Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
34.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.35, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.725 kcal/mol/HA)
✓ Good fit quality (FQ -7.52)
✓ Good H-bonds (3 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Very high strain energy (34.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-28.262
kcal/mol
LE
-0.725
kcal/mol/HA
Fit Quality
-7.52
FQ (Leeson)
HAC
39
heavy atoms
MW
563
Da
LogP
5.00
cLogP
Final rank
3.7948
rank score
Inter norm
-0.709
normalised
Contacts
23
H-bonds 7
Interaction summary
HBD 1
HBA 2
HY 8
PI 2
CLASH 2
Interaction summary
HBD 1
HBA 2
HY 8
PI 2
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5S9T | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA365
ARG228
ARG331
GLY229
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL366
| ||
| Current overlap | 9 | Native recall | 0.75 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
1033 residues
| Protein target | T17 | Atoms | 15160 |
|---|---|---|---|
| Residues | 1033 | Chains | 2 |
| Residue summary | VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408 | ||
Receptor context
2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
B:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 475 | 1.280287287729594 | -0.617165 | -25.0747 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 463 | 2.6296067961054295 | -0.682535 | -26.5323 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 514 | 3.7948270720513495 | -0.709367 | -28.2621 | 7 | 23 | 9 | 0.75 | 0.00 | - | no | Current |
| 473 | 4.655184917891928 | -0.82917 | -34.339 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 457 | 5.557439725654371 | -0.634517 | -20.1581 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 460 | 5.792579168189608 | -0.711207 | -22.3926 | 8 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.262kcal/mol
Ligand efficiency (LE)
-0.7247kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.521
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
563.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.00
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
118.49kcal/mol
Minimised FF energy
84.50kcal/mol
SASA & burial
✓ computed
SASA (unbound)
854.0Ų
Total solvent-accessible surface area of free ligand
BSA total
685.4Ų
Buried surface area upon binding
BSA apolar
569.0Ų
Hydrophobic contacts buried
BSA polar
116.4Ų
Polar contacts buried
Fraction buried
80.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6672.9Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2120.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)