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
17.0 kcal/mol
Protein clashes
3
Internal clashes
10
Native overlap
contact recall 0.75, Jaccard 0.67, H-bond role recall 0.00
Reason: 10 internal clashes
3 protein-contact clashes
10 intramolecular clashes
39% of hydrophobic surface appears solvent-exposed (7/18 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 (-0.747 kcal/mol/HA)
✓ Good fit quality (FQ -6.79)
✓ Good H-bonds (4 bonds)
✓ Good burial (55% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Moderate strain (17.0 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (10)
Score
-18.662
kcal/mol
LE
-0.747
kcal/mol/HA
Fit Quality
-6.79
FQ (Leeson)
HAC
25
heavy atoms
MW
379
Da
LogP
3.05
cLogP
Interaction summary
HB 4
HY 11
PI 1
CLASH 0
⚠ Exposure 38%
Interaction summary
HB 4
HY 11
PI 1
CLASH 0
⚠ Exposure 38%
Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18
Buried (contacted) 11
Exposed 7
LogP 3.05
H-bonds 4
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 0.992 | Score | -18.662 |
|---|---|---|---|
| Inter norm | -0.761 | Intra norm | 0.015 |
| Top1000 | no | Excluded | no |
| Contacts | 7 | H-bonds | 4 |
| Artifact reason | geometry warning; 10 clashes; 3 protein contact clashes | ||
| Residues |
ASN402
GLU467
LEU399
LYS407
PHE396
PRO398
THR397
| ||
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 | 0.67 | 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 |
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
No clash · clashes detected for this pose.
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-18.662kcal/mol
Ligand efficiency (LE)
-0.7465kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.786
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
378.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.05
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-67.22kcal/mol
Minimised FF energy
-84.23kcal/mol
SASA & burial
✓ computed
SASA (unbound)
636.7Ų
Total solvent-accessible surface area of free ligand
BSA total
348.7Ų
Buried surface area upon binding
BSA apolar
295.7Ų
Hydrophobic contacts buried
BSA polar
53.0Ų
Polar contacts buried
Fraction buried
54.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3066.2Ų
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
1534.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)