# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 03:41:28 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (2R,3R,4R,5R,6R)-5-(acetylamino)-6-[(1R)-1,3-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]1[C@H](O)CCO)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
 9SP  9SP  '(2R,3R,4R,5R,6R)-5-(acetylamino)-6-[(1R)-1,3-dihydroxypropyl]-2,3-difluoro-4-hydroxytetrahydro-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_9SP
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
 9SP  OAC  O  OH1   0  -0.577  -1.3817   3.3374  -1.4774
 9SP  CAO  C  C     0   0.459  -0.3099   2.6475  -1.1470
 9SP  OAE  O  O     0  -0.398   0.6832   2.5362  -1.8085
 9SP  CAV  C  CT    0   0.540  -0.4616   2.0171   0.2570
 9SP  FAJ  F  F     0  -0.345  -0.2499   3.0542   1.1273
 9SP  CAS  C  CH1   0   0.091  -1.8416   1.4193   0.5277
 9SP  FAI  F  F     0  -0.368  -1.8965   1.1383   1.8831
 9SP  CAR  C  CH1   0   0.000  -2.0152   0.1247  -0.2524
 9SP  OAF  O  OH1   0  -0.653  -3.2263  -0.4999   0.0537
 9SP  OAM  O  O2    0  -0.493   0.5354   1.1160   0.5089
 9SP  CAU  C  CH1   0  -0.011   0.4698  -0.1266  -0.1872
 9SP  CAQ  C  CH1   0   0.012   1.6854  -0.9453   0.2376
 9SP  CAP  C  CH2   0  -0.481   2.9904  -0.2171  -0.0798
 9SP  CAK  C  CH2   0  -0.140   4.1865  -1.1467   0.0074
 9SP  OAD  O  OH1   0  -0.675   5.3541  -0.4073  -0.2810
 9SP  OAG  O  OH1   0  -0.657   1.6113  -1.3581   1.5811
 9SP  CAT  C  CH1   0  -0.112  -0.8660  -0.8282   0.0863
 9SP  NAL  N  NH1   0  -0.638  -0.9521  -2.0333  -0.6907
 9SP  CAN  C  C     0   0.530  -1.2975  -3.2356  -0.1839
 9SP  OAB  O  O     0  -0.495  -1.5242  -3.4248   1.0008
 9SP  CAA  C  CH3   0  -0.782  -1.3678  -4.3534  -1.1931
 9SP  H1   H  HOH1  0   0.498  -1.2686   3.7596  -2.3444
 9SP  H2   H  HCH1  0   0.274  -2.6385   2.1324   0.3048
 9SP  H3   H  HCH1  0   0.238  -1.9552   0.3689  -1.3243
 9SP  H4   H  HOH1  0   0.463  -3.9269  -0.0962  -0.4678
 9SP  H5   H  HCH1  0   0.248   0.5617   0.0426  -1.2688
 9SP  H6   H  HCH1  0   0.248   1.6501  -1.8617  -0.3592
 9SP  H7   H  HCH2  0   0.235   2.9307   0.2017  -1.0887
 9SP  H8   H  HCH2  0   0.236   3.1261   0.6257   0.6042
 9SP  H9   H  HCH2  0   0.195   4.2341  -1.5937   1.0073
 9SP  H10  H  HCH2  0   0.190   4.0513  -1.9724  -0.7046
 9SP  H11  H  HOH1  0   0.453   6.1088  -0.9967  -0.1968
 9SP  H12  H  HOH1  0   0.446   1.6935  -0.5822   2.1464
 9SP  H13  H  HCH1  0   0.281  -0.9254  -1.1064   1.1386
 9SP  H14  H  HNH1  0   0.401  -0.8326  -1.9555  -1.6890
 9SP  H15  H  HCH3  0   0.248  -1.1552  -4.0376  -2.2124
 9SP  H16  H  HCH3  0   0.268  -0.6573  -5.1325  -0.9167
 9SP  H17  H  HCH3  0   0.267  -2.3619  -4.7995  -1.1701

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
 9SP  CAA  CAN  single  1.508  0.020  1.508
 9SP  OAE  CAO  double  1.198  0.020  1.198
 9SP  NAL  CAN  single  1.350  0.020  1.350
 9SP  NAL  CAT  single  1.436  0.020  1.436
 9SP  OAC  CAO  single  1.317  0.020  1.317
 9SP  CAO  CAV  single  1.547  0.020  1.547
 9SP  CAR  OAF  single  1.397  0.020  1.397
 9SP  CAR  CAT  single  1.531  0.020  1.531
 9SP  CAR  CAS  single  1.521  0.020  1.521
 9SP  CAN  OAB  double  1.221  0.020  1.221
 9SP  CAT  CAU  single  1.533  0.020  1.533
 9SP  CAS  CAV  single  1.528  0.020  1.528
 9SP  CAS  FAI  single  1.385  0.020  1.385
 9SP  CAU  OAM  single  1.426  0.020  1.426
 9SP  CAU  CAQ  single  1.526  0.020  1.526
 9SP  CAV  OAM  single  1.367  0.020  1.367
 9SP  CAV  FAJ  single  1.370  0.020  1.370
 9SP  CAP  CAQ  single  1.528  0.020  1.528
 9SP  CAP  CAK  single  1.517  0.020  1.517
 9SP  CAQ  OAG  single  1.407  0.020  1.407
 9SP  CAK  OAD  single  1.412  0.020  1.412
 9SP  OAC  H1   single  0.850  0.020  0.980
 9SP  CAS  H2   single  0.970  0.020  1.090
 9SP  CAR  H3   single  0.970  0.020  1.090
 9SP  OAF  H4   single  0.850  0.020  0.980
 9SP  CAU  H5   single  0.970  0.020  1.090
 9SP  CAQ  H6   single  0.970  0.020  1.090
 9SP  CAP  H7   single  0.970  0.020  1.090
 9SP  CAP  H8   single  0.970  0.020  1.090
 9SP  CAK  H9   single  0.970  0.020  1.090
 9SP  CAK  H10  single  0.970  0.020  1.090
 9SP  OAD  H11  single  0.850  0.020  0.980
 9SP  OAG  H12  single  0.850  0.020  0.980
 9SP  CAT  H13  single  0.970  0.020  1.090
 9SP  NAL  H14  single  0.860  0.020  1.020
 9SP  CAA  H15  single  0.970  0.020  1.090
 9SP  CAA  H16  single  0.970  0.020  1.090
 9SP  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
 9SP  H1   OAC  CAO  110.92  3.000
 9SP  CAV  CAO  OAE  123.00  3.000
 9SP  CAV  CAO  OAC  111.19  3.000
 9SP  OAE  CAO  OAC  125.78  3.000
 9SP  OAM  CAV  CAS  111.60  3.000
 9SP  OAM  CAV  FAJ  105.61  3.000
 9SP  CAS  CAV  FAJ  108.86  3.000
 9SP  FAJ  CAV  CAO  104.65  3.000
 9SP  OAM  CAV  CAO  111.37  3.000
 9SP  CAS  CAV  CAO  114.13  3.000
 9SP  H2   CAS  CAR  111.57  3.000
 9SP  H2   CAS  FAI  107.65  3.000
 9SP  CAR  CAS  FAI  108.94  3.000
 9SP  H2   CAS  CAV  111.55  3.000
 9SP  FAI  CAS  CAV  106.76  3.000
 9SP  CAR  CAS  CAV  110.19  3.000
 9SP  H3   CAR  CAT  108.21  3.000
 9SP  H3   CAR  OAF  111.09  3.000
 9SP  CAT  CAR  OAF  108.91  3.000
 9SP  H3   CAR  CAS  107.71  3.000
 9SP  CAT  CAR  CAS  109.30  3.000
 9SP  OAF  CAR  CAS  111.54  3.000
 9SP  H4   OAF  CAR  108.97  3.000
 9SP  CAU  OAM  CAV  116.80  3.000
 9SP  H5   CAU  CAT  108.60  3.000
 9SP  H5   CAU  CAQ  106.86  3.000
 9SP  CAT  CAU  CAQ  113.51  3.000
 9SP  H5   CAU  OAM  110.04  3.000
 9SP  CAQ  CAU  OAM  107.16  3.000
 9SP  CAT  CAU  OAM  110.59  3.000
 9SP  H6   CAQ  OAG  105.86  3.000
 9SP  H6   CAQ  CAP  108.27  3.000
 9SP  OAG  CAQ  CAP  112.53  3.000
 9SP  H6   CAQ  CAU  105.77  3.000
 9SP  OAG  CAQ  CAU  112.41  3.000
 9SP  CAP  CAQ  CAU  111.53  3.000
 9SP  H8   CAP  H7   106.77  3.000
 9SP  H8   CAP  CAK  109.77  3.000
 9SP  H7   CAP  CAK  109.30  3.000
 9SP  H8   CAP  CAQ  110.08  3.000
 9SP  H7   CAP  CAQ  109.12  3.000
 9SP  CAK  CAP  CAQ  111.68  3.000
 9SP  H10  CAK  H9   106.85  3.000
 9SP  H10  CAK  OAD  111.29  3.000
 9SP  H9   CAK  OAD  111.35  3.000
 9SP  H10  CAK  CAP  109.04  3.000
 9SP  H9   CAK  CAP  109.66  3.000
 9SP  OAD  CAK  CAP  108.62  3.000
 9SP  H11  OAD  CAK  108.07  3.000
 9SP  H12  OAG  CAQ  108.62  3.000
 9SP  H13  CAT  NAL  107.74  3.000
 9SP  H13  CAT  CAU  109.66  3.000
 9SP  NAL  CAT  CAU  109.85  3.000
 9SP  H13  CAT  CAR  109.36  3.000
 9SP  CAU  CAT  CAR  109.25  3.000
 9SP  NAL  CAT  CAR  110.95  3.000
 9SP  H14  NAL  CAN  118.08  3.000
 9SP  H14  NAL  CAT  117.62  3.000
 9SP  CAN  NAL  CAT  124.03  3.000
 9SP  CAA  CAN  OAB  121.74  3.000
 9SP  OAB  CAN  NAL  123.36  3.000
 9SP  CAA  CAN  NAL  114.90  3.000
 9SP  H17  CAA  H16  107.26  3.000
 9SP  H17  CAA  H15  108.48  3.000
 9SP  H16  CAA  H15  108.52  3.000
 9SP  H17  CAA  CAN  109.38  3.000
 9SP  H16  CAA  CAN  109.25  3.000
 9SP  H15  CAA  CAN  113.75  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
 9SP  CONST_01  CAA  CAN  NAL  CAT   180.00   0.0  0
 9SP  CONST_02  OAB  CAN  NAL  CAT     0.00   0.0  0
 9SP  CONST_03  H1   OAC  CAO  CAV   180.00   0.0  0
 9SP  CONST_04  H14  NAL  CAN  OAB   180.00   0.0  0
 9SP  Var_01    OAD  CAK  CAP  CAQ  -179.32  30.0  3
 9SP  Var_02    H15  CAA  CAN  NAL    -1.56  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
 9SP  chir_01  CAV  CAS  OAM  FAJ  positiv
 9SP  chir_02  CAS  FAI  CAV  CAR  negativ
 9SP  chir_03  CAR  OAF  CAS  CAT  negativ
 9SP  chir_04  CAU  OAM  CAT  CAQ  positiv
 9SP  chir_05  CAQ  OAG  CAU  CAP  negativ
 9SP  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
 9SP  plan-1  CAT  0.020
 9SP  plan-1  NAL  0.020
 9SP  plan-1  CAN  0.020
 9SP  plan-1  OAB  0.020
 9SP  plan-1  CAA  0.020
 9SP  plan-1  H14  0.020
 9SP  plan-2  OAC  0.020
 9SP  plan-2  CAO  0.020
 9SP  plan-2  OAE  0.020
 9SP  plan-2  CAV  0.020
 9SP  plan-2  H1   0.020

