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 (-0.486 kcal/mol/HA)
✓ Good fit quality (FQ -4.94)
✗ Very high strain energy (27.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-17.482
kcal/mol
LE
-0.486
kcal/mol/HA
Fit Quality
-4.94
FQ (Leeson)
HAC
36
heavy atoms
MW
489
Da
LogP
1.96
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 27.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 55.36173360024159 | Score | -17.4817 |
|---|---|---|---|
| Inter norm | -0.576599 | Intra norm | 0.0909971 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 1 |
| Artifact reason | geometry warning; 16 clashes; 8 protein contact clashes | ||
| Residues | A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR54;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 | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1245 | 4.4306380730178185 | -0.606102 | -20.8405 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 1246 | 5.3872920867225975 | -0.62423 | -17.9378 | 1 | 20 | 20 | 1.00 | 0.20 | - | no | Open |
| 1229 | 5.404401572207389 | -0.607958 | -19.3261 | 1 | 19 | 18 | 0.90 | 0.20 | - | no | Open |
| 1242 | 5.98611853887622 | -0.696002 | -21.0367 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1232 | 6.004731805075224 | -0.646315 | -21.3251 | 1 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1237 | 6.251298696225477 | -0.61299 | -17.7252 | 0 | 18 | 18 | 0.90 | 0.00 | - | no | Open |
| 1234 | 6.714870461435001 | -0.662239 | -17.8936 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1235 | 7.3075751974473615 | -0.608466 | -15.2661 | 1 | 16 | 13 | 0.65 | 0.00 | - | no | Open |
| 1230 | 7.34913807404363 | -0.58841 | -20.2461 | 0 | 17 | 16 | 0.80 | 0.00 | - | no | Open |
| 1228 | 54.82918465162599 | -0.725702 | -24.3179 | 1 | 18 | 17 | 0.85 | 0.00 | - | no | Open |
| 1226 | 54.95485638987272 | -0.688856 | -15.8515 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1227 | 55.265762013166466 | -0.661696 | -20.4429 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1243 | 55.36173360024159 | -0.576599 | -17.4817 | 1 | 14 | 13 | 0.65 | 0.00 | - | no | Current |
| 1236 | 55.97995732720602 | -0.601365 | -18.4471 | 2 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1248 | 56.16249071225274 | -0.588969 | -20.493 | 2 | 16 | 15 | 0.75 | 0.00 | - | no | Open |
| 1247 | 55.3930187655408 | -0.657954 | -21.6563 | 1 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1231 | 55.547837032106905 | -0.631401 | -20.879 | 1 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1240 | 56.15690734697094 | -0.699923 | -21.6386 | 1 | 21 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1233 | 56.54627405906763 | -0.599813 | -16.8071 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1244 | 56.55860113683269 | -0.619297 | -13.6313 | 1 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1241 | 57.015873841227716 | -0.648293 | -16.6316 | 2 | 17 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1225 | 57.837613817495765 | -0.604481 | -17.6905 | 1 | 18 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1239 | 58.12679329729943 | -0.656246 | -21.7259 | 1 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1238 | 61.699418316931606 | -0.653003 | -16.473 | 2 | 21 | 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
-17.482kcal/mol
Ligand efficiency (LE)
-0.4856kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.936
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
488.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.96
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
178.24kcal/mol
Minimised FF energy
150.35kcal/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.