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 (-0.794 kcal/mol/HA)
✓ Good fit quality (FQ -7.81)
✓ Good H-bonds (3 bonds)
✗ High strain energy (14.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.416
kcal/mol
LE
-0.794
kcal/mol/HA
Fit Quality
-7.81
FQ (Leeson)
HAC
32
heavy atoms
MW
437
Da
LogP
5.43
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 14.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 23
π–π 0
Clashes 7
Severe clashes 0
| Final rank | 3.803316269253096 | Score | -25.4162 |
|---|---|---|---|
| Inter norm | -0.688789 | Intra norm | -0.105583 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 7 protein contact clashes; moderate strain Δ 14.9 | ||
| Residues | A:ARG48;A:GLU216;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:PRO50;A:PRO88;A:SER44;A:SER86;A:THR83;A:TRP47;A:VAL156;A:VAL49;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 | 9 | Native recall | 0.45 |
| Jaccard | 0.35 | 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2016 | 3.803316269253096 | -0.688789 | -25.4162 | 3 | 15 | 9 | 0.45 | 0.20 | - | no | Current |
| 2010 | 5.130515823666404 | -0.697741 | -24.2214 | 1 | 19 | 18 | 0.90 | 0.00 | - | no | Open |
| 2015 | 5.318882177305842 | -0.718507 | -25.2735 | 4 | 17 | 16 | 0.80 | 0.20 | - | yes | Open |
| 2011 | 55.582931288676235 | -0.706759 | -24.6874 | 4 | 19 | 19 | 0.95 | 0.00 | - | yes | Open |
| 2014 | 55.900523597097155 | -0.623923 | -22.7101 | 3 | 14 | 10 | 0.50 | 0.00 | - | yes | Open |
| 2009 | 55.924292848842214 | -0.767688 | -24.5529 | 4 | 19 | 19 | 0.95 | 0.00 | - | yes | Open |
| 2013 | 56.56933712158421 | -0.687308 | -22.6969 | 3 | 19 | 19 | 0.95 | 0.00 | - | yes | Open |
| 2012 | 57.84880918230601 | -0.713407 | -22.186 | 4 | 17 | 16 | 0.80 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.416kcal/mol
Ligand efficiency (LE)
-0.7943kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.811
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
436.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.43
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
92.42kcal/mol
Minimised FF energy
78.02kcal/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.