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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
31.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.53, H-bond role recall 0.50
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (8/13 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.285 kcal/mol/HA)
✓ Good fit quality (FQ -11.16)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Very high strain energy (31.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-28.276
kcal/mol
LE
-1.285
kcal/mol/HA
Fit Quality
-11.16
FQ (Leeson)
HAC
22
heavy atoms
MW
338
Da
LogP
1.43
cLogP
Final rank
3.6331
rank score
Inter norm
-1.273
normalised
Contacts
13
H-bonds 10
Interaction summary
HBD 1
HBA 8
HY 2
PI 2
CLASH 3
Interaction summary
HBD 1
HBA 8
HY 2
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
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 | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 10 | Native recall | 0.62 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| HB same residue | 5 | HB residue recall | 0.50 |
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
Receptor context
1 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 1
Excluded HETATM 0
Kept cofactors / ions
A:CSD72
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 398 | 1.5248638740335199 | -1.15468 | -25.087 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 413 | 2.7878711962634726 | -1.18251 | -26.3486 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 330 | 3.551134365003259 | -1.40054 | -31.674 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 303 | 3.6330777644416266 | -1.27327 | -28.2762 | 10 | 13 | 10 | 0.62 | 0.50 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.276kcal/mol
Ligand efficiency (LE)
-1.2853kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.159
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
338.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.43
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-70.37kcal/mol
Minimised FF energy
-101.48kcal/mol
SASA & burial
✓ computed
SASA (unbound)
542.3Ų
Total solvent-accessible surface area of free ligand
BSA total
391.6Ų
Buried surface area upon binding
BSA apolar
266.9Ų
Hydrophobic contacts buried
BSA polar
124.7Ų
Polar contacts buried
Fraction buried
72.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2068.4Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
779.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)