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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.951 kcal/mol/HA)
✓ Good fit quality (FQ -9.17)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (11.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.526
kcal/mol
LE
-0.951
kcal/mol/HA
Fit Quality
-9.17
FQ (Leeson)
HAC
30
heavy atoms
MW
399
Da
LogP
2.84
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 11.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 3
Clashes 6
Severe clashes 0
| Final rank | 4.415693416521252 | Score | -28.5256 |
|---|---|---|---|
| Inter norm | -0.929381 | Intra norm | -0.0214715 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 8 |
| Artifact reason | geometry warning; 16 clashes; 6 protein contact clashes | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU179;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:PHE91;A:THR180;A:TYR162;A:TYR178;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 | 0.67 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 223 | 3.1858172775679083 | -1.23148 | -37.5009 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 89 | 3.421159330711923 | -1.30787 | -39.8328 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 99 | 3.4721198023924362 | -1.23393 | -38.4263 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 90 | 3.555956026672406 | -1.35194 | -41.1881 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 268 | 3.6445191534565207 | -0.802406 | -19.5407 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 91 | 3.7167456352456476 | -1.32763 | -40.8812 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 101 | 4.058612320414625 | -1.27331 | -37.5337 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 96 | 4.095656485850893 | -0.795921 | -22.6999 | 9 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 225 | 4.328742379177729 | -1.25317 | -37.4868 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 299 | 4.415693416521252 | -0.929381 | -28.5256 | 8 | 20 | 16 | 0.80 | 0.40 | - | no | Current |
| 100 | 4.534880202538158 | -1.3248 | -40.6867 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 195 | 4.893796472953285 | -0.83355 | -23.7941 | 6 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 224 | 5.332544073186912 | -1.31566 | -36.354 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 300 | 5.523605867480585 | -0.974715 | -29.3448 | 10 | 20 | 16 | 0.80 | 0.60 | - | no | Open |
| 97 | 6.888145404060353 | -1.07747 | -28.4735 | 11 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 196 | 7.120607776593641 | -1.07569 | -27.4595 | 10 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 301 | 8.645619895076276 | -0.994304 | -25.3242 | 10 | 18 | 15 | 0.75 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.526kcal/mol
Ligand efficiency (LE)
-0.9509kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.172
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
399.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.84
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
123.24kcal/mol
Minimised FF energy
111.93kcal/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.