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 (-1.373 kcal/mol/HA)
✓ Good fit quality (FQ -11.49)
✓ Strong H-bond network (9 bonds)
✗ High strain energy (14.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.451
kcal/mol
LE
-1.373
kcal/mol/HA
Fit Quality
-11.49
FQ (Leeson)
HAC
20
heavy atoms
MW
313
Da
LogP
0.81
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 14.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 23
π–π 2
Clashes 7
Severe clashes 0
| Final rank | 3.0541287092040164 | Score | -27.4507 |
|---|---|---|---|
| Inter norm | -1.39656 | Intra norm | 0.0240278 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 9 |
| Artifact reason | geometry warning; 7 clashes; 7 protein contact clashes; high strain Δ 21.4 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU179;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:THR180;A:TRP47;A:TYR178;A:VAL30;A:VAL31;A:VAL49 | ||
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 | 9 | Native recall | 0.45 |
| Jaccard | 0.35 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1105 | 1.8015874941263035 | -1.22106 | -23.8238 | 6 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 2831 | 2.5139021948811577 | -1.42069 | -28.4485 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2833 | 2.7791407295584194 | -1.17948 | -23.9444 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1104 | 2.8381851261886735 | -1.20093 | -22.9423 | 10 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 746 | 2.868570517146959 | -1.21841 | -24.7196 | 10 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 2204 | 3.0541287092040164 | -1.39656 | -27.4507 | 9 | 15 | 9 | 0.45 | 0.20 | - | no | Current |
| 2832 | 3.1395205386738922 | -1.07893 | -21.965 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2834 | 3.4036078106990635 | -1.42934 | -28.6624 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1325 | 3.4497104562140786 | -1.12493 | -21.7001 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2967 | 3.7286585480073686 | -1.61668 | -32.5631 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1620 | 4.125792971760725 | -0.968003 | -19.9316 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 747 | 3.956035189097958 | -1.23041 | -24.2745 | 10 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1619 | 4.047711587760167 | -0.846947 | -17.2118 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1322 | 4.371389475374939 | -1.15147 | -24.1277 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 745 | 4.523362317522636 | -1.22705 | -23.2376 | 12 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 748 | 4.809200614036901 | -1.21732 | -23.7106 | 7 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1324 | 5.169339532707856 | -1.18436 | -24.0621 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1323 | 6.177057243412305 | -1.09512 | -22.0049 | 7 | 13 | 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
-27.451kcal/mol
Ligand efficiency (LE)
-1.3725kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.486
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
313.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.81
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-4.40kcal/mol
Minimised FF energy
-18.68kcal/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.