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
17.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.54, H-bond role recall 1.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.764 kcal/mol/HA)
✓ Good fit quality (FQ -7.04)
✓ Good H-bonds (5 bonds)
✓ Good burial (58% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (17.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-19.858
kcal/mol
LE
-0.764
kcal/mol/HA
Fit Quality
-7.04
FQ (Leeson)
HAC
26
heavy atoms
MW
364
Da
LogP
1.67
cLogP
Interaction summary
HB 5
HY 15
PI 1
CLASH 3
Interaction summary
HB 5
HY 15
PI 1
CLASH 3
| Final rank | 2.530 | Score | -19.858 |
|---|---|---|---|
| Inter norm | -0.770 | Intra norm | 0.006 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ASN402
GLU466
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 | 0.54 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 522 | 2.261262159608891 | -0.956395 | -21.4623 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 2.445465122574451 | -0.93199 | -23.3803 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 500 | 2.521021803203339 | -1.41509 | -32.6993 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 2.5299445645219074 | -0.770281 | -19.8585 | 5 | 12 | 7 | 0.88 | 1.00 | - | no | Current |
| 509 | 3.262137122905528 | -1.06992 | -27.791 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 544 | 3.481530108671423 | -0.925088 | -22.453 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 4.064661269329177 | -1.16787 | -30.0605 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 551 | 4.1785443525306984 | -0.940747 | -23.0358 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 505 | 4.605833726720881 | -1.07502 | -27.6675 | 13 | 20 | 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
-19.858kcal/mol
Ligand efficiency (LE)
-0.7638kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.037
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
364.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.67
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.98kcal/mol
Minimised FF energy
42.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
571.2Ų
Total solvent-accessible surface area of free ligand
BSA total
331.5Ų
Buried surface area upon binding
BSA apolar
236.3Ų
Hydrophobic contacts buried
BSA polar
95.3Ų
Polar contacts buried
Fraction buried
58.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2954.4Ų
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
1501.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)