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 (-0.812 kcal/mol/HA)
✓ Good fit quality (FQ -8.19)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (53.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.414
kcal/mol
LE
-0.812
kcal/mol/HA
Fit Quality
-8.19
FQ (Leeson)
HAC
35
heavy atoms
MW
473
Da
LogP
1.61
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 53.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 3
Clashes 6
Severe clashes 1
| Final rank | 8.71285521030407 | Score | -28.4143 |
|---|---|---|---|
| Inter norm | -0.754055 | Intra norm | -0.0577812 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 19 clashes; 1 protein clash; high strain Δ 50.8 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:THR54;A:TRP47;A:VAL49;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 | 12 | Native recall | 0.60 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 362 | 6.051947950059093 | -0.725491 | -24.7876 | 3 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 564 | 6.435097382084817 | -0.76336 | -25.367 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 562 | 6.622736186688672 | -0.724749 | -25.7739 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 433 | 6.929139539328095 | -0.831483 | -32.4761 | 2 | 19 | 17 | 0.85 | 0.40 | - | no | Open |
| 360 | 7.081412667625094 | -0.792379 | -30.8426 | 1 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 432 | 7.6897862423845496 | -0.666396 | -18.4122 | 0 | 19 | 18 | 0.90 | 0.00 | - | no | Open |
| 563 | 7.724099824193679 | -0.651589 | -24.4701 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 434 | 7.864725185190762 | -0.79809 | -18.4317 | 2 | 20 | 18 | 0.90 | 0.20 | - | yes | Open |
| 431 | 8.71285521030407 | -0.754055 | -28.4143 | 3 | 16 | 12 | 0.60 | 0.00 | - | yes | Current |
| 565 | 10.179313852503258 | -0.718414 | -28.9632 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 430 | 10.606329162344084 | -0.804457 | -25.0823 | 2 | 16 | 11 | 0.55 | 0.20 | - | yes | Open |
| 361 | 10.634335700671578 | -0.604498 | -24.2566 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 363 | 11.3447361950399 | -0.648163 | -29.5202 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 435 | 12.16063322607444 | -0.832458 | -26.8363 | 3 | 15 | 13 | 0.65 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.414kcal/mol
Ligand efficiency (LE)
-0.8118kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.189
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
472.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.61
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
53.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
8.21kcal/mol
Minimised FF energy
-45.16kcal/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.