# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 20:57:17 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  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_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  OC    -1  -0.579  -1.2037   2.8922  -1.7819
 9SM  CAO  C  C      0   0.336  -0.1848   2.5724  -1.1448
 9SM  OAE  O  O      0  -0.574   1.0013   2.6496  -1.4876
 9SM  CAV  C  CT     0   0.470  -0.4347   2.0456   0.3037
 9SM  FAJ  F  F      0  -0.373  -0.2152   3.1199   1.1446
 9SM  CAS  C  CH1    0   0.109  -1.8491   1.5377   0.5386
 9SM  FAI  F  F      0  -0.385  -2.0093   1.3184   1.9065
 9SM  CAR  C  CH1    0  -0.001  -2.0565   0.2184  -0.1891
 9SM  OAG  O  OH1    0  -0.661  -3.3043  -0.3508   0.1008
 9SM  OAM  O  O2     0  -0.496   0.4811   1.0967   0.7188
 9SM  CAU  C  CH1    0   0.040   0.4191  -0.1359   0.0216
 9SM  CAQ  C  CH2    0  -0.488   1.5399  -1.0035   0.5603
 9SM  CAP  C  CH1    0  -0.001   2.9260  -0.5403   0.1175
 9SM  CAK  C  CH2    0  -0.157   3.9950  -1.3203   0.8639
 9SM  OAD  O  OH1    0  -0.670   5.2666  -0.8539   0.4812
 9SM  OAF  O  OH1    0  -0.660   3.0835  -0.6291  -1.2819
 9SM  CAT  C  CH1    0  -0.123  -0.9649  -0.7785   0.2057
 9SM  NAL  N  NH1    0  -0.630  -1.0667  -1.9719  -0.5928
 9SM  CAN  C  C      0   0.524  -1.4469  -3.1757  -0.1240
 9SM  OAB  O  O      0  -0.501  -1.6843  -3.3952   1.0552
 9SM  CAA  C  CH3    0  -0.782  -1.5594  -4.2578  -1.1688
 9SM  H2   H  HCH1   0   0.243  -2.5910   2.2780   0.2333
 9SM  H3   H  HCH1   0   0.231  -1.9563   0.4252  -1.2628
 9SM  H4   H  HOH1   0   0.457  -3.9718   0.0800  -0.4414
 9SM  H5   H  HCH1   0   0.229   0.5823   0.0329  -1.0527
 9SM  H6   H  HCH2   0   0.241   1.4780  -1.0178   1.6527
 9SM  H7   H  HCH2   0   0.244   1.3886  -2.0356   0.2306
 9SM  H8   H  HCH1   0   0.232   3.0413   0.5212   0.3560
 9SM  H9   H  HCH2   0   0.199   3.8247  -1.1965   1.9413
 9SM  H10  H  HCH2   0   0.189   3.8744  -2.3932   0.6489
 9SM  H11  H  HOH1   0   0.454   5.9259  -1.3530   0.9710
 9SM  H12  H  HOH1   0   0.439   2.9968  -1.5538  -1.5390
 9SM  H13  H  HCH1   0   0.267  -1.0951  -1.0645   1.2515
 9SM  H14  H  HNH1   0   0.399  -0.9228  -1.8737  -1.5861
 9SM  H15  H  HCH3   0   0.248  -1.1921  -3.9588  -2.1484
 9SM  H16  H  HCH3   0   0.264  -1.0066  -5.1378  -0.8424
 9SM  H17  H  HCH3   0   0.268  -2.6048  -4.5512  -1.2703

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  deloc   1.237  0.020  1.237
 9SM  CAA  CAN  single  1.508  0.020  1.508
 9SM  OAC  CAO  deloc   1.244  0.020  1.244
 9SM  CAO  CAV  single  1.562  0.020  1.562
 9SM  NAL  CAN  single  1.347  0.020  1.347
 9SM  NAL  CAT  single  1.440  0.020  1.440
 9SM  CAR  OAG  single  1.402  0.020  1.402
 9SM  CAR  CAT  single  1.530  0.020  1.530
 9SM  CAR  CAS  single  1.521  0.020  1.521
 9SM  CAN  OAB  double  1.223  0.020  1.223
 9SM  OAF  CAP  single  1.411  0.020  1.411
 9SM  CAT  CAU  single  1.537  0.020  1.537
 9SM  CAS  CAV  single  1.521  0.020  1.521
 9SM  CAS  FAI  single  1.395  0.020  1.395
 9SM  CAU  OAM  single  1.418  0.020  1.418
 9SM  CAU  CAQ  single  1.516  0.020  1.516
 9SM  CAV  OAM  single  1.382  0.020  1.382
 9SM  CAV  FAJ  single  1.382  0.020  1.382
 9SM  CAP  CAQ  single  1.527  0.020  1.527
 9SM  CAP  CAK  single  1.519  0.020  1.519
 9SM  CAK  OAD  single  1.407  0.020  1.407
 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  CAV  CAO  OAE  115.56  3.000
 9SM  CAV  CAO  OAC  115.53  3.000
 9SM  OAE  CAO  OAC  128.88  3.000
 9SM  OAM  CAV  CAS  109.91  3.000
 9SM  OAM  CAV  FAJ  104.22  3.000
 9SM  CAS  CAV  FAJ  108.26  3.000
 9SM  FAJ  CAV  CAO  106.07  3.000
 9SM  OAM  CAV  CAO  113.83  3.000
 9SM  CAS  CAV  CAO  113.87  3.000
 9SM  H2   CAS  CAR  111.21  3.000
 9SM  H2   CAS  FAI  107.63  3.000
 9SM  CAR  CAS  FAI  108.49  3.000
 9SM  H2   CAS  CAV  111.25  3.000
 9SM  FAI  CAS  CAV  108.11  3.000
 9SM  CAR  CAS  CAV  110.03  3.000
 9SM  H3   CAR  CAT  108.06  3.000
 9SM  H3   CAR  OAG  111.09  3.000
 9SM  CAT  CAR  OAG  108.49  3.000
 9SM  H3   CAR  CAS  106.98  3.000
 9SM  CAT  CAR  CAS  110.15  3.000
 9SM  OAG  CAR  CAS  112.01  3.000
 9SM  H4   OAG  CAR  108.62  3.000
 9SM  CAU  OAM  CAV  114.84  3.000
 9SM  H5   CAU  CAT  108.35  3.000
 9SM  H5   CAU  CAQ  108.98  3.000
 9SM  CAT  CAU  CAQ  112.57  3.000
 9SM  H5   CAU  OAM  109.91  3.000
 9SM  CAQ  CAU  OAM  106.88  3.000
 9SM  CAT  CAU  OAM  110.12  3.000
 9SM  H7   CAQ  H6   106.30  3.000
 9SM  H7   CAQ  CAP  108.92  3.000
 9SM  H6   CAQ  CAP  110.17  3.000
 9SM  H7   CAQ  CAU  109.30  3.000
 9SM  H6   CAQ  CAU  108.69  3.000
 9SM  CAP  CAQ  CAU  113.23  3.000
 9SM  H8   CAP  OAF  105.39  3.000
 9SM  H8   CAP  CAK  108.47  3.000
 9SM  OAF  CAP  CAK  112.11  3.000
 9SM  H8   CAP  CAQ  109.07  3.000
 9SM  CAK  CAP  CAQ  109.91  3.000
 9SM  OAF  CAP  CAQ  111.71  3.000
 9SM  H10  CAK  H9   106.53  3.000
 9SM  H10  CAK  OAD  111.65  3.000
 9SM  H9   CAK  OAD  111.69  3.000
 9SM  H10  CAK  CAP  109.11  3.000
 9SM  H9   CAK  CAP  108.37  3.000
 9SM  OAD  CAK  CAP  109.39  3.000
 9SM  H11  OAD  CAK  108.00  3.000
 9SM  H12  OAF  CAP  108.35  3.000
 9SM  H13  CAT  NAL  107.80  3.000
 9SM  H13  CAT  CAU  109.37  3.000
 9SM  NAL  CAT  CAU  110.11  3.000
 9SM  H13  CAT  CAR  109.43  3.000
 9SM  CAU  CAT  CAR  109.82  3.000
 9SM  NAL  CAT  CAR  110.28  3.000
 9SM  H14  NAL  CAN  118.05  3.000
 9SM  H14  NAL  CAT  117.10  3.000
 9SM  CAN  NAL  CAT  124.60  3.000
 9SM  CAA  CAN  OAB  121.65  3.000
 9SM  OAB  CAN  NAL  123.44  3.000
 9SM  CAA  CAN  NAL  114.91  3.000
 9SM  H17  CAA  H16  107.28  3.000
 9SM  H17  CAA  H15  108.28  3.000
 9SM  H16  CAA  H15  108.69  3.000
 9SM  H17  CAA  CAN  109.21  3.000
 9SM  H16  CAA  CAN  109.52  3.000
 9SM  H15  CAA  CAN  113.66  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  H14  NAL  CAN  OAB  180.00   0.0  0
 9SM  Var_01    H15  CAA  CAN  NAL    7.61  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

