FAIRMol

NMT-TY0957

Pose ID 5052 Compound 264 Pose 311

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
T08
T. brucei PTR1 T. brucei
Ligand NMT-TY0957
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
25.1 kcal/mol
Protein clashes
4
Internal clashes
6
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.40
Burial
91%
Hydrophobic fit
77%
Reason: 6 internal clashes
4 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.060 kcal/mol/HA) ✓ Good fit quality (FQ -10.01) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ High strain energy (25.1 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (12)
Score
-29.688
kcal/mol
LE
-1.060
kcal/mol/HA
Fit Quality
-10.01
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.07
cLogP
Strain ΔE
25.1 kcal/mol
SASA buried
91%
Lipo contact
77% BSA apolar/total
SASA unbound
638 Ų
Apolar buried
447 Ų

Interaction summary

HB 9 HY 21 PI 2 CLASH 6
Final rank1.323Score-29.688
Inter norm-1.160Intra norm0.100
Top1000noExcludedno
Contacts15H-bonds9
Artifact reasongeometry warning; 12 clashes; 7 protein contact clashes; 2 severe cofactor-context clashes; moderate strain Δ 25.1
Residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 NAP301 PHE97 PRO210 SER207 SER95 TRP221 TYR174 VAL206 VAL211

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap14Native recall0.74
Jaccard0.70RMSD-
HB strict3Strict recall0.50
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

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
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 14 0.74 0.40 - no Current
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 0 0.00 0.00 - no Open
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 0 0.00 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 -29.688kcal/mol
Ligand efficiency (LE) -1.0603kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.010
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) 25.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -16.98kcal/mol
Minimised FF energy -42.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 637.5Ų
Total solvent-accessible surface area of free ligand
BSA total 579.6Ų
Buried surface area upon binding
BSA apolar 447.2Ų
Hydrophobic contacts buried
BSA polar 132.4Ų
Polar contacts buried
Fraction buried 90.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1618.4Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 926.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)