# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 06:26:00 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (2R,3R,5R,6R)-5-(acetylamino)-2,3-difluoro-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]1C[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
 9SG  9SG  '(2R,3R,5R,6R)-5-(acetylamino)-2,3-difluoro-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-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_9SG
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
 9SG  OAB  O  O     0  -0.488  -1.2089   3.6639  -0.8284
 9SG  CAN  C  C     0   0.508  -1.2045   3.3715   0.3566
 9SG  CAA  C  CH3   0  -0.788  -1.2339   4.4041   1.4568
 9SG  NAL  N  NH1   0  -0.632  -1.1697   2.0956   0.8026
 9SG  CAT  C  CH1   0  -0.101  -1.1379   0.9297  -0.0432
 9SG  CAR  C  CH2   0  -0.544  -2.3574   0.0462   0.2091
 9SG  CAS  C  CH1   0   0.116  -2.2559  -1.2363  -0.5795
 9SG  FAI  F  F     0  -0.370  -2.2173  -0.9398  -1.9356
 9SG  CAU  C  CH1   0   0.032   0.1595   0.1551   0.2197
 9SG  OAM  O  O2    0  -0.510   0.1455  -1.1391  -0.3896
 9SG  CAV  C  CT    0   0.556  -0.9468  -1.9492  -0.2449
 9SG  FAJ  F  F     0  -0.347  -0.7558  -2.9736  -1.1338
 9SG  CAO  C  C     0   0.456  -0.9910  -2.6062   1.1511
 9SG  OAE  O  O     0  -0.398  -0.2452  -2.3173   2.0441
 9SG  OAC  O  OH1   0  -0.577  -1.9436  -3.5142   1.2097
 9SG  CAQ  C  CH1   0  -0.025   1.3793   0.8633  -0.3705
 9SG  OAG  O  OH1   0  -0.657   1.3119   0.9126  -1.7734
 9SG  CAP  C  CH1   0  -0.025   2.7035   0.2611   0.1349
 9SG  OAF  O  OH1   0  -0.657   2.7631   0.3151   1.5413
 9SG  CAK  C  CH2   0  -0.160   3.8951   0.9492  -0.5138
 9SG  OAD  O  OH1   0  -0.670   5.0770   0.3601  -0.0244
 9SG  H1   H  HCH3  0   0.262  -1.2434   5.4058   1.0360
 9SG  H2   H  HCH3  0   0.267  -2.1190   4.2780   2.0818
 9SG  H3   H  HCH3  0   0.266  -0.3620   4.3034   2.1045
 9SG  H4   H  HNH1  0   0.402  -1.1965   1.9452   1.8001
 9SG  H5   H  HCH1  0   0.278  -1.1529   1.2769  -1.0756
 9SG  H6   H  HCH2  0   0.263  -2.4447  -0.1937   1.2740
 9SG  H7   H  HCH2  0   0.295  -3.2728   0.5738  -0.0620
 9SG  H8   H  HCH1  0   0.271  -3.1136  -1.8884  -0.4062
 9SG  H9   H  HCH1  0   0.253   0.2928   0.0501   1.3009
 9SG  H10  H  HOH1  0   0.496  -1.9687  -3.9316   2.0856
 9SG  H11  H  HCH1  0   0.248   1.3421   1.9049  -0.0322
 9SG  H12  H  HOH1  0   0.447   1.2850   0.0105  -2.1116
 9SG  H13  H  HCH1  0   0.235   2.7400  -0.8039  -0.1200
 9SG  H14  H  HOH1  0   0.444   2.8220   1.2377   1.8142
 9SG  H15  H  HCH2  0   0.210   3.8169   0.8507  -1.6008
 9SG  H16  H  HCH2  0   0.188   3.8560   2.0272  -0.2896
 9SG  H17  H  HOH1  0   0.455   5.8132   0.7135  -0.5310

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
 9SG  OAE  CAO  double  1.199  0.020  1.199
 9SG  CAA  CAN  single  1.509  0.020  1.509
 9SG  OAC  CAO  single  1.317  0.020  1.317
 9SG  CAO  CAV  single  1.543  0.020  1.543
 9SG  NAL  CAN  single  1.352  0.020  1.352
 9SG  NAL  CAT  single  1.441  0.020  1.441
 9SG  CAR  CAT  single  1.527  0.020  1.527
 9SG  CAR  CAS  single  1.509  0.020  1.509
 9SG  CAN  OAB  double  1.221  0.020  1.221
 9SG  OAF  CAP  single  1.409  0.020  1.409
 9SG  CAT  CAU  single  1.534  0.020  1.534
 9SG  CAU  CAQ  single  1.529  0.020  1.529
 9SG  CAU  OAM  single  1.431  0.020  1.431
 9SG  CAS  CAV  single  1.528  0.020  1.528
 9SG  CAS  FAI  single  1.389  0.020  1.389
 9SG  CAV  OAM  single  1.368  0.020  1.368
 9SG  CAV  FAJ  single  1.370  0.020  1.370
 9SG  CAQ  CAP  single  1.540  0.020  1.540
 9SG  CAQ  OAG  single  1.405  0.020  1.405
 9SG  CAP  CAK  single  1.521  0.020  1.521
 9SG  CAK  OAD  single  1.408  0.020  1.408
 9SG  CAA  H1   single  0.970  0.020  1.090
 9SG  CAA  H2   single  0.970  0.020  1.090
 9SG  CAA  H3   single  0.970  0.020  1.090
 9SG  NAL  H4   single  0.860  0.020  1.020
 9SG  CAT  H5   single  0.970  0.020  1.090
 9SG  CAR  H6   single  0.970  0.020  1.090
 9SG  CAR  H7   single  0.970  0.020  1.090
 9SG  CAS  H8   single  0.970  0.020  1.090
 9SG  CAU  H9   single  0.970  0.020  1.090
 9SG  OAC  H10  single  0.850  0.020  0.980
 9SG  CAQ  H11  single  0.970  0.020  1.090
 9SG  OAG  H12  single  0.850  0.020  0.980
 9SG  CAP  H13  single  0.970  0.020  1.090
 9SG  OAF  H14  single  0.850  0.020  0.980
 9SG  CAK  H15  single  0.970  0.020  1.090
 9SG  CAK  H16  single  0.970  0.020  1.090
 9SG  OAD  H17  single  0.850  0.020  0.980

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
 9SG  NAL  CAN  CAA  113.93  3.000
 9SG  NAL  CAN  OAB  123.12  3.000
 9SG  CAA  CAN  OAB  122.95  3.000
 9SG  H3   CAA  H2   107.32  3.000
 9SG  H3   CAA  H1   108.80  3.000
 9SG  H2   CAA  H1   108.74  3.000
 9SG  H3   CAA  CAN  110.74  3.000
 9SG  H2   CAA  CAN  110.75  3.000
 9SG  H1   CAA  CAN  110.40  3.000
 9SG  H4   NAL  CAT  117.40  3.000
 9SG  H4   NAL  CAN  117.78  3.000
 9SG  CAT  NAL  CAN  124.79  3.000
 9SG  H5   CAT  CAU  109.58  3.000
 9SG  H5   CAT  CAR  109.27  3.000
 9SG  CAU  CAT  CAR  110.80  3.000
 9SG  H5   CAT  NAL  107.34  3.000
 9SG  CAU  CAT  NAL  109.07  3.000
 9SG  CAR  CAT  NAL  110.71  3.000
 9SG  H7   CAR  H6   106.30  3.000
 9SG  H7   CAR  CAS  109.73  3.000
 9SG  H6   CAR  CAS  109.11  3.000
 9SG  H7   CAR  CAT  110.45  3.000
 9SG  H6   CAR  CAT  110.56  3.000
 9SG  CAS  CAR  CAT  110.59  3.000
 9SG  H8   CAS  CAV  111.08  3.000
 9SG  H8   CAS  FAI  107.73  3.000
 9SG  CAV  CAS  FAI  106.84  3.000
 9SG  H8   CAS  CAR  111.84  3.000
 9SG  FAI  CAS  CAR  109.32  3.000
 9SG  CAV  CAS  CAR  109.86  3.000
 9SG  H9   CAU  CAQ  109.19  3.000
 9SG  H9   CAU  OAM  109.58  3.000
 9SG  CAQ  CAU  OAM  105.22  3.000
 9SG  H9   CAU  CAT  108.71  3.000
 9SG  OAM  CAU  CAT  112.06  3.000
 9SG  CAQ  CAU  CAT  112.01  3.000
 9SG  CAV  OAM  CAU  119.91  3.000
 9SG  CAO  CAV  FAJ  105.82  3.000
 9SG  FAJ  CAV  OAM  105.24  3.000
 9SG  CAO  CAV  OAM  111.76  3.000
 9SG  FAJ  CAV  CAS  109.05  3.000
 9SG  OAM  CAV  CAS  112.63  3.000
 9SG  CAO  CAV  CAS  111.85  3.000
 9SG  OAC  CAO  OAE  125.65  3.000
 9SG  OAC  CAO  CAV  110.76  3.000
 9SG  OAE  CAO  CAV  123.60  3.000
 9SG  H10  OAC  CAO  110.82  3.000
 9SG  H11  CAQ  CAP  107.43  3.000
 9SG  H11  CAQ  OAG  105.86  3.000
 9SG  CAP  CAQ  OAG  112.49  3.000
 9SG  H11  CAQ  CAU  107.10  3.000
 9SG  OAG  CAQ  CAU  111.30  3.000
 9SG  CAP  CAQ  CAU  112.22  3.000
 9SG  H12  OAG  CAQ  108.59  3.000
 9SG  H13  CAP  CAK  108.32  3.000
 9SG  H13  CAP  OAF  105.55  3.000
 9SG  CAK  CAP  OAF  112.04  3.000
 9SG  H13  CAP  CAQ  109.41  3.000
 9SG  CAK  CAP  CAQ  110.90  3.000
 9SG  OAF  CAP  CAQ  110.43  3.000
 9SG  H14  OAF  CAP  108.78  3.000
 9SG  H16  CAK  H15  106.72  3.000
 9SG  H16  CAK  OAD  111.61  3.000
 9SG  H15  CAK  OAD  111.56  3.000
 9SG  H16  CAK  CAP  109.15  3.000
 9SG  H15  CAK  CAP  109.08  3.000
 9SG  OAD  CAK  CAP  108.66  3.000
 9SG  H17  OAD  CAK  107.81  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
 9SG  CONST_01  CAT  NAL  CAN  OAB    0.00   0.0  0
 9SG  CONST_02  CAT  NAL  CAN  CAA  180.00   0.0  0
 9SG  CONST_03  H10  OAC  CAO  CAV  180.00   0.0  0
 9SG  CONST_04  H4   NAL  CAN  OAB  180.00   0.0  0
 9SG  Var_01    H1   CAA  CAN  OAB   -0.84  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
 9SG  chir_01  CAT  NAL  CAR  CAU  positiv
 9SG  chir_02  CAS  FAI  CAV  CAR  negativ
 9SG  chir_03  CAU  OAM  CAT  CAQ  positiv
 9SG  chir_04  CAV  OAM  CAS  CAO  positiv
 9SG  chir_05  CAQ  OAG  CAU  CAP  negativ
 9SG  chir_06  CAP  OAF  CAQ  CAK  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
 9SG  plan-1  OAB  0.020
 9SG  plan-1  CAN  0.020
 9SG  plan-1  CAA  0.020
 9SG  plan-1  NAL  0.020
 9SG  plan-1  CAT  0.020
 9SG  plan-1  H4   0.020
 9SG  plan-2  CAV  0.020
 9SG  plan-2  CAO  0.020
 9SG  plan-2  OAE  0.020
 9SG  plan-2  OAC  0.020
 9SG  plan-2  H10  0.020

