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 (-0.688 kcal/mol/HA)
✓ Good fit quality (FQ -7.04)
✗ Very high strain energy (23.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.462
kcal/mol
LE
-0.688
kcal/mol/HA
Fit Quality
-7.04
FQ (Leeson)
HAC
37
heavy atoms
MW
502
Da
LogP
2.91
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 23.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 1
Clashes 8
Severe clashes 0
| Final rank | 55.65695515321564 | Score | -25.4616 |
|---|---|---|---|
| Inter norm | -0.687655 | Intra norm | -0.000497364 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 1 |
| Artifact reason | geometry warning; 19 clashes; 8 protein contact clashes | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR180;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 | 17 | Native recall | 0.85 |
| Jaccard | 0.71 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 863 | 5.826832996361648 | -0.612361 | -21.3562 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 853 | 6.8545418299215815 | -0.634715 | -24.4221 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 858 | 7.026082115349668 | -0.639914 | -23.4179 | 1 | 18 | 16 | 0.80 | 0.00 | - | no | Open |
| 861 | 55.13020410717958 | -0.681926 | -28.5794 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 857 | 55.43296456756019 | -0.612013 | -23.7548 | 0 | 16 | 10 | 0.50 | 0.00 | - | no | Open |
| 862 | 55.65695515321564 | -0.687655 | -25.4616 | 1 | 21 | 17 | 0.85 | 0.00 | - | no | Current |
| 859 | 55.694168718488555 | -0.642566 | -23.8417 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 850 | 55.71266576151602 | -0.606735 | -25.6067 | 3 | 18 | 16 | 0.80 | 0.20 | - | no | Open |
| 851 | 55.973343807024506 | -0.587312 | -18.6632 | 1 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 852 | 56.30761623593743 | -0.623054 | -23.0971 | 2 | 19 | 15 | 0.75 | 0.20 | - | no | Open |
| 864 | 56.32650457400241 | -0.685256 | -21.1933 | 2 | 15 | 13 | 0.65 | 0.20 | - | no | Open |
| 860 | 56.326735481538485 | -0.646653 | -23.2102 | 1 | 15 | 13 | 0.65 | 0.00 | - | yes | Open |
| 849 | 56.335324044010726 | -0.625277 | -19.4549 | 0 | 17 | 15 | 0.75 | 0.00 | - | yes | Open |
| 855 | 56.53192445380316 | -0.640449 | -21.9921 | 0 | 20 | 15 | 0.75 | 0.00 | - | yes | Open |
| 856 | 57.47542477194421 | -0.611717 | -22.2531 | 0 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 854 | 62.25269122204826 | -0.659561 | -22.6848 | 1 | 20 | 17 | 0.85 | 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
-25.462kcal/mol
Ligand efficiency (LE)
-0.6882kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.045
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
501.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.91
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
155.36kcal/mol
Minimised FF energy
131.55kcal/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.