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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
48.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.92, Jaccard 0.60
Reason: strain 48.7 kcal/mol
strain ΔE 48.7 kcal/mol
1 protein-contact 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.597 kcal/mol/HA)
✓ Good fit quality (FQ -6.34)
✓ Good burial (65% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Extreme strain energy (48.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (23)
Score
-25.658
kcal/mol
LE
-0.597
kcal/mol/HA
Fit Quality
-6.34
FQ (Leeson)
HAC
43
heavy atoms
MW
593
Da
LogP
1.86
cLogP
Final rank
2.3605
rank score
Inter norm
-0.555
normalised
Contacts
19
H-bonds 2
Interaction summary
HBA 1
HY 7
PI 1
CLASH 1
Interaction summary
HBA 1
HY 7
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
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 | 9IFF | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA209
ARG74
ASN208
GLY214
GLY215
GLY85
LEU73
LYS211
MET70
PHE83
PRO212
PRO213
VAL88
| ||
| Current overlap | 12 | Native recall | 0.92 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
489 residues
| Protein target | T15 | Atoms | 7420 |
|---|---|---|---|
| Residues | 489 | 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:204 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 487 | 2.3604512045472505 | -0.554818 | -25.6583 | 2 | 19 | 12 | 0.92 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.658kcal/mol
Ligand efficiency (LE)
-0.5967kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.342
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
43HA
Physicochemical properties
Molecular weight
592.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.86
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
48.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
297.44kcal/mol
Minimised FF energy
248.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
912.8Ų
Total solvent-accessible surface area of free ligand
BSA total
590.7Ų
Buried surface area upon binding
BSA apolar
550.1Ų
Hydrophobic contacts buried
BSA polar
40.6Ų
Polar contacts buried
Fraction buried
64.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3289.4Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1544.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)