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 (-0.579 kcal/mol/HA)
✓ Good fit quality (FQ -5.89)
✗ Very high strain energy (35.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.855
kcal/mol
LE
-0.579
kcal/mol/HA
Fit Quality
-5.89
FQ (Leeson)
HAC
36
heavy atoms
MW
544
Da
LogP
2.44
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 35.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 1
Clashes 12
Severe clashes 0
| Final rank | 8.060644977181651 | Score | -20.8548 |
|---|---|---|---|
| Inter norm | -0.688871 | Intra norm | 0.109571 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 16 clashes; 12 protein contact clashes; high strain Δ 41.6 | ||
| 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:THR54;A:THR83;A:TYR162;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 | 19 | Native recall | 0.95 |
| Jaccard | 0.95 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3396 | 5.075642098667443 | -0.568762 | -20.8405 | 1 | 12 | 1 | 0.05 | 0.00 | - | no | Open |
| 3248 | 5.921699636584039 | -0.580927 | -18.8535 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2541 | 8.060644977181651 | -0.688871 | -20.8548 | 2 | 19 | 19 | 0.95 | 0.00 | - | no | Current |
| 3247 | 6.724302548501824 | -0.632066 | -22.366 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2540 | 6.80471431965059 | -0.63323 | -15.1639 | 2 | 14 | 12 | 0.60 | 0.20 | - | yes | Open |
| 3245 | 8.521677291511232 | -0.694278 | -20.7511 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3395 | 11.62466945348613 | -0.582048 | -21.3875 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3394 | 12.076759942037933 | -0.63054 | -21.3015 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2538 | 13.120393901929614 | -0.809269 | -21.7186 | 4 | 19 | 18 | 0.90 | 0.20 | - | yes | Open |
| 3246 | 58.16908594110197 | -0.590369 | -20.5428 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3393 | 60.50679734883546 | -0.565195 | -16.572 | 2 | 12 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2539 | 62.21865048326576 | -0.695065 | -15.6846 | 3 | 22 | 16 | 0.80 | 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
-20.855kcal/mol
Ligand efficiency (LE)
-0.5793kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.888
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
543.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.44
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
45.38kcal/mol
Minimised FF energy
10.19kcal/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.