FAIRMol

NMT-TY0612

Pose ID 5700 Compound 93 Pose 282

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-TY0612

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
37.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.00
Burial
83%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.811 kcal/mol/HA) ✓ Good fit quality (FQ -7.90) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (37.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-25.134
kcal/mol
LE
-0.811
kcal/mol/HA
Fit Quality
-7.90
FQ (Leeson)
HAC
31
heavy atoms
MW
460
Da
LogP
2.69
cLogP
Final rank
2.3565
rank score
Inter norm
-0.839
normalised
Contacts
19
H-bonds 6
Strain ΔE
37.9 kcal/mol
SASA buried
83%
Lipo contact
74% BSA apolar/total
SASA unbound
741 Ų
Apolar buried
454 Ų

Interaction summary

HBA 2 HY 11 PI 2 CLASH 2

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 overlap14Native recall0.67
Jaccard0.54RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
302 0.8971350997771225 -0.807855 -20.869 4 21 1 0.05 0.00 - no Open
370 0.9210647889777489 -0.875749 -27.0837 6 20 0 0.00 0.00 - no Open
340 1.252813065356264 -0.77723 -24.1077 3 20 0 0.00 0.00 - no Open
329 1.522074512203647 -0.723208 -21.4941 6 12 0 0.00 0.00 - no Open
353 2.2704929493478354 -0.823986 -23.5041 4 19 0 0.00 0.00 - no Open
282 2.3565383036457663 -0.839266 -25.1335 6 19 14 0.67 0.00 - no Current
289 3.040071703780371 -0.988061 -31.4748 14 24 0 0.00 0.00 - no Open
285 3.1293627715196166 -1.09642 -30.3765 10 15 0 0.00 0.00 - no Open
418 3.533831568613022 -0.797244 -23.8892 10 16 0 0.00 0.00 - no Open
388 3.6343383937469538 -0.749265 -22.332 7 13 0 0.00 0.00 - no Open
262 4.143948027164196 -0.952432 -27.504 10 22 0 0.00 0.00 - no Open
322 4.563724517232619 -0.858686 -25.0504 13 18 0 0.00 0.00 - no Open
319 4.877370290226992 -0.746215 -21.9956 8 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 -25.134kcal/mol
Ligand efficiency (LE) -0.8108kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.899
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 459.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.69
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -68.99kcal/mol
Minimised FF energy -106.88kcal/mol

SASA & burial

✓ computed
SASA (unbound) 741.0Ų
Total solvent-accessible surface area of free ligand
BSA total 618.1Ų
Buried surface area upon binding
BSA apolar 454.2Ų
Hydrophobic contacts buried
BSA polar 163.9Ų
Polar contacts buried
Fraction buried 83.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3305.3Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1664.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)