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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
20.4 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.33, Jaccard 0.19
Reason: 12 internal clashes
12 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.850 kcal/mol/HA)
✓ Good fit quality (FQ -8.02)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (20.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-23.791
kcal/mol
LE
-0.850
kcal/mol/HA
Fit Quality
-8.02
FQ (Leeson)
HAC
28
heavy atoms
MW
402
Da
LogP
2.52
cLogP
Final rank
3.0796
rank score
Inter norm
-0.835
normalised
Contacts
13
H-bonds 3
Interaction summary
HBA 2
HY 4
PI 0
CLASH 0
Interaction summary
HBA 2
HY 4
PI 0
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 4 | Native recall | 0.33 |
| Jaccard | 0.19 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| Residues | 493 | 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:276; 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 585 | 3.079593660312151 | -0.834571 | -23.7912 | 3 | 13 | 4 | 0.33 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.791kcal/mol
Ligand efficiency (LE)
-0.8497kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.021
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
401.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.52
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.52kcal/mol
Minimised FF energy
24.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
683.2Ų
Total solvent-accessible surface area of free ligand
BSA total
472.9Ų
Buried surface area upon binding
BSA apolar
396.1Ų
Hydrophobic contacts buried
BSA polar
76.8Ų
Polar contacts buried
Fraction buried
69.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3180.5Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1476.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)