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
15.2 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.62, Jaccard 0.44
Reason: 15 internal clashes
15 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.687 kcal/mol/HA)
✓ Good fit quality (FQ -6.82)
✓ Good H-bonds (3 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ Moderate strain (15.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-22.672
kcal/mol
LE
-0.687
kcal/mol/HA
Fit Quality
-6.82
FQ (Leeson)
HAC
33
heavy atoms
MW
489
Da
LogP
3.54
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
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.
| Final rank | 2.162 | Score | -22.672 |
|---|---|---|---|
| Inter norm | -0.670 | Intra norm | -0.017 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
| ||
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.44 | 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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.672kcal/mol
Ligand efficiency (LE)
-0.6870kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.817
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
489.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.54
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
73.05kcal/mol
Minimised FF energy
57.81kcal/mol
SASA & burial
✓ computed
SASA (unbound)
703.9Ų
Total solvent-accessible surface area of free ligand
BSA total
483.1Ų
Buried surface area upon binding
BSA apolar
437.0Ų
Hydrophobic contacts buried
BSA polar
46.0Ų
Polar contacts buried
Fraction buried
68.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3210.1Ų
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
1492.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)