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 (-0.535 kcal/mol/HA)
✓ Good fit quality (FQ -5.40)
✗ Very high strain energy (30.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-18.732
kcal/mol
LE
-0.535
kcal/mol/HA
Fit Quality
-5.40
FQ (Leeson)
HAC
35
heavy atoms
MW
475
Da
LogP
2.77
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 30.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 0
Clashes 6
Severe clashes 1
| Final rank | 56.58171206767925 | Score | -18.7324 |
|---|---|---|---|
| Inter norm | -0.593117 | Intra norm | 0.0579046 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 0 |
| Artifact reason | excluded; geometry warning; 19 clashes; 1 protein clash | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49;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: permissive.
| 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 | 0.67 | 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: permissive. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1300 | 4.555857565094415 | -0.60493 | -19.907 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1344 | 4.9799483296797655 | -0.601428 | -21.9741 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1297 | 5.244466538905405 | -0.500449 | -17.0248 | 0 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1303 | 5.637321520904174 | -0.662306 | -13.6507 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1301 | 5.726610762635013 | -0.523042 | -15.422 | 0 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1338 | 6.047136029653834 | -0.679113 | -20.7976 | 1 | 18 | 15 | 0.75 | 0.20 | - | no | Open |
| 1341 | 6.337101594940998 | -0.600904 | -16.184 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1304 | 6.468472890150392 | -0.625835 | -18.5876 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1295 | 6.747113878668843 | -0.710131 | -21.8836 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1340 | 55.16938544266331 | -0.569329 | -14.2791 | 2 | 19 | 16 | 0.80 | 0.20 | - | no | Open |
| 1339 | 55.50035050122407 | -0.717686 | -13.743 | 2 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 1308 | 55.82020903503072 | -0.679444 | -12.4578 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1306 | 56.09400295700925 | -0.587279 | -16.4634 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1299 | 56.252858993048164 | -0.630877 | -19.44 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1343 | 56.58171206767925 | -0.593117 | -18.7324 | 0 | 20 | 16 | 0.80 | 0.00 | - | yes | Current |
| 1296 | 56.75508483750029 | -0.605185 | -18.341 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1293 | 57.41876212549005 | -0.516353 | -15.6478 | 0 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1298 | 57.58696093524178 | -0.648825 | -19.3347 | 1 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1294 | 57.624361680316774 | -0.442974 | -15.843 | 0 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1305 | 57.904867024689636 | -0.597529 | -14.2795 | 0 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1307 | 57.9524792571854 | -0.603131 | -18.7156 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1337 | 58.25014671994387 | -0.608506 | -19.1334 | 1 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1342 | 58.62815423115328 | -0.666167 | -20.1895 | 3 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1302 | 59.27704030738866 | -0.465251 | -15.6072 | 0 | 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
-18.732kcal/mol
Ligand efficiency (LE)
-0.5352kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.398
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
474.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.77
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
138.42kcal/mol
Minimised FF energy
108.42kcal/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.