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 (-0.716 kcal/mol/HA)
✓ Good fit quality (FQ -7.17)
✗ Very high strain energy (22.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.350
kcal/mol
LE
-0.716
kcal/mol/HA
Fit Quality
-7.17
FQ (Leeson)
HAC
34
heavy atoms
MW
489
Da
LogP
2.38
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 22.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 1
Clashes 5
Severe clashes 0
| Final rank | 5.115558746971648 | Score | -24.3503 |
|---|---|---|---|
| Inter norm | -0.769265 | Intra norm | 0.0530787 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 2 |
| Artifact reason | geometry warning; 16 clashes; 5 protein contact clashes; high strain Δ 29.5 | ||
| Residues | A:ALA32;A:ASN58;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:THR180;A:THR54;A:THR83;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 | 0.73 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 804 | 4.698750806825013 | -0.728687 | -23.6792 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2130 | 5.115558746971648 | -0.769265 | -24.3503 | 2 | 18 | 16 | 0.80 | 0.00 | - | no | Current |
| 2922 | 5.166151796112486 | -0.580291 | -18.9912 | 4 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 1072 | 5.901424933283021 | -0.632762 | -20.7927 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1253 | 6.576783161576039 | -0.498922 | -15.1141 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2921 | 6.720197609011943 | -0.777885 | -25.0506 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2923 | 6.756572032207131 | -0.574614 | -15.6519 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 806 | 8.367830593164323 | -0.688128 | -19.8948 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1074 | 9.024504968163807 | -0.765126 | -25.2273 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2925 | 6.379744825863821 | -0.782028 | -25.3532 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 803 | 7.529535868918771 | -0.734062 | -20.7551 | 9 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2131 | 8.285163220641225 | -0.790782 | -24.7584 | 3 | 14 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1254 | 8.2871329434483 | -0.6785 | -19.7342 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2920 | 9.14980645339217 | -0.675625 | -22.1813 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 805 | 9.204133832824493 | -0.910439 | -24.7912 | 13 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1073 | 9.302495416278923 | -0.626145 | -22.7031 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2924 | 9.742701659770987 | -0.744163 | -20.6681 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1075 | 10.633832423620813 | -0.7134 | -22.7123 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1070 | 10.884464645666295 | -0.754019 | -25.5115 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1071 | 13.22170472102836 | -0.573657 | -16.943 | 8 | 12 | 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
-24.350kcal/mol
Ligand efficiency (LE)
-0.7162kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.166
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
488.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.38
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
107.11kcal/mol
Minimised FF energy
84.63kcal/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.