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 but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
19.7 kcal/mol
Protein clashes
0
Internal clashes
7
Native overlap
contact recall 0.75, Jaccard 0.55, H-bond role recall 0.00
Reason: 7 internal clashes
7 intramolecular clashes
44% of hydrophobic surface appears solvent-exposed (7/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.695 kcal/mol/HA)
✓ Good fit quality (FQ -6.13)
✓ Good H-bonds (5 bonds)
✓ Good burial (55% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (19.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-15.980
kcal/mol
LE
-0.695
kcal/mol/HA
Fit Quality
-6.13
FQ (Leeson)
HAC
23
heavy atoms
MW
328
Da
LogP
2.78
cLogP
Interaction summary
HB 5
HY 9
PI 1
CLASH 0
⚠ Exposure 43%
Interaction summary
HB 5
HY 9
PI 1
CLASH 0
⚠ Exposure 43%
Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (7/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 9
Exposed 7
LogP 2.78
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.891 | Score | -15.980 |
|---|---|---|---|
| Inter norm | -0.815 | Intra norm | 0.120 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 5 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes | ||
| Residues |
ASN402
GLU466
GLU467
LEU399
LYS407
PHE396
PRO398
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 | 0.55 | 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
-15.980kcal/mol
Ligand efficiency (LE)
-0.6948kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.132
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
328.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.78
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.17kcal/mol
Minimised FF energy
85.48kcal/mol
SASA & burial
✓ computed
SASA (unbound)
557.9Ų
Total solvent-accessible surface area of free ligand
BSA total
307.2Ų
Buried surface area upon binding
BSA apolar
227.3Ų
Hydrophobic contacts buried
BSA polar
79.8Ų
Polar contacts buried
Fraction buried
55.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2955.9Ų
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
1492.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)