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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
32.2 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.62, Jaccard 0.33, H-bond role recall 1.00
Reason: 9 internal clashes
9 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.816 kcal/mol/HA)
✓ Good fit quality (FQ -7.31)
✓ Good H-bonds (4 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Very high strain energy (32.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-19.574
kcal/mol
LE
-0.816
kcal/mol/HA
Fit Quality
-7.31
FQ (Leeson)
HAC
24
heavy atoms
MW
323
Da
LogP
0.40
cLogP
Final rank
3.9549
rank score
Inter norm
-0.853
normalised
Contacts
12
H-bonds 4
Interaction summary
HBD 3
HBA 1
HY 5
PI 2
CLASH 0
Interaction summary
HBD 3
HBA 1
HY 5
PI 2
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 5 | Native recall | 0.62 |
| Jaccard | 0.33 | RMSD | - |
| HB strict | 1 | Strict recall | 0.50 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
Protein summary
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221 | ||
Receptor context
1 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 1
Excluded HETATM 0
Kept cofactors / ions
A: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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 186 | 1.0785366487636192 | -1.33554 | -31.2401 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 233 | 3.9549272373036755 | -0.852733 | -19.5737 | 4 | 12 | 5 | 0.62 | 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
-19.574kcal/mol
Ligand efficiency (LE)
-0.8156kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.309
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
323.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.40
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
85.99kcal/mol
Minimised FF energy
53.81kcal/mol
SASA & burial
✓ computed
SASA (unbound)
598.3Ų
Total solvent-accessible surface area of free ligand
BSA total
371.7Ų
Buried surface area upon binding
BSA apolar
344.1Ų
Hydrophobic contacts buried
BSA polar
27.6Ų
Polar contacts buried
Fraction buried
62.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3117.6Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1501.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)