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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
31.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.42
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.042 kcal/mol/HA)
✓ Good fit quality (FQ -9.20)
✓ Good H-bonds (5 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Very high strain energy (31.5 kcal/mol)
✗ Geometry warnings
Score
-23.962
kcal/mol
LE
-1.042
kcal/mol/HA
Fit Quality
-9.20
FQ (Leeson)
HAC
23
heavy atoms
MW
347
Da
LogP
2.81
cLogP
Final rank
2.2557
rank score
Inter norm
-1.122
normalised
Contacts
15
H-bonds 9
Interaction summary
HBD 2
HBA 3
HY 6
PI 0
CLASH 2
Interaction summary
HBD 2
HBA 3
HY 6
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 8 | Native recall | 0.67 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 449 | 1.045777710503296 | -1.44495 | -31.7812 | 11 | 15 | 0 | 0.00 | - | - | no | Open |
| 516 | 2.2557420363874656 | -1.1221 | -23.9617 | 9 | 15 | 8 | 0.67 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.962kcal/mol
Ligand efficiency (LE)
-1.0418kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.195
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.81
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
102.39kcal/mol
Minimised FF energy
70.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
554.7Ų
Total solvent-accessible surface area of free ligand
BSA total
432.4Ų
Buried surface area upon binding
BSA apolar
289.1Ų
Hydrophobic contacts buried
BSA polar
143.3Ų
Polar contacts buried
Fraction buried
77.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2980.6Ų
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
1469.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)