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
30.8 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.88, Jaccard 0.58, H-bond role recall 1.00
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.467 kcal/mol/HA)
✓ Good fit quality (FQ -4.67)
✓ Good H-bonds (3 bonds)
✓ Good burial (54% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (30.8 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (8)
✗ Many internal clashes (13)
Score
-15.873
kcal/mol
LE
-0.467
kcal/mol/HA
Fit Quality
-4.67
FQ (Leeson)
HAC
34
heavy atoms
MW
534
Da
LogP
5.11
cLogP
Final rank
2.1346
rank score
Inter norm
-0.571
normalised
Contacts
11
H-bonds 3
Interaction summary
HBD 2
HBA 1
HY 4
PI 2
CLASH 5
Interaction summary
HBD 2
HBA 1
HY 4
PI 2
CLASH 5
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 | 7 | Native recall | 0.88 |
| Jaccard | 0.58 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 407 | 0.4460464701571234 | -0.902398 | -26.5386 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 2.134597253516552 | -0.571051 | -15.873 | 3 | 11 | 7 | 0.88 | 1.00 | - | no | Current |
| 476 | 3.207803087429654 | -0.828298 | -24.7951 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 520 | 3.4286161390837204 | -0.715677 | -26.832 | 8 | 18 | 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
-15.873kcal/mol
Ligand efficiency (LE)
-0.4669kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.671
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
534.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.11
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.08kcal/mol
Minimised FF energy
56.26kcal/mol
SASA & burial
✓ computed
SASA (unbound)
757.8Ų
Total solvent-accessible surface area of free ligand
BSA total
407.0Ų
Buried surface area upon binding
BSA apolar
334.0Ų
Hydrophobic contacts buried
BSA polar
73.0Ų
Polar contacts buried
Fraction buried
53.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3070.9Ų
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
1588.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)