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 high
Native strong
SASA done
Strain ΔE
27.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.39
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.721 kcal/mol/HA)
✓ Good fit quality (FQ -7.09)
✓ Deep burial (65% SASA buried)
✓ Lipophilic contacts well-matched (100%)
✗ High strain energy (27.8 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (14)
Score
-23.060
kcal/mol
LE
-0.721
kcal/mol/HA
Fit Quality
-7.09
FQ (Leeson)
HAC
32
heavy atoms
MW
432
Da
LogP
2.38
cLogP
Interaction summary
HB 2
HY 24
PI 0
CLASH 2
Interaction summary
HB 2
HY 24
PI 0
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 1.602 | Score | -23.060 |
|---|---|---|---|
| Inter norm | -0.713 | Intra norm | -0.008 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 2 |
| Artifact reason | geometry warning; 14 clashes; 4 protein contact clashes; moderate strain Δ 27.8 | ||
| Residues |
ALA209
ALA90
GLY214
GLY215
LEU73
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
TYR210
VAL88
| ||
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 | 7 | Native recall | 0.58 |
| Jaccard | 0.39 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 223 | 1.5330440062416233 | -0.796142 | -24.9055 | 1 | 21 | 0 | 0.00 | - | - | no | Open |
| 254 | 1.6024421340643777 | -0.712841 | -23.0597 | 2 | 13 | 7 | 0.58 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.060kcal/mol
Ligand efficiency (LE)
-0.7206kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.087
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
431.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.38
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
64.92kcal/mol
Minimised FF energy
37.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
725.0Ų
Total solvent-accessible surface area of free ligand
BSA total
472.8Ų
Buried surface area upon binding
BSA apolar
472.8Ų
Hydrophobic contacts buried
BSA polar
0.0Ų
Polar contacts buried
Fraction buried
65.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
100.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3337.3Ų
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
1464.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)