FAIRMol

NMT-TY0169

Pose ID 5671 Compound 3265 Pose 253

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
T09
L. major DHFR-TS L. major
Ligand NMT-TY0169

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
15.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.57, Jaccard 0.50, H-bond role recall 0.50
Burial
96%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.624 kcal/mol/HA) ✓ Good fit quality (FQ -12.70) ✓ Good H-bonds (3 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Moderate strain (15.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-27.615
kcal/mol
LE
-1.624
kcal/mol/HA
Fit Quality
-12.70
FQ (Leeson)
HAC
17
heavy atoms
MW
248
Da
LogP
1.53
cLogP
Final rank
2.1361
rank score
Inter norm
-1.639
normalised
Contacts
15
H-bonds 9
Strain ΔE
15.1 kcal/mol
SASA buried
96%
Lipo contact
72% BSA apolar/total
SASA unbound
446 Ų
Apolar buried
308 Ų

Interaction summary

HBD 3 HY 8 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap12Native recall0.57
Jaccard0.50RMSD-
HB strict3Strict recall0.43
HB same residue+role3HB role recall0.50
HB same residue3HB residue recall0.50

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
253 2.1361295612437563 -1.6385 -27.6152 9 15 12 0.57 0.50 - 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 -27.615kcal/mol
Ligand efficiency (LE) -1.6244kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.702
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 17HA

Physicochemical properties
Molecular weight 248.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.53
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -11.43kcal/mol
Minimised FF energy -26.57kcal/mol

SASA & burial

✓ computed
SASA (unbound) 446.4Ų
Total solvent-accessible surface area of free ligand
BSA total 426.1Ų
Buried surface area upon binding
BSA apolar 308.4Ų
Hydrophobic contacts buried
BSA polar 117.7Ų
Polar contacts buried
Fraction buried 95.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3083.8Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1672.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)