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 mixed
SASA done
Strain ΔE
38.8 kcal/mol
Protein clashes
3
Internal clashes
9
Native overlap
contact recall 0.54, Jaccard 0.37
Reason: 9 internal clashes
3 protein-contact clashes
9 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.109 kcal/mol/HA)
✓ Good fit quality (FQ -9.94)
✓ Good H-bonds (3 bonds)
✓ Deep burial (65% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Very high strain energy (38.8 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (9)
Score
-26.620
kcal/mol
LE
-1.109
kcal/mol/HA
Fit Quality
-9.94
FQ (Leeson)
HAC
24
heavy atoms
MW
409
Da
LogP
4.56
cLogP
Final rank
0.7063
rank score
Inter norm
-0.950
normalised
Contacts
13
H-bonds 7
Interaction summary
HBD 2
HBA 1
HY 5
PI 1
CLASH 0
Interaction summary
HBD 2
HBA 1
HY 5
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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: 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 | 0.37 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 391 | 0.21700719466234605 | -1.39302 | -32.2253 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 444 | 0.7062920106538152 | -0.950209 | -26.6197 | 7 | 13 | 7 | 0.54 | - | - | no | Current |
| 420 | 1.2623877638131078 | -1.35339 | -29.6607 | 9 | 10 | 0 | 0.00 | - | - | no | Open |
| 404 | 1.8802542420593948 | -0.990568 | -25.18 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 447 | 3.109982217759302 | -1.12173 | -24.7218 | 9 | 12 | 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
-26.620kcal/mol
Ligand efficiency (LE)
-1.1092kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.940
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
409.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.56
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.72kcal/mol
Minimised FF energy
75.89kcal/mol
SASA & burial
✓ computed
SASA (unbound)
621.3Ų
Total solvent-accessible surface area of free ligand
BSA total
406.3Ų
Buried surface area upon binding
BSA apolar
298.9Ų
Hydrophobic contacts buried
BSA polar
107.4Ų
Polar contacts buried
Fraction buried
65.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3061.7Ų
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
1500.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)