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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
32.2 kcal/mol
Protein clashes
3
Internal clashes
7
Native overlap
contact recall 0.69, Jaccard 0.50
Reason: 7 internal clashes
3 protein-contact clashes
7 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.558 kcal/mol/HA)
✓ Good fit quality (FQ -5.07)
✓ Good H-bonds (3 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (32.2 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (7)
Score
-13.954
kcal/mol
LE
-0.558
kcal/mol/HA
Fit Quality
-5.07
FQ (Leeson)
HAC
25
heavy atoms
MW
356
Da
LogP
2.23
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
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
No clash · clashes detected for this pose.
| Final rank | 0.536 | Score | -13.954 |
|---|---|---|---|
| Inter norm | -0.834 | Intra norm | 0.276 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | geometry warning; 7 clashes; 3 protein contact clashes; high strain Δ 32.2 | ||
| Residues |
ASP116
CYS52
GLU18
GLY13
GLY49
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 617 | 0.5364488371058826 | -0.833997 | -13.9538 | 3 | 14 | 9 | 0.69 | - | - | no | Current |
| 604 | 0.6708383599777297 | -1.32744 | -32.2148 | 8 | 18 | 0 | 0.00 | - | - | no | Open |
| 613 | 0.7074283955056254 | -1.05323 | -22.6416 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 595 | 1.5992888634610638 | -1.2484 | -27.5859 | 9 | 14 | 0 | 0.00 | - | - | no | Open |
| 595 | 1.664204163524461 | -1.35261 | -34.5795 | 9 | 20 | 0 | 0.00 | - | - | no | Open |
| 597 | 2.999156072789758 | -1.11196 | -25.6511 | 5 | 14 | 0 | 0.00 | - | - | no | Open |
| 635 | 3.783002463306349 | -1.33508 | -29.8721 | 12 | 23 | 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
-13.954kcal/mol
Ligand efficiency (LE)
-0.5582kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.074
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
356.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.23
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
96.12kcal/mol
Minimised FF energy
63.90kcal/mol
SASA & burial
✓ computed
SASA (unbound)
624.7Ų
Total solvent-accessible surface area of free ligand
BSA total
469.3Ų
Buried surface area upon binding
BSA apolar
341.8Ų
Hydrophobic contacts buried
BSA polar
127.5Ų
Polar contacts buried
Fraction buried
75.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3057.4Ų
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
1464.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)