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 (-0.443 kcal/mol/HA)
✓ Good fit quality (FQ -4.60)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (23.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-17.270
kcal/mol
LE
-0.443
kcal/mol/HA
Fit Quality
-4.60
FQ (Leeson)
HAC
39
heavy atoms
MW
529
Da
LogP
6.17
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 1
Clashes 13
Severe clashes 2
| Final rank | 9.928660641867628 | Score | -17.2702 |
|---|---|---|---|
| Inter norm | -0.606812 | Intra norm | 0.163987 |
| Top1000 | no | Excluded | yes |
| Contacts | 12 | H-bonds | 8 |
| Artifact reason | excluded; geometry warning; 16 clashes; 2 protein clashes; high strain Δ 25.3 | ||
| Residues | A:ALA32;A:ARG97;A:ASN58;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:PHE56;A:PHE91;A:PRO50;A:THR54 | ||
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 | 10 | Native recall | 0.50 |
| Jaccard | 0.45 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.43 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1170 | 5.06268909189742 | -0.378276 | -9.76776 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2046 | 7.683265756501406 | -0.628246 | -19.03 | 3 | 17 | 11 | 0.55 | 0.00 | - | no | Open |
| 1169 | 6.4184126052151145 | -0.411389 | -18.3599 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1167 | 8.362434380008889 | -0.42812 | -11.9708 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2048 | 9.23219460399084 | -0.881205 | -25.7326 | 5 | 20 | 14 | 0.70 | 0.20 | - | yes | Open |
| 2043 | 9.928660641867628 | -0.606812 | -17.2702 | 8 | 12 | 10 | 0.50 | 0.40 | - | yes | Current |
| 2045 | 10.485068897759103 | -0.665369 | -23.8114 | 7 | 10 | 7 | 0.35 | 0.20 | - | yes | Open |
| 2044 | 16.601103047703894 | -0.692056 | -22.7877 | 5 | 22 | 17 | 0.85 | 0.20 | - | yes | Open |
| 2047 | 58.55738027161178 | -0.699369 | -19.8558 | 4 | 16 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1168 | 59.82585829806636 | -0.513525 | -11.719 | 5 | 16 | 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
-17.270kcal/mol
Ligand efficiency (LE)
-0.4428kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.596
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
528.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.17
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
117.94kcal/mol
Minimised FF energy
94.23kcal/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.