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 (-0.432 kcal/mol/HA)
✓ Good fit quality (FQ -4.43)
✗ Very high strain energy (33.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-16.002
kcal/mol
LE
-0.432
kcal/mol/HA
Fit Quality
-4.43
FQ (Leeson)
HAC
37
heavy atoms
MW
498
Da
LogP
1.78
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 33.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 3
Clashes 9
Severe clashes 0
| Final rank | 7.788912091769055 | Score | -16.0024 |
|---|---|---|---|
| Inter norm | -0.706373 | Intra norm | 0.273875 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 1 |
| Artifact reason | geometry warning; 20 clashes; 9 protein contact clashes; high strain Δ 40.1 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER86;A:THR83;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.70 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2354 | 7.788912091769055 | -0.706373 | -16.0024 | 1 | 19 | 16 | 0.80 | 0.20 | - | no | Current |
| 2264 | 8.595845420859218 | -0.721513 | -14.5688 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 2263 | 8.70281808950016 | -0.730134 | -30.2242 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2261 | 9.354700937203685 | -0.706215 | -18.9074 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2353 | 10.389135930715625 | -0.695053 | -17.7037 | 9 | 18 | 17 | 0.85 | 0.60 | - | yes | Open |
| 2258 | 10.703179511398789 | -0.802117 | -22.9256 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2259 | 11.58318201983802 | -0.785486 | -19.4382 | 8 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2348 | 11.600033956497237 | -0.673656 | -9.65434 | 6 | 13 | 9 | 0.45 | 0.20 | - | yes | Open |
| 2352 | 11.653462317437256 | -0.691451 | -19.0194 | 7 | 16 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2349 | 11.665318430276963 | -0.704 | -18.0764 | 5 | 12 | 10 | 0.50 | 0.20 | - | yes | Open |
| 2350 | 11.708328637900559 | -0.707532 | -13.1969 | 4 | 18 | 16 | 0.80 | 0.20 | - | yes | Open |
| 2351 | 13.567004586321818 | -0.634842 | -6.02874 | 3 | 15 | 13 | 0.65 | 0.20 | - | yes | Open |
| 2262 | 15.08221594995705 | -0.659669 | -22.5681 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2260 | 15.384022826561807 | -0.745063 | -24.6879 | 7 | 17 | 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
-16.002kcal/mol
Ligand efficiency (LE)
-0.4325kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.428
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
497.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.78
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
89.20kcal/mol
Minimised FF energy
55.30kcal/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.