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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
8.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.94, Jaccard 0.88, H-bond role recall 0.40
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (8/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.105 kcal/mol/HA)
✓ Good fit quality (FQ -9.91)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (8.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-26.530
kcal/mol
LE
-1.105
kcal/mol/HA
Fit Quality
-9.91
FQ (Leeson)
HAC
24
heavy atoms
MW
336
Da
LogP
3.00
cLogP
Final rank
4.4930
rank score
Inter norm
-1.179
normalised
Contacts
16
H-bonds 10
Interaction summary
HBA 9
HY 3
PI 4
CLASH 4
Interaction summary
HBA 9
HY 3
PI 4
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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: 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 | 15 | Native recall | 0.94 |
| Jaccard | 0.88 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | 1.7255116500284249 | -1.06127 | -20.8401 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 507 | 2.2454245298281488 | -0.79818 | -16.7349 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 486 | 2.4557881244034303 | -1.17165 | -27.4838 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 524 | 2.656306600203591 | -1.08008 | -25.1332 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 494 | 3.2626283087821317 | -1.31748 | -28.7197 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 4.493007696400588 | -1.17875 | -26.5297 | 10 | 16 | 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
-26.530kcal/mol
Ligand efficiency (LE)
-1.1054kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.907
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
336.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.00
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
61.76kcal/mol
Minimised FF energy
53.30kcal/mol
SASA & burial
✓ computed
SASA (unbound)
578.1Ų
Total solvent-accessible surface area of free ligand
BSA total
429.9Ų
Buried surface area upon binding
BSA apolar
280.7Ų
Hydrophobic contacts buried
BSA polar
149.2Ų
Polar contacts buried
Fraction buried
74.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2089.5Ų
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
789.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)