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 (-0.616 kcal/mol/HA)
✓ Good fit quality (FQ -6.21)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (22.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.563
kcal/mol
LE
-0.616
kcal/mol/HA
Fit Quality
-6.21
FQ (Leeson)
HAC
35
heavy atoms
MW
476
Da
LogP
2.37
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 22.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 2
Clashes 14
Severe clashes 1
| Final rank | 57.953355141174896 | Score | -21.5627 |
|---|---|---|---|
| Inter norm | -0.669037 | Intra norm | 0.0529601 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;A:SER86;A:THR54;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 | 12 | Native recall | 0.60 |
| Jaccard | 0.57 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 743 | 5.312649088795534 | -0.697944 | -22.1828 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 735 | 5.358840675675725 | -0.735058 | -27.4357 | 1 | 18 | 16 | 0.80 | 0.00 | - | no | Open |
| 742 | 5.8280697387163505 | -0.639962 | -19.6847 | 1 | 18 | 16 | 0.80 | 0.20 | - | no | Open |
| 748 | 5.991231384420915 | -0.536771 | -17.2393 | 0 | 19 | 17 | 0.85 | 0.00 | - | no | Open |
| 737 | 6.465642965761124 | -0.600779 | -24.3981 | 0 | 17 | 16 | 0.80 | 0.00 | - | no | Open |
| 733 | 7.325949884476672 | -0.648071 | -15.2017 | 1 | 18 | 14 | 0.70 | 0.20 | - | no | Open |
| 734 | 55.970368576341656 | -0.63518 | -22.0222 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 745 | 56.04093165427253 | -0.536413 | -22.3617 | 1 | 14 | 10 | 0.50 | 0.00 | - | yes | Open |
| 747 | 56.45539408939962 | -0.606222 | -14.0555 | 2 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 746 | 56.8408066330601 | -0.729956 | -24.3105 | 0 | 21 | 17 | 0.85 | 0.00 | - | yes | Open |
| 736 | 57.26595064328689 | -0.66536 | -23.2109 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 738 | 57.344414955275006 | -0.760862 | -23.0834 | 0 | 22 | 19 | 0.95 | 0.00 | - | yes | Open |
| 739 | 57.43229816905028 | -0.609796 | -18.9747 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 744 | 57.953355141174896 | -0.669037 | -21.5627 | 3 | 13 | 12 | 0.60 | 0.20 | - | yes | Current |
| 740 | 58.44335644739914 | -0.546153 | -13.3073 | 0 | 17 | 17 | 0.85 | 0.00 | - | yes | Open |
| 741 | 59.42672335531421 | -0.679073 | -19.7259 | 1 | 17 | 12 | 0.60 | 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
-21.563kcal/mol
Ligand efficiency (LE)
-0.6161kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.214
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
475.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.37
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
125.99kcal/mol
Minimised FF energy
103.72kcal/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.