FAIRMol

Z20255081

Pose ID 13311 Compound 678 Pose 432

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z20255081
PDB9IFH↗

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
22.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 0.00
Burial
49%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 40% of hydrophobic surface appears solvent-exposed (8/20 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 (-0.582 kcal/mol/HA) ✓ Good fit quality (FQ -5.61) ✓ Strong H-bond network (6 bonds) ✓ Good burial (49% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (22.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-17.454
kcal/mol
LE
-0.582
kcal/mol/HA
Fit Quality
-5.61
FQ (Leeson)
HAC
30
heavy atoms
MW
459
Da
LogP
4.59
cLogP
Strain ΔE
22.9 kcal/mol
SASA buried
49%
Lipo contact
72% BSA apolar/total
SASA unbound
675 Ų
Apolar buried
239 Ų

Interaction summary

HB 6 HY 15 PI 1 CLASH 3 ⚠ Exposure 40%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
⚠️Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (8/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20 Buried (contacted) 12 Exposed 8 LogP 4.59 H-bonds 6
Exposed fragments: phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.434Score-17.454
Inter norm-0.660Intra norm0.078
Top1000noExcludedno
Contacts10H-bonds6
Artifact reasongeometry warning; 8 clashes; 1 protein clash; moderate strain Δ 21.6
Residues
ASN402 GLU467 LEU399 LYS407 LYS410 PHE396 PRO398 SER394 SER395 THR397

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap7Native recall0.88
Jaccard0.64RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221

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:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
396 -0.11056417959593262 -1.19533 -34.8331 9 17 0 0.00 0.00 - no Open
419 0.3271797508948459 -0.839972 -24.243 2 13 0 0.00 0.00 - no Open
480 0.4575261200251558 -0.989236 -25.5218 1 21 0 0.00 0.00 - no Open
388 1.3247621968802203 -0.97422 -27.5305 8 15 0 0.00 0.00 - no Open
429 1.5682838105176942 -0.894601 -23.8867 4 14 0 0.00 0.00 - no Open
452 1.7973468440035216 -0.986403 -22.7906 5 13 0 0.00 0.00 - no Open
450 1.8532223899879046 -0.707052 -19.9579 8 16 0 0.00 0.00 - no Open
442 2.056146307025179 -0.886151 -21.9132 8 18 0 0.00 0.00 - no Open
402 2.1313085350777627 -1.15443 -29.8157 14 17 0 0.00 0.00 - no Open
432 2.4339812204281435 -0.65996 -17.4537 6 10 7 0.88 0.00 - no Current
469 2.992470262134781 -0.896028 -22.0828 6 18 0 0.00 0.00 - no Open
408 3.228580280103112 -0.944403 -24.0255 6 19 0 0.00 0.00 - no Open
426 3.390641675980678 -0.781192 -18.2749 8 14 0 0.00 0.00 - no Open
398 3.736159295282282 -0.857475 -20.4087 13 15 0 0.00 0.00 - no Open
409 3.9602894299335802 -0.833689 -21.2615 10 15 0 0.00 0.00 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -17.454kcal/mol
Ligand efficiency (LE) -0.5818kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.612
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 458.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.59
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 32.03kcal/mol
Minimised FF energy 9.18kcal/mol

SASA & burial

✓ computed
SASA (unbound) 675.4Ų
Total solvent-accessible surface area of free ligand
BSA total 331.8Ų
Buried surface area upon binding
BSA apolar 239.5Ų
Hydrophobic contacts buried
BSA polar 92.3Ų
Polar contacts buried
Fraction buried 49.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3021.6Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1518.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)