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
27.7 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.67, Jaccard 0.42
Reason: 16 internal clashes
16 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (32/32 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 (-0.638 kcal/mol/HA)
✓ Good fit quality (FQ -6.53)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ High strain energy (27.7 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-23.611
kcal/mol
LE
-0.638
kcal/mol/HA
Fit Quality
-6.53
FQ (Leeson)
HAC
37
heavy atoms
MW
503
Da
LogP
1.49
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 (32/32 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 32
Buried (contacted) 0
Exposed 32
LogP 1.49
H-bonds 0
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 4.980 | Score | -23.611 |
|---|---|---|---|
| Inter norm | -0.684 | Intra norm | 0.045 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | geometry warning; 16 clashes; 3 protein clashes; moderate strain Δ 27.7 | ||
| Residues |
ALA90
ASN91
GLY214
GLY215
GLY85
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
SER86
TRP92
TYR210
VAL88
| ||
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 | ||
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 | - |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 228 | 4.979755918122773 | -0.683613 | -23.6113 | 4 | 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
-23.611kcal/mol
Ligand efficiency (LE)
-0.6381kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.533
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
502.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.49
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
231.91kcal/mol
Minimised FF energy
204.20kcal/mol
SASA & burial
✓ computed
SASA (unbound)
816.0Ų
Total solvent-accessible surface area of free ligand
BSA total
550.7Ų
Buried surface area upon binding
BSA apolar
526.0Ų
Hydrophobic contacts buried
BSA polar
24.7Ų
Polar contacts buried
Fraction buried
67.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
95.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3412.7Ų
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
1455.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)