FAIRMol

NMT-TY0555

Pose ID 3674 Compound 515 Pose 288

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-TY0555
PDB8RHT↗

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 high Native strong SASA done
Strain ΔE
22.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.76, Jaccard 0.73, H-bond role recall 1.00
Burial
100%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.092 kcal/mol/HA) ✓ Good fit quality (FQ -9.14) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (100% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ High strain energy (22.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-21.838
kcal/mol
LE
-1.092
kcal/mol/HA
Fit Quality
-9.14
FQ (Leeson)
HAC
20
heavy atoms
MW
296
Da
LogP
-0.68
cLogP
Strain ΔE
22.8 kcal/mol
SASA buried
100%
Lipo contact
66% BSA apolar/total
SASA unbound
483 Ų
Apolar buried
317 Ų

Interaction summary

HB 10 HY 19 PI 2 CLASH 2
Final rank2.273Score-21.838
Inter norm-1.201Intra norm0.109
Top1000noExcludedno
Contacts17H-bonds10
Artifact reasongeometry warning; 7 clashes; 2 protein clashes; moderate strain Δ 22.8
Residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 MET82 NDP301 PHE58 THR184 THR86 TYR166 TYR57 VAL32 VAL33

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

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 overlap16Native recall0.76
Jaccard0.73RMSD-
HB strict4Strict recall0.80
HB same residue+role4HB role recall1.00
HB same residue4HB residue recall1.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
291 1.1342832901296953 -1.47243 -28.1213 7 13 0 0.00 0.00 - no Open
308 1.1407956598243199 -1.47271 -28.0966 7 13 0 0.00 0.00 - no Open
287 1.425854450107728 -1.57638 -29.017 10 15 0 0.00 0.00 - no Open
294 1.4368563653499584 -1.58614 -29.0417 10 15 0 0.00 0.00 - no Open
340 1.5199875327590986 -1.30421 -24.1616 12 16 0 0.00 0.00 - no Open
325 1.8929444358902847 -1.09972 -20.59 10 11 0 0.00 0.00 - no Open
264 2.0213778030470935 -1.28263 -24.1424 8 15 1 0.05 0.00 - no Open
272 2.07930378903586 -1.19931 -21.6886 10 17 16 0.76 1.00 - no Open
288 2.272686469792997 -1.20072 -21.8379 10 17 16 0.76 1.00 - no Current
255 2.604134178216891 -1.55444 -29.5672 11 18 1 0.05 0.00 - no Open
395 2.618228131873109 -1.34198 -25.4179 10 16 0 0.00 0.00 - no Open
307 2.6395815071657873 -1.216 -22.6881 12 17 0 0.00 0.00 - no Open
324 2.719858307570968 -0.962258 -19.339 7 11 0 0.00 0.00 - no Open
272 2.890185804928903 -1.24872 -23.3539 7 15 0 0.00 0.00 - no Open
354 2.894301988851109 -1.46517 -27.278 13 19 0 0.00 0.00 - no Open
248 2.9955573621189955 -1.44392 -27.8137 14 18 0 0.00 0.00 - no Open
346 3.086475756889026 -1.42333 -26.6003 13 19 0 0.00 0.00 - no Open
299 3.1992481359795537 -1.24642 -23.7166 13 17 0 0.00 0.00 - no Open
285 3.2187089349618714 -1.29682 -23.427 10 17 0 0.00 0.00 - no Open
379 3.2560466957189305 -1.35838 -25.6607 9 16 0 0.00 0.00 - no Open
369 3.4560880962334983 -1.32647 -25.5936 9 16 0 0.00 0.00 - no Open
254 3.4642926757389616 -1.30203 -24.5606 9 15 1 0.05 0.00 - no Open
406 3.67636034041161 -1.29246 -24.4616 10 16 0 0.00 0.00 - no Open
333 3.717795610400825 -1.4146 -26.5109 10 14 1 0.05 0.00 - no Open
241 3.724783035797209 -1.26416 -21.7498 15 13 0 0.00 0.00 - no Open
251 3.7829044977730146 -1.35705 -25.1409 11 19 0 0.00 0.00 - no Open
330 3.7929991462566486 -0.942708 -18.8834 6 11 0 0.00 0.00 - no Open
241 4.010694369049239 -1.38136 -25.2742 11 19 0 0.00 0.00 - no Open
226 4.299065349056032 -1.39557 -26.9943 14 15 0 0.00 0.00 - no Open
257 4.359761779337785 -1.65662 -30.294 16 22 0 0.00 0.00 - no Open
274 4.532558280468934 -1.63443 -31.073 16 21 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 -21.838kcal/mol
Ligand efficiency (LE) -1.0919kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.137
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 296.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.68
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -93.08kcal/mol
Minimised FF energy -115.85kcal/mol

SASA & burial

✓ computed
SASA (unbound) 482.6Ų
Total solvent-accessible surface area of free ligand
BSA total 481.4Ų
Buried surface area upon binding
BSA apolar 317.5Ų
Hydrophobic contacts buried
BSA polar 163.9Ų
Polar contacts buried
Fraction buried 99.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1532.3Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 594.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)