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 (-0.546 kcal/mol/HA)
✓ Good fit quality (FQ -5.84)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (59.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.047
kcal/mol
LE
-0.546
kcal/mol/HA
Fit Quality
-5.84
FQ (Leeson)
HAC
44
heavy atoms
MW
610
Da
LogP
0.40
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 59.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 1
Clashes 5
Severe clashes 0
| Final rank | 7.350464938752037 | Score | -24.0475 |
|---|---|---|---|
| Inter norm | -0.624398 | Intra norm | 0.0778634 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 5 |
| Artifact reason | geometry warning; 16 clashes; 5 protein contact clashes; high strain Δ 63.4 | ||
| Residues | A:ALA32;A:ARG97;A:GLY157;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:THR54;A:TYR162;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 | 0.70 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.43 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 168 | 7.023665339492769 | -0.427398 | -17.79 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 153 | 7.330311277315124 | -0.557948 | -22.6725 | 6 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 265 | 7.350464938752037 | -0.624398 | -24.0475 | 5 | 19 | 16 | 0.80 | 0.60 | - | no | Current |
| 164 | 7.674133302235749 | -0.459738 | -21.7239 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 263 | 7.786447145288811 | -0.601009 | -22.8534 | 4 | 19 | 17 | 0.85 | 0.60 | - | no | Open |
| 185 | 7.888633566124654 | -0.541852 | -19.7561 | 4 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 155 | 7.922049680456461 | -0.507246 | -20.0911 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 163 | 7.956018962221468 | -0.419388 | -15.9905 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 262 | 8.956853229979028 | -0.63853 | -22.0415 | 6 | 19 | 16 | 0.80 | 0.60 | - | no | Open |
| 166 | 9.030198863594844 | -0.464352 | -19.1092 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 171 | 9.18959634695467 | -0.649389 | -27.0531 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 264 | 9.389217612215772 | -0.508652 | -14.0927 | 2 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 260 | 9.430921070530088 | -0.583211 | -19.2894 | 3 | 21 | 17 | 0.85 | 0.60 | - | no | Open |
| 184 | 8.320188869547547 | -0.495622 | -26.1935 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 167 | 9.755807243465343 | -0.506314 | -20.4667 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 152 | 10.509612507824277 | -0.384727 | -16.1175 | 5 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 172 | 11.97617580348897 | -0.696189 | -25.0881 | 8 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 154 | 13.278137543188803 | -0.516905 | -20.8765 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 261 | 56.64284635921081 | -0.580188 | -24.5406 | 3 | 19 | 12 | 0.60 | 0.00 | - | yes | Open |
| 165 | 58.754962801835134 | -0.660802 | -27.1569 | 4 | 21 | 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
-24.047kcal/mol
Ligand efficiency (LE)
-0.5465kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.840
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
44HA
Physicochemical properties
Molecular weight
609.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.40
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
59.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.03kcal/mol
Minimised FF energy
37.63kcal/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.