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 (-0.597 kcal/mol/HA)
✓ Good fit quality (FQ -6.02)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (45.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-20.891
kcal/mol
LE
-0.597
kcal/mol/HA
Fit Quality
-6.02
FQ (Leeson)
HAC
35
heavy atoms
MW
479
Da
LogP
2.03
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 45.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 24
π–π 2
Clashes 6
Severe clashes 1
| Final rank | 7.772060174584413 | Score | -20.8914 |
|---|---|---|---|
| Inter norm | -0.71998 | Intra norm | 0.123083 |
| Top1000 | no | Excluded | yes |
| Contacts | 21 | H-bonds | 10 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash; high strain Δ 45.2 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE55;A:PHE56;A:PHE91;A:PRO88;A:SER86;A:THR180;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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 87 | 4.643498246436422 | -1.05255 | -36.6414 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 70 | 5.476196025311045 | -0.739124 | -24.709 | 12 | 22 | 19 | 0.95 | 0.80 | - | no | Open |
| 33 | 6.480727755154504 | -0.81612 | -23.4258 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 95 | 7.87152207715595 | -0.794446 | -29.5766 | 6 | 22 | 1 | 0.05 | 0.00 | - | no | Open |
| 88 | 6.701023002482439 | -1.03729 | -39.6339 | 6 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 86 | 6.891187406146223 | -1.04094 | -29.6961 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 69 | 7.772060174584413 | -0.71998 | -20.8914 | 10 | 21 | 18 | 0.90 | 0.80 | - | yes | Current |
| 71 | 9.113995759443968 | -0.727321 | -29.2617 | 10 | 22 | 18 | 0.90 | 0.80 | - | yes | Open |
| 32 | 10.755888868764302 | -0.9847 | -29.0807 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 94 | 12.364613215489982 | -0.722233 | -24.7408 | 9 | 21 | 1 | 0.05 | 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
-20.891kcal/mol
Ligand efficiency (LE)
-0.5969kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.021
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
478.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.03
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
45.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.81kcal/mol
Minimised FF energy
60.49kcal/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.