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 high
Native strong
SASA done
Strain ΔE
21.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
53% of hydrophobic surface appears solvent-exposed (9/17 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 (-0.775 kcal/mol/HA)
✓ Good fit quality (FQ -6.84)
✓ Good H-bonds (4 bonds)
✓ Good burial (56% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (21.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-17.819
kcal/mol
LE
-0.775
kcal/mol/HA
Fit Quality
-6.84
FQ (Leeson)
HAC
23
heavy atoms
MW
307
Da
LogP
2.41
cLogP
Final rank
3.9255
rank score
Inter norm
-0.849
normalised
Contacts
11
H-bonds 8
Interaction summary
HBD 2
HBA 2
HY 3
PI 1
CLASH 2
Interaction summary
HBD 2
HBA 2
HY 3
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 76 | 0.45381324785065 | -1.22085 | -25.7889 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 70 | 2.442684569188187 | -1.10683 | -21.3506 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 40 | 3.807615652205658 | -1.32736 | -26.423 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 103 | 3.9254576003142985 | -0.849229 | -17.819 | 8 | 11 | 6 | 0.75 | 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
-17.819kcal/mol
Ligand efficiency (LE)
-0.7747kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.838
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
307.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.41
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
90.86kcal/mol
Minimised FF energy
69.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
541.2Ų
Total solvent-accessible surface area of free ligand
BSA total
302.2Ų
Buried surface area upon binding
BSA apolar
214.3Ų
Hydrophobic contacts buried
BSA polar
87.9Ų
Polar contacts buried
Fraction buried
55.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2976.1Ų
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
1513.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)