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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
27.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.75, Jaccard 0.55, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
47% of hydrophobic surface appears solvent-exposed (8/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.676 kcal/mol/HA)
✓ Good fit quality (FQ -6.14)
✓ Good H-bonds (3 bonds)
✓ Good burial (58% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (27.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Many internal clashes (10)
Score
-16.897
kcal/mol
LE
-0.676
kcal/mol/HA
Fit Quality
-6.14
FQ (Leeson)
HAC
25
heavy atoms
MW
347
Da
LogP
2.92
cLogP
Final rank
1.5668
rank score
Inter norm
-0.750
normalised
Contacts
9
H-bonds 4
Interaction summary
HBA 3
HY 2
PI 1
CLASH 4
Interaction summary
HBA 3
HY 2
PI 1
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
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 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 484 | 0.28110153307647273 | -1.31495 | -32.5414 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 469 | 0.6106312707921285 | -1.25752 | -30.0688 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 459 | 0.9059983743946403 | -1.20032 | -29.5096 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 490 | 1.4021700669349333 | -0.92032 | -22.5041 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 494 | 1.5668201695242128 | -0.749892 | -16.897 | 4 | 9 | 6 | 0.75 | 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
-16.897kcal/mol
Ligand efficiency (LE)
-0.6759kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.92
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
112.38kcal/mol
Minimised FF energy
84.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
588.0Ų
Total solvent-accessible surface area of free ligand
BSA total
339.3Ų
Buried surface area upon binding
BSA apolar
259.2Ų
Hydrophobic contacts buried
BSA polar
80.1Ų
Polar contacts buried
Fraction buried
57.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3024.5Ų
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
1515.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)