FAIRMol

NMT-TY0625

Pose ID 8402 Compound 587 Pose 272

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand NMT-TY0625
PDB1F3T↗

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
27.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.64, H-bond role recall 0.57
Burial
76%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.110 kcal/mol/HA) ✓ Good fit quality (FQ -10.36) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (27.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-29.976
kcal/mol
LE
-1.110
kcal/mol/HA
Fit Quality
-10.36
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
27.3 kcal/mol
SASA buried
76%
Lipo contact
72% BSA apolar/total
SASA unbound
648 Ų
Apolar buried
357 Ų

Interaction summary

HB 9 HY 18 PI 3 CLASH 1

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 rank4.200Score-29.976
Inter norm-1.169Intra norm0.059
Top1000noExcludedno
Contacts17H-bonds9
Artifact reasongeometry warning; 10 clashes; 3 protein clashes; moderate strain Δ 27.2
Residues
ALA67 ARG277 ASN327 ASP332 ASP88 GLU274 GLY199 GLY236 GLY237 GLY276 GLY393 HIS197 LYS69 PRO275 SER200 TYR331 TYR389

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap14Native recall0.74
Jaccard0.64RMSD-
HB strict4Strict recall0.44
HB same residue+role4HB role recall0.57
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
324 0.20723889343453514 -0.951386 -23.6661 1 14 0 0.00 0.00 - no Open
275 0.9061196009967781 -1.22993 -32.9032 9 20 0 0.00 0.00 - no Open
292 1.1768621845493887 -1.20358 -35.0455 10 11 0 0.00 0.00 - no Open
291 1.218230612835466 -1.06543 -26.4823 10 13 0 0.00 0.00 - no Open
310 1.511827099897129 -0.901999 -22.8948 4 17 0 0.00 0.00 - no Open
330 1.9924960648131407 -0.979613 -23.342 4 14 0 0.00 0.00 - no Open
343 2.359267355874073 -0.89635 -23.6694 9 12 0 0.00 0.00 - no Open
426 2.4909161669113518 -0.907217 -24.1632 10 17 0 0.00 0.00 - no Open
278 2.509428388171617 -1.0319 -28.1397 6 13 0 0.00 0.00 - no Open
297 2.63967730557778 -1.25147 -33.606 12 23 0 0.00 0.00 - no Open
355 3.229453768262364 -1.09247 -22.9997 10 19 0 0.00 0.00 - no Open
311 3.2950567359488305 -0.981974 -28.1708 9 14 0 0.00 0.00 - no Open
395 3.4109746243775096 -0.855223 -23.6426 8 13 0 0.00 0.00 - no Open
350 3.483682559989441 -0.96476 -27.5634 8 19 0 0.00 0.00 - no Open
381 3.5214059746730104 -1.11325 -28.0276 6 14 0 0.00 0.00 - no Open
364 4.0288364719309 -1.09005 -30.4446 8 17 0 0.00 0.00 - no Open
272 4.1996467964885476 -1.16921 -29.9755 9 17 14 0.74 0.57 - no Current
332 4.352390042161908 -0.822496 -24.9609 10 15 0 0.00 0.00 - no Open
271 4.392965189680496 -1.27398 -34.4428 11 15 0 0.00 0.00 - no Open
330 5.564206722433145 -0.904232 -20.3369 11 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 -29.976kcal/mol
Ligand efficiency (LE) -1.1102kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.358
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -53.76kcal/mol
Minimised FF energy -81.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 647.5Ų
Total solvent-accessible surface area of free ligand
BSA total 493.7Ų
Buried surface area upon binding
BSA apolar 357.3Ų
Hydrophobic contacts buried
BSA polar 136.4Ų
Polar contacts buried
Fraction buried 76.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2558.7Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1384.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)