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
21.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.807 kcal/mol/HA)
✓ Good fit quality (FQ -7.70)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ High strain energy (21.9 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (12)
Score
-23.394
kcal/mol
LE
-0.807
kcal/mol/HA
Fit Quality
-7.70
FQ (Leeson)
HAC
29
heavy atoms
MW
386
Da
LogP
2.41
cLogP
Interaction summary
HB 1
HY 24
PI 1
CLASH 1
Interaction summary
HB 1
HY 24
PI 1
CLASH 1
| Final rank | 0.830 | Score | -23.394 |
|---|---|---|---|
| Inter norm | -0.869 | Intra norm | 0.062 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 1 |
| Artifact reason | geometry warning; 12 clashes; 2 protein contact clashes; moderate strain Δ 21.9 | ||
| Residues |
ALA209
ALA67
ALA90
ARG74
GLY66
LEU73
LYS211
LYS89
MET70
PHE83
PRO212
PRO213
TYR210
TYR69
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 | ||
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
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 | 9 | Native recall | 0.75 |
| 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
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 301 | 0.8299988440391093 | -0.868696 | -23.3941 | 1 | 15 | 9 | 0.75 | - | - | no | Current |
| 309 | 1.2385326888611823 | -0.833339 | -23.4234 | 1 | 15 | 0 | 0.00 | - | - | no | Open |
| 192 | 2.5621721981230094 | -1.16385 | -29.9358 | 7 | 20 | 0 | 0.00 | - | - | no | Open |
| 191 | 2.6900465268149696 | -0.791766 | -20.1184 | 4 | 12 | 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
-23.394kcal/mol
Ligand efficiency (LE)
-0.8067kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.700
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
386.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.41
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
78.84kcal/mol
Minimised FF energy
56.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
659.9Ų
Total solvent-accessible surface area of free ligand
BSA total
526.8Ų
Buried surface area upon binding
BSA apolar
473.4Ų
Hydrophobic contacts buried
BSA polar
53.4Ų
Polar contacts buried
Fraction buried
79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3187.9Ų
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
1446.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)