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 (-0.820 kcal/mol/HA)
✓ Good fit quality (FQ -7.99)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (72.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.411
kcal/mol
LE
-0.820
kcal/mol/HA
Fit Quality
-7.99
FQ (Leeson)
HAC
31
heavy atoms
MW
463
Da
LogP
2.68
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 72.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 12
Severe clashes 0
| Final rank | 8.88138262817425 | Score | -25.4109 |
|---|---|---|---|
| Inter norm | -0.888089 | Intra norm | 0.0683826 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | geometry warning; 12 clashes; 12 protein contact clashes; high strain Δ 69.9 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:THR180;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.73 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1553 | 6.601880644187128 | -0.684491 | -19.2384 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1555 | 6.90713370680132 | -0.573933 | -20.9566 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 990 | 6.930463648518177 | -1.00086 | -30.9453 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1556 | 6.947998446299967 | -0.623446 | -18.3229 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 991 | 7.090500327981782 | -0.905384 | -27.2375 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2336 | 8.594890553733196 | -0.862672 | -26.3082 | 4 | 19 | 17 | 0.85 | 0.20 | - | no | Open |
| 2333 | 8.88138262817425 | -0.888089 | -25.4109 | 4 | 18 | 16 | 0.80 | 0.20 | - | no | Current |
| 1312 | 9.037584743771923 | -0.685118 | -17.9932 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1013 | 9.756171458439853 | -0.760022 | -18.0829 | 6 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 2335 | 10.191125855054768 | -0.819935 | -24.2471 | 3 | 17 | 15 | 0.75 | 0.20 | - | no | Open |
| 1554 | 8.142524541997904 | -0.654268 | -20.6614 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1552 | 10.460058322921274 | -0.592255 | -17.0898 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1311 | 10.560313631394987 | -0.528716 | -16.067 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1011 | 10.617958091953554 | -0.739378 | -21.387 | 3 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 988 | 11.240600527676973 | -1.05613 | -31.7257 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2334 | 12.129028651584083 | -0.771508 | -21.5589 | 4 | 18 | 16 | 0.80 | 0.20 | - | yes | Open |
| 989 | 12.29539830789036 | -0.979574 | -31.5648 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1009 | 16.044625114120628 | -0.770772 | -20.0033 | 7 | 21 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1010 | 16.93007262161361 | -0.74178 | -15.5227 | 7 | 20 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1012 | 17.95856237458152 | -0.589167 | -16.8745 | 5 | 19 | 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
-25.411kcal/mol
Ligand efficiency (LE)
-0.8197kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.986
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
462.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.68
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
72.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.17kcal/mol
Minimised FF energy
-20.68kcal/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.