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
10.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.42, Jaccard 0.23, 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 (-0.815 kcal/mol/HA)
✓ Good fit quality (FQ -7.20)
✓ Good H-bonds (4 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (10.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-18.751
kcal/mol
LE
-0.815
kcal/mol/HA
Fit Quality
-7.20
FQ (Leeson)
HAC
23
heavy atoms
MW
315
Da
LogP
1.60
cLogP
Final rank
1.9065
rank score
Inter norm
-0.990
normalised
Contacts
15
H-bonds 5
Interaction summary
HBD 2
HBA 2
HY 5
PI 1
CLASH 1
Interaction summary
HBD 2
HBA 2
HY 5
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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: permissive.
| 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 | 1 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 623 | -0.21493581621955696 | -1.3166 | -29.3146 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 636 | 1.9065028710157321 | -0.990453 | -18.7513 | 5 | 15 | 5 | 0.42 | 1.00 | - | no | Current |
| 638 | 2.078718061437694 | -1.03904 | -19.278 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 640 | 2.4645938733667183 | -1.04408 | -17.2106 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 629 | 3.425746121157447 | -1.25604 | -25.7731 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 625 | 3.6012935560196184 | -1.2648 | -22.3059 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 648 | 4.1058842412556915 | -1.39928 | -29.419 | 12 | 18 | 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
-18.751kcal/mol
Ligand efficiency (LE)
-0.8153kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.195
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
315.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.60
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
79.78kcal/mol
Minimised FF energy
68.88kcal/mol
SASA & burial
✓ computed
SASA (unbound)
573.3Ų
Total solvent-accessible surface area of free ligand
BSA total
457.4Ų
Buried surface area upon binding
BSA apolar
368.4Ų
Hydrophobic contacts buried
BSA polar
89.1Ų
Polar contacts buried
Fraction buried
79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6426.9Ų
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
2089.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)