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 mixed
SASA done
Strain ΔE
27.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.54, Jaccard 0.41
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.833 kcal/mol/HA)
✓ Good fit quality (FQ -8.04)
✓ Strong H-bond network (6 bonds)
✓ Good burial (56% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ High strain energy (27.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-24.996
kcal/mol
LE
-0.833
kcal/mol/HA
Fit Quality
-8.04
FQ (Leeson)
HAC
30
heavy atoms
MW
439
Da
LogP
3.86
cLogP
Interaction summary
HB 6
HY 24
PI 1
CLASH 3
Interaction summary
HB 6
HY 24
PI 1
CLASH 3
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
| Final rank | 5.414 | Score | -24.996 |
|---|---|---|---|
| Inter norm | -0.787 | Intra norm | -0.046 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 6 |
| Artifact reason | geometry warning; 17 clashes; 3 protein clashes; moderate strain Δ 27.3 | ||
| Residues |
CYS52
GLU18
GLY13
ILE339
LEU17
MET113
SER14
THR335
TRP21
TYR110
VAL58
| ||
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 | 7 | Native recall | 0.54 |
| Jaccard | 0.41 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 565 | 1.1937598601304344 | -1.12119 | -33.975 | 8 | 11 | 0 | 0.00 | - | - | no | Open |
| 581 | 1.851678950788277 | -0.849421 | -25.582 | 3 | 12 | 0 | 0.00 | - | - | no | Open |
| 567 | 2.455088140425625 | -1.06535 | -31.144 | 6 | 20 | 0 | 0.00 | - | - | no | Open |
| 583 | 2.510939092973108 | -0.961098 | -28.3281 | 3 | 13 | 0 | 0.00 | - | - | no | Open |
| 597 | 5.414259517488726 | -0.787138 | -24.9962 | 6 | 11 | 7 | 0.54 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.996kcal/mol
Ligand efficiency (LE)
-0.8332kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.037
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
438.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
27.17kcal/mol
Minimised FF energy
-0.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
704.6Ų
Total solvent-accessible surface area of free ligand
BSA total
396.4Ų
Buried surface area upon binding
BSA apolar
248.9Ų
Hydrophobic contacts buried
BSA polar
147.5Ų
Polar contacts buried
Fraction buried
56.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3083.9Ų
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
1496.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)