# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 18:17:32 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  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_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  -0.493  -1.2418   3.6934  -0.7392
 9SG  CAN  C  C      0   0.505  -1.2249   3.3362   0.4289
 9SG  CAA  C  CH3    0  -0.787  -1.2676   4.3103   1.5817
 9SG  NAL  N  NH1    0  -0.629  -1.1701   2.0411   0.8057
 9SG  CAT  C  CH1    0  -0.092  -1.1335   0.9172  -0.0982
 9SG  CAR  C  CH2    0  -0.533  -2.3426   0.0093   0.1296
 9SG  CAS  C  CH1    0   0.137  -2.2264  -1.2699  -0.6666
 9SG  FAI  F  F      0  -0.388  -2.2594  -0.9552  -2.0287
 9SG  CAU  C  CH1    0   0.028   0.1686   0.1307   0.1055
 9SG  OAM  O  O2     0  -0.515   0.1484  -1.0734  -0.6441
 9SG  CAV  C  CT     0   0.486  -0.8950  -1.9395  -0.3694
 9SG  FAJ  F  F      0  -0.374  -0.7147  -2.9766  -1.2647
 9SG  CAO  C  C      0   0.334  -0.8278  -2.5767   1.0550
 9SG  OAE  O  O      0  -0.569   0.2965  -2.6520   1.5654
 9SG  OAC  O  OC    -1  -0.585  -1.9160  -2.9766   1.5051
 9SG  CAQ  C  CH1    0  -0.014   1.3994   0.8976  -0.3782
 9SG  OAG  O  OH1    0  -0.663   1.3918   1.0355  -1.7782
 9SG  CAP  C  CH1    0  -0.025   2.7013   0.2690   0.1524
 9SG  OAF  O  OH1    0  -0.658   2.7324   0.3382   1.5601
 9SG  CAK  C  CH2    0  -0.160   3.9250   0.9184  -0.4749
 9SG  OAD  O  OH1    0  -0.671   5.0793   0.3099   0.0570
 9SG  H1   H  HCH3   0   0.261  -1.2420   5.3327   1.2145
 9SG  H2   H  HCH3   0   0.267  -2.1785   4.1725   2.1662
 9SG  H3   H  HCH3   0   0.263  -0.4238   4.1569   2.2554
 9SG  H4   H  HNH1   0   0.399  -1.1918   1.8380   1.7940
 9SG  H5   H  HCH1   0   0.265  -1.1595   1.3128  -1.1131
 9SG  H6   H  HCH2   0   0.251  -2.4211  -0.2524   1.1885
 9SG  H7   H  HCH2   0   0.274  -3.2647   0.5321  -0.1310
 9SG  H8   H  HCH1   0   0.241  -3.0574  -1.9453  -0.4661
 9SG  H9   H  HCH1   0   0.238   0.2834  -0.0907   1.1741
 9SG  H11  H  HCH1   0   0.240   1.3397   1.9159   0.0221
 9SG  H12  H  HOH1   0   0.446   1.2899   0.1587  -2.1658
 9SG  H13  H  HCH1   0   0.233   2.7112  -0.7996  -0.0883
 9SG  H14  H  HOH1   0   0.442   2.7992   1.2635   1.8215
 9SG  H15  H  HCH2   0   0.207   3.8754   0.8033  -1.5620
 9SG  H16  H  HCH2   0   0.186   3.9068   2.0005  -0.2692
 9SG  H17  H  HOH1   0   0.454   5.8418   0.6813  -0.3950

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  deloc   1.237  0.020  1.237
 9SG  CAA  CAN  single  1.510  0.020  1.510
 9SG  OAC  CAO  deloc   1.244  0.020  1.244
 9SG  CAO  CAV  single  1.562  0.020  1.562
 9SG  NAL  CAN  single  1.350  0.020  1.350
 9SG  NAL  CAT  single  1.443  0.020  1.443
 9SG  CAR  CAT  single  1.529  0.020  1.529
 9SG  CAR  CAS  single  1.511  0.020  1.511
 9SG  CAN  OAB  double  1.222  0.020  1.222
 9SG  OAF  CAP  single  1.410  0.020  1.410
 9SG  CAT  CAU  single  1.535  0.020  1.535
 9SG  CAU  CAQ  single  1.529  0.020  1.529
 9SG  CAU  OAM  single  1.419  0.020  1.419
 9SG  CAS  CAV  single  1.520  0.020  1.520
 9SG  CAS  FAI  single  1.398  0.020  1.398
 9SG  CAV  OAM  single  1.384  0.020  1.384
 9SG  CAV  FAJ  single  1.382  0.020  1.382
 9SG  CAQ  CAP  single  1.540  0.020  1.540
 9SG  CAQ  OAG  single  1.407  0.020  1.407
 9SG  CAP  CAK  single  1.521  0.020  1.521
 9SG  CAK  OAD  single  1.409  0.020  1.409
 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  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  114.02  3.000
 9SG  NAL  CAN  OAB  123.23  3.000
 9SG  CAA  CAN  OAB  122.75  3.000
 9SG  H3   CAA  H2   107.29  3.000
 9SG  H3   CAA  H1   108.83  3.000
 9SG  H2   CAA  H1   108.64  3.000
 9SG  H3   CAA  CAN  111.04  3.000
 9SG  H2   CAA  CAN  110.56  3.000
 9SG  H1   CAA  CAN  110.39  3.000
 9SG  H4   NAL  CAT  117.21  3.000
 9SG  H4   NAL  CAN  117.75  3.000
 9SG  CAT  NAL  CAN  125.00  3.000
 9SG  H5   CAT  CAU  109.26  3.000
 9SG  H5   CAT  CAR  109.60  3.000
 9SG  CAU  CAT  CAR  110.30  3.000
 9SG  H5   CAT  NAL  107.46  3.000
 9SG  CAU  CAT  NAL  109.73  3.000
 9SG  CAR  CAT  NAL  110.44  3.000
 9SG  H7   CAR  H6   106.57  3.000
 9SG  H7   CAR  CAS  110.16  3.000
 9SG  H6   CAR  CAS  108.25  3.000
 9SG  H7   CAR  CAT  110.37  3.000
 9SG  H6   CAR  CAT  110.06  3.000
 9SG  CAS  CAR  CAT  111.30  3.000
 9SG  H8   CAS  CAV  111.05  3.000
 9SG  H8   CAS  FAI  107.50  3.000
 9SG  CAV  CAS  FAI  108.08  3.000
 9SG  H8   CAS  CAR  111.66  3.000
 9SG  FAI  CAS  CAR  108.71  3.000
 9SG  CAV  CAS  CAR  109.72  3.000
 9SG  H9   CAU  CAQ  108.97  3.000
 9SG  H9   CAU  OAM  110.17  3.000
 9SG  CAQ  CAU  OAM  105.67  3.000
 9SG  H9   CAU  CAT  108.74  3.000
 9SG  OAM  CAU  CAT  110.66  3.000
 9SG  CAQ  CAU  CAT  112.59  3.000
 9SG  CAV  OAM  CAU  115.93  3.000
 9SG  CAO  CAV  FAJ  106.20  3.000
 9SG  FAJ  CAV  OAM  104.05  3.000
 9SG  CAO  CAV  OAM  113.83  3.000
 9SG  FAJ  CAV  CAS  108.56  3.000
 9SG  OAM  CAV  CAS  110.25  3.000
 9SG  CAO  CAV  CAS  113.31  3.000
 9SG  OAC  CAO  OAE  128.78  3.000
 9SG  OAC  CAO  CAV  115.06  3.000
 9SG  OAE  CAO  CAV  116.12  3.000
 9SG  H11  CAQ  CAP  107.43  3.000
 9SG  H11  CAQ  OAG  105.79  3.000
 9SG  CAP  CAQ  OAG  112.79  3.000
 9SG  H11  CAQ  CAU  107.86  3.000
 9SG  OAG  CAQ  CAU  111.08  3.000
 9SG  CAP  CAQ  CAU  111.52  3.000
 9SG  H12  OAG  CAQ  108.15  3.000
 9SG  H13  CAP  CAK  108.58  3.000
 9SG  H13  CAP  OAF  105.49  3.000
 9SG  CAK  CAP  OAF  111.91  3.000
 9SG  H13  CAP  CAQ  109.28  3.000
 9SG  CAK  CAP  CAQ  111.34  3.000
 9SG  OAF  CAP  CAQ  110.04  3.000
 9SG  H14  OAF  CAP  108.63  3.000
 9SG  H16  CAK  H15  106.74  3.000
 9SG  H16  CAK  OAD  111.55  3.000
 9SG  H15  CAK  OAD  111.51  3.000
 9SG  H16  CAK  CAP  109.22  3.000
 9SG  H15  CAK  CAP  109.17  3.000
 9SG  OAD  CAK  CAP  108.61  3.000
 9SG  H17  OAD  CAK  107.79  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  H4   NAL  CAN  OAB  180.00   0.0  0
 9SG  Var_01    H1   CAA  CAN  OAB   -4.03  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

