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
7.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.67, Jaccard 0.40, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.4 kcal/mol)
✓ Excellent LE (-0.996 kcal/mol/HA)
✓ Good fit quality (FQ -8.79)
✓ Good H-bonds (4 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-22.901
kcal/mol
LE
-0.996
kcal/mol/HA
Fit Quality
-8.79
FQ (Leeson)
HAC
23
heavy atoms
MW
528
Da
LogP
4.23
cLogP
Interaction summary
HB 4
HY 12
PI 1
CLASH 4
Interaction summary
HB 4
HY 12
PI 1
CLASH 4
| Final rank | 3.069 | Score | -22.901 |
|---|---|---|---|
| Inter norm | -1.010 | Intra norm | 0.014 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes | ||
| Residues |
ALA365
ARG361
CYS375
GLY229
GLY376
HIS428
ILE378
LEU332
LEU334
LEU377
PHE230
SER364
THR374
VAL362
VAL366
VAL381
| ||
Protein summary
1033 residues
| Protein target | T17 | Atoms | 15160 |
|---|---|---|---|
| Residues | 1033 | Chains | 2 |
| Residue summary | VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408 | ||
Receptor context
2 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 2
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
B:FAD501
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5S9T | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA365
ARG228
ARG331
GLY229
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL366
| ||
| Current overlap | 8 | Native recall | 0.67 |
| Jaccard | 0.40 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 675 | 0.08932108552118626 | -1.53139 | -33.7137 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 1.4623494220460063 | -1.20535 | -27.015 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 670 | 1.4838971022548233 | -1.01085 | -19.596 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 1.5296363297884992 | -1.24398 | -27.7842 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 1.6127658204479765 | -1.16325 | -26.2443 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 668 | 1.813401811970726 | -1.08305 | -23.0344 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 2.618099765994593 | -1.24331 | -24.7088 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 677 | 2.650135671650861 | -0.972587 | -21.0295 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 2.7068022141827996 | -1.03337 | -23.1766 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 670 | 3.068566625982152 | -1.0102 | -22.9013 | 4 | 16 | 8 | 0.67 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.901kcal/mol
Ligand efficiency (LE)
-0.9957kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.788
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
528.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.23
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.29kcal/mol
Minimised FF energy
47.94kcal/mol
SASA & burial
✓ computed
SASA (unbound)
592.0Ų
Total solvent-accessible surface area of free ligand
BSA total
484.5Ų
Buried surface area upon binding
BSA apolar
470.4Ų
Hydrophobic contacts buried
BSA polar
14.1Ų
Polar contacts buried
Fraction buried
81.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6565.8Ų
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
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2074.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)