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
26.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.88, Jaccard 0.70, H-bond role recall 0.50
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
63% of hydrophobic surface is solvent-exposed (12/19 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 (-0.754 kcal/mol/HA)
✓ Good fit quality (FQ -7.12)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ High strain energy (26.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-21.117
kcal/mol
LE
-0.754
kcal/mol/HA
Fit Quality
-7.12
FQ (Leeson)
HAC
28
heavy atoms
MW
401
Da
LogP
2.23
cLogP
Final rank
4.8322
rank score
Inter norm
-1.072
normalised
Contacts
18
H-bonds 13
Interaction summary
HBD 1
HBA 9
HY 3
PI 1
CLASH 5
Interaction summary
HBD 1
HBA 9
HY 3
PI 1
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
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 | 14 | Native recall | 0.88 |
| Jaccard | 0.70 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 548 | 0.6067675643089019 | -0.91307 | -10.311 | 5 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 556 | 1.728252009536883 | -1.22489 | -21.6697 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 549 | 2.20929891941585 | -1.10472 | -30.4504 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 3.200521320066378 | -0.853064 | -13.3418 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 558 | 3.460830310890564 | -0.973641 | -25.0281 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 4.136553907887692 | -1.13429 | -23.1701 | 16 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 582 | 4.298262327047228 | -0.796914 | -17.889 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 556 | 4.83223480932776 | -1.07236 | -21.1171 | 13 | 18 | 14 | 0.88 | 0.50 | - | no | Current |
| 560 | 5.628665404275403 | -0.846398 | -11.7793 | 13 | 17 | 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
-21.117kcal/mol
Ligand efficiency (LE)
-0.7542kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.120
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
401.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.23
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-31.43kcal/mol
Minimised FF energy
-57.82kcal/mol
SASA & burial
✓ computed
SASA (unbound)
664.9Ų
Total solvent-accessible surface area of free ligand
BSA total
483.0Ų
Buried surface area upon binding
BSA apolar
302.0Ų
Hydrophobic contacts buried
BSA polar
181.0Ų
Polar contacts buried
Fraction buried
72.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2143.2Ų
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
789.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)