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
52.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.43
Reason: strain 52.4 kcal/mol
strain ΔE 52.4 kcal/mol
2 protein-contact clashes
48% of hydrophobic surface appears solvent-exposed (12/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.764 kcal/mol/HA)
✓ Good fit quality (FQ -7.65)
✓ Good H-bonds (4 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Extreme strain energy (52.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.985
kcal/mol
LE
-0.764
kcal/mol/HA
Fit Quality
-7.65
FQ (Leeson)
HAC
34
heavy atoms
MW
464
Da
LogP
3.46
cLogP
Final rank
3.5638
rank score
Inter norm
-0.668
normalised
Contacts
18
H-bonds 5
Interaction summary
HBD 4
HY 8
PI 0
CLASH 2
Interaction summary
HBD 4
HY 8
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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 | 9 | Native recall | 0.75 |
| Jaccard | 0.43 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 90 | 3.563816881290357 | -0.6681 | -25.9847 | 5 | 18 | 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
-25.985kcal/mol
Ligand efficiency (LE)
-0.7643kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.647
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
463.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.46
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
52.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
7.68kcal/mol
Minimised FF energy
-44.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
749.2Ų
Total solvent-accessible surface area of free ligand
BSA total
516.7Ų
Buried surface area upon binding
BSA apolar
443.7Ų
Hydrophobic contacts buried
BSA polar
73.0Ų
Polar contacts buried
Fraction buried
69.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3256.8Ų
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
1458.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)