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 strong
SASA done
Strain ΔE
36.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.77, Jaccard 0.62
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 (-0.711 kcal/mol/HA)
✓ Good fit quality (FQ -6.86)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Very high strain energy (36.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-21.319
kcal/mol
LE
-0.711
kcal/mol/HA
Fit Quality
-6.86
FQ (Leeson)
HAC
30
heavy atoms
MW
407
Da
LogP
2.87
cLogP
Interaction summary
HB 8
HY 22
PI 3
CLASH 3
Interaction summary
HB 8
HY 22
PI 3
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 | 3.504 | Score | -21.319 |
|---|---|---|---|
| Inter norm | -0.797 | Intra norm | 0.087 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 36.3 | ||
| Residues |
ASP116
GLU18
GLY112
GLY13
ILE339
LEU17
MET113
SER109
SER14
THR117
THR335
TRP21
TYR110
| ||
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 | 10 | Native recall | 0.77 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 333 | 0.8165892997804749 | -1.03679 | -23.7942 | 12 | 14 | 0 | 0.00 | - | - | no | Open |
| 441 | 1.1685211136412954 | -0.880713 | -26.4243 | 8 | 15 | 0 | 0.00 | - | - | no | Open |
| 356 | 1.6407871253580555 | -0.869268 | -22.1003 | 7 | 20 | 0 | 0.00 | - | - | no | Open |
| 403 | 1.795979106920546 | -0.975825 | -28.8271 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 383 | 3.452527861957111 | -0.914722 | -19.2993 | 3 | 13 | 0 | 0.00 | - | - | no | Open |
| 457 | 3.460735189732118 | -0.830068 | -17.489 | 5 | 17 | 0 | 0.00 | - | - | no | Open |
| 391 | 3.50428813078884 | -0.797361 | -21.3187 | 8 | 13 | 10 | 0.77 | - | - | no | Current |
| 352 | 3.756650634369295 | -1.01987 | -25.7771 | 9 | 19 | 0 | 0.00 | - | - | no | Open |
| 318 | 4.326972274753828 | -1.10335 | -32.5603 | 12 | 23 | 0 | 0.00 | - | - | no | Open |
| 380 | 5.4593238784164 | -0.932728 | -21.1296 | 13 | 15 | 0 | 0.00 | - | - | no | Open |
| 421 | 5.842856067255379 | -0.879322 | -23.9742 | 11 | 20 | 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
-21.319kcal/mol
Ligand efficiency (LE)
-0.7106kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.855
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
407.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.87
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
107.00kcal/mol
Minimised FF energy
70.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
662.7Ų
Total solvent-accessible surface area of free ligand
BSA total
458.4Ų
Buried surface area upon binding
BSA apolar
348.2Ų
Hydrophobic contacts buried
BSA polar
110.2Ų
Polar contacts buried
Fraction buried
69.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3109.0Ų
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
1481.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)