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 (-0.761 kcal/mol/HA)
✓ Good fit quality (FQ -7.18)
✗ Very high strain energy (20.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-21.308
kcal/mol
LE
-0.761
kcal/mol/HA
Fit Quality
-7.18
FQ (Leeson)
HAC
28
heavy atoms
MW
406
Da
LogP
5.56
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 20.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 10
Severe clashes 0
| Final rank | 4.874806654884296 | Score | -21.3083 |
|---|---|---|---|
| Inter norm | -0.773568 | Intra norm | 0.0125574 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 1 |
| Artifact reason | geometry warning; 9 clashes; 10 protein contact clashes; high strain Δ 20.4 | ||
| Residues | A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR83;A:VAL156;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 | 13 | Native recall | 0.65 |
| Jaccard | 0.59 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2522 | 3.603100088384475 | -0.753208 | -20.2271 | 1 | 15 | 13 | 0.65 | 0.00 | - | no | Open |
| 1046 | 4.115524958213157 | -0.877037 | -21.4858 | 1 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1045 | 4.334165538881587 | -0.924931 | -23.7852 | 1 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1048 | 4.664008092419392 | -0.82573 | -20.6883 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2524 | 4.874806654884296 | -0.773568 | -21.3083 | 1 | 15 | 13 | 0.65 | 0.00 | - | no | Current |
| 1047 | 5.052657343141703 | -0.898838 | -21.5124 | 1 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1567 | 5.509606217872089 | -0.912214 | -16.18 | 4 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 1566 | 5.372919973915165 | -0.7248 | -19.5067 | 2 | 12 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1568 | 5.79009765527818 | -0.701841 | -20.5574 | 3 | 12 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1569 | 6.581816602297611 | -0.837093 | -14.3369 | 1 | 20 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2521 | 7.828736633834243 | -0.957989 | -17.416 | 4 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 2523 | 8.472204082026884 | -0.938303 | -16.0871 | 3 | 14 | 13 | 0.65 | 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
-21.308kcal/mol
Ligand efficiency (LE)
-0.7610kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.184
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
405.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.56
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
72.79kcal/mol
Minimised FF energy
52.42kcal/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.