FAIRMol

NMT-TY0624

Pose ID 7722 Compound 616 Pose 270

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 NMT-TY0624
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
22.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.82, H-bond role recall 0.40
Burial
73%
Hydrophobic fit
67%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 38% of hydrophobic surface appears solvent-exposed (6/16 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 (-1.158 kcal/mol/HA) ✓ Good fit quality (FQ -10.66) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ High strain energy (22.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-30.097
kcal/mol
LE
-1.158
kcal/mol/HA
Fit Quality
-10.66
FQ (Leeson)
HAC
26
heavy atoms
MW
396
Da
LogP
2.16
cLogP
Strain ΔE
22.4 kcal/mol
SASA buried
73%
Lipo contact
67% BSA apolar/total
SASA unbound
631 Ų
Apolar buried
310 Ų

Interaction summary

HB 8 HY 8 PI 2 CLASH 3 ⚠ Exposure 37%

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
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16 Buried (contacted) 10 Exposed 6 LogP 2.16 H-bonds 8
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank3.524Score-30.097
Inter norm-1.137Intra norm-0.021
Top1000noExcludedno
Contacts15H-bonds8
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; moderate strain Δ 22.4
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 ARG46 CYS72 GLY73 GLY77 HIS14 ILE15 ILE76 SER74 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
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
Jaccard0.82RMSD-
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
323 0.604003958058523 -0.942657 -21.1902 4 15 0 0.00 0.00 - no Open
291 0.6323186320960439 -1.22038 -30.9952 10 13 0 0.00 0.00 - no Open
329 1.875810958250805 -0.873591 -23.2439 4 10 0 0.00 0.00 - no Open
290 2.002828557753335 -1.14993 -29.8501 9 14 0 0.00 0.00 - no Open
310 2.224044674964138 -0.998085 -25.5439 8 18 0 0.00 0.00 - no Open
274 2.2594370727836455 -1.19735 -30.4625 8 17 0 0.00 0.00 - no Open
363 2.3368706908166565 -1.24065 -32.9492 6 14 0 0.00 0.00 - no Open
296 2.3850699368176747 -1.30385 -33.7876 14 22 0 0.00 0.00 - no Open
256 2.4947555472898184 -0.974719 -18.8557 12 13 5 0.31 0.20 - no Open
354 2.712760058770864 -1.25519 -32.5296 10 15 0 0.00 0.00 - no Open
425 3.1536405973770054 -1.02037 -26.076 10 16 0 0.00 0.00 - no Open
270 3.5240590701875685 -1.13687 -30.0974 8 15 14 0.88 0.40 - no Current
349 3.8084335922387926 -0.992658 -26.3696 8 20 0 0.00 0.00 - no Open
380 3.892965236960112 -1.26373 -32.5926 8 16 0 0.00 0.00 - no Open
394 4.604769733373062 -0.872118 -21.6077 9 12 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 -30.097kcal/mol
Ligand efficiency (LE) -1.1576kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.665
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 395.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.16
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -53.99kcal/mol
Minimised FF energy -76.43kcal/mol

SASA & burial

✓ computed
SASA (unbound) 630.7Ų
Total solvent-accessible surface area of free ligand
BSA total 462.5Ų
Buried surface area upon binding
BSA apolar 309.8Ų
Hydrophobic contacts buried
BSA polar 152.7Ų
Polar contacts buried
Fraction buried 73.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2156.6Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 760.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)