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
13.4 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.75, Jaccard 0.53
Reason: 13 internal clashes
13 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
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.887 kcal/mol/HA)
✓ Good fit quality (FQ -8.47)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (99%)
✗ Moderate strain (13.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-25.732
kcal/mol
LE
-0.887
kcal/mol/HA
Fit Quality
-8.47
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
4.82
cLogP
Final rank
3.1734
rank score
Inter norm
-0.902
normalised
Contacts
14
H-bonds 2
Interaction summary
HBD 2
HY 9
PI 0
CLASH 0
Interaction summary
HBD 2
HY 9
PI 0
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
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: strict.
| 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 | 9 | Native recall | 0.75 |
| Jaccard | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 241 | 3.11230577479569 | -0.938584 | -25.7805 | 2 | 14 | 0 | 0.00 | - | - | no | Open |
| 212 | 3.1733977709319365 | -0.901724 | -25.7316 | 2 | 14 | 9 | 0.75 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.732kcal/mol
Ligand efficiency (LE)
-0.8873kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.470
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
430.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.82
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
92.40kcal/mol
Minimised FF energy
78.96kcal/mol
SASA & burial
✓ computed
SASA (unbound)
677.6Ų
Total solvent-accessible surface area of free ligand
BSA total
499.0Ų
Buried surface area upon binding
BSA apolar
492.9Ų
Hydrophobic contacts buried
BSA polar
6.2Ų
Polar contacts buried
Fraction buried
73.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
98.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3276.4Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1470.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)