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 (-0.945 kcal/mol/HA)
✓ Good fit quality (FQ -9.02)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (62.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-27.410
kcal/mol
LE
-0.945
kcal/mol/HA
Fit Quality
-9.02
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.24
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 62.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 3
Clashes 14
Severe clashes 1
| Final rank | 10.483720617878864 | Score | -27.4097 |
|---|---|---|---|
| Inter norm | -0.919382 | Intra norm | -0.0257803 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 14 clashes; 1 protein clash; high strain Δ 58.1 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:THR54;A:TYR162;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 | 0.73 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1522 | 6.077153081704872 | -0.570691 | -15.2459 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 775 | 6.780725509257474 | -0.763705 | -21.6087 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 773 | 7.234636789597247 | -0.866466 | -24.6234 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2299 | 7.337268243542633 | -0.933728 | -27.318 | 4 | 18 | 16 | 0.80 | 0.20 | - | no | Open |
| 772 | 7.533356747099689 | -0.810243 | -23.5505 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 959 | 8.551485862305917 | -0.859526 | -24.8294 | 4 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 961 | 8.944243680337374 | -0.830023 | -24.4069 | 3 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 958 | 9.288348351619724 | -0.832583 | -21.0199 | 5 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 774 | 8.31909033934569 | -0.787048 | -24.7493 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1521 | 8.758434517595909 | -0.691866 | -19.5138 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 770 | 8.960850695797632 | -0.956826 | -26.5786 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2298 | 9.522546551421629 | -0.93625 | -27.0964 | 4 | 19 | 17 | 0.85 | 0.20 | - | yes | Open |
| 771 | 9.763341147940448 | -0.901756 | -23.9196 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1520 | 10.05211856012855 | -0.688802 | -19.7515 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2300 | 10.420028469361384 | -0.967058 | -25.9968 | 4 | 17 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2301 | 10.483720617878864 | -0.919382 | -27.4097 | 4 | 18 | 16 | 0.80 | 0.20 | - | yes | Current |
| 962 | 12.71328158612714 | -0.692733 | -19.3747 | 7 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2302 | 13.082441100512261 | -0.953077 | -25.7443 | 5 | 18 | 16 | 0.80 | 0.20 | - | yes | Open |
| 960 | 13.762167842419784 | -0.636862 | -17.1413 | 7 | 20 | 1 | 0.05 | 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
-27.410kcal/mol
Ligand efficiency (LE)
-0.9452kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.022
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.24
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
62.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
36.02kcal/mol
Minimised FF energy
-26.32kcal/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.