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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
38.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.73, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (8/21 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 (-0.674 kcal/mol/HA)
✓ Good fit quality (FQ -6.44)
✓ Good H-bonds (4 bonds)
✓ Good burial (54% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Very high strain energy (38.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-19.561
kcal/mol
LE
-0.674
kcal/mol/HA
Fit Quality
-6.44
FQ (Leeson)
HAC
29
heavy atoms
MW
408
Da
LogP
3.56
cLogP
Final rank
3.4236
rank score
Inter norm
-0.729
normalised
Contacts
11
H-bonds 7
Interaction summary
HBD 2
HBA 2
HY 4
PI 1
CLASH 1
Interaction summary
HBD 2
HBA 2
HY 4
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 8 | Native recall | 1.00 |
| Jaccard | 0.73 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 611 | 1.6858718437942672 | -0.784032 | -24.4732 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 2.3411592116053694 | -0.856245 | -22.0048 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 2.4430336134887645 | -0.800422 | -21.2984 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 633 | 2.8693333061383006 | -1.14047 | -28.4808 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 3.423589934689467 | -0.728846 | -19.561 | 7 | 11 | 8 | 1.00 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.561kcal/mol
Ligand efficiency (LE)
-0.6745kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.439
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
408.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.56
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
68.82kcal/mol
Minimised FF energy
30.65kcal/mol
SASA & burial
✓ computed
SASA (unbound)
702.6Ų
Total solvent-accessible surface area of free ligand
BSA total
380.0Ų
Buried surface area upon binding
BSA apolar
302.8Ų
Hydrophobic contacts buried
BSA polar
77.2Ų
Polar contacts buried
Fraction buried
54.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3081.3Ų
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
1533.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)