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
Weak or marginal quality
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
31.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.50, Jaccard 0.29
Reason: no major geometry red flags detected
5 protein-contact clashes
5 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.
Not B (BCF≤2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.758 kcal/mol/HA)
✓ Good fit quality (FQ -7.58)
✓ Good H-bonds (3 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Very high strain energy (31.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-25.763
kcal/mol
LE
-0.758
kcal/mol/HA
Fit Quality
-7.58
FQ (Leeson)
HAC
34
heavy atoms
MW
467
Da
LogP
5.71
cLogP
Final rank
2.7973
rank score
Inter norm
-0.681
normalised
Contacts
15
H-bonds 4
Interaction summary
HBD 1
HBA 2
HY 7
PI 0
CLASH 5
Interaction summary
HBD 1
HBA 2
HY 7
PI 0
CLASH 5
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
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 | 6 | Native recall | 0.50 |
| Jaccard | 0.29 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 578 | 1.3654910373235143 | -0.826977 | -20.9854 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 588 | 2.0183812075455676 | -0.956391 | -29.4261 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 597 | 2.797313622627395 | -0.680997 | -25.7631 | 4 | 15 | 6 | 0.50 | - | - | no | Current |
| 600 | 3.498820415806573 | -0.729848 | -23.2377 | 5 | 13 | 0 | 0.00 | - | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.763kcal/mol
Ligand efficiency (LE)
-0.7577kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.582
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
466.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.71
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.85kcal/mol
Minimised FF energy
66.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
733.8Ų
Total solvent-accessible surface area of free ligand
BSA total
525.5Ų
Buried surface area upon binding
BSA apolar
469.5Ų
Hydrophobic contacts buried
BSA polar
56.0Ų
Polar contacts buried
Fraction buried
71.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3226.5Ų
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
1484.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)