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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
13.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.62, Jaccard 0.56, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
55% of hydrophobic surface appears solvent-exposed (11/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.618 kcal/mol/HA)
✓ Good fit quality (FQ -5.70)
✓ Strong H-bond network (7 bonds)
✓ Good burial (45% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (13.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-16.072
kcal/mol
LE
-0.618
kcal/mol/HA
Fit Quality
-5.70
FQ (Leeson)
HAC
26
heavy atoms
MW
347
Da
LogP
3.00
cLogP
Interaction summary
HB 7
HY 10
PI 0
CLASH 4
⚠ Exposure 55%
Interaction summary
HB 7
HY 10
PI 0
CLASH 4
⚠ Exposure 55%
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
Partial hydrophobic solvent exposure
55% of hydrophobic surface appears solvent-exposed (11/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 9
Exposed 11
LogP 3.0
H-bonds 7
Exposed fragments:
phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.723 | Score | -16.072 |
|---|---|---|---|
| Inter norm | -0.723 | Intra norm | 0.105 |
| Top1000 | no | Excluded | no |
| Contacts | 6 | H-bonds | 7 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes | ||
| Residues |
ASN402
LEU399
LYS407
PHE396
PRO398
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 | 5 | Native recall | 0.62 |
| Jaccard | 0.56 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 96 | 3.723167484514075 | -0.723487 | -16.0721 | 7 | 6 | 5 | 0.62 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-16.072kcal/mol
Ligand efficiency (LE)
-0.6182kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.695
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.00
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
67.69kcal/mol
Minimised FF energy
54.58kcal/mol
SASA & burial
✓ computed
SASA (unbound)
586.1Ų
Total solvent-accessible surface area of free ligand
BSA total
261.4Ų
Buried surface area upon binding
BSA apolar
184.9Ų
Hydrophobic contacts buried
BSA polar
76.5Ų
Polar contacts buried
Fraction buried
44.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3019.0Ų
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
1543.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)