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 (-0.556 kcal/mol/HA)
✓ Good fit quality (FQ -5.65)
✗ Very high strain energy (30.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.003
kcal/mol
LE
-0.556
kcal/mol/HA
Fit Quality
-5.65
FQ (Leeson)
HAC
36
heavy atoms
MW
489
Da
LogP
3.16
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 30.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 2
Clashes 3
Severe clashes 0
| Final rank | 5.188235886259246 | Score | -20.0025 |
|---|---|---|---|
| Inter norm | -0.539784 | Intra norm | -0.0158406 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 2 |
| Artifact reason | geometry warning; 18 clashes; 3 protein contact clashes; high strain Δ 28.6 | ||
| Residues | A:ALA10;A:ARG29;A:ASN65;A:ASP22;A:GLU31;A:LEU23;A:LEU28;A:NAP201;A:PHE32;A:PHE35;A:PRO26;A:PRO27;A:TRP25 | ||
Protein summary
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 5 |
| IFP residues | A:ALA10; A:ASN65; A:ASP22; A:GLN36; A:GLU31; A:GLY117; A:GLY21; A:ILE61; A:ILE8; A:LEU23; A:LEU68; A:NAP201; A:PHE32; A:PHE35; A:PRO62; A:SER60; A:THR137; A:THR57; A:TYR122; A:VAL116; A:VAL9 | ||
| Current overlap | 8 | Native recall | 0.38 |
| Jaccard | 0.31 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1372 | 5.044055811807285 | -0.407003 | -15.892 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1234 | 5.188235886259246 | -0.539784 | -20.0025 | 2 | 13 | 8 | 0.38 | 0.20 | - | no | Current |
| 1378 | 5.7106218720905595 | -0.476363 | -17.7692 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1244 | 5.9436369114202385 | -0.632196 | -10.9002 | 0 | 19 | 17 | 0.81 | 0.00 | - | no | Open |
| 1245 | 6.18917561147906 | -0.523533 | -17.8831 | 0 | 14 | 9 | 0.43 | 0.00 | - | no | Open |
| 1379 | 6.454001891979365 | -0.494448 | -17.9458 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1239 | 54.79295080535171 | -0.641297 | -12.8386 | 2 | 19 | 16 | 0.76 | 0.00 | - | no | Open |
| 1240 | 55.169732431923656 | -0.603836 | -18.5478 | 1 | 18 | 15 | 0.71 | 0.00 | - | no | Open |
| 1237 | 55.52845111736323 | -0.523143 | -19.3698 | 0 | 14 | 9 | 0.43 | 0.00 | - | no | Open |
| 1248 | 55.93304539126796 | -0.590623 | -18.7666 | 1 | 18 | 15 | 0.71 | 0.00 | - | no | Open |
| 1376 | 55.94293522658833 | -0.563996 | -17.1747 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1235 | 55.99721462987739 | -0.603998 | -18.6243 | 1 | 22 | 19 | 0.90 | 0.00 | - | no | Open |
| 1246 | 56.57698613667258 | -0.652961 | -22.6782 | 0 | 21 | 17 | 0.81 | 0.00 | - | no | Open |
| 1238 | 56.87417687840242 | -0.625825 | -10.2107 | 0 | 21 | 18 | 0.86 | 0.00 | - | no | Open |
| 1373 | 54.84407956432683 | -0.567573 | -20.0898 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1236 | 55.8222131650429 | -0.644917 | -21.8499 | 1 | 18 | 16 | 0.76 | 0.00 | - | yes | Open |
| 1377 | 56.40988628958356 | -0.546873 | -18.7777 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1233 | 57.6486353788669 | -0.485692 | -19.7246 | 0 | 17 | 12 | 0.57 | 0.00 | - | yes | Open |
| 1247 | 57.97382691924889 | -0.527593 | -14.0999 | 1 | 18 | 15 | 0.71 | 0.00 | - | yes | Open |
| 1374 | 58.387261403604455 | -0.568279 | -20.8506 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1242 | 58.85576732575499 | -0.468116 | -14.6945 | 0 | 15 | 15 | 0.71 | 0.00 | - | yes | Open |
| 1243 | 59.05249809493202 | -0.558154 | -13.8579 | 0 | 21 | 19 | 0.90 | 0.00 | - | yes | Open |
| 1375 | 59.23405019807555 | -0.457517 | -16.0638 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1241 | 59.261314779649915 | -0.52192 | -16.4875 | 0 | 13 | 13 | 0.62 | 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
-20.003kcal/mol
Ligand efficiency (LE)
-0.5556kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.647
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
488.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.16
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
136.05kcal/mol
Minimised FF energy
106.06kcal/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.