FAIRMol

NMT-TY0920

Pose ID 3706 Compound 544 Pose 320

DB SELECTIONDocking 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
T06
T. brucei DHFR T. brucei
Ligand NMT-TY0920
PDB8RHT↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
33.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.62, Jaccard 0.54, H-bond role recall 0.00
Burial
94%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.123 kcal/mol/HA) ✓ Good fit quality (FQ -10.60) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (33.1 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (10)
Score
-31.451
kcal/mol
LE
-1.123
kcal/mol/HA
Fit Quality
-10.60
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Final rank
1.0669
rank score
Inter norm
-0.878
normalised
Contacts
16
H-bonds 3
Strain ΔE
33.1 kcal/mol
SASA buried
94%
Lipo contact
74% BSA apolar/total
SASA unbound
643 Ų
Apolar buried
445 Ų

Interaction summary

HB 0 PC 1 HY 9 PI 4 CLASH 4

HBD/HBA · H-bonds (geometric)
No hbd/hba · h-bonds (geometric) detected for this pose.

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap13Native recall0.62
Jaccard0.54RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

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 0.5239567590025211 -1.18433 -30.604 9 13 0 0.00 0.00 - no Open
319 0.9940520654587742 -0.944043 -25.3008 5 13 0 0.00 0.00 - no Open
320 1.0669444827431311 -0.878088 -31.4505 3 16 13 0.62 0.00 - no Current
345 1.1134646347622539 -0.877657 -23.1229 3 15 0 0.00 0.00 - no Open
369 1.570299553280359 -0.935163 -25.1037 6 14 0 0.00 0.00 - no Open
285 1.846962516011115 -1.10054 -35.0271 11 16 0 0.00 0.00 - no Open
333 2.430240854014312 -0.961348 -34.1213 11 17 0 0.00 0.00 - no Open
313 2.7355217655896267 -0.945999 -28.0195 7 18 1 0.05 0.00 - no Open
388 3.1357764599548372 -1.01979 -35.0482 6 16 0 0.00 0.00 - no Open
366 3.33349022232488 -1.04252 -32.8619 6 15 0 0.00 0.00 - no Open
313 3.427850034969361 -1.24397 -30.3675 11 26 0 0.00 0.00 - no Open
342 3.492057571577017 -0.785111 -22.7794 9 15 0 0.00 0.00 - no Open
295 3.616137840018539 -0.981468 -32.0097 7 17 0 0.00 0.00 - no Open
437 3.855523120955258 -0.937716 -27.4849 10 13 0 0.00 0.00 - no Open
349 4.8296015227220686 -0.681525 -25.7042 8 9 0 0.00 0.00 - no Open
361 5.231781681702861 -0.899682 -33.3801 11 16 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 -31.451kcal/mol
Ligand efficiency (LE) -1.1232kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.604
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.31
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -34.01kcal/mol
Minimised FF energy -67.08kcal/mol

SASA & burial

✓ computed
SASA (unbound) 643.2Ų
Total solvent-accessible surface area of free ligand
BSA total 601.4Ų
Buried surface area upon binding
BSA apolar 444.8Ų
Hydrophobic contacts buried
BSA polar 156.7Ų
Polar contacts buried
Fraction buried 93.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1708.6Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 585.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)