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 medium
Native strong
SASA done
Strain ΔE
14.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 1.00, Jaccard 0.73, H-bond role recall 1.00
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.828 kcal/mol/HA)
✓ Good fit quality (FQ -8.07)
✓ Strong H-bond network (10 bonds)
✓ Good burial (52% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (14.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-25.674
kcal/mol
LE
-0.828
kcal/mol/HA
Fit Quality
-8.07
FQ (Leeson)
HAC
31
heavy atoms
MW
414
Da
LogP
2.35
cLogP
Interaction summary
HB 10
HY 13
PI 3
CLASH 5
Interaction summary
HB 10
HY 13
PI 3
CLASH 5
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
| Final rank | 3.695 | Score | -25.674 |
|---|---|---|---|
| Inter norm | -0.630 | Intra norm | -0.198 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 10 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
PHE396
PRO398
SER394
SER395
SER470
THR397
| ||
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 | 0.73 | RMSD | - |
| HB strict | 2 | Strict recall | 1.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 117 | 0.4816532383386699 | -0.819823 | -31.7131 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 121 | 0.8528228617151145 | -1.04358 | -33.743 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 116 | 0.994354898836697 | -0.86191 | -27.8752 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 88 | 1.6774821073098232 | -1.10093 | -32.8614 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 127 | 2.448460325432168 | -0.829026 | -22.9346 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 81 | 2.757958246941406 | -0.758658 | -26.9153 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 86 | 3.5513891838815015 | -0.79038 | -20.7592 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 125 | 3.6953505570332297 | -0.629977 | -25.6744 | 10 | 11 | 8 | 1.00 | 1.00 | - | no | Current |
| 49 | 4.429218295957923 | -1.0087 | -27.8555 | 16 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 73 | 6.223113891236293 | -1.0244 | -28.8817 | 9 | 22 | 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
-25.674kcal/mol
Ligand efficiency (LE)
-0.8282kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.069
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
414.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.35
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-22.29kcal/mol
Minimised FF energy
-36.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
691.4Ų
Total solvent-accessible surface area of free ligand
BSA total
362.0Ų
Buried surface area upon binding
BSA apolar
272.5Ų
Hydrophobic contacts buried
BSA polar
89.5Ų
Polar contacts buried
Fraction buried
52.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3100.0Ų
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
1524.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)