Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Receptor not available — ligand geometry only, interactions disabled.
Viewer legend
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
23.0 kcal/mol
Protein clashes
0
Internal clashes
17
Native overlap
contact recall 0.69, Jaccard 0.50
Reason: 17 internal clashes
17 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (30/30 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.447 kcal/mol/HA)
✓ Good fit quality (FQ -4.48)
✓ Good burial (63% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ High strain energy (23.0 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-15.213
kcal/mol
LE
-0.447
kcal/mol/HA
Fit Quality
-4.48
FQ (Leeson)
HAC
34
heavy atoms
MW
454
Da
LogP
4.41
cLogP
Interaction summary
HB 0
HY 0
PI 0
CLASH 0
⚠ Exposure 100%
Interaction summary
HB 0
HY 0
PI 0
CLASH 0
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (30/30 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 30
Buried (contacted) 0
Exposed 30
LogP 4.41
H-bonds 0
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.701 | Score | -15.213 |
|---|---|---|---|
| Inter norm | -0.635 | Intra norm | 0.188 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | geometry warning; 17 clashes; 2 protein clashes; moderate strain Δ 23.0 | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
ILE106
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
| ||
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 | ||
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 | 9 | Native recall | 0.69 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
HB · H-bonds
No hb · h-bonds detected for this pose.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.
CLASH · Clashes
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 181 | 3.7012638504671385 | -0.635428 | -15.2131 | 4 | 14 | 9 | 0.69 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.213kcal/mol
Ligand efficiency (LE)
-0.4474kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.477
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
453.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.41
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
75.16kcal/mol
Minimised FF energy
52.20kcal/mol
SASA & burial
✓ computed
SASA (unbound)
713.1Ų
Total solvent-accessible surface area of free ligand
BSA total
448.5Ų
Buried surface area upon binding
BSA apolar
391.4Ų
Hydrophobic contacts buried
BSA polar
57.1Ų
Polar contacts buried
Fraction buried
62.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3247.1Ų
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
1484.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)