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
19.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.63, H-bond role recall 0.50
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.133 kcal/mol/HA)
✓ Good fit quality (FQ -10.44)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (68% SASA buried)
✗ Moderate strain (19.9 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (10)
✗ Many internal clashes (10)
Score
-29.451
kcal/mol
LE
-1.133
kcal/mol/HA
Fit Quality
-10.44
FQ (Leeson)
HAC
26
heavy atoms
MW
402
Da
LogP
4.26
cLogP
Final rank
1.6426
rank score
Inter norm
-1.165
normalised
Contacts
15
H-bonds 11
Interaction summary
HBA 9
HY 3
PI 3
CLASH 3
Interaction summary
HBA 9
HY 3
PI 3
CLASH 3
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 | 12 | Native recall | 0.75 |
| Jaccard | 0.63 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| HB same residue | 6 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 441 | 0.5899340868847586 | -0.993845 | -21.5367 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 448 | 1.6426460868017652 | -1.16491 | -29.4515 | 11 | 15 | 12 | 0.75 | 0.50 | - | no | Current |
| 464 | 1.8145094087744755 | -0.992491 | -23.6741 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 451 | 2.3917671125321918 | -0.9311 | -24.3609 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 487 | 2.5123127086348505 | -0.935305 | -19.7957 | 5 | 13 | 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
-29.451kcal/mol
Ligand efficiency (LE)
-1.1327kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.436
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
401.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.26
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
1.12kcal/mol
Minimised FF energy
-18.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
653.5Ų
Total solvent-accessible surface area of free ligand
BSA total
441.2Ų
Buried surface area upon binding
BSA apolar
251.0Ų
Hydrophobic contacts buried
BSA polar
190.2Ų
Polar contacts buried
Fraction buried
67.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
56.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2106.4Ų
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
787.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)