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 (-0.550 kcal/mol/HA)
✓ Good fit quality (FQ -5.55)
✗ Very high strain energy (37.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-19.263
kcal/mol
LE
-0.550
kcal/mol/HA
Fit Quality
-5.55
FQ (Leeson)
HAC
35
heavy atoms
MW
478
Da
LogP
1.38
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 37.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 6.864698401985375 | Score | -19.2629 |
|---|---|---|---|
| Inter norm | -0.695347 | Intra norm | 0.144978 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 1 |
| Artifact reason | geometry warning; 17 clashes; 8 protein contact clashes; high strain Δ 36.4 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER86;A:THR54;A:THR83;A:TRP47;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.65 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1421 | 5.473295963852082 | -0.57299 | -13.3783 | 2 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1430 | 5.685526359698427 | -0.827578 | -24.4334 | 0 | 22 | 18 | 0.90 | 0.00 | - | no | Open |
| 1432 | 6.164391591248511 | -0.598069 | -15.9362 | 0 | 19 | 16 | 0.80 | 0.00 | - | no | Open |
| 1420 | 6.239280501301899 | -0.60655 | -21.015 | 0 | 17 | 15 | 0.75 | 0.00 | - | no | Open |
| 1424 | 6.864698401985375 | -0.695347 | -19.2629 | 1 | 18 | 15 | 0.75 | 0.00 | - | no | Current |
| 1427 | 6.875176731589589 | -0.612404 | -18.5871 | 1 | 17 | 12 | 0.60 | 0.20 | - | no | Open |
| 1428 | 55.10269589130165 | -0.547882 | -13.4513 | 1 | 21 | 17 | 0.85 | 0.20 | - | no | Open |
| 1429 | 55.271287060443406 | -0.588299 | -13.8733 | 1 | 16 | 12 | 0.60 | 0.00 | - | no | Open |
| 1431 | 55.35927685864007 | -0.605875 | -18.03 | 0 | 15 | 12 | 0.60 | 0.00 | - | no | Open |
| 1423 | 55.63877896826486 | -0.668684 | -22.5258 | 0 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1418 | 56.641114782809275 | -0.694927 | -18.4229 | 1 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1426 | 56.721878113067774 | -0.560873 | -14.4276 | 0 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1417 | 56.89785487863341 | -0.619338 | -18.0701 | 2 | 18 | 18 | 0.90 | 0.20 | - | yes | Open |
| 1419 | 57.11881744063439 | -0.634502 | -15.6261 | 2 | 17 | 17 | 0.85 | 0.20 | - | yes | Open |
| 1425 | 57.22997951682644 | -0.643093 | -21.3214 | 1 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1422 | 58.05593181786347 | -0.736516 | -22.3067 | 0 | 21 | 18 | 0.90 | 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
-19.263kcal/mol
Ligand efficiency (LE)
-0.5504kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.551
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
477.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.38
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
183.39kcal/mol
Minimised FF energy
145.92kcal/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.