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
26.5 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.58, Jaccard 0.39
Reason: 16 internal clashes
16 intramolecular clashes
45% of hydrophobic surface appears solvent-exposed (14/31 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.619 kcal/mol/HA)
✓ Good fit quality (FQ -6.29)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ High strain energy (26.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-22.295
kcal/mol
LE
-0.619
kcal/mol/HA
Fit Quality
-6.29
FQ (Leeson)
HAC
36
heavy atoms
MW
489
Da
LogP
1.05
cLogP
Final rank
2.7215
rank score
Inter norm
-0.660
normalised
Contacts
13
H-bonds 2
Interaction summary
HBD 1
HBA 1
HY 8
PI 1
CLASH 0
Interaction summary
HBD 1
HBA 1
HY 8
PI 1
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
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | 7 | Native recall | 0.58 |
| 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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 262 | 2.721476534011668 | -0.659609 | -22.2947 | 2 | 13 | 7 | 0.58 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.295kcal/mol
Ligand efficiency (LE)
-0.6193kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.294
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
488.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.05
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
269.73kcal/mol
Minimised FF energy
243.25kcal/mol
SASA & burial
✓ computed
SASA (unbound)
763.4Ų
Total solvent-accessible surface area of free ligand
BSA total
536.8Ų
Buried surface area upon binding
BSA apolar
517.5Ų
Hydrophobic contacts buried
BSA polar
19.3Ų
Polar contacts buried
Fraction buried
70.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
96.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3353.1Ų
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
1460.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)