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
33.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.42, Jaccard 0.25, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
40% of hydrophobic surface appears solvent-exposed (4/10 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 (-1.175 kcal/mol/HA)
✓ Good fit quality (FQ -9.63)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Very high strain energy (33.0 kcal/mol)
✗ Geometry warnings
Score
-22.334
kcal/mol
LE
-1.175
kcal/mol/HA
Fit Quality
-9.63
FQ (Leeson)
HAC
19
heavy atoms
MW
287
Da
LogP
-1.07
cLogP
Final rank
2.7229
rank score
Inter norm
-1.193
normalised
Contacts
13
H-bonds 8
Interaction summary
HBD 2
HBA 4
HY 7
PI 1
CLASH 3
Interaction summary
HBD 2
HBA 4
HY 7
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | 5S9T | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA365
ARG228
ARG331
GLY229
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL366
| ||
| Current overlap | 5 | Native recall | 0.42 |
| Jaccard | 0.25 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
1033 residues
| Protein target | T17 | Atoms | 15160 |
|---|---|---|---|
| Residues | 1033 | Chains | 2 |
| Residue summary | VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408 | ||
Receptor context
2 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 2
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
B: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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 176 | 2.1235620534942115 | -1.649 | -32.7179 | 12 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 173 | 2.2097958068481676 | -1.68052 | -33.3208 | 16 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 140 | 2.6837438727649325 | -1.50508 | -31.2958 | 16 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 216 | 2.7228918607595345 | -1.1931 | -22.3343 | 8 | 13 | 5 | 0.42 | 0.00 | - | no | Current |
| 129 | 3.546185683732613 | -1.45232 | -30.7445 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 122 | 4.021631400475942 | -1.49408 | -32.5526 | 12 | 15 | 0 | 0.00 | 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
-22.334kcal/mol
Ligand efficiency (LE)
-1.1755kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.635
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
286.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.07
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
111.30kcal/mol
Minimised FF energy
78.25kcal/mol
SASA & burial
✓ computed
SASA (unbound)
464.3Ų
Total solvent-accessible surface area of free ligand
BSA total
368.6Ų
Buried surface area upon binding
BSA apolar
254.3Ų
Hydrophobic contacts buried
BSA polar
114.3Ų
Polar contacts buried
Fraction buried
79.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6320.9Ų
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
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2062.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)