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
28.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.67, Jaccard 0.36
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.844 kcal/mol/HA)
✓ Good fit quality (FQ -8.14)
✓ Good H-bonds (3 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (28.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (8)
✗ Internal clashes (9)
Score
-25.327
kcal/mol
LE
-0.844
kcal/mol/HA
Fit Quality
-8.14
FQ (Leeson)
HAC
30
heavy atoms
MW
451
Da
LogP
5.36
cLogP
Final rank
1.4735
rank score
Inter norm
-0.827
normalised
Contacts
18
H-bonds 3
Interaction summary
HBD 1
HBA 2
HY 9
PI 1
CLASH 4
Interaction summary
HBD 1
HBA 2
HY 9
PI 1
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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 | 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 | 0.36 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 343 | -0.016781169744085098 | -1.00863 | -28.5549 | 5 | 14 | 0 | 0.00 | - | - | no | Open |
| 361 | 0.39586097939460907 | -0.943264 | -20.6961 | 1 | 18 | 0 | 0.00 | - | - | no | Open |
| 464 | 1.4734933962778927 | -0.826777 | -25.3273 | 3 | 18 | 8 | 0.67 | - | - | no | Current |
| 326 | 1.5781974143203685 | -1.09282 | -32.0683 | 3 | 22 | 0 | 0.00 | - | - | no | Open |
| 389 | 1.943848181712128 | -0.926403 | -25.5192 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 361 | 2.8436288692052334 | -0.924051 | -28.9454 | 10 | 16 | 0 | 0.00 | - | - | no | Open |
| 364 | 3.019765575265047 | -0.826602 | -24.7265 | 5 | 12 | 0 | 0.00 | - | - | no | Open |
| 356 | 3.4461648256018282 | -0.916897 | -26.8047 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 386 | 3.5274002705054572 | -0.814362 | -24.8371 | 7 | 11 | 0 | 0.00 | - | - | no | Open |
| 363 | 3.5536977263405602 | -1.05422 | -31.1436 | 10 | 19 | 0 | 0.00 | - | - | no | Open |
| 402 | 3.832040767874197 | -0.721821 | -22.5586 | 9 | 12 | 0 | 0.00 | - | - | no | Open |
| 330 | 3.8955722111935605 | -0.975688 | -30.3598 | 6 | 14 | 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
-25.327kcal/mol
Ligand efficiency (LE)
-0.8442kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
450.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.36
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.81kcal/mol
Minimised FF energy
31.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
696.5Ų
Total solvent-accessible surface area of free ligand
BSA total
566.1Ų
Buried surface area upon binding
BSA apolar
398.0Ų
Hydrophobic contacts buried
BSA polar
168.1Ų
Polar contacts buried
Fraction buried
81.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3087.8Ų
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
1465.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)