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 high
Native strong
SASA done
Strain ΔE
15.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.70, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.697 kcal/mol/HA)
✓ Good fit quality (FQ -6.25)
✓ Good H-bonds (5 bonds)
✓ Good burial (50% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (15.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-16.735
kcal/mol
LE
-0.697
kcal/mol/HA
Fit Quality
-6.25
FQ (Leeson)
HAC
24
heavy atoms
MW
336
Da
LogP
3.00
cLogP
Interaction summary
HB 5
HY 9
PI 1
CLASH 2
⚠ Exposure 37%
Interaction summary
HB 5
HY 9
PI 1
CLASH 2
⚠ Exposure 37%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 10
Exposed 6
LogP 3.0
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 2.245 | Score | -16.735 |
|---|---|---|---|
| Inter norm | -0.798 | Intra norm | 0.101 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 5 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ASN402
GLU467
LEU399
LYS407
LYS410
PHE396
PRO398
SER394
THR397
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 7 | Native recall | 0.88 |
| Jaccard | 0.70 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | 1.7255116500284249 | -1.06127 | -20.8401 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 507 | 2.2454245298281488 | -0.79818 | -16.7349 | 5 | 9 | 7 | 0.88 | 0.00 | - | no | Current |
| 486 | 2.4557881244034303 | -1.17165 | -27.4838 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 524 | 2.656306600203591 | -1.08008 | -25.1332 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 494 | 3.2626283087821317 | -1.31748 | -28.7197 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 4.493007696400588 | -1.17875 | -26.5297 | 10 | 16 | 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
-16.735kcal/mol
Ligand efficiency (LE)
-0.6973kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.249
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
336.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.00
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
68.49kcal/mol
Minimised FF energy
53.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
566.9Ų
Total solvent-accessible surface area of free ligand
BSA total
282.2Ų
Buried surface area upon binding
BSA apolar
183.8Ų
Hydrophobic contacts buried
BSA polar
98.4Ų
Polar contacts buried
Fraction buried
49.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2939.1Ų
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
1527.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)