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
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
38.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.54, Jaccard 0.39
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (9/24 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.588 kcal/mol/HA)
✓ Good fit quality (FQ -5.98)
✓ Good burial (57% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Very high strain energy (38.0 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (13)
Score
-21.175
kcal/mol
LE
-0.588
kcal/mol/HA
Fit Quality
-5.98
FQ (Leeson)
HAC
36
heavy atoms
MW
544
Da
LogP
2.44
cLogP
Final rank
1.7214
rank score
Inter norm
-0.605
normalised
Contacts
12
H-bonds 3
Interaction summary
HBA 1
HY 7
PI 2
CLASH 3
Interaction summary
HBA 1
HY 7
PI 2
CLASH 3
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 | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 7 | Native recall | 0.54 |
| Jaccard | 0.39 | 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 | T18 | Atoms | 7550 |
|---|---|---|---|
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 439 | 1.7214337114526863 | -0.605114 | -21.175 | 3 | 12 | 7 | 0.54 | - | - | no | Current |
| 460 | 2.9277789990819674 | -0.643045 | -22.9231 | 2 | 18 | 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
-21.175kcal/mol
Ligand efficiency (LE)
-0.5882kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.978
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
543.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.44
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
37.15kcal/mol
Minimised FF energy
-0.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
784.3Ų
Total solvent-accessible surface area of free ligand
BSA total
444.2Ų
Buried surface area upon binding
BSA apolar
312.3Ų
Hydrophobic contacts buried
BSA polar
131.9Ų
Polar contacts buried
Fraction buried
56.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3143.0Ų
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
1477.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)