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 medium
Native strong
SASA done
Strain ΔE
31.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.58, Jaccard 0.37
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
43% of hydrophobic surface appears solvent-exposed (10/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.691 kcal/mol/HA)
✓ Good fit quality (FQ -6.60)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (31.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-20.052
kcal/mol
LE
-0.691
kcal/mol/HA
Fit Quality
-6.60
FQ (Leeson)
HAC
29
heavy atoms
MW
417
Da
LogP
6.21
cLogP
Final rank
2.7019
rank score
Inter norm
-0.791
normalised
Contacts
14
H-bonds 3
Interaction summary
HBD 1
HBA 1
HY 8
PI 0
CLASH 4
Interaction summary
HBD 1
HBA 1
HY 8
PI 0
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
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 | 7 | Native recall | 0.58 |
| Jaccard | 0.37 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 432 | 0.8623178535349165 | -1.00322 | -24.6609 | 2 | 16 | 0 | 0.00 | - | - | no | Open |
| 403 | 1.0636572058242943 | -0.810058 | -23.5364 | 6 | 12 | 0 | 0.00 | - | - | no | Open |
| 351 | 1.341002587485065 | -1.2482 | -38.7245 | 2 | 22 | 0 | 0.00 | - | - | no | Open |
| 401 | 1.4146208906347317 | -1.12411 | -35.086 | 4 | 19 | 0 | 0.00 | - | - | no | Open |
| 501 | 1.9050517117857513 | -0.874468 | -26.9335 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 479 | 2.7019193094242033 | -0.790757 | -20.0516 | 3 | 14 | 7 | 0.58 | - | - | no | Current |
| 448 | 2.865866465048615 | -0.810026 | -23.0742 | 6 | 17 | 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
-20.052kcal/mol
Ligand efficiency (LE)
-0.6914kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.600
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.21
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.27kcal/mol
Minimised FF energy
72.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
675.3Ų
Total solvent-accessible surface area of free ligand
BSA total
486.7Ų
Buried surface area upon binding
BSA apolar
383.4Ų
Hydrophobic contacts buried
BSA polar
103.3Ų
Polar contacts buried
Fraction buried
72.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3139.8Ų
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
1494.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)