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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
19.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.58, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.614 kcal/mol/HA)
✓ Good fit quality (FQ -5.86)
✓ Good H-bonds (4 bonds)
✓ Good burial (55% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Moderate strain (19.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-17.812
kcal/mol
LE
-0.614
kcal/mol/HA
Fit Quality
-5.86
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
3.90
cLogP
Interaction summary
HB 4
HY 21
PI 2
CLASH 2
Interaction summary
HB 4
HY 21
PI 2
CLASH 2
| Final rank | 2.621 | Score | -17.812 |
|---|---|---|---|
| Inter norm | -0.647 | Intra norm | 0.032 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash | ||
| Residues |
ASN402
GLU467
LEU399
MET400
PHE396
PRO398
SER394
SER395
SER464
THR397
THR463
| ||
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
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 | 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 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 32 | 0.6350295306883202 | -0.947993 | -25.7194 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 49 | 1.06598484236764 | -0.902347 | -25.0526 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 46 | 1.247594231706635 | -0.849387 | -24.2208 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 66 | 1.2746015132081996 | -0.940681 | -26.7167 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 56 | 1.4067512650930576 | -0.892365 | -25.6003 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 37 | 1.4316038385936012 | -0.9755 | -25.7021 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 2.6209386879172865 | -0.646672 | -17.8124 | 4 | 11 | 7 | 0.88 | 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
-17.812kcal/mol
Ligand efficiency (LE)
-0.6142kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.863
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
432.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.90
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
4.31kcal/mol
Minimised FF energy
-15.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
685.8Ų
Total solvent-accessible surface area of free ligand
BSA total
379.7Ų
Buried surface area upon binding
BSA apolar
308.3Ų
Hydrophobic contacts buried
BSA polar
71.4Ų
Polar contacts buried
Fraction buried
55.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3107.4Ų
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
1559.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)