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
8.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.956 kcal/mol/HA)
✓ Good fit quality (FQ -8.15)
✓ Good H-bonds (4 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Moderate strain (8.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-20.076
kcal/mol
LE
-0.956
kcal/mol/HA
Fit Quality
-8.15
FQ (Leeson)
HAC
21
heavy atoms
MW
276
Da
LogP
3.02
cLogP
Interaction summary
HB 4
HY 23
PI 2
CLASH 1
Interaction summary
HB 4
HY 23
PI 2
CLASH 1
| Final rank | 2.223 | Score | -20.076 |
|---|---|---|---|
| Inter norm | -0.945 | Intra norm | -0.011 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
MET400
PHE396
PRO398
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 | 6 | Native recall | 0.75 |
| Jaccard | 0.46 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 661 | 1.3301225924586448 | -1.53409 | -29.212 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 669 | 1.5700738045781129 | -1.13597 | -17.9714 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 657 | 1.577400629558791 | -1.10426 | -22.553 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 2.2225127768025614 | -0.945388 | -20.0759 | 4 | 11 | 6 | 0.75 | 1.00 | - | no | Current |
| 676 | 2.614827992980293 | -1.31059 | -26.4268 | 4 | 19 | 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
-20.076kcal/mol
Ligand efficiency (LE)
-0.9560kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.154
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
276.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.02
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.23kcal/mol
Minimised FF energy
47.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
509.6Ų
Total solvent-accessible surface area of free ligand
BSA total
362.7Ų
Buried surface area upon binding
BSA apolar
353.0Ų
Hydrophobic contacts buried
BSA polar
9.7Ų
Polar contacts buried
Fraction buried
71.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3072.2Ų
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
1494.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)