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 medium
Native strong
SASA done
Strain ΔE
14.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.94, Jaccard 0.79, H-bond role recall 0.40
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
63% of hydrophobic surface is solvent-exposed (12/19 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
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.982 kcal/mol/HA)
✓ Good fit quality (FQ -9.27)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (14.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-27.488
kcal/mol
LE
-0.982
kcal/mol/HA
Fit Quality
-9.27
FQ (Leeson)
HAC
28
heavy atoms
MW
422
Da
LogP
2.13
cLogP
Final rank
6.7713
rank score
Inter norm
-0.964
normalised
Contacts
18
H-bonds 13
Interaction summary
HBD 1
HBA 7
HY 3
PI 2
CLASH 5
Interaction summary
HBD 1
HBA 7
HY 3
PI 2
CLASH 5
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.79 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 411 | 4.094844457063474 | -1.30783 | -34.6245 | 10 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 6.771266076426603 | -0.963748 | -27.4884 | 13 | 18 | 15 | 0.94 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.488kcal/mol
Ligand efficiency (LE)
-0.9817kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.268
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
421.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-112.67kcal/mol
Minimised FF energy
-127.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
692.7Ų
Total solvent-accessible surface area of free ligand
BSA total
469.4Ų
Buried surface area upon binding
BSA apolar
318.1Ų
Hydrophobic contacts buried
BSA polar
151.3Ų
Polar contacts buried
Fraction buried
67.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2152.4Ų
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
797.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)