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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
18.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.33, Jaccard 0.21, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.981 kcal/mol/HA)
✓ Good fit quality (FQ -8.66)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (18.7 kcal/mol)
✗ Geometry warnings
Score
-22.561
kcal/mol
LE
-0.981
kcal/mol/HA
Fit Quality
-8.66
FQ (Leeson)
HAC
23
heavy atoms
MW
322
Da
LogP
3.29
cLogP
Final rank
2.7169
rank score
Inter norm
-1.032
normalised
Contacts
11
H-bonds 8
Interaction summary
HBD 2
HBA 4
HY 3
PI 1
CLASH 2
Interaction summary
HBD 2
HBA 4
HY 3
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.
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 | 4 | Native recall | 0.33 |
| Jaccard | 0.21 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 503 | 1.540954670453168 | -0.937327 | -21.175 | 4 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 515 | 2.716896115329566 | -1.03151 | -22.561 | 8 | 11 | 4 | 0.33 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.561kcal/mol
Ligand efficiency (LE)
-0.9809kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.657
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
322.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.29
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
60.66kcal/mol
Minimised FF energy
41.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
550.1Ų
Total solvent-accessible surface area of free ligand
BSA total
416.0Ų
Buried surface area upon binding
BSA apolar
313.9Ų
Hydrophobic contacts buried
BSA polar
102.0Ų
Polar contacts buried
Fraction buried
75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6446.2Ų
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
2064.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)