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 (-0.973 kcal/mol/HA)
✓ Good fit quality (FQ -8.72)
✓ Strong H-bond network (12 bonds)
✗ Very high strain energy (35.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-23.342
kcal/mol
LE
-0.973
kcal/mol/HA
Fit Quality
-8.72
FQ (Leeson)
HAC
24
heavy atoms
MW
369
Da
LogP
1.63
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 35.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 12
Hydrophobic 20
π–π 2
Clashes 7
Severe clashes 1
| Final rank | 6.088552464205872 | Score | -23.3419 |
|---|---|---|---|
| Inter norm | -1.0349 | Intra norm | 0.0623203 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 9 clashes; 1 protein clash; high strain Δ 38.0 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49 | ||
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: permissive.
| 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 | 10 | Native recall | 0.50 |
| Jaccard | 0.42 | 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: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2253 | 3.420161364834467 | -0.980113 | -23.4347 | 3 | 15 | 11 | 0.55 | 0.40 | - | no | Open |
| 2251 | 3.7541282467480235 | -1.01449 | -21.0972 | 9 | 14 | 10 | 0.50 | 0.80 | - | no | Open |
| 2175 | 3.7664680118373135 | -1.14015 | -26.1926 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1144 | 3.821890714115333 | -0.883315 | -20.0234 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1141 | 3.856949942136315 | -1.03898 | -24.7483 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1139 | 3.93864664759149 | -1.03385 | -23.8524 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2256 | 4.139830257890376 | -1.32222 | -31.3752 | 9 | 15 | 11 | 0.55 | 0.80 | - | no | Open |
| 2907 | 4.203761026289352 | -1.03419 | -24.3577 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2904 | 4.361478499891133 | -1.097 | -25.9648 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2905 | 4.4156613226880825 | -1.16817 | -29.4909 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2912 | 4.555056647206074 | -0.936033 | -22.184 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2258 | 4.603012486605365 | -1.19496 | -26.4091 | 10 | 15 | 11 | 0.55 | 0.80 | - | no | Open |
| 2176 | 4.634902936056227 | -1.17359 | -27.9475 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2178 | 4.844625435605755 | -1.0904 | -24.6641 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2903 | 4.92104624319408 | -0.867192 | -19.35 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1140 | 5.17083171579989 | -0.899789 | -20.8822 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2259 | 5.376082781010201 | -1.12361 | -20.328 | 10 | 16 | 11 | 0.55 | 0.80 | - | no | Open |
| 1143 | 5.493060296203853 | -0.953861 | -23.8738 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2177 | 5.829656891162102 | -0.950372 | -23.9669 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2911 | 5.933561974660224 | -0.977531 | -22.1696 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2260 | 6.043406487668909 | -1.03032 | -22.6453 | 7 | 15 | 11 | 0.55 | 0.60 | - | yes | Open |
| 1138 | 6.08397495360762 | -0.877014 | -20.989 | 5 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2257 | 6.088552464205872 | -1.0349 | -23.3419 | 9 | 14 | 10 | 0.50 | 0.80 | - | yes | Current |
| 2906 | 6.107806367669729 | -0.946393 | -23.9953 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2908 | 6.796857614618233 | -0.718013 | -16.1162 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2252 | 7.085923933798884 | -0.860813 | -22.5682 | 3 | 16 | 14 | 0.70 | 0.40 | - | yes | Open |
| 2255 | 7.500494196108233 | -1.06491 | -26.1039 | 5 | 11 | 10 | 0.50 | 0.40 | - | yes | Open |
| 2909 | 7.821530294600496 | -0.964594 | -21.9257 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1145 | 8.703058575631912 | -0.882441 | -18.2066 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2254 | 12.562948423570543 | -0.987372 | -25.644 | 9 | 11 | 8 | 0.40 | 0.20 | - | yes | Open |
| 1142 | 54.46503986078015 | -0.958105 | -22.4837 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2910 | 57.28611185104623 | -0.996789 | -22.2427 | 10 | 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
-23.342kcal/mol
Ligand efficiency (LE)
-0.9726kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.716
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
369.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.63
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
3.86kcal/mol
Minimised FF energy
-31.74kcal/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.