Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.824 kcal/mol/HA)
✓ Good fit quality (FQ -7.59)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (31.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-21.426
kcal/mol
LE
-0.824
kcal/mol/HA
Fit Quality
-7.59
FQ (Leeson)
HAC
26
heavy atoms
MW
391
Da
LogP
2.82
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 31.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 22
π–π 1
Clashes 8
Severe clashes 0
| Final rank | 4.94558020240054 | Score | -21.4264 |
|---|---|---|---|
| Inter norm | -0.817679 | Intra norm | -0.00641285 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 4 |
| Artifact reason | geometry warning; 7 clashes; 8 protein contact clashes; high strain Δ 37.9 | ||
| Residues | A:ALA32;A:ARG48;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO46;A:PRO88;A:SER44;A:SER86;A:TRP47;A:TYR162;A:VAL156;A:VAL31;A:VAL87 | ||
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87 | ||
| Current overlap | 13 | Native recall | 0.65 |
| Jaccard | 0.54 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3351 | 3.700166410105763 | -0.694355 | -24.1012 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 3356 | 4.060259190723226 | -0.57646 | -16.2213 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2708 | 4.066908340758205 | -0.882299 | -23.5614 | 7 | 19 | 14 | 0.70 | 0.20 | - | no | Open |
| 2713 | 4.397339357329831 | -0.882041 | -26.1356 | 7 | 9 | 7 | 0.35 | 0.20 | - | no | Open |
| 3357 | 4.52185972612399 | -0.614849 | -12.8325 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2721 | 4.600408778455224 | -0.734888 | -14.8762 | 8 | 18 | 13 | 0.65 | 0.00 | - | no | Open |
| 2709 | 4.8485224772625015 | -1.05932 | -24.7891 | 6 | 17 | 14 | 0.70 | 0.20 | - | no | Open |
| 2722 | 4.94558020240054 | -0.817679 | -21.4264 | 4 | 17 | 13 | 0.65 | 0.00 | - | no | Current |
| 2716 | 4.9667622754639424 | -0.825218 | -24.6944 | 6 | 17 | 14 | 0.70 | 0.20 | - | no | Open |
| 3347 | 5.520272521802061 | -0.783828 | -21.1306 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2711 | 5.671810626257038 | -0.730073 | -28.0194 | 5 | 16 | 13 | 0.65 | 0.20 | - | no | Open |
| 3343 | 4.907718538764667 | -0.926049 | -23.919 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3355 | 5.327273340927074 | -0.804704 | -22.4335 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2717 | 5.51011414711577 | -0.80878 | -22.5146 | 2 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 3348 | 5.535934980262025 | -0.922918 | -24.4857 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3352 | 5.967136058308274 | -0.615596 | -19.4533 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2714 | 6.03655169233735 | -0.825675 | -22.2478 | 6 | 14 | 11 | 0.55 | 0.20 | - | yes | Open |
| 3353 | 6.388856661844819 | -0.711742 | -18.4431 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2712 | 6.455154962785032 | -0.883812 | -24.8654 | 4 | 17 | 14 | 0.70 | 0.00 | - | yes | Open |
| 3349 | 6.512434389319291 | -0.694102 | -20.8902 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3346 | 7.02004168331491 | -0.681302 | -27.0085 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2719 | 7.518280240178267 | -0.766525 | -20.3131 | 2 | 17 | 15 | 0.75 | 0.00 | - | yes | Open |
| 2723 | 7.537187184503247 | -0.751544 | -18.5869 | 6 | 14 | 11 | 0.55 | 0.20 | - | yes | Open |
| 3345 | 8.74043112610656 | -0.721575 | -19.8508 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2715 | 55.78029250972965 | -0.834686 | -21.8621 | 4 | 14 | 10 | 0.50 | 0.00 | - | yes | Open |
| 3350 | 55.941164464406576 | -0.62208 | -19.4593 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3358 | 56.52519508621056 | -0.700347 | -20.783 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2720 | 57.276901634848244 | -0.858543 | -23.2142 | 6 | 17 | 14 | 0.70 | 0.20 | - | yes | Open |
| 2710 | 57.34572465987451 | -1.00114 | -24.3262 | 6 | 16 | 13 | 0.65 | 0.20 | - | yes | Open |
| 3344 | 57.94765240802333 | -0.74487 | -23.0944 | 8 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3354 | 58.007845546614455 | -0.811484 | -21.7359 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2718 | 58.43349222570747 | -0.970525 | -25.3633 | 6 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.426kcal/mol
Ligand efficiency (LE)
-0.8241kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.593
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
391.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.82
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
111.47kcal/mol
Minimised FF energy
80.47kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.