FAIRMol

NMT-TY0957

Pose ID 3721 Compound 264 Pose 335

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-TY0957
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
33.6 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.90, Jaccard 0.83, H-bond role recall 0.50
Burial
97%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.940 kcal/mol/HA) ✓ Good fit quality (FQ -8.88) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (97% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Very high strain energy (33.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (8) ✗ Many internal clashes (12)
Score
-26.329
kcal/mol
LE
-0.940
kcal/mol/HA
Fit Quality
-8.88
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.07
cLogP
Strain ΔE
33.6 kcal/mol
SASA buried
97%
Lipo contact
72% BSA apolar/total
SASA unbound
639 Ų
Apolar buried
446 Ų

Interaction summary

HB 6 HY 24 PI 3 CLASH 5

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
Final rank1.726Score-26.329
Inter norm-0.999Intra norm0.059
Top1000noExcludedno
Contacts21H-bonds6
Artifact reasongeometry warning; 12 clashes; 8 protein contact clashes; 1 cofactor-context clash; high strain Δ 33.6
Residues
ALA34 ARG100 ARG59 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 THR184 THR86 TYR166 TYR57 VAL32 VAL33

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 overlap19Native recall0.90
Jaccard0.83RMSD-
HB strict2Strict recall0.40
HB same residue+role2HB role recall0.50
HB same residue2HB residue recall0.50

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
349 0.7278409086070636 -0.881455 -21.5148 2 14 0 0.00 0.00 - no Open
311 1.3229509224018154 -1.16017 -29.6884 9 15 0 0.00 0.00 - no Open
334 1.51730203346956 -0.851135 -24.9989 8 16 0 0.00 0.00 - no Open
335 1.7260732089299 -0.999198 -26.3291 6 21 19 0.90 0.50 - no Current
403 1.7481430375200544 -0.991243 -27.3069 7 18 0 0.00 0.00 - no Open
347 2.3447902198011827 -0.753436 -19.3121 7 15 0 0.00 0.00 - no Open
389 2.786111419208295 -1.0956 -28.7016 6 16 0 0.00 0.00 - no Open
289 3.0086401503696756 -1.24814 -30.9089 9 21 0 0.00 0.00 - no Open
301 3.1451083125642456 -1.02377 -27.2511 8 23 0 0.00 0.00 - no Open
357 3.2475516904388395 -0.897972 -24.0584 9 11 0 0.00 0.00 - no Open
377 3.304488419434868 -0.914277 -26.47 6 16 0 0.00 0.00 - no Open
379 3.3253823915120413 -1.07446 -31.7967 5 19 1 0.05 0.00 - no Open
414 3.598164167482077 -0.922403 -23.4985 9 14 0 0.00 0.00 - no Open
332 3.624289409705216 -0.937648 -25.3511 7 11 0 0.00 0.00 - no Open
330 4.212597954691834 -0.897031 -24.2894 4 14 0 0.00 0.00 - no Open
451 4.456710646262987 -0.898418 -22.7057 8 16 0 0.00 0.00 - no Open
324 5.157273396991818 -1.11879 -29.0355 13 26 0 0.00 0.00 - no Open
284 5.171548217517241 -0.94018 -23.463 14 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 -26.329kcal/mol
Ligand efficiency (LE) -0.9403kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.877
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.07
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -10.43kcal/mol
Minimised FF energy -44.01kcal/mol

SASA & burial

✓ computed
SASA (unbound) 638.9Ų
Total solvent-accessible surface area of free ligand
BSA total 621.2Ų
Buried surface area upon binding
BSA apolar 445.6Ų
Hydrophobic contacts buried
BSA polar 175.6Ų
Polar contacts buried
Fraction buried 97.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1693.5Ų
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 578.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)