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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
15.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.67, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
45% of hydrophobic surface appears solvent-exposed (5/11 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.084 kcal/mol/HA)
✓ Good fit quality (FQ -8.69)
✓ Good H-bonds (5 bonds)
✓ Good burial (52% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Moderate strain (15.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-19.508
kcal/mol
LE
-1.084
kcal/mol/HA
Fit Quality
-8.69
FQ (Leeson)
HAC
18
heavy atoms
MW
265
Da
LogP
1.99
cLogP
Final rank
3.1264
rank score
Inter norm
-1.051
normalised
Contacts
7
H-bonds 8
Interaction summary
HBA 5
HY 3
PI 1
CLASH 2
Interaction summary
HBA 5
HY 3
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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 | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 6 | Native recall | 0.75 |
| Jaccard | 0.67 | 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
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | 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:264; 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 422 | -0.8907234777815304 | -2.02838 | -36.1327 | 10 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 1.9931956817253402 | -1.63432 | -29.4343 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 455 | 2.0710051739731803 | -1.52558 | -25.3293 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 462 | 3.126377367149108 | -1.05077 | -19.5077 | 8 | 7 | 6 | 0.75 | 0.00 | - | no | Current |
| 430 | 4.252899622902689 | -1.50839 | -27.014 | 14 | 17 | 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
-19.508kcal/mol
Ligand efficiency (LE)
-1.0838kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.686
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
264.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.99
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
93.06kcal/mol
Minimised FF energy
77.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
473.3Ų
Total solvent-accessible surface area of free ligand
BSA total
248.5Ų
Buried surface area upon binding
BSA apolar
174.9Ų
Hydrophobic contacts buried
BSA polar
73.5Ų
Polar contacts buried
Fraction buried
52.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2908.6Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1522.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)