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 (-0.707 kcal/mol/HA)
✓ Good fit quality (FQ -7.13)
✓ Strong H-bond network (11 bonds)
✗ High strain energy (18.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.734
kcal/mol
LE
-0.707
kcal/mol/HA
Fit Quality
-7.13
FQ (Leeson)
HAC
35
heavy atoms
MW
475
Da
LogP
1.25
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 18.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 11
Hydrophobic 24
π–π 2
Clashes 18
Severe clashes 1
| Final rank | 10.165401781668859 | Score | -24.7338 |
|---|---|---|---|
| Inter norm | -0.863725 | Intra norm | 0.157046 |
| Top1000 | no | Excluded | yes |
| Contacts | 22 | H-bonds | 11 |
| Artifact reason | excluded; geometry warning; 19 clashes; 1 protein clash; moderate strain Δ 18.2 | ||
| 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:PRO93;A:THR180;A:THR83;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 | 17 | Native recall | 0.85 |
| Jaccard | 0.68 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.43 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 64 | 4.858665488273645 | -1.02689 | -36.7571 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 65 | 5.015518803068915 | -1.0193 | -35.8529 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 40 | 5.8441805025495155 | -0.766897 | -22.8523 | 9 | 22 | 18 | 0.90 | 0.80 | - | no | Open |
| 63 | 6.026232947336428 | -1.06159 | -32.4057 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 16 | 6.383987949259197 | -0.631431 | -17.8227 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 41 | 9.648872102527655 | -0.810558 | -26.7218 | 9 | 23 | 19 | 0.95 | 0.80 | - | yes | Open |
| 39 | 10.165401781668859 | -0.863725 | -24.7338 | 11 | 22 | 17 | 0.85 | 0.60 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.734kcal/mol
Ligand efficiency (LE)
-0.7067kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.128
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
474.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.25
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
78.22kcal/mol
Minimised FF energy
59.52kcal/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.