Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
25.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 1.00, Jaccard 0.89, H-bond role recall 0.50
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
70% of hydrophobic surface is solvent-exposed (19/27 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 (-0.679 kcal/mol/HA)
✓ Good fit quality (FQ -6.85)
✓ Strong H-bond network (12 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (25.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-23.783
kcal/mol
LE
-0.679
kcal/mol/HA
Fit Quality
-6.85
FQ (Leeson)
HAC
35
heavy atoms
MW
502
Da
LogP
3.84
cLogP
Interaction summary
HB 12
HY 8
PI 1
CLASH 4
⚠ Exposure 70%
Interaction summary
HB 12
HY 8
PI 1
CLASH 4
⚠ Exposure 70%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
70% of hydrophobic surface is solvent-exposed (19/27 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 27
Buried (contacted) 8
Exposed 19
LogP 3.84
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 2.921 | Score | -23.783 |
|---|---|---|---|
| Inter norm | -0.769 | Intra norm | 0.089 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; moderate strain Δ 25.4 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
MET78
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 | 16 | Native recall | 1.00 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 202 | 2.920845647842995 | -0.768631 | -23.783 | 12 | 18 | 16 | 1.00 | 0.50 | - | no | Current |
| 187 | 5.304898904136661 | -0.742379 | -21.8396 | 12 | 16 | 5 | 0.31 | 0.20 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.783kcal/mol
Ligand efficiency (LE)
-0.6795kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.854
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
501.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.84
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
78.39kcal/mol
Minimised FF energy
52.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
831.7Ų
Total solvent-accessible surface area of free ligand
BSA total
515.2Ų
Buried surface area upon binding
BSA apolar
411.8Ų
Hydrophobic contacts buried
BSA polar
103.4Ų
Polar contacts buried
Fraction buried
61.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2390.7Ų
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
786.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)