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
38.3 kcal/mol
Protein clashes
4
Internal clashes
6
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 1.00
Reason: 6 internal clashes
4 protein-contact clashes
6 intramolecular clashes
43% of hydrophobic surface appears solvent-exposed (13/30 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 (-0.566 kcal/mol/HA)
✓ Good fit quality (FQ -5.71)
✓ Strong H-bond network (6 bonds)
✓ Good burial (50% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Very high strain energy (38.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (6)
Score
-19.809
kcal/mol
LE
-0.566
kcal/mol/HA
Fit Quality
-5.71
FQ (Leeson)
HAC
35
heavy atoms
MW
489
Da
LogP
5.18
cLogP
Interaction summary
HB 6
HY 11
PI 0
CLASH 0
⚠ Exposure 43%
Interaction summary
HB 6
HY 11
PI 0
CLASH 0
⚠ Exposure 43%
Partial hydrophobic solvent exposure
43% of hydrophobic surface appears solvent-exposed (13/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 30
Buried (contacted) 17
Exposed 13
LogP 5.18
H-bonds 6
Exposed fragments:
cyclohexyl (6/6 atoms exposed)cyclohexyl (4/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 0.902 | Score | -19.809 |
|---|---|---|---|
| Inter norm | -0.571 | Intra norm | 0.005 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 6 |
| Artifact reason | geometry warning; 6 clashes; 4 protein contact clashes; high strain Δ 38.3 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
PHE396
PRO398
PRO462
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 | 1 | Strict recall | 0.50 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 90 | 0.9024379389445512 | -0.571056 | -19.8093 | 6 | 11 | 6 | 0.75 | 1.00 | - | no | Current |
| 79 | 1.0021972144081828 | -0.564156 | -20.1316 | 6 | 11 | 6 | 0.75 | 1.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.809kcal/mol
Ligand efficiency (LE)
-0.5660kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.709
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
488.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.18
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
145.11kcal/mol
Minimised FF energy
106.77kcal/mol
SASA & burial
✓ computed
SASA (unbound)
681.7Ų
Total solvent-accessible surface area of free ligand
BSA total
338.4Ų
Buried surface area upon binding
BSA apolar
284.2Ų
Hydrophobic contacts buried
BSA polar
54.2Ų
Polar contacts buried
Fraction buried
49.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3193.5Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1465.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)