Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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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
16.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.42, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.031 kcal/mol/HA)
✓ Good fit quality (FQ -9.10)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Moderate strain (16.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-23.713
kcal/mol
LE
-1.031
kcal/mol/HA
Fit Quality
-9.10
FQ (Leeson)
HAC
23
heavy atoms
MW
328
Da
LogP
2.78
cLogP
Interaction summary
HB 7
HY 24
PI 3
CLASH 2
Interaction summary
HB 7
HY 24
PI 3
CLASH 2
| Final rank | 1.594 | Score | -23.713 |
|---|---|---|---|
| Inter norm | -1.058 | Intra norm | 0.027 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ALA284
ALA365
ARG287
GLY195
GLY197
GLY286
ILE199
LEU332
LEU334
MET333
PHE198
PHE230
SER200
SER364
VAL366
| ||
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 | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 438 | 1.5935778613322662 | -1.05764 | -23.7128 | 7 | 15 | 8 | 0.67 | 0.00 | - | no | Current |
| 383 | 1.8986792723681687 | -1.0428 | -22.2131 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 495 | 2.850161246790037 | -1.0661 | -22.9728 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 370 | 3.4477172158172777 | -1.11623 | -21.359 | 11 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 466 | 3.509598316790688 | -1.13775 | -23.8142 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 469 | 4.372722701036715 | -1.15166 | -25.5918 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 4.56124354577558 | -1.22661 | -24.6376 | 10 | 11 | 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
-23.713kcal/mol
Ligand efficiency (LE)
-1.0310kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.099
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
328.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.78
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
110.24kcal/mol
Minimised FF energy
94.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
524.9Ų
Total solvent-accessible surface area of free ligand
BSA total
463.5Ų
Buried surface area upon binding
BSA apolar
318.4Ų
Hydrophobic contacts buried
BSA polar
145.2Ų
Polar contacts buried
Fraction buried
88.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6346.6Ų
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
2074.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)