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
32.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.94, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.198 kcal/mol/HA)
✓ Good fit quality (FQ -10.74)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Very high strain energy (32.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-28.750
kcal/mol
LE
-1.198
kcal/mol/HA
Fit Quality
-10.74
FQ (Leeson)
HAC
24
heavy atoms
MW
369
Da
LogP
0.79
cLogP
Interaction summary
HB 11
HY 7
PI 2
CLASH 2
Interaction summary
HB 11
HY 7
PI 2
CLASH 2
| Final rank | 3.744 | Score | -28.750 |
|---|---|---|---|
| Inter norm | -1.276 | Intra norm | 0.078 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 11 |
| Artifact reason | geometry warning; 5 clashes; 3 protein clashes; high strain Δ 32.1 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
MET78
SER74
TYR49
| ||
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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 16 | Native recall | 1.00 |
| Jaccard | 0.94 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| HB same residue | 6 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 374 | 2.0865146822246143 | -1.38198 | -34.324 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 413 | 2.6943961769928566 | -0.984124 | -21.2873 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 410 | 2.7399256456858576 | -1.07947 | -26.8497 | 10 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 459 | 3.458566031907076 | -1.03078 | -25.5076 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 392 | 3.7441207624658626 | -1.27643 | -28.7503 | 11 | 17 | 16 | 1.00 | 0.50 | - | no | Current |
| 387 | 4.41582415185168 | -1.27937 | -27.7085 | 14 | 16 | 5 | 0.31 | 0.30 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.750kcal/mol
Ligand efficiency (LE)
-1.1979kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.736
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
369.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.79
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
32.64kcal/mol
Minimised FF energy
0.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
628.2Ų
Total solvent-accessible surface area of free ligand
BSA total
488.4Ų
Buried surface area upon binding
BSA apolar
321.1Ų
Hydrophobic contacts buried
BSA polar
167.3Ų
Polar contacts buried
Fraction buried
77.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2106.3Ų
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
759.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)