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 high
Native strong
SASA done
Strain ΔE
15.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.42
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.599 kcal/mol/HA)
✓ Good fit quality (FQ -5.71)
✓ Good H-bonds (4 bonds)
✓ Good burial (65% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (15.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-17.359
kcal/mol
LE
-0.599
kcal/mol/HA
Fit Quality
-5.71
FQ (Leeson)
HAC
29
heavy atoms
MW
385
Da
LogP
4.86
cLogP
Interaction summary
HB 4
HY 24
PI 2
CLASH 2
Interaction summary
HB 4
HY 24
PI 2
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 | 2.404 | Score | -17.359 |
|---|---|---|---|
| Inter norm | -0.778 | Intra norm | 0.179 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash | ||
| Residues |
ASP116
CYS52
GLU18
GLY13
GLY49
GLY50
ILE339
LEU17
MET113
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 348 | 0.7097099713471693 | -0.928736 | -24.4899 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 321 | 0.7414515178002574 | -1.28064 | -37.1559 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 457 | 1.0013317596324351 | -0.895256 | -16.9261 | 5 | 16 | 0 | 0.00 | - | - | no | Open |
| 346 | 1.3116209126168636 | -1.01701 | -27.3469 | 8 | 17 | 0 | 0.00 | - | - | no | Open |
| 386 | 1.6562451370699631 | -0.778291 | -20.4118 | 8 | 17 | 0 | 0.00 | - | - | no | Open |
| 313 | 1.869078421749205 | -1.05744 | -21.2439 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 355 | 2.4041395187131402 | -0.777914 | -17.359 | 4 | 14 | 8 | 0.62 | - | - | no | Current |
| 419 | 3.1271929319738234 | -0.869189 | -23.9867 | 6 | 18 | 0 | 0.00 | - | - | no | Open |
| 359 | 3.178043498913507 | -0.693471 | -19.6333 | 4 | 13 | 0 | 0.00 | - | - | no | Open |
| 295 | 3.228938024541079 | -1.08489 | -29.5785 | 6 | 21 | 0 | 0.00 | - | - | no | Open |
| 337 | 4.121022873227579 | -1.06073 | -26.5805 | 8 | 21 | 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
-17.359kcal/mol
Ligand efficiency (LE)
-0.5986kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.714
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
385.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.86
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
79.68kcal/mol
Minimised FF energy
63.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
680.7Ų
Total solvent-accessible surface area of free ligand
BSA total
440.4Ų
Buried surface area upon binding
BSA apolar
351.7Ų
Hydrophobic contacts buried
BSA polar
88.7Ų
Polar contacts buried
Fraction buried
64.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3123.2Ų
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
1507.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)