Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
71.6 kcal/mol
Protein clashes
0
Internal clashes
18
Native overlap
contact recall 0.88, Jaccard 0.54, H-bond role recall 0.00
Reason: 18 internal clashes, strain 71.6 kcal/mol
strain ΔE 71.6 kcal/mol
18 intramolecular clashes
68% of hydrophobic surface is solvent-exposed (17/25 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.442 kcal/mol/HA)
✓ Good fit quality (FQ -4.59)
✓ Good H-bonds (5 bonds)
✓ Good burial (50% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Extreme strain energy (71.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-17.239
kcal/mol
LE
-0.442
kcal/mol/HA
Fit Quality
-4.59
FQ (Leeson)
HAC
39
heavy atoms
MW
570
Da
LogP
3.57
cLogP
Final rank
4.4487
rank score
Inter norm
-0.510
normalised
Contacts
12
H-bonds 7
Interaction summary
HBD 2
HBA 3
HY 3
PI 1
CLASH 0
Interaction summary
HBD 2
HBA 3
HY 3
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
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 | 0.54 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 488 | 1.672200773331258 | -0.719774 | -22.9505 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 447 | 1.9322741281478826 | -0.717572 | -28.5262 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 1.992766089379955 | -0.587649 | -23.5693 | 5 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 462 | 3.0789642120118357 | -0.8542 | -33.1254 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 440 | 3.7496370630942577 | -0.624881 | -21.4116 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 509 | 3.921737239173272 | -0.684945 | -27.1972 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 423 | 4.448396986697342 | -0.829802 | -27.9931 | 13 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 4.44869914518263 | -0.509693 | -17.2386 | 7 | 12 | 7 | 0.88 | 0.00 | - | no | Current |
| 443 | 4.693852668046735 | -0.811438 | -26.2177 | 12 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 5.195508061932922 | -0.713708 | -25.239 | 7 | 16 | 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
-17.239kcal/mol
Ligand efficiency (LE)
-0.4420kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.587
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
569.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.57
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
71.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
61.04kcal/mol
Minimised FF energy
-10.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
824.2Ų
Total solvent-accessible surface area of free ligand
BSA total
413.7Ų
Buried surface area upon binding
BSA apolar
294.3Ų
Hydrophobic contacts buried
BSA polar
119.4Ų
Polar contacts buried
Fraction buried
50.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3154.7Ų
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
1497.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)