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 (-0.963 kcal/mol/HA)
✓ Good fit quality (FQ -9.29)
✓ Good H-bonds (4 bonds)
✗ Moderate strain (8.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.892
kcal/mol
LE
-0.963
kcal/mol/HA
Fit Quality
-9.29
FQ (Leeson)
HAC
30
heavy atoms
MW
429
Da
LogP
4.30
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
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 3
Clashes 5
Severe clashes 0
| Final rank | 2.94602425672637 | Score | -28.8915 |
|---|---|---|---|
| Inter norm | -0.992564 | Intra norm | 0.0295132 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | geometry warning; 11 clashes; 5 protein contact clashes; moderate strain Δ 12.1 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO93;A:THR83;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.73 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2065 | 2.94602425672637 | -0.992564 | -28.8915 | 4 | 18 | 16 | 0.80 | 0.20 | - | no | Current |
| 1191 | 3.768089679049951 | -0.719092 | -19.5389 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1962 | 3.9333827126534873 | -0.900549 | -22.9333 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1080 | 5.339181214027544 | -0.929592 | -23.1893 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 583 | 5.630799113426268 | -1.04133 | -26.5489 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1961 | 4.909886224393236 | -0.90485 | -24.7932 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2064 | 6.977560368249202 | -0.921564 | -27.0509 | 5 | 15 | 10 | 0.50 | 0.00 | - | yes | Open |
| 1190 | 7.1157636358790235 | -0.674942 | -19.2002 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 582 | 8.463256946645911 | -0.924977 | -28.5631 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1079 | 9.918314688126125 | -0.901996 | -22.4202 | 13 | 16 | 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
-28.892kcal/mol
Ligand efficiency (LE)
-0.9631kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.290
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
428.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.30
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.19kcal/mol
Minimised FF energy
77.33kcal/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.