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 mixed
SASA done
Strain ΔE
19.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.42, Jaccard 0.23, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.780 kcal/mol/HA)
✓ Good fit quality (FQ -7.36)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (19.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-21.838
kcal/mol
LE
-0.780
kcal/mol/HA
Fit Quality
-7.36
FQ (Leeson)
HAC
28
heavy atoms
MW
417
Da
LogP
2.68
cLogP
Final rank
2.6135
rank score
Inter norm
-0.809
normalised
Contacts
15
H-bonds 2
Interaction summary
HBD 1
HBA 1
HY 6
PI 1
CLASH 1
Interaction summary
HBD 1
HBA 1
HY 6
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 5 | Native recall | 0.42 |
| Jaccard | 0.23 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 621 | 1.4345497717291078 | -1.0318 | -28.9875 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 1.9005361944032626 | -0.963332 | -23.5994 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 633 | 2.034066149755648 | -0.997448 | -27.4985 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 2.1205691892069596 | -1.06766 | -31.8052 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 2.21543994317517 | -0.943733 | -25.4581 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 636 | 2.2733624275643116 | -0.935816 | -24.4034 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 631 | 2.613527185358712 | -0.808865 | -21.8381 | 2 | 15 | 5 | 0.42 | 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
-21.838kcal/mol
Ligand efficiency (LE)
-0.7799kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.363
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.68
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
23.24kcal/mol
Minimised FF energy
3.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
647.6Ų
Total solvent-accessible surface area of free ligand
BSA total
512.8Ų
Buried surface area upon binding
BSA apolar
380.8Ų
Hydrophobic contacts buried
BSA polar
131.9Ų
Polar contacts buried
Fraction buried
79.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6446.1Ų
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
2082.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)