# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 04:30:42 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R,3R,4R,5R)-3-(acetylamino)-6-carboxy-2-[(1R)-1,3-dihydroxypropyl]-5-fluoro-4-hydroxy-2,3,4,5-tetrahydropyranium (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(=[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
 9SD  9SD  '(2R,3R,4R,5R)-3-(acetylamino)-6-carboxy-2-[(1R)-1,3-dihydroxypropyl]-5-fluoro-4-hydroxy-2,3,4,5-tetrahydropyranium (non-preferred name)'  ligand  37  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9SD
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
 9SD  O1B  O  O     0  -0.346   1.5602  -4.0727   0.1338
 9SD  C1   C  C     0   0.563   1.8360  -2.9104   0.1174
 9SD  O1A  O  OH1   0  -0.546   2.9851  -2.3296  -0.0539
 9SD  C2   C  C     0   0.390   0.7286  -1.8830   0.3261
 9SD  C3   C  CH1   0   0.079  -0.7077  -2.3216   0.2678
 9SD  F1   F  F     0  -0.336  -0.8839  -2.5206  -1.0900
 9SD  C4   C  CH1   0   0.032  -1.6553  -1.2535   0.7922
 9SD  O6   O  OC2   1  -0.282   1.0809  -0.7133   0.4810
 9SD  C6   C  CH1   0  -0.016   0.1711   0.4622   0.6271
 9SD  C7   C  CH1   0  -0.001   0.8149   1.5699  -0.2050
 9SD  C8   C  CH2   0  -0.513   2.1755   1.9919   0.3348
 9SD  C9   C  CH2   0  -0.133   2.6856   3.2497  -0.3484
 9SD  O9   O  OH1   0  -0.670   3.9059   3.6091   0.2573
 9SD  O7   O  OH1   0  -0.648   0.8274   1.2193  -1.5620
 9SD  C5   C  CH1   0  -0.177  -1.2552   0.1043   0.2152
 9SD  N5   N  NH1   0  -0.642  -2.1166   1.1492   0.6781
 9SD  C10  C  C     0   0.536  -2.8843   1.9021  -0.1503
 9SD  O10  O  O     0  -0.477  -2.8428   1.7959  -1.3630
 9SD  C11  C  CH3   0  -0.781  -3.7791   2.8934   0.5435
 9SD  O4   O  OH1   0  -0.641  -2.9581  -1.5457   0.4120
 9SD  H1   H  HOH1  0   0.523   3.6997  -2.9757  -0.1873
 9SD  H3   H  HCH1  0   0.332  -0.8341  -3.2701   0.7926
 9SD  H4   H  HCH1  0   0.286  -1.5339  -1.2309   1.8836
 9SD  H5   H  HCH1  0   0.352   0.2375   0.6891   1.6939
 9SD  H6   H  HCH1  0   0.281   0.1282   2.4165  -0.0947
 9SD  H7   H  HCH2  0   0.260   2.0795   2.1838   1.4066
 9SD  H8   H  HCH2  0   0.251   2.9075   1.1857   0.2182
 9SD  H9   H  HCH2  0   0.201   2.8114   3.0686  -1.4220
 9SD  H10  H  HCH2  0   0.199   1.9330   4.0430  -0.2452
 9SD  H11  H  HOH1  0   0.457   4.2682   4.3597  -0.2218
 9SD  H12  H  HOH1  0   0.461   1.6700   0.8097  -1.7872
 9SD  H13  H  HCH1  0   0.318  -1.3253   0.0739  -0.8749
 9SD  H14  H  HNH1  0   0.414  -2.2413   1.2519   1.6738
 9SD  H15  H  HCH3  0   0.254  -3.7151   2.8560   1.6288
 9SD  H16  H  HCH3  0   0.274  -3.5201   3.9000   0.2164
 9SD  H17  H  HCH3  0   0.274  -4.8125   2.7118   0.2498
 9SD  H18  H  HOH1  0   0.476  -3.3984  -2.0262   1.1201

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
 9SD  C11  C10  single  1.505  0.020  1.505
 9SD  O9   C9   single  1.409  0.020  1.409
 9SD  N5   C10  single  1.357  0.020  1.357
 9SD  N5   C5   single  1.431  0.020  1.431
 9SD  C10  O10  double  1.218  0.020  1.218
 9SD  C8   C9   single  1.520  0.020  1.520
 9SD  C8   C7   single  1.523  0.020  1.523
 9SD  C7   C6   single  1.528  0.020  1.528
 9SD  C7   O7   single  1.402  0.020  1.402
 9SD  C6   C5   single  1.527  0.020  1.527
 9SD  C6   O6   single  1.494  0.020  1.494
 9SD  C4   C5   single  1.529  0.020  1.529
 9SD  C4   O4   single  1.388  0.020  1.388
 9SD  C4   C3   single  1.521  0.020  1.521
 9SD  O6   C2   double  1.231  0.020  1.231
 9SD  C3   C2   single  1.503  0.020  1.503
 9SD  C3   F1   single  1.384  0.020  1.384
 9SD  C2   C1   single  1.525  0.020  1.525
 9SD  C1   O1B  double  1.195  0.020  1.195
 9SD  C1   O1A  single  1.299  0.020  1.299
 9SD  O1A  H1   single  0.850  0.020  0.980
 9SD  C3   H3   single  0.970  0.020  1.090
 9SD  C4   H4   single  0.970  0.020  1.090
 9SD  C6   H5   single  0.970  0.020  1.090
 9SD  C7   H6   single  0.970  0.020  1.090
 9SD  C8   H7   single  0.970  0.020  1.090
 9SD  C8   H8   single  0.970  0.020  1.090
 9SD  C9   H9   single  0.970  0.020  1.090
 9SD  C9   H10  single  0.970  0.020  1.090
 9SD  O9   H11  single  0.850  0.020  0.980
 9SD  O7   H12  single  0.850  0.020  0.980
 9SD  C5   H13  single  0.970  0.020  1.090
 9SD  N5   H14  single  0.860  0.020  1.020
 9SD  C11  H15  single  0.970  0.020  1.090
 9SD  C11  H16  single  0.970  0.020  1.090
 9SD  C11  H17  single  0.970  0.020  1.090
 9SD  O4   H18  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
 9SD  C2   C1   O1A  111.05  3.000
 9SD  O1A  C1   O1B  129.87  3.000
 9SD  C2   C1   O1B  119.07  3.000
 9SD  H1   O1A  C1   111.78  3.000
 9SD  O6   C2   C3   123.74  3.000
 9SD  C3   C2   C1   119.48  3.000
 9SD  O6   C2   C1   116.71  3.000
 9SD  H3   C3   C4   111.86  3.000
 9SD  H3   C3   F1   109.40  3.000
 9SD  C4   C3   F1   111.10  3.000
 9SD  H3   C3   C2   110.22  3.000
 9SD  F1   C3   C2   101.64  3.000
 9SD  C4   C3   C2   112.16  3.000
 9SD  H4   C4   O4   112.35  3.000
 9SD  H4   C4   C5   109.14  3.000
 9SD  O4   C4   C5   109.22  3.000
 9SD  H4   C4   C3   106.75  3.000
 9SD  O4   C4   C3   110.03  3.000
 9SD  C5   C4   C3   109.30  3.000
 9SD  C6   O6   C2   125.85  3.000
 9SD  H5   C6   C5   111.63  3.000
 9SD  H5   C6   C7   110.83  3.000
 9SD  C5   C6   C7   114.62  3.000
 9SD  H5   C6   O6   102.83  3.000
 9SD  C5   C6   O6   110.98  3.000
 9SD  C7   C6   O6   105.11  3.000
 9SD  H6   C7   O7   107.24  3.000
 9SD  H6   C7   C8   108.06  3.000
 9SD  O7   C7   C8   113.86  3.000
 9SD  H6   C7   C6   103.96  3.000
 9SD  O7   C7   C6   110.47  3.000
 9SD  C8   C7   C6   112.59  3.000
 9SD  H8   C8   H7   107.01  3.000
 9SD  H8   C8   C9   109.70  3.000
 9SD  H7   C8   C9   108.96  3.000
 9SD  H8   C8   C7   110.81  3.000
 9SD  H7   C8   C7   108.52  3.000
 9SD  C9   C8   C7   111.70  3.000
 9SD  H10  C9   H9   106.86  3.000
 9SD  H10  C9   O9   111.64  3.000
 9SD  H9   C9   O9   111.34  3.000
 9SD  H10  C9   C8   109.01  3.000
 9SD  H9   C9   C8   110.01  3.000
 9SD  O9   C9   C8   107.98  3.000
 9SD  H11  O9   C9   108.14  3.000
 9SD  H12  O7   C7   109.90  3.000
 9SD  H13  C5   N5   107.72  3.000
 9SD  H13  C5   C6   109.60  3.000
 9SD  N5   C5   C6   107.68  3.000
 9SD  H13  C5   C4   109.58  3.000
 9SD  C6   C5   C4   110.54  3.000
 9SD  N5   C5   C4   111.65  3.000
 9SD  H14  N5   C10  118.43  3.000
 9SD  H14  N5   C5   117.91  3.000
 9SD  C10  N5   C5   123.23  3.000
 9SD  C11  C10  O10  122.46  3.000
 9SD  O10  C10  N5   122.69  3.000
 9SD  C11  C10  N5   114.85  3.000
 9SD  H17  C11  H16  107.37  3.000
 9SD  H17  C11  H15  108.60  3.000
 9SD  H16  C11  H15  108.49  3.000
 9SD  H17  C11  C10  109.26  3.000
 9SD  H16  C11  C10  109.20  3.000
 9SD  H15  C11  C10  113.72  3.000
 9SD  H18  O4   C4   109.45  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
 9SD  CONST_01  C11  C10  N5   C5   180.00   0.0  0
 9SD  CONST_02  O10  C10  N5   C5     0.00   0.0  0
 9SD  CONST_03  H1   O1A  C1   C2   180.00   0.0  0
 9SD  CONST_04  H14  N5   C10  O10  180.00   0.0  0
 9SD  Var_01    O6   C2   C1   O1B  170.52  30.0  2
 9SD  Var_02    O9   C9   C8   C7   176.84  30.0  3
 9SD  Var_03    H15  C11  C10  N5    -1.75  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
 9SD  chir_01  C3  C4  C2  F1  positiv
 9SD  chir_02  C4  O4  C3  C5  negativ
 9SD  chir_03  C6  O6  C5  C7  positiv
 9SD  chir_04  C7  O7  C6  C8  negativ
 9SD  chir_05  C5  N5  C6  C4  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
 9SD  plan-1  C5   0.020
 9SD  plan-1  N5   0.020
 9SD  plan-1  C10  0.020
 9SD  plan-1  O10  0.020
 9SD  plan-1  C11  0.020
 9SD  plan-1  H14  0.020
 9SD  plan-2  O1B  0.020
 9SD  plan-2  C1   0.020
 9SD  plan-2  O1A  0.020
 9SD  plan-2  C2   0.020
 9SD  plan-2  H1   0.020

