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
34.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.69, Jaccard 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.888 kcal/mol/HA)
✓ Good fit quality (FQ -7.96)
✓ Good H-bonds (5 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Very high strain energy (34.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-21.317
kcal/mol
LE
-0.888
kcal/mol/HA
Fit Quality
-7.96
FQ (Leeson)
HAC
24
heavy atoms
MW
369
Da
LogP
1.63
cLogP
Interaction summary
HB 5
HY 24
PI 3
CLASH 2
Interaction summary
HB 5
HY 24
PI 3
CLASH 2
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 | 1.930 | Score | -21.317 |
|---|---|---|---|
| Inter norm | -0.919 | Intra norm | 0.031 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; high strain Δ 34.7 | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
ILE106
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
| ||
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 | 9 | Native recall | 0.69 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 284 | 1.2287391940559973 | -1.3373 | -31.3251 | 7 | 20 | 0 | 0.00 | - | - | no | Open |
| 318 | 1.930390520989664 | -0.919352 | -21.3172 | 5 | 14 | 9 | 0.69 | - | - | no | Current |
| 300 | 2.612500458198002 | -1.05598 | -26.007 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 352 | 2.8133704680740235 | -1.21926 | -27.8314 | 8 | 15 | 0 | 0.00 | - | - | no | Open |
| 387 | 2.8591922961429583 | -1.08354 | -26.5012 | 9 | 16 | 0 | 0.00 | - | - | no | Open |
| 280 | 3.2557473016876934 | -1.09158 | -26.8763 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 417 | 3.6436717196830264 | -1.11799 | -25.5635 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 368 | 3.6861116489491605 | -1.16757 | -26.4681 | 8 | 15 | 0 | 0.00 | - | - | no | Open |
| 250 | 4.820320240349916 | -1.03701 | -23.767 | 11 | 13 | 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
-21.317kcal/mol
Ligand efficiency (LE)
-0.8882kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.960
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
369.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.63
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-22.00kcal/mol
Minimised FF energy
-56.69kcal/mol
SASA & burial
✓ computed
SASA (unbound)
598.1Ų
Total solvent-accessible surface area of free ligand
BSA total
452.6Ų
Buried surface area upon binding
BSA apolar
303.7Ų
Hydrophobic contacts buried
BSA polar
148.9Ų
Polar contacts buried
Fraction buried
75.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3035.8Ų
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
1453.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)