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
30.7 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.50, Jaccard 0.30
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.747 kcal/mol/HA)
✓ Good fit quality (FQ -7.28)
✓ Good H-bonds (4 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Very high strain energy (30.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-23.148
kcal/mol
LE
-0.747
kcal/mol/HA
Fit Quality
-7.28
FQ (Leeson)
HAC
31
heavy atoms
MW
406
Da
LogP
5.43
cLogP
Final rank
4.0410
rank score
Inter norm
-0.765
normalised
Contacts
14
H-bonds 4
Interaction summary
HBD 1
HBA 3
HY 5
PI 0
CLASH 6
Interaction summary
HBD 1
HBA 3
HY 5
PI 0
CLASH 6
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: strict.
| 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 | 6 | Native recall | 0.50 |
| Jaccard | 0.30 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 457 | 2.3334579004819758 | -0.796377 | -20.7486 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 497 | 3.5983764184525246 | -0.777505 | -23.4879 | 5 | 17 | 0 | 0.00 | - | - | no | Open |
| 425 | 3.8222514009867794 | -1.05411 | -30.6961 | 4 | 21 | 0 | 0.00 | - | - | no | Open |
| 518 | 4.0410304952851 | -0.765173 | -23.1476 | 4 | 14 | 6 | 0.50 | - | - | no | Current |
| 467 | 6.791932017520767 | -0.670596 | -20.6493 | 8 | 8 | 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
-23.148kcal/mol
Ligand efficiency (LE)
-0.7467kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.275
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
406.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.43
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.10kcal/mol
Minimised FF energy
83.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
687.4Ų
Total solvent-accessible surface area of free ligand
BSA total
468.8Ų
Buried surface area upon binding
BSA apolar
387.2Ų
Hydrophobic contacts buried
BSA polar
81.6Ų
Polar contacts buried
Fraction buried
68.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3144.4Ų
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
1518.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)