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
36.9 kcal/mol
Protein clashes
2
Internal clashes
13
Native overlap
contact recall 0.85, Jaccard 0.65
Reason: 13 internal clashes
2 protein-contact clashes
13 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Good LE (-0.351 kcal/mol/HA)
✓ Good fit quality (FQ -3.57)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ Very high strain energy (36.9 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (13)
Score
-12.649
kcal/mol
LE
-0.351
kcal/mol/HA
Fit Quality
-3.57
FQ (Leeson)
HAC
36
heavy atoms
MW
490
Da
LogP
3.15
cLogP
Final rank
1.2564
rank score
Inter norm
-0.634
normalised
Contacts
15
H-bonds 2
Interaction summary
HBA 1
HY 5
PI 2
CLASH 0
Interaction summary
HBA 1
HY 5
PI 2
CLASH 0
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
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 | 11 | Native recall | 0.85 |
| Jaccard | 0.65 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 183 | 1.2563795323931104 | -0.633522 | -12.6493 | 2 | 15 | 11 | 0.85 | - | - | no | Current |
| 169 | 4.01991839815854 | -0.697339 | -22.1539 | 4 | 15 | 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
-12.649kcal/mol
Ligand efficiency (LE)
-0.3514kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.571
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
489.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.15
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
123.23kcal/mol
Minimised FF energy
86.33kcal/mol
SASA & burial
✓ computed
SASA (unbound)
785.0Ų
Total solvent-accessible surface area of free ligand
BSA total
489.8Ų
Buried surface area upon binding
BSA apolar
427.4Ų
Hydrophobic contacts buried
BSA polar
62.4Ų
Polar contacts buried
Fraction buried
62.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3319.2Ų
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
1479.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)