FAIRMol

Z45676441

Pose ID 7940 Compound 3005 Pose 488

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T12
T. brucei R5P T. brucei
Ligand Z45676441
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
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
31.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.74, H-bond role recall 0.40
Burial
73%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
1 protein-contact clashes 36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.006 kcal/mol/HA) ✓ Good fit quality (FQ -9.60) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Very high strain energy (31.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-29.168
kcal/mol
LE
-1.006
kcal/mol/HA
Fit Quality
-9.60
FQ (Leeson)
HAC
29
heavy atoms
MW
410
Da
LogP
4.63
cLogP
Final rank
3.5008
rank score
Inter norm
-1.059
normalised
Contacts
17
H-bonds 9
Strain ΔE
31.3 kcal/mol
SASA buried
73%
Lipo contact
82% BSA apolar/total
SASA unbound
655 Ų
Apolar buried
390 Ų

Interaction summary

HBA 8 HY 5 PI 2 CLASH 1

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.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap14Native recall0.88
Jaccard0.74RMSD-
HB strict6Strict recall0.50
HB same residue+role4HB role recall0.40
HB same residue4HB residue recall0.40

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG: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

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
498 0.5871717741191601 -1.12718 -28.0639 8 14 0 0.00 0.00 - no Open
517 2.7807087543543414 -0.834066 -19.5908 8 17 0 0.00 0.00 - no Open
488 3.500773342012578 -1.05944 -29.1681 9 17 14 0.88 0.40 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -29.168kcal/mol
Ligand efficiency (LE) -1.0058kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.601
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 410.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.63
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 76.27kcal/mol
Minimised FF energy 44.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 655.4Ų
Total solvent-accessible surface area of free ligand
BSA total 476.4Ų
Buried surface area upon binding
BSA apolar 389.7Ų
Hydrophobic contacts buried
BSA polar 86.7Ų
Polar contacts buried
Fraction buried 72.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2232.3Ų
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 785.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)