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 (-0.560 kcal/mol/HA)
✓ Good fit quality (FQ -5.70)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (33.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-20.172
kcal/mol
LE
-0.560
kcal/mol/HA
Fit Quality
-5.70
FQ (Leeson)
HAC
36
heavy atoms
MW
530
Da
LogP
3.75
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 33.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 20
π–π 2
Clashes 13
Severe clashes 3
| Final rank | 10.566036805630187 | Score | -20.1719 |
|---|---|---|---|
| Inter norm | -0.64857 | Intra norm | 0.0882392 |
| Top1000 | no | Excluded | yes |
| Contacts | 12 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 11 clashes; 3 protein clashes; high strain Δ 33.1 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;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 | 11 | Native recall | 0.55 |
| Jaccard | 0.52 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2987 | 7.09278694836947 | -0.627069 | -15.0973 | 2 | 14 | 12 | 0.60 | 0.20 | - | no | Open |
| 2985 | 6.495081029953481 | -0.630192 | -22.0912 | 1 | 15 | 13 | 0.65 | 0.20 | - | yes | Open |
| 2984 | 9.630537457327685 | -0.727134 | -17.0781 | 4 | 17 | 16 | 0.80 | 0.20 | - | yes | Open |
| 2986 | 10.566036805630187 | -0.64857 | -20.1719 | 6 | 12 | 11 | 0.55 | 0.20 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.172kcal/mol
Ligand efficiency (LE)
-0.5603kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.695
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
530.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.75
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
65.73kcal/mol
Minimised FF energy
32.63kcal/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.