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 (-0.932 kcal/mol/HA)
✓ Good fit quality (FQ -8.99)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (11.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.975
kcal/mol
LE
-0.932
kcal/mol/HA
Fit Quality
-8.99
FQ (Leeson)
HAC
30
heavy atoms
MW
400
Da
LogP
2.26
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 11.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 3
Clashes 9
Severe clashes 0
| Final rank | 6.1211022903103665 | Score | -27.9753 |
|---|---|---|---|
| Inter norm | -0.920577 | Intra norm | -0.0119322 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 8 |
| Artifact reason | geometry warning; 16 clashes; 9 protein contact clashes; high strain Δ 28.0 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU179;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:PHE91;A:THR180;A:TYR162;A:TYR178;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 | 0.67 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 200 | 2.918645301259482 | -1.28939 | -35.1713 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 198 | 3.4857649756395244 | -1.30032 | -39.2797 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 199 | 3.5384688680939567 | -1.33737 | -41.1817 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 73 | 4.871554615950786 | -0.977028 | -29.0743 | 11 | 20 | 16 | 0.80 | 0.60 | - | no | Open |
| 72 | 4.920939656575616 | -0.906016 | -27.9161 | 8 | 20 | 16 | 0.80 | 0.40 | - | no | Open |
| 114 | 5.61739952751597 | -0.968364 | -24.1252 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 74 | 6.1211022903103665 | -0.920577 | -27.9753 | 8 | 20 | 16 | 0.80 | 0.40 | - | no | Current |
| 23 | 6.177839531044456 | -0.789709 | -22.5077 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 250 | 6.191922249279758 | -0.716483 | -20.0669 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 48 | 7.529586783836525 | -0.603942 | -19.1316 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 115 | 8.529431868867388 | -0.800001 | -22.4192 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 113 | 9.396995160084744 | -1.12397 | -31.1384 | 5 | 15 | 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
-27.975kcal/mol
Ligand efficiency (LE)
-0.9325kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.995
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.26
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
123.50kcal/mol
Minimised FF energy
111.93kcal/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.