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 (-0.992 kcal/mol/HA)
✓ Good fit quality (FQ -9.02)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (26.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.796
kcal/mol
LE
-0.992
kcal/mol/HA
Fit Quality
-9.02
FQ (Leeson)
HAC
25
heavy atoms
MW
384
Da
LogP
2.12
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 26.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 23
π–π 2
Clashes 6
Severe clashes 0
| Final rank | 3.371564328633747 | Score | -24.7962 |
|---|---|---|---|
| Inter norm | -1.00215 | Intra norm | 0.0103004 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | geometry warning; 6 clashes; 6 protein contact clashes; high strain Δ 28.8 | ||
| Residues | A:ALA32;A:ARG92;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:TYR162;A:VAL156;A:VAL30;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.65 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2205 | 2.581941834211034 | -1.00758 | -23.7477 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2206 | 2.8923045762853272 | -1.21237 | -31.1001 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2296 | 3.371564328633747 | -1.00215 | -24.7962 | 5 | 18 | 15 | 0.75 | 0.20 | - | no | Current |
| 2297 | 4.236341045711411 | -1.01247 | -22.307 | 7 | 16 | 11 | 0.55 | 0.20 | - | no | Open |
| 2949 | 4.785411910617647 | -1.01908 | -21.7728 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1230 | 6.209533730850848 | -0.97911 | -23.9362 | 5 | 21 | 1 | 0.05 | 0.00 | - | no | Open |
| 2207 | 4.87556894993375 | -1.10037 | -28.928 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2208 | 7.073537330136175 | -0.932216 | -23.3501 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2209 | 7.5124107863560985 | -1.05725 | -21.172 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1229 | 7.901848525229564 | -0.906066 | -23.6173 | 8 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.796kcal/mol
Ligand efficiency (LE)
-0.9918kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.017
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
383.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.12
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
4.68kcal/mol
Minimised FF energy
-21.47kcal/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.