# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 05:16:56 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2S,3R,4R,5R)-3-(acetylamino)-6-carboxy-2-[(2S)-2,3-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]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
 9S4  9S4  '(2S,3R,4R,5R)-3-(acetylamino)-6-carboxy-2-[(2S)-2,3-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_9S4
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
 9S4  O1B  O  O     0  -0.350   0.3546  -4.3503   0.2929
 9S4  C1   C  C     0   0.559   0.9213  -3.3154   0.1028
 9S4  O1A  O  OH1   0  -0.545   2.1539  -3.0942  -0.2429
 9S4  C2   C  C     0   0.399   0.1565  -2.0076   0.2791
 9S4  C3   C  CH1   0   0.080  -1.3451  -2.0399   0.3399
 9S4  F1   F  F     0  -0.336  -1.6760  -2.3401  -0.9681
 9S4  O6   O  OC2   1  -0.279   0.8238  -0.9748   0.3112
 9S4  C6   C  CH1   0   0.003   0.2754   0.4204   0.4323
 9S4  C7   C  CH2   0  -0.513   1.1659   1.2815  -0.4278
 9S4  C8   C  CH1   0  -0.003   2.6504   1.2265  -0.0537
 9S4  C9   C  CH2   0  -0.158   3.4068   2.2600  -0.8708
 9S4  O9   O  OH1   0  -0.667   4.7836   2.1079  -0.6363
 9S4  O8   O  OH1   0  -0.656   2.8485   1.3779   1.3317
 9S4  C5   C  CH1   0  -0.173  -1.2027   0.4323   0.0490
 9S4  C4   C  CH1   0   0.028  -1.9384  -0.7025   0.7624
 9S4  O4   O  OH1   0  -0.642  -3.2866  -0.6555   0.4332
 9S4  N5   N  NH1   0  -0.640  -1.7473   1.7088   0.3993
 9S4  C10  C  C     0   0.536  -2.2742   2.5662  -0.5104
 9S4  O10  O  O     0  -0.479  -2.2431   2.3533  -1.7098
 9S4  C11  C  CH3   0  -0.781  -2.8978   3.8042   0.0747
 9S4  H1   H  HOH1  0   0.522   2.6504  -3.9225  -0.3578
 9S4  H3   H  HCH1  0   0.329  -1.6754  -2.8511   0.9920
 9S4  H4   H  HCH1  0   0.343   0.4137   0.6302   1.4951
 9S4  H5   H  HCH2  0   0.282   1.0298   1.0253  -1.4809
 9S4  H6   H  HCH2  0   0.284   0.7996   2.3051  -0.3028
 9S4  H7   H  HCH1  0   0.249   3.0497   0.2393  -0.3046
 9S4  H8   H  HCH2  0   0.205   3.1534   2.1204  -1.9298
 9S4  H9   H  HCH2  0   0.201   3.0515   3.2624  -0.5910
 9S4  H10  H  HOH1  0   0.458   5.2462   2.8127  -1.0981
 9S4  H11  H  HOH1  0   0.449   2.5950   2.2725   1.5870
 9S4  H12  H  HCH1  0   0.316  -1.2994   0.3153  -1.0339
 9S4  H13  H  HCH1  0   0.287  -1.7685  -0.6089   1.8435
 9S4  H14  H  HOH1  0   0.476  -3.8098  -0.9493   1.1856
 9S4  H15  H  HNH1  0   0.414  -1.8517   1.9239   1.3793
 9S4  H16  H  HCH3  0   0.254  -2.7648   3.8929   1.1509
 9S4  H17  H  HCH3  0   0.273  -2.4718   4.6850  -0.4038
 9S4  H18  H  HCH3  0   0.275  -3.9665   3.8004  -0.1407

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
 9S4  C11  C10  single  1.505  0.020  1.505
 9S4  O8   C8   single  1.408  0.020  1.408
 9S4  N5   C10  single  1.357  0.020  1.357
 9S4  N5   C5   single  1.431  0.020  1.431
 9S4  O9   C9   single  1.405  0.020  1.405
 9S4  C10  O10  double  1.219  0.020  1.219
 9S4  C8   C7   single  1.532  0.020  1.532
 9S4  C8   C9   single  1.519  0.020  1.519
 9S4  C7   C6   single  1.508  0.020  1.508
 9S4  C6   C5   single  1.527  0.020  1.527
 9S4  C6   O6   single  1.504  0.020  1.504
 9S4  C4   C5   single  1.529  0.020  1.529
 9S4  C4   O4   single  1.389  0.020  1.389
 9S4  C4   C3   single  1.523  0.020  1.523
 9S4  O6   C2   double  1.230  0.020  1.230
 9S4  C3   C2   single  1.503  0.020  1.503
 9S4  C3   F1   single  1.382  0.020  1.382
 9S4  C2   C1   single  1.525  0.020  1.525
 9S4  C1   O1B  double  1.195  0.020  1.195
 9S4  C1   O1A  single  1.299  0.020  1.299
 9S4  O1A  H1   single  0.850  0.020  0.980
 9S4  C3   H3   single  0.970  0.020  1.090
 9S4  C6   H4   single  0.970  0.020  1.090
 9S4  C7   H5   single  0.970  0.020  1.090
 9S4  C7   H6   single  0.970  0.020  1.090
 9S4  C8   H7   single  0.970  0.020  1.090
 9S4  C9   H8   single  0.970  0.020  1.090
 9S4  C9   H9   single  0.970  0.020  1.090
 9S4  O9   H10  single  0.850  0.020  0.980
 9S4  O8   H11  single  0.850  0.020  0.980
 9S4  C5   H12  single  0.970  0.020  1.090
 9S4  C4   H13  single  0.970  0.020  1.090
 9S4  O4   H14  single  0.850  0.020  0.980
 9S4  N5   H15  single  0.860  0.020  1.020
 9S4  C11  H16  single  0.970  0.020  1.090
 9S4  C11  H17  single  0.970  0.020  1.090
 9S4  C11  H18  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
 9S4  C2   C1   O1A  111.13  3.000
 9S4  O1A  C1   O1B  129.76  3.000
 9S4  C2   C1   O1B  119.10  3.000
 9S4  H1   O1A  C1   111.76  3.000
 9S4  O6   C2   C3   123.98  3.000
 9S4  C3   C2   C1   119.15  3.000
 9S4  O6   C2   C1   116.81  3.000
 9S4  H3   C3   C4   111.65  3.000
 9S4  H3   C3   F1   109.35  3.000
 9S4  C4   C3   F1   111.10  3.000
 9S4  H3   C3   C2   110.01  3.000
 9S4  F1   C3   C2   101.86  3.000
 9S4  C4   C3   C2   112.43  3.000
 9S4  C6   O6   C2   125.68  3.000
 9S4  H4   C6   C5   111.43  3.000
 9S4  H4   C6   C7   111.75  3.000
 9S4  C5   C6   C7   115.08  3.000
 9S4  H4   C6   O6   102.15  3.000
 9S4  C5   C6   O6   109.87  3.000
 9S4  C7   C6   O6   105.57  3.000
 9S4  H6   C7   H5   106.73  3.000
 9S4  H6   C7   C8   109.27  3.000
 9S4  H5   C7   C8   110.35  3.000
 9S4  H6   C7   C6   105.74  3.000
 9S4  H5   C7   C6   110.02  3.000
 9S4  C8   C7   C6   114.36  3.000
 9S4  H7   C8   O8   105.74  3.000
 9S4  H7   C8   C9   107.99  3.000
 9S4  O8   C8   C9   112.71  3.000
 9S4  H7   C8   C7   109.27  3.000
 9S4  C9   C8   C7   109.07  3.000
 9S4  O8   C8   C7   111.89  3.000
 9S4  H9   C9   H8   106.67  3.000
 9S4  H9   C9   O9   111.89  3.000
 9S4  H8   C9   O9   111.93  3.000
 9S4  H9   C9   C8   108.81  3.000
 9S4  H8   C9   C8   108.50  3.000
 9S4  O9   C9   C8   108.94  3.000
 9S4  H10  O9   C9   108.18  3.000
 9S4  H11  O8   C8   108.86  3.000
 9S4  H12  C5   N5   107.71  3.000
 9S4  H12  C5   C4   109.88  3.000
 9S4  N5   C5   C4   111.39  3.000
 9S4  H12  C5   C6   109.47  3.000
 9S4  C4   C5   C6   110.05  3.000
 9S4  N5   C5   C6   108.28  3.000
 9S4  H13  C4   O4   112.37  3.000
 9S4  H13  C4   C5   108.75  3.000
 9S4  O4   C4   C5   109.35  3.000
 9S4  H13  C4   C3   106.72  3.000
 9S4  O4   C4   C3   110.02  3.000
 9S4  C5   C4   C3   109.57  3.000
 9S4  H14  O4   C4   109.40  3.000
 9S4  H15  N5   C10  118.45  3.000
 9S4  H15  N5   C5   117.87  3.000
 9S4  C10  N5   C5   123.18  3.000
 9S4  C11  C10  O10  122.48  3.000
 9S4  O10  C10  N5   122.67  3.000
 9S4  C11  C10  N5   114.85  3.000
 9S4  H18  C11  H17  107.43  3.000
 9S4  H18  C11  H16  108.39  3.000
 9S4  H17  C11  H16  108.71  3.000
 9S4  H18  C11  C10  109.06  3.000
 9S4  H17  C11  C10  109.42  3.000
 9S4  H16  C11  C10  113.64  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
 9S4  CONST_01  C11  C10  N5   C5   180.00   0.0  0
 9S4  CONST_02  O10  C10  N5   C5     0.00   0.0  0
 9S4  CONST_03  H1   O1A  C1   C2   180.00   0.0  0
 9S4  CONST_04  H15  N5   C10  O10  180.00   0.0  0
 9S4  Var_01    O6   C2   C1   O1B  167.32  30.0  2
 9S4  Var_02    H16  C11  C10  N5     5.21  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
 9S4  chir_01  C3  C4  C2  F1  positiv
 9S4  chir_02  C6  O6  C5  C7  positiv
 9S4  chir_03  C8  O8  C9  C7  positiv
 9S4  chir_04  C5  N5  C4  C6  positiv
 9S4  chir_05  C4  O4  C5  C3  positiv

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
 9S4  plan-1  C5   0.020
 9S4  plan-1  N5   0.020
 9S4  plan-1  C10  0.020
 9S4  plan-1  O10  0.020
 9S4  plan-1  C11  0.020
 9S4  plan-1  H15  0.020
 9S4  plan-2  O1B  0.020
 9S4  plan-2  C1   0.020
 9S4  plan-2  O1A  0.020
 9S4  plan-2  C2   0.020
 9S4  plan-2  H1   0.020

