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
54.0 kcal/mol
Protein clashes
2
Internal clashes
33
Native overlap
contact recall 0.92, Jaccard 0.57
Reason: 33 internal clashes, strain 54.0 kcal/mol
strain ΔE 54.0 kcal/mol
2 protein-contact clashes
33 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.
vB — Very bioaccumulative (BCF>5000)
Persistent
Yes
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.430 kcal/mol/HA)
✓ Good fit quality (FQ -4.83)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Extreme strain energy (54.0 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (33)
Score
-24.055
kcal/mol
LE
-0.430
kcal/mol/HA
Fit Quality
-4.83
FQ (Leeson)
HAC
56
heavy atoms
MW
756
Da
LogP
6.99
cLogP
Final rank
3.3689
rank score
Inter norm
-0.493
normalised
Contacts
20
H-bonds 3
Interaction summary
HBA 2
HY 6
PI 1
CLASH 0
Interaction summary
HBA 2
HY 6
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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: 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 | 0.57 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 489 | 3.3688942044824595 | -0.493103 | -24.0555 | 3 | 20 | 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
-24.055kcal/mol
Ligand efficiency (LE)
-0.4296kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.828
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
56HA
Physicochemical properties
Molecular weight
755.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.99
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
54.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
231.70kcal/mol
Minimised FF energy
177.67kcal/mol
SASA & burial
✓ computed
SASA (unbound)
1086.3Ų
Total solvent-accessible surface area of free ligand
BSA total
734.2Ų
Buried surface area upon binding
BSA apolar
634.0Ų
Hydrophobic contacts buried
BSA polar
100.2Ų
Polar contacts buried
Fraction buried
67.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3405.6Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1556.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)