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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
26.5 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 0.00
Reason: 13 internal clashes
13 intramolecular clashes
52% of hydrophobic surface appears solvent-exposed (11/21 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 (-0.648 kcal/mol/HA)
✓ Good fit quality (FQ -6.31)
✓ Good H-bonds (4 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (26.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-20.092
kcal/mol
LE
-0.648
kcal/mol/HA
Fit Quality
-6.31
FQ (Leeson)
HAC
31
heavy atoms
MW
442
Da
LogP
0.80
cLogP
Interaction summary
HB 4
HY 14
PI 0
CLASH 0
⚠ Exposure 52%
Interaction summary
HB 4
HY 14
PI 0
CLASH 0
⚠ Exposure 52%
Partial hydrophobic solvent exposure
52% of hydrophobic surface appears solvent-exposed (11/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 10
Exposed 11
LogP 0.8
H-bonds 4
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.081 | Score | -20.092 |
|---|---|---|---|
| Inter norm | -0.680 | Intra norm | 0.032 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes; moderate strain Δ 22.8 | ||
| Residues |
ASN402
GLU467
HIS461
LEU399
LYS407
LYS410
PHE396
PRO398
SER464
THR397
THR463
| ||
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
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 | 6 | Native recall | 0.75 |
| Jaccard | 0.46 | 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 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
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.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 355 | 1.6026500140535416 | -0.743905 | -21.8571 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 354 | 1.7306580484949365 | -0.923116 | -29.7352 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 407 | 2.0338986117039672 | -0.876746 | -27.1056 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 358 | 2.1591494369409356 | -0.901399 | -28.0656 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 3.080838426070046 | -0.679833 | -20.0918 | 4 | 11 | 6 | 0.75 | 0.00 | - | no | Current |
| 357 | 4.492732902768604 | -1.03651 | -31.4245 | 13 | 23 | 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
-20.092kcal/mol
Ligand efficiency (LE)
-0.6481kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.314
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
442.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.80
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
17.53kcal/mol
Minimised FF energy
-8.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
711.3Ų
Total solvent-accessible surface area of free ligand
BSA total
424.2Ų
Buried surface area upon binding
BSA apolar
326.1Ų
Hydrophobic contacts buried
BSA polar
98.0Ų
Polar contacts buried
Fraction buried
59.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3074.8Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1512.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)