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
25.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.62, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
79% of hydrophobic surface is solvent-exposed (19/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.595 kcal/mol/HA)
✓ Good fit quality (FQ -5.95)
✓ Good H-bonds (4 bonds)
✓ Good burial (54% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (25.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-20.224
kcal/mol
LE
-0.595
kcal/mol/HA
Fit Quality
-5.95
FQ (Leeson)
HAC
34
heavy atoms
MW
491
Da
LogP
0.68
cLogP
Final rank
3.2500
rank score
Inter norm
-0.663
normalised
Contacts
13
H-bonds 6
Interaction summary
HBD 3
HBA 1
HY 3
PI 0
CLASH 2
Interaction summary
HBD 3
HBA 1
HY 3
PI 0
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
No pi · π–π interactions detected for this pose.
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 | 8 | Native recall | 1.00 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 137 | 1.4250442280306628 | -0.831035 | -24.9586 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 95 | 2.2939910034529745 | -0.74699 | -23.0218 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 134 | 3.2500437522289114 | -0.663106 | -20.2236 | 6 | 13 | 8 | 1.00 | 1.00 | - | no | Current |
| 118 | 3.530922444984885 | -0.659476 | -18.0355 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 140 | 4.13901343086955 | -0.78708 | -24.095 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.224kcal/mol
Ligand efficiency (LE)
-0.5948kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.952
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
490.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.68
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
219.24kcal/mol
Minimised FF energy
193.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
782.3Ų
Total solvent-accessible surface area of free ligand
BSA total
425.9Ų
Buried surface area upon binding
BSA apolar
332.2Ų
Hydrophobic contacts buried
BSA polar
93.7Ų
Polar contacts buried
Fraction buried
54.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3170.9Ų
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
1544.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)