Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
48.4 kcal/mol
Protein clashes
3
Internal clashes
16
Native overlap
contact recall 0.77, Jaccard 0.56
Reason: 16 internal clashes, strain 48.4 kcal/mol
strain ΔE 48.4 kcal/mol
3 protein-contact clashes
16 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.597 kcal/mol/HA)
✓ Good fit quality (FQ -6.27)
✓ Good H-bonds (4 bonds)
✓ Good burial (65% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Extreme strain energy (48.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (16)
Score
-24.478
kcal/mol
LE
-0.597
kcal/mol/HA
Fit Quality
-6.27
FQ (Leeson)
HAC
41
heavy atoms
MW
560
Da
LogP
4.89
cLogP
Interaction summary
HB 4
HY 24
PI 2
CLASH 0
Interaction summary
HB 4
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 | 1.793 | Score | -24.478 |
|---|---|---|---|
| Inter norm | -0.563 | Intra norm | -0.034 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | geometry warning; 16 clashes; 3 protein contact clashes; high strain Δ 37.3 | ||
| Residues |
ASP116
CYS52
CYS57
GLU18
ILE339
LEU17
LYS61
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
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 | 10 | Native recall | 0.77 |
| Jaccard | 0.56 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 279 | 1.0067627352935882 | -0.667315 | -24.5471 | 3 | 21 | 0 | 0.00 | - | - | no | Open |
| 255 | 1.793231673535512 | -0.562886 | -24.4781 | 4 | 15 | 10 | 0.77 | - | - | no | Current |
| 284 | 5.116584945356977 | -0.506709 | -20.233 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 286 | 5.160385032940554 | -0.643864 | -15.4755 | 6 | 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
-24.478kcal/mol
Ligand efficiency (LE)
-0.5970kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.273
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
559.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.89
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
48.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
119.35kcal/mol
Minimised FF energy
70.90kcal/mol
SASA & burial
✓ computed
SASA (unbound)
855.9Ų
Total solvent-accessible surface area of free ligand
BSA total
555.8Ų
Buried surface area upon binding
BSA apolar
458.4Ų
Hydrophobic contacts buried
BSA polar
97.3Ų
Polar contacts buried
Fraction buried
64.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3309.0Ų
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
1495.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)