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
12.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.75, Jaccard 0.47, 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.
✓ Excellent LE (-0.831 kcal/mol/HA)
✓ Good fit quality (FQ -7.55)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (12.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-20.768
kcal/mol
LE
-0.831
kcal/mol/HA
Fit Quality
-7.55
FQ (Leeson)
HAC
25
heavy atoms
MW
340
Da
LogP
3.91
cLogP
Interaction summary
HB 6
HY 24
PI 2
CLASH 4
Interaction summary
HB 6
HY 24
PI 2
CLASH 4
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 | 2.137 | Score | -20.768 |
|---|---|---|---|
| Inter norm | -0.970 | Intra norm | 0.140 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash | ||
| Residues |
ALA363
ALA365
ARG331
ARG361
CYS375
GLY376
HIS359
LEU332
LEU334
PHE198
PHE230
SER364
THR360
THR374
VAL362
VAL366
| ||
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 | 9 | Native recall | 0.75 |
| Jaccard | 0.47 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 66 | 0.8305093453479375 | -0.860099 | -15.002 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 74 | 2.1373659912864653 | -0.970433 | -20.7683 | 6 | 16 | 9 | 0.75 | 0.00 | - | no | Current |
| 29 | 2.600107939307177 | -1.01846 | -24.5258 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 65 | 2.6022736026417634 | -0.939392 | -18.7025 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 3.0349276914671437 | -1.1562 | -26.1336 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 43 | 3.222270151018671 | -1.10798 | -20.2889 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 79 | 3.5206894931967216 | -1.022 | -18.8867 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 90 | 3.7209462673393525 | -1.01938 | -22.3114 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 4.14130884921673 | -1.0316 | -21.4621 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 77 | 4.326743905642506 | -0.753896 | -17.6426 | 7 | 12 | 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
-20.768kcal/mol
Ligand efficiency (LE)
-0.8307kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.552
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.91
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
84.14kcal/mol
Minimised FF energy
71.92kcal/mol
SASA & burial
✓ computed
SASA (unbound)
614.7Ų
Total solvent-accessible surface area of free ligand
BSA total
498.0Ų
Buried surface area upon binding
BSA apolar
395.2Ų
Hydrophobic contacts buried
BSA polar
102.8Ų
Polar contacts buried
Fraction buried
81.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6483.6Ų
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
2061.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)