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 (-0.772 kcal/mol/HA)
✓ Good fit quality (FQ -7.91)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (24.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.573
kcal/mol
LE
-0.772
kcal/mol/HA
Fit Quality
-7.91
FQ (Leeson)
HAC
37
heavy atoms
MW
495
Da
LogP
3.17
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 24.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 24
π–π 4
Clashes 3
Severe clashes 0
| Final rank | 4.618637155274895 | Score | -28.5727 |
|---|---|---|---|
| Inter norm | -0.803058 | Intra norm | 0.0308225 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 10 |
| Artifact reason | geometry warning; 17 clashes; 3 protein contact clashes; high strain Δ 29.1 | ||
| Residues | A:ALA32;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR180;A:THR54;A:TYR162;A:TYR178;A:VAL156;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 | 18 | Native recall | 0.90 |
| Jaccard | 0.78 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.57 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 304 | 4.618637155274895 | -0.803058 | -28.5727 | 10 | 21 | 18 | 0.90 | 0.80 | - | no | Current |
| 227 | 4.823152433370709 | -1.14683 | -33.4245 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 197 | 4.832421871029605 | -0.633104 | -20.201 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 197 | 5.121721553289744 | -0.649791 | -18.9976 | 4 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 207 | 5.142565175193588 | -0.544743 | -15.1314 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 204 | 5.158661328225735 | -1.11363 | -36.2955 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 228 | 5.235002079928121 | -0.934212 | -30.9377 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 178 | 6.391970965155197 | -0.611124 | -18.0149 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 7.1983409405374275 | -0.537335 | -16.6239 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 196 | 7.475422160355843 | -0.717527 | -22.2933 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 302 | 7.904069850528994 | -0.906033 | -25.6212 | 7 | 24 | 19 | 0.95 | 0.20 | - | no | Open |
| 226 | 7.351286921462457 | -1.00732 | -33.1264 | 4 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 201 | 7.373429719771494 | -1.03536 | -33.075 | 7 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 202 | 7.880459488386842 | -1.14596 | -33.7036 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 252 | 7.895986744012289 | -0.711971 | -23.6267 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 203 | 8.070886547796118 | -1.0222 | -30.5113 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 229 | 8.291873648095919 | -1.0842 | -35.0367 | 11 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 303 | 8.45361427934496 | -0.798578 | -23.1576 | 8 | 22 | 19 | 0.95 | 0.40 | - | yes | Open |
| 205 | 8.645287298237387 | -0.511082 | -14.8838 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 176 | 9.267056293692587 | -0.607051 | -16.0283 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 305 | 10.742603935914689 | -0.965604 | -29.7543 | 10 | 21 | 17 | 0.85 | 0.60 | - | yes | Open |
| 177 | 10.93161836458181 | -0.600757 | -17.5629 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 206 | 11.386361520289974 | -0.546086 | -14.5867 | 6 | 14 | 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
-28.573kcal/mol
Ligand efficiency (LE)
-0.7722kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.906
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
494.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.17
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.83kcal/mol
Minimised FF energy
81.74kcal/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.