Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
10.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.67, Jaccard 0.47, H-bond role recall 1.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular 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
Yes
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.002 kcal/mol/HA)
✓ Good fit quality (FQ -8.84)
✓ Good H-bonds (5 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ Moderate strain (10.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-23.040
kcal/mol
LE
-1.002
kcal/mol/HA
Fit Quality
-8.84
FQ (Leeson)
HAC
23
heavy atoms
MW
344
Da
LogP
5.05
cLogP
Final rank
2.0659
rank score
Inter norm
-1.049
normalised
Contacts
13
H-bonds 6
Interaction summary
HBD 3
HBA 2
HY 8
PI 2
CLASH 4
Interaction summary
HBD 3
HBA 2
HY 8
PI 2
CLASH 4
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 | 8 | Native recall | 0.67 |
| Jaccard | 0.47 | RMSD | - |
| HB strict | 1 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 668 | 2.0659225395616754 | -1.04937 | -23.0401 | 6 | 13 | 8 | 0.67 | 1.00 | - | no | Current |
| 676 | 2.867767247140579 | -0.817557 | -18.3964 | 4 | 8 | 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
-23.040kcal/mol
Ligand efficiency (LE)
-1.0017kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.841
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
344.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.05
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
71.73kcal/mol
Minimised FF energy
61.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
555.6Ų
Total solvent-accessible surface area of free ligand
BSA total
471.0Ų
Buried surface area upon binding
BSA apolar
450.2Ų
Hydrophobic contacts buried
BSA polar
20.7Ų
Polar contacts buried
Fraction buried
84.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
95.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6525.6Ų
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
2070.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)