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 mixed
SASA done
Strain ΔE
28.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.44, Jaccard 0.44, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (14/14 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 (-1.254 kcal/mol/HA)
✓ Good fit quality (FQ -10.69)
✓ Strong H-bond network (10 bonds)
✓ Good burial (58% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (28.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-26.325
kcal/mol
LE
-1.254
kcal/mol/HA
Fit Quality
-10.69
FQ (Leeson)
HAC
21
heavy atoms
MW
300
Da
LogP
3.01
cLogP
Interaction summary
HB 10
HY 0
PI 0
CLASH 3
⚠ Exposure 100%
Interaction summary
HB 10
HY 0
PI 0
CLASH 3
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (14/14 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 14
Buried (contacted) 0
Exposed 14
LogP 3.01
H-bonds 10
Exposed fragments:
phenyl (3/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.414 | Score | -26.325 |
|---|---|---|---|
| Inter norm | -1.277 | Intra norm | 0.023 |
| Top1000 | no | Excluded | no |
| Contacts | 7 | H-bonds | 10 |
| Artifact reason | geometry warning; 12 clashes; 3 protein clashes; moderate strain Δ 28.6 | ||
| Residues |
ARG140
ARG144
HIS105
HIS141
ARG46
HIS14
ILE15
| ||
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 | 7 | Native recall | 0.44 |
| Jaccard | 0.44 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 5 | HB residue recall | 0.50 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 195 | 2.9854798527494473 | -1.42807 | -29.9038 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 149 | 4.41376731960565 | -1.27665 | -26.3249 | 10 | 7 | 7 | 0.44 | 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
-26.325kcal/mol
Ligand efficiency (LE)
-1.2536kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.692
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
299.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.01
Lipinski: ≤ 5
Rotatable bonds
1
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
108.75kcal/mol
Minimised FF energy
80.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
470.4Ų
Total solvent-accessible surface area of free ligand
BSA total
275.2Ų
Buried surface area upon binding
BSA apolar
210.9Ų
Hydrophobic contacts buried
BSA polar
64.3Ų
Polar contacts buried
Fraction buried
58.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2023.5Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
801.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)