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 (-0.534 kcal/mol/HA)
✓ Good fit quality (FQ -5.30)
✗ Very high strain energy (28.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-17.619
kcal/mol
LE
-0.534
kcal/mol/HA
Fit Quality
-5.30
FQ (Leeson)
HAC
33
heavy atoms
MW
486
Da
LogP
4.13
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 28.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 3
Clashes 8
Severe clashes 0
| Final rank | 5.431450296883614 | Score | -17.6195 |
|---|---|---|---|
| Inter norm | -0.64754 | Intra norm | 0.113617 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 2 |
| Artifact reason | geometry warning; 11 clashes; 8 protein contact clashes; high strain Δ 30.8 | ||
| Residues | A:ARG48;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:THR83;A:TRP47;A:VAL156;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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 548 | 5.081908569193422 | -0.690502 | -13.1265 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 547 | 5.0950710599395475 | -0.555746 | -13.9644 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 545 | 5.105363872234837 | -0.588521 | -13.335 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 572 | 5.431450296883614 | -0.64754 | -17.6195 | 2 | 16 | 12 | 0.60 | 0.20 | - | no | Current |
| 546 | 5.466427687060774 | -0.590049 | -15.2907 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1978 | 5.83503777108036 | -0.706863 | -15.9242 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 528 | 5.952437885347036 | -0.583201 | -15.6926 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 6.515163930159474 | -0.647493 | -14.6638 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 311 | 6.536219478007521 | -0.68128 | -15.7724 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1980 | 6.57386179958214 | -0.652397 | -14.6786 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 527 | 7.302718540145861 | -0.639006 | -20.2417 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 571 | 6.659052124756004 | -0.74966 | -23.8694 | 3 | 17 | 16 | 0.80 | 0.20 | - | yes | Open |
| 525 | 6.751843990980415 | -0.707534 | -17.5975 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 573 | 7.365291258555342 | -0.752769 | -21.0427 | 3 | 16 | 12 | 0.60 | 0.20 | - | yes | Open |
| 526 | 7.604629144541703 | -0.609451 | -19.5701 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1979 | 9.388373661081921 | -0.70394 | -14.3394 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1977 | 9.52335982345675 | -0.749603 | -15.8986 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 574 | 57.26584774044052 | -0.689563 | -15.7303 | 3 | 17 | 12 | 0.60 | 0.20 | - | yes | Open |
| 312 | 59.780855866016466 | -0.67002 | -13.1303 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 310 | 60.46822861850252 | -0.694192 | -15.1833 | 6 | 15 | 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
-17.619kcal/mol
Ligand efficiency (LE)
-0.5339kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.298
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
485.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.13
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.55kcal/mol
Minimised FF energy
72.88kcal/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.