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
32.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.77, Jaccard 0.56
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.455 kcal/mol/HA)
✓ Good fit quality (FQ -4.72)
✓ Good H-bonds (5 bonds)
✓ Good burial (63% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Very high strain energy (32.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-17.744
kcal/mol
LE
-0.455
kcal/mol/HA
Fit Quality
-4.72
FQ (Leeson)
HAC
39
heavy atoms
MW
542
Da
LogP
6.08
cLogP
Final rank
2.9279
rank score
Inter norm
-0.538
normalised
Contacts
15
H-bonds 5
Interaction summary
HBD 2
HBA 3
HY 9
PI 2
CLASH 1
Interaction summary
HBD 2
HBA 3
HY 9
PI 2
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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: permissive.
| 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 | 10 | Native recall | 0.77 |
| Jaccard | 0.56 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 37 | 1.5732684149285006 | -0.704108 | -23.8103 | 2 | 19 | 0 | 0.00 | - | - | no | Open |
| 16 | 1.8005443252370026 | -0.628939 | -25.1446 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 30 | 2.2979834550987546 | -0.814208 | -25.2991 | 8 | 20 | 0 | 0.00 | - | - | no | Open |
| 33 | 2.884676074939267 | -0.710818 | -19.5307 | 2 | 17 | 0 | 0.00 | - | - | no | Open |
| 26 | 2.9279468816303753 | -0.53796 | -17.7445 | 5 | 15 | 10 | 0.77 | - | - | no | Current |
| 15 | 4.821358207898677 | -0.725329 | -23.8624 | 12 | 19 | 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
-17.744kcal/mol
Ligand efficiency (LE)
-0.4550kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.722
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
542.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.08
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
72.62kcal/mol
Minimised FF energy
40.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
845.0Ų
Total solvent-accessible surface area of free ligand
BSA total
534.8Ų
Buried surface area upon binding
BSA apolar
467.8Ų
Hydrophobic contacts buried
BSA polar
67.1Ų
Polar contacts buried
Fraction buried
63.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3275.6Ų
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
1527.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)