FAIRMol

NMT-TY0566

Pose ID 5683 Compound 1408 Pose 265

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-TY0566

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 medium Native strong SASA done
Strain ΔE
18.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.81, Jaccard 0.77, H-bond role recall 0.67
Burial
94%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.303 kcal/mol/HA) ✓ Good fit quality (FQ -10.68) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Moderate strain (18.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-24.762
kcal/mol
LE
-1.303
kcal/mol/HA
Fit Quality
-10.68
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
0.02
cLogP
Final rank
3.3810
rank score
Inter norm
-1.352
normalised
Contacts
18
H-bonds 11
Strain ΔE
18.8 kcal/mol
SASA buried
94%
Lipo contact
68% BSA apolar/total
SASA unbound
482 Ų
Apolar buried
311 Ų

Interaction summary

HBD 7 HY 5 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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 overlap17Native recall0.81
Jaccard0.77RMSD-
HB strict4Strict recall0.57
HB same residue+role4HB role recall0.67
HB same residue4HB residue recall0.67

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
312 -0.12698051497752788 -1.4099 -25.1999 5 13 0 0.00 0.00 - no Open
409 1.5618486583435398 -1.25392 -19.5039 8 16 0 0.00 0.00 - no Open
329 1.810958723850599 -1.17778 -21.5875 6 14 0 0.00 0.00 - no Open
267 3.3656450884601203 -1.63439 -30.9104 5 17 0 0.00 0.00 - no Open
265 3.3810319513898386 -1.35166 -24.7621 11 18 17 0.81 0.67 - no Current
341 3.5339212025300557 -1.51737 -27.3765 9 15 1 0.05 0.00 - no Open
382 3.8196564752012465 -1.26937 -21.4516 9 16 0 0.00 0.00 - no Open
288 4.003072569334565 -1.34735 -23.6626 10 17 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 -24.762kcal/mol
Ligand efficiency (LE) -1.3033kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.683
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.02
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -121.55kcal/mol
Minimised FF energy -140.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 482.1Ų
Total solvent-accessible surface area of free ligand
BSA total 455.7Ų
Buried surface area upon binding
BSA apolar 310.7Ų
Hydrophobic contacts buried
BSA polar 145.0Ų
Polar contacts buried
Fraction buried 94.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3092.2Ų
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 1670.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)