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 (-0.538 kcal/mol/HA)
✓ Good fit quality (FQ -5.47)
✗ Very high strain energy (33.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-19.381
kcal/mol
LE
-0.538
kcal/mol/HA
Fit Quality
-5.47
FQ (Leeson)
HAC
36
heavy atoms
MW
491
Da
LogP
1.74
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 33.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 55.168442638495705 | Score | -19.3811 |
|---|---|---|---|
| Inter norm | -0.597273 | Intra norm | 0.0589095 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | geometry warning; 16 clashes; 8 protein contact clashes | ||
| Residues | A:ALA32;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.76 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1277 | 4.955390243682244 | -0.633304 | -23.2003 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1284 | 5.266590438213333 | -0.589116 | -20.5555 | 0 | 21 | 16 | 0.80 | 0.00 | - | no | Open |
| 1273 | 5.420218368573264 | -0.69434 | -23.3365 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1276 | 5.63123130661502 | -0.577185 | -19.3035 | 0 | 23 | 18 | 0.90 | 0.00 | - | no | Open |
| 1266 | 5.916219393702416 | -0.505792 | -20.3863 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1268 | 6.237408435825435 | -0.504901 | -16.749 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1271 | 6.677440558013149 | -0.671078 | -20.2642 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1282 | 7.103710860788376 | -0.529393 | -16.305 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1283 | 8.149754730529782 | -0.703227 | -24.5366 | 0 | 22 | 19 | 0.95 | 0.00 | - | no | Open |
| 1272 | 55.168442638495705 | -0.597273 | -19.3811 | 1 | 17 | 16 | 0.80 | 0.00 | - | no | Current |
| 1267 | 55.22585166049036 | -0.722343 | -24.5284 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1278 | 55.34802207569263 | -0.59464 | -20.3427 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 1274 | 55.90467238694108 | -0.577796 | -19.3768 | 1 | 15 | 14 | 0.70 | 0.00 | - | no | Open |
| 1279 | 55.15930333170979 | -0.54678 | -18.2212 | 0 | 20 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1269 | 55.430613126236565 | -0.56603 | -20.9268 | 0 | 20 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1286 | 55.94254527420868 | -0.723334 | -26.5795 | 1 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1275 | 56.10591493197533 | -0.739461 | -28.2783 | 1 | 21 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1288 | 56.22278985082605 | -0.484989 | -14.9191 | 0 | 16 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1281 | 56.69113764342162 | -0.65413 | -21.5281 | 2 | 17 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1287 | 56.77900350542991 | -0.639226 | -21.8545 | 1 | 20 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1285 | 57.09888257553469 | -0.639662 | -22.3896 | 1 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1270 | 57.15492175021484 | -0.704798 | -28.3287 | 1 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1265 | 57.22681303945254 | -0.593801 | -19.0446 | 2 | 16 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1280 | 57.580035907571485 | -0.481053 | -17.2959 | 0 | 16 | 12 | 0.60 | 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
-19.381kcal/mol
Ligand efficiency (LE)
-0.5384kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.472
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
490.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.74
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
185.77kcal/mol
Minimised FF energy
152.45kcal/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.