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 (-0.822 kcal/mol/HA)
✓ Good fit quality (FQ -8.00)
✗ Very high strain energy (22.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.468
kcal/mol
LE
-0.822
kcal/mol/HA
Fit Quality
-8.00
FQ (Leeson)
HAC
31
heavy atoms
MW
495
Da
LogP
5.32
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 22.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 3
Clashes 6
Severe clashes 0
| Final rank | 3.5008472835249673 | Score | -25.4677 |
|---|---|---|---|
| Inter norm | -0.870202 | Intra norm | 0.048664 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 8 clashes; 6 protein contact clashes; high strain Δ 23.4 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:THR54;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49 | ||
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: permissive.
| 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 | 13 | Native recall | 0.65 |
| Jaccard | 0.57 | 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: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3012 | 3.5008472835249673 | -0.870202 | -25.4677 | 1 | 16 | 13 | 0.65 | 0.20 | - | no | Current |
| 3009 | 4.264649485556495 | -0.753425 | -20.4229 | 1 | 19 | 14 | 0.70 | 0.20 | - | no | Open |
| 3720 | 4.475432255147078 | -0.751547 | -19.326 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3010 | 4.790951199612363 | -0.817278 | -22.2339 | 2 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 3008 | 4.858289331297003 | -0.843065 | -23.3011 | 1 | 20 | 15 | 0.75 | 0.20 | - | no | Open |
| 2380 | 5.24130423855188 | -0.811071 | -16.3744 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 3718 | 5.792623022588414 | -0.793719 | -19.1784 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2381 | 7.448464549887253 | -0.557376 | -13.3976 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3719 | 5.9005778059473 | -0.60549 | -17.3397 | 3 | 13 | 1 | 0.05 | 0.00 | - | yes | Open |
| 3007 | 6.1757752049124175 | -0.832563 | -27.2041 | 5 | 12 | 8 | 0.40 | 0.20 | - | yes | Open |
| 3722 | 6.849041389449994 | -0.667376 | -18.1777 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3725 | 7.448040269178322 | -0.82762 | -23.9417 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3723 | 7.965956982335391 | -0.560396 | -17.3366 | 1 | 11 | 1 | 0.05 | 0.00 | - | yes | Open |
| 3013 | 10.929889634825173 | -0.807686 | -22.6922 | 5 | 10 | 8 | 0.40 | 0.20 | - | yes | Open |
| 2378 | 11.179971303207955 | -0.754788 | -15.394 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3006 | 55.93644300771782 | -0.828189 | -21.6678 | 1 | 17 | 13 | 0.65 | 0.20 | - | yes | Open |
| 3721 | 56.60980540699392 | -0.693809 | -19.969 | 4 | 14 | 1 | 0.05 | 0.00 | - | yes | Open |
| 3724 | 58.202409408943545 | -0.707799 | -21.3846 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3011 | 60.190750819326425 | -0.834988 | -26.4709 | 4 | 11 | 8 | 0.40 | 0.20 | - | yes | Open |
| 2379 | 62.23524893153547 | -0.584708 | -19.083 | 13 | 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
-25.468kcal/mol
Ligand efficiency (LE)
-0.8215kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.004
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
495.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.32
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
74.19kcal/mol
Minimised FF energy
51.82kcal/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.