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 mixed
SASA done
Strain ΔE
29.2 kcal/mol
Protein clashes
0
Internal clashes
3
Native overlap
contact recall 0.42, Jaccard 0.25
Reason: no major geometry red flags detected
3 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (10/16 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.823 kcal/mol/HA)
✓ Good fit quality (FQ -7.48)
✓ Good H-bonds (4 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (60%)
✗ High strain energy (29.2 kcal/mol)
✗ Geometry warnings
Score
-20.578
kcal/mol
LE
-0.823
kcal/mol/HA
Fit Quality
-7.48
FQ (Leeson)
HAC
25
heavy atoms
MW
413
Da
LogP
4.11
cLogP
Final rank
2.5487
rank score
Inter norm
-0.945
normalised
Contacts
13
H-bonds 5
Interaction summary
HBA 4
HY 4
PI 0
CLASH 0
Interaction summary
HBA 4
HY 4
PI 0
CLASH 0
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
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 | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 5 | Native recall | 0.42 |
| Jaccard | 0.25 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 179 | 0.2594283999296635 | -1.04511 | -22.959 | 2 | 17 | 0 | 0.00 | - | - | no | Open |
| 81 | 0.6081118924852887 | -1.10405 | -22.8093 | 1 | 12 | 0 | 0.00 | - | - | no | Open |
| 158 | 1.254972404675908 | -0.864476 | -21.5275 | 2 | 11 | 0 | 0.00 | - | - | no | Open |
| 94 | 2.4282509243657286 | -1.07214 | -22.1872 | 8 | 18 | 0 | 0.00 | - | - | no | Open |
| 128 | 2.548700631037403 | -0.945102 | -20.5783 | 5 | 13 | 5 | 0.42 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.578kcal/mol
Ligand efficiency (LE)
-0.8231kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.483
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
412.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.11
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
16.12kcal/mol
Minimised FF energy
-13.13kcal/mol
SASA & burial
✓ computed
SASA (unbound)
646.2Ų
Total solvent-accessible surface area of free ligand
BSA total
456.7Ų
Buried surface area upon binding
BSA apolar
275.6Ų
Hydrophobic contacts buried
BSA polar
181.1Ų
Polar contacts buried
Fraction buried
70.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3039.5Ų
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
1472.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)