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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
19.5 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.75, Jaccard 0.75, H-bond role recall 0.50
Reason: 11 internal clashes
11 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.321 kcal/mol/HA)
✓ Good fit quality (FQ -10.83)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Moderate strain (19.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-25.098
kcal/mol
LE
-1.321
kcal/mol/HA
Fit Quality
-10.83
FQ (Leeson)
HAC
19
heavy atoms
MW
254
Da
LogP
2.41
cLogP
Interaction summary
HB 8
HY 6
PI 3
CLASH 0
Interaction summary
HB 8
HY 6
PI 3
CLASH 0
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
No clash · clashes detected for this pose.
| Final rank | 3.016 | Score | -25.098 |
|---|---|---|---|
| Inter norm | -1.443 | Intra norm | 0.122 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 8 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes | ||
| Residues |
ARG140
ARG144
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
HIS14
ILE15
SER74
TYR49
| ||
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 | 12 | Native recall | 0.75 |
| Jaccard | 0.75 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 599 | 1.774607054232465 | -1.34971 | -23.3525 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 2.9890510231618737 | -1.2951 | -22.6337 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 609 | 3.0159037591829456 | -1.44252 | -25.0979 | 8 | 12 | 12 | 0.75 | 0.50 | - | no | Current |
| 624 | 3.0872971814603587 | -1.32537 | -23.3887 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 618 | 3.1835171244642915 | -1.27025 | -21.0326 | 7 | 13 | 5 | 0.31 | 0.20 | - | no | Open |
| 600 | 3.7608836455983226 | -1.51756 | -26.9668 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 620 | 3.8864306304714464 | -1.45494 | -23.8158 | 7 | 16 | 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
-25.098kcal/mol
Ligand efficiency (LE)
-1.3209kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.827
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
254.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.41
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
23.33kcal/mol
Minimised FF energy
3.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
461.1Ų
Total solvent-accessible surface area of free ligand
BSA total
342.6Ų
Buried surface area upon binding
BSA apolar
239.3Ų
Hydrophobic contacts buried
BSA polar
103.3Ų
Polar contacts buried
Fraction buried
74.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2035.0Ų
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
775.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)