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 (-1.073 kcal/mol/HA)
✓ Good fit quality (FQ -9.62)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (22.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.759
kcal/mol
LE
-1.073
kcal/mol/HA
Fit Quality
-9.62
FQ (Leeson)
HAC
24
heavy atoms
MW
364
Da
LogP
3.09
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 22.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 24
π–π 1
Clashes 4
Severe clashes 0
| Final rank | 2.9583132347911665 | Score | -25.7588 |
|---|---|---|---|
| Inter norm | -1.20346 | Intra norm | 0.130172 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 10 |
| Artifact reason | geometry warning; 10 clashes; 4 protein contact clashes; high strain Δ 23.3 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE45;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:THR180;A:TRP47;A:TYR162;A:TYR178;A:VAL156;A:VAL30;A:VAL31;A:VAL49 | ||
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 | 11 | Native recall | 0.55 |
| Jaccard | 0.42 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.57 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 172 | 2.9583132347911665 | -1.20346 | -25.7588 | 10 | 17 | 11 | 0.55 | 0.80 | - | no | Current |
| 119 | 3.0411416082296214 | -1.18879 | -29.0207 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 117 | 3.3037872853401975 | -1.18971 | -29.2661 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 170 | 4.451495078205778 | -1.16923 | -25.0891 | 6 | 16 | 11 | 0.55 | 0.80 | - | no | Open |
| 118 | 5.18116131436111 | -1.15484 | -25.0514 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 122 | 5.471817934988997 | -0.743153 | -15.0498 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 120 | 5.6539743183894 | -1.12904 | -24.6433 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 171 | 4.618794082020386 | -1.18707 | -21.4229 | 11 | 16 | 11 | 0.55 | 0.80 | - | yes | Open |
| 173 | 54.02556249294625 | -1.20338 | -22.2631 | 9 | 16 | 11 | 0.55 | 0.80 | - | yes | Open |
| 123 | 59.382537021470505 | -0.878394 | -19.1316 | 6 | 19 | 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
-25.759kcal/mol
Ligand efficiency (LE)
-1.0733kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.619
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
364.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.09
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-127.40kcal/mol
Minimised FF energy
-150.04kcal/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.