FAIRMol

NMT-TY0957

Pose ID 14562 Compound 264 Pose 324

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
T22
L. donovani rab5a L. donovani
Ligand NMT-TY0957

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 medium Native strong SASA done
Strain ΔE
33.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.90, Jaccard 0.68, H-bond role recall 0.45
Burial
90%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 56% of hydrophobic surface appears solvent-exposed (10/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.037 kcal/mol/HA) ✓ Good fit quality (FQ -9.79) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Very high strain energy (33.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-29.035
kcal/mol
LE
-1.037
kcal/mol/HA
Fit Quality
-9.79
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Strain ΔE
33.4 kcal/mol
SASA buried
90%
Lipo contact
71% BSA apolar/total
SASA unbound
671 Ų
Apolar buried
428 Ų

Interaction summary

HB 13 HY 6 PI 1 CLASH 5 ⚠ Exposure 55%

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
⚠️Partial hydrophobic solvent exposure
56% of hydrophobic surface appears solvent-exposed (10/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18 Buried (contacted) 8 Exposed 10 LogP 2.31 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)
Final rank5.157Score-29.035
Inter norm-1.119Intra norm0.082
Top1000noExcludedno
Contacts26H-bonds13
Artifact reasongeometry warning; 10 clashes; 3 protein clashes; high strain Δ 33.4
Residues
ALA158 ALA24 ALA40 ALA70 ASN126 ASN41 ASP129 ASP68 GLU73 GLY23 GLY25 GLY47 GLY71 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28 THR44 THR45 THR69

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap19Native recall0.90
Jaccard0.68RMSD-
HB strict5Strict recall0.33
HB same residue+role5HB role recall0.45
HB same residue5HB residue recall0.45

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

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 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 19 0.90 0.45 - no Current
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 -29.035kcal/mol
Ligand efficiency (LE) -1.0370kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.789
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) 33.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -53.13kcal/mol
Minimised FF energy -86.53kcal/mol

SASA & burial

✓ computed
SASA (unbound) 671.2Ų
Total solvent-accessible surface area of free ligand
BSA total 603.6Ų
Buried surface area upon binding
BSA apolar 428.4Ų
Hydrophobic contacts buried
BSA polar 175.2Ų
Polar contacts buried
Fraction buried 89.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1355.2Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 496.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)