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 (-0.706 kcal/mol/HA)
✓ Good fit quality (FQ -7.00)
✗ Very high strain energy (22.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.292
kcal/mol
LE
-0.706
kcal/mol/HA
Fit Quality
-7.00
FQ (Leeson)
HAC
33
heavy atoms
MW
446
Da
LogP
2.77
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 22.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 1
Clashes 7
Severe clashes 0
| Final rank | 5.053914738507422 | Score | -23.2919 |
|---|---|---|---|
| Inter norm | -0.65804 | Intra norm | -0.0477767 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 1 |
| Artifact reason | geometry warning; 13 clashes; 7 protein contact clashes; high strain Δ 24.9 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR83;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 | 17 | Native recall | 0.85 |
| Jaccard | 0.81 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1216 | 4.013882301094123 | -0.502014 | -17.8447 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1212 | 4.396990726588747 | -0.454885 | -15.7572 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1664 | 4.642272634384539 | -0.786068 | -23.9847 | 1 | 19 | 18 | 0.90 | 0.20 | - | no | Open |
| 1213 | 4.82058525967209 | -0.519629 | -17.2292 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1660 | 5.053914738507422 | -0.65804 | -23.2919 | 1 | 18 | 17 | 0.85 | 0.20 | - | no | Current |
| 1662 | 5.609317620858329 | -0.694604 | -24.6632 | 1 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1215 | 54.014337055346104 | -0.565989 | -17.3348 | 2 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1211 | 54.49758931621311 | -0.545004 | -15.1878 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1658 | 54.67424900407422 | -0.722052 | -24.1029 | 1 | 12 | 9 | 0.45 | 0.20 | - | no | Open |
| 1663 | 54.95178217854325 | -0.70715 | -22.7696 | 1 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 1210 | 55.012375243918925 | -0.493339 | -18.3483 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1214 | 55.050565107588966 | -0.502724 | -18.594 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1661 | 55.52037280295748 | -0.780499 | -26.2914 | 1 | 18 | 15 | 0.75 | 0.20 | - | no | Open |
| 1209 | 54.94606519573975 | -0.359535 | -13.2979 | 1 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1657 | 56.02607467946437 | -0.705187 | -20.9165 | 0 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1659 | 58.524733583480845 | -0.729517 | -24.9158 | 1 | 19 | 16 | 0.80 | 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
-23.292kcal/mol
Ligand efficiency (LE)
-0.7058kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.003
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
445.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.77
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.44kcal/mol
Minimised FF energy
75.15kcal/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.