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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
30.2 kcal/mol
Protein clashes
2
Internal clashes
12
Native overlap
contact recall 0.62, Jaccard 0.44
Reason: 12 internal clashes
2 protein-contact clashes
12 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.748 kcal/mol/HA)
✓ Good fit quality (FQ -6.80)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (30.2 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (12)
Score
-18.690
kcal/mol
LE
-0.748
kcal/mol/HA
Fit Quality
-6.80
FQ (Leeson)
HAC
25
heavy atoms
MW
348
Da
LogP
4.03
cLogP
Final rank
0.8791
rank score
Inter norm
-0.830
normalised
Contacts
13
H-bonds 4
Interaction summary
HBD 2
HY 7
PI 3
CLASH 0
Interaction summary
HBD 2
HY 7
PI 3
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
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.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 0.44 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 602 | 0.11430096132212113 | -1.27135 | -29.7382 | 5 | 12 | 0 | 0.00 | - | - | no | Open |
| 616 | 0.8791360147483075 | -0.830152 | -18.6899 | 4 | 13 | 8 | 0.62 | - | - | no | Current |
| 601 | 1.2194364801494049 | -1.02909 | -25.5113 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 612 | 1.5874584481341056 | -1.13378 | -28.2176 | 3 | 15 | 0 | 0.00 | - | - | no | Open |
| 595 | 1.8006179207427564 | -1.05666 | -24.4722 | 5 | 11 | 0 | 0.00 | - | - | no | Open |
| 599 | 3.4431675101061257 | -0.887757 | -22.4323 | 8 | 13 | 0 | 0.00 | - | - | no | Open |
| 611 | 4.478348342907414 | -1.13978 | -27.4314 | 7 | 9 | 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
-18.690kcal/mol
Ligand efficiency (LE)
-0.7476kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.796
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
348.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.03
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.24kcal/mol
Minimised FF energy
5.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
549.1Ų
Total solvent-accessible surface area of free ligand
BSA total
394.5Ų
Buried surface area upon binding
BSA apolar
320.3Ų
Hydrophobic contacts buried
BSA polar
74.2Ų
Polar contacts buried
Fraction buried
71.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3049.1Ų
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
1467.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)