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 (-0.630 kcal/mol/HA)
✓ Good fit quality (FQ -6.49)
✗ Very high strain energy (34.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.928
kcal/mol
LE
-0.630
kcal/mol/HA
Fit Quality
-6.49
FQ (Leeson)
HAC
38
heavy atoms
MW
518
Da
LogP
0.25
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 34.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 0
Clashes 6
Severe clashes 0
| Final rank | 6.327385608477396 | Score | -23.9276 |
|---|---|---|---|
| Inter norm | -0.639833 | Intra norm | 0.0101597 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 2 |
| Artifact reason | geometry warning; 17 clashes; 6 protein contact clashes; high strain Δ 38.4 | ||
| Residues | A:ARG48;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR54;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 | 14 | Native recall | 0.70 |
| Jaccard | 0.58 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1487 | 6.07442385679683 | -0.598465 | -21.2855 | 0 | 16 | 10 | 0.50 | 0.00 | - | no | Open |
| 1485 | 6.128643862147477 | -0.656681 | -25.6495 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1466 | 6.281945054188164 | -0.590364 | -20.2439 | 1 | 14 | 13 | 0.65 | 0.00 | - | no | Open |
| 1473 | 6.327385608477396 | -0.639833 | -23.9276 | 2 | 18 | 14 | 0.70 | 0.20 | - | no | Current |
| 1486 | 6.527479266737894 | -0.696956 | -23.4597 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1470 | 6.726688335486472 | -0.67102 | -22.9118 | 2 | 19 | 14 | 0.70 | 0.20 | - | no | Open |
| 1477 | 6.953141207531191 | -0.645843 | -25.7231 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1474 | 7.063905860182462 | -0.619327 | -23.5325 | 0 | 22 | 18 | 0.90 | 0.00 | - | no | Open |
| 1469 | 7.529055820696406 | -0.638843 | -24.3611 | 0 | 16 | 13 | 0.65 | 0.00 | - | no | Open |
| 1475 | 55.2556795840474 | -0.707408 | -22.4918 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1483 | 55.632865880912476 | -0.660896 | -23.9709 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1479 | 56.221072351477474 | -0.633789 | -22.09 | 1 | 15 | 11 | 0.55 | 0.00 | - | no | Open |
| 1467 | 56.390513999081726 | -0.629654 | -20.4108 | 1 | 18 | 14 | 0.70 | 0.20 | - | no | Open |
| 1472 | 55.84251286533656 | -0.562083 | -24.5622 | 0 | 13 | 10 | 0.50 | 0.00 | - | yes | Open |
| 1465 | 55.9688263974557 | -0.543463 | -20.0128 | 1 | 19 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1476 | 56.2577780226393 | -0.536044 | -19.4575 | 1 | 14 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1471 | 56.27140459003314 | -0.56118 | -21.939 | 0 | 11 | 7 | 0.35 | 0.00 | - | yes | Open |
| 1478 | 56.363579973362626 | -0.576383 | -20.352 | 0 | 19 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1484 | 56.71193077325185 | -0.634285 | -21.9024 | 1 | 17 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1482 | 57.329954179358666 | -0.674064 | -23.524 | 1 | 17 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1480 | 57.531690712131635 | -0.571147 | -19.841 | 0 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1488 | 57.68304463232018 | -0.5574 | -18.9736 | 0 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1468 | 57.87042742147217 | -0.573335 | -22.7619 | 1 | 19 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1481 | 58.77975156866493 | -0.672406 | -24.1235 | 3 | 13 | 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
-23.928kcal/mol
Ligand efficiency (LE)
-0.6297kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.491
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
517.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.25
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
282.70kcal/mol
Minimised FF energy
248.61kcal/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.