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
46.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.85, Jaccard 0.55
Reason: strain 46.0 kcal/mol
strain ΔE 46.0 kcal/mol
2 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (9/24 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 (-0.753 kcal/mol/HA)
✓ Good fit quality (FQ -7.60)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Extreme strain energy (46.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-26.367
kcal/mol
LE
-0.753
kcal/mol/HA
Fit Quality
-7.60
FQ (Leeson)
HAC
35
heavy atoms
MW
525
Da
LogP
4.92
cLogP
Final rank
3.8501
rank score
Inter norm
-0.590
normalised
Contacts
18
H-bonds 3
Interaction summary
HBA 2
HY 8
PI 3
CLASH 2
Interaction summary
HBA 2
HY 8
PI 3
CLASH 2
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 | 11 | Native recall | 0.85 |
| Jaccard | 0.55 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 480 | 3.850114216244941 | -0.589954 | -26.3667 | 3 | 18 | 11 | 0.85 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.367kcal/mol
Ligand efficiency (LE)
-0.7533kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.598
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
524.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.92
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
46.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
49.45kcal/mol
Minimised FF energy
3.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
874.0Ų
Total solvent-accessible surface area of free ligand
BSA total
572.9Ų
Buried surface area upon binding
BSA apolar
401.6Ų
Hydrophobic contacts buried
BSA polar
171.3Ų
Polar contacts buried
Fraction buried
65.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3237.2Ų
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
1485.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)