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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
6.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.67, Jaccard 0.50
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
67% of hydrophobic surface is solvent-exposed (12/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (6.7 kcal/mol)
✓ Excellent LE (-1.008 kcal/mol/HA)
✓ Good fit quality (FQ -8.89)
✓ Good H-bonds (3 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-23.177
kcal/mol
LE
-1.008
kcal/mol/HA
Fit Quality
-8.89
FQ (Leeson)
HAC
23
heavy atoms
MW
528
Da
LogP
4.23
cLogP
Final rank
2.7068
rank score
Inter norm
-1.033
normalised
Contacts
12
H-bonds 3
Interaction summary
HBD 3
HY 5
PI 0
CLASH 3
Interaction summary
HBD 3
HY 5
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 8 | Native recall | 0.67 |
| 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 | T16 | Atoms | 7551 |
|---|---|---|---|
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 675 | 0.08932108552118626 | -1.53139 | -33.7137 | 3 | 15 | 0 | 0.00 | - | - | no | Open |
| 671 | 1.4623494220460063 | -1.20535 | -27.015 | 3 | 18 | 1 | 0.08 | - | - | no | Open |
| 670 | 1.4838971022548233 | -1.01085 | -19.596 | 1 | 19 | 0 | 0.00 | - | - | no | Open |
| 660 | 1.5296363297884992 | -1.24398 | -27.7842 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 659 | 1.6127658204479765 | -1.16325 | -26.2443 | 2 | 19 | 0 | 0.00 | - | - | no | Open |
| 668 | 1.813401811970726 | -1.08305 | -23.0344 | 3 | 13 | 0 | 0.00 | - | - | no | Open |
| 673 | 2.618099765994593 | -1.24331 | -24.7088 | 5 | 19 | 1 | 0.08 | - | - | no | Open |
| 677 | 2.650135671650861 | -0.972587 | -21.0295 | 4 | 11 | 0 | 0.00 | - | - | no | Open |
| 659 | 2.7068022141827996 | -1.03337 | -23.1766 | 3 | 12 | 8 | 0.67 | - | - | no | Current |
| 670 | 3.068566625982152 | -1.0102 | -22.9013 | 4 | 16 | 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
-23.177kcal/mol
Ligand efficiency (LE)
-1.0077kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.894
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
528.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.23
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
6.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.21kcal/mol
Minimised FF energy
47.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
562.7Ų
Total solvent-accessible surface area of free ligand
BSA total
386.9Ų
Buried surface area upon binding
BSA apolar
376.6Ų
Hydrophobic contacts buried
BSA polar
10.3Ų
Polar contacts buried
Fraction buried
68.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3145.0Ų
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
1479.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)