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
15.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.68, Jaccard 0.54, H-bond role recall 0.43
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.948 kcal/mol/HA)
✓ Good fit quality (FQ -8.74)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (15.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.652
kcal/mol
LE
-0.948
kcal/mol/HA
Fit Quality
-8.74
FQ (Leeson)
HAC
26
heavy atoms
MW
350
Da
LogP
2.45
cLogP
Interaction summary
HB 12
HY 6
PI 3
CLASH 2
Interaction summary
HB 12
HY 6
PI 3
CLASH 2
| Final rank | 3.258 | Score | -24.652 |
|---|---|---|---|
| Inter norm | -1.054 | Intra norm | 0.106 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASN112
ASP88
GLU274
GLY199
GLY235
GLY236
GLY237
GLY276
HIS197
LYS69
PHE170
PRO113
SER200
TYR389
| ||
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 13 | Native recall | 0.68 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| HB same residue+role | 3 | HB role recall | 0.43 |
| HB same residue | 3 | HB residue recall | 0.43 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 232 | 0.22512664578509115 | -0.982056 | -23.3495 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 203 | 0.6142823023382752 | -1.00213 | -23.6948 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 285 | 1.1222800013457437 | -0.984396 | -22.608 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 238 | 1.9179388927226144 | -1.20382 | -29.2649 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 234 | 2.1949120016563737 | -1.18622 | -28.0822 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 341 | 2.442548170009624 | -0.972273 | -22.0173 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 213 | 2.9637696841486436 | -1.24057 | -28.6769 | 16 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 167 | 3.258232707517787 | -1.05416 | -24.6519 | 12 | 18 | 13 | 0.68 | 0.43 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.652kcal/mol
Ligand efficiency (LE)
-0.9482kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.736
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
350.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.45
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.67kcal/mol
Minimised FF energy
27.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
585.1Ų
Total solvent-accessible surface area of free ligand
BSA total
472.0Ų
Buried surface area upon binding
BSA apolar
370.0Ų
Hydrophobic contacts buried
BSA polar
102.0Ų
Polar contacts buried
Fraction buried
80.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2550.5Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1391.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)