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
20.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.75, Jaccard 0.63, 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 (11/22 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 (-0.966 kcal/mol/HA)
✓ Good fit quality (FQ -9.50)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ High strain energy (20.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-30.908
kcal/mol
LE
-0.966
kcal/mol/HA
Fit Quality
-9.50
FQ (Leeson)
HAC
32
heavy atoms
MW
467
Da
LogP
4.70
cLogP
Final rank
2.5793
rank score
Inter norm
-0.931
normalised
Contacts
15
H-bonds 7
Interaction summary
HBA 7
HY 4
PI 4
CLASH 4
Interaction summary
HBA 7
HY 4
PI 4
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| 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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 481 | 0.833260595904217 | -0.99353 | -31.3183 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 488 | 0.9430789113896668 | -0.763464 | -24.1793 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 469 | 2.5792744908747576 | -0.930947 | -30.9076 | 7 | 15 | 12 | 0.75 | 0.40 | - | no | Current |
| 482 | 2.61080621143186 | -0.91774 | -24.0255 | 12 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 503 | 2.6537518010083168 | -0.872065 | -27.8131 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 537 | 2.741837643516047 | -0.70956 | -24.207 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 476 | 2.8526863726121 | -0.830155 | -26.7459 | 15 | 14 | 5 | 0.31 | 0.20 | - | no | Open |
| 495 | 3.187958920184594 | -0.765818 | -26.7542 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 3.9807987113699346 | -0.690298 | -20.9193 | 5 | 14 | 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
-30.908kcal/mol
Ligand efficiency (LE)
-0.9659kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.498
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
466.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.70
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.27kcal/mol
Minimised FF energy
27.57kcal/mol
SASA & burial
✓ computed
SASA (unbound)
749.1Ų
Total solvent-accessible surface area of free ligand
BSA total
499.5Ų
Buried surface area upon binding
BSA apolar
331.8Ų
Hydrophobic contacts buried
BSA polar
167.8Ų
Polar contacts buried
Fraction buried
66.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2200.4Ų
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)