CAT  CAU  CAQ  112.02  3.000
 9T7  H5   CAU  OAM  110.12  3.000
 9T7  CAQ  CAU  OAM  106.14  3.000
 9T7  CAT  CAU  OAM  110.86  3.000
 9T7  H6   CAQ  OAG  106.02  3.000
 9T7  H6   CAQ  CAP  107.24  3.000
 9T7  OAG  CAQ  CAP  112.24  3.000
 9T7  H6   CAQ  CAU  107.71  3.000
 9T7  OAG  CAQ  CAU  111.15  3.000
 9T7  CAP  CAQ  CAU  112.10  3.000
 9T7  H7   CAP  OAF  105.36  3.000
 9T7  H7   CAP  CAK  108.94  3.000
 9T7  OAF  CAP  CAK  111.39  3.000
 9T7  H7   CAP  CAQ  109.06  3.000
 9T7  CAK  CAP  CAQ  111.84  3.000
 9T7  OAF  CAP  CAQ  110.01  3.000
 9T7  H10  CAK  H9   107.68  3.000
 9T7  H10  CAK  H8   107.72  3.000
 9T7  H9   CAK  H8   107.99  3.000
 9T7  H10  CAK  CAP  111.88  3.000
 9T7  H9   CAK  CAP  110.14  3.000
 9T7  H8   CAK  CAP  111.25  3.000
 9T7  H11  OAF  CAP  108.13  3.000
 9T7  H12  OAG  CAQ  108.39  3.000
 9T7  H13  CAT  NAL  107.88  3.000
 9T7  H13  CAT  CAU  109.17  3.000
 9T7  NAL  CAT  CAU  109.72  3.000
 9T7  H13  CAT  CAR  109.30  3.000
 9T7  CAU  CAT  CAR  110.38  3.000
 9T7  NAL  CAT  CAR  110.33  3.000
 9T7  H14  NAL  CAN  117.76  3.000
 9T7  H14  NAL  CAT  117.16  3.000
 9T7  CAN  NAL  CAT  124.78  3.000
 9T7  CAA  CAN  OAB  121.66  3.000
 9T7  OAB  CAN  NAL  123.51  3.000
 9T7  CAA  CAN  NAL  114.83  3.000
 9T7  H17  CAA  H16  108.36  3.000
 9T7  H17  CAA  H15  108.45  3.000
 9T7  H16  CAA  H15  107.35  3.000
 9T7  H17  CAA  CAN  113.75  3.000
 9T7  H16  CAA  CAN  109.34  3.000
 9T7  H15  CAA  CAN  109.40  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
 9T7  CONST_01  CAA  CAN  NAL  CAT  180.00   0.0  0
 9T7  CONST_02  OAB  CAN  NAL  CAT    0.00   0.0  0
 9T7  CONST_03  H14  NAL  CAN  OAB  180.00   0.0  0
 9T7  Var_01    H15  CAA  CAN  NAL  124.71  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
 9T7  chir_01  CAV  CAS  OAM  FAJ  positiv
 9T7  chir_02  CAS  FAI  CAR  CAV  positiv
 9T7  chir_03  CAR  OAD  CAS  CAT  negativ
 9T7  chir_04  CAU  OAM  CAT  CAQ  positiv
 9T7  chir_05  CAQ  OAG  CAU  CAP  negativ
 9T7  chir_06  CAP  OAF  CAQ  CAK  negativ
 9T7  chir_07  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
 9T7  plan-1  CAT  0.020
 9T7  plan-1  NAL  0.020
 9T7  plan-1  CAN  0.020
 9T7  plan-1  OAB  0.020
 9T7  plan-1  CAA  0.020
 9T7  plan-1  H14  0.020
 9T7  plan-2  OAC  0.020
 9T7  plan-2  CAO  0.020
 9T7  plan-2  OAE  0.020
 9T7  plan-2  CAV  0.020

