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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.985 kcal/mol/HA)
✓ Good fit quality (FQ -8.82)
✓ Strong H-bond network (9 bonds)
✗ High strain energy (15.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.629
kcal/mol
LE
-0.985
kcal/mol/HA
Fit Quality
-8.82
FQ (Leeson)
HAC
24
heavy atoms
MW
337
Da
LogP
2.44
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 15.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 22
π–π 1
Clashes 4
Severe clashes 0
| Final rank | 2.5672039559790862 | Score | -23.6293 |
|---|---|---|---|
| Inter norm | -1.09574 | Intra norm | 0.11119 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | geometry warning; 10 clashes; 4 protein contact clashes; moderate strain Δ 15.9 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE45;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:SER44;A:THR180;A:TRP47;A:TYR162;A:TYR178;A:VAL156;A:VAL30;A:VAL31;A:VAL49 | ||
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 | 11 | Native recall | 0.55 |
| Jaccard | 0.41 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.57 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 637 | 2.5672039559790862 | -1.09574 | -23.6293 | 9 | 18 | 11 | 0.55 | 0.80 | - | no | Current |
| 638 | 2.6296410864150035 | -1.1164 | -23.2172 | 6 | 17 | 14 | 0.70 | 0.80 | - | no | Open |
| 789 | 2.7432954351345193 | -1.08725 | -25.1706 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 790 | 3.032726691043519 | -1.04896 | -25.2603 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 590 | 3.865463360881475 | -1.0613 | -21.5743 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 591 | 4.71655630422342 | -0.985426 | -21.1748 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 636 | 3.9866736171028982 | -1.12236 | -21.9231 | 11 | 16 | 14 | 0.70 | 0.80 | - | yes | Open |
| 788 | 5.138745413827386 | -1.1223 | -25.4623 | 2 | 17 | 0 | 0.00 | 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
-23.629kcal/mol
Ligand efficiency (LE)
-0.9846kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.823
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.44
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-136.18kcal/mol
Minimised FF energy
-151.52kcal/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.