FAIRMol

NMT-TY0612

Pose ID 14527 Compound 93 Pose 289

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-TY0612

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
32.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.41, H-bond role recall 0.36
Burial
89%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
2 protein-contact clashes 65% of hydrophobic surface is solvent-exposed (13/20 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.015 kcal/mol/HA) ✓ Good fit quality (FQ -9.89) ✓ Strong H-bond network (14 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Very high strain energy (32.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-31.475
kcal/mol
LE
-1.015
kcal/mol/HA
Fit Quality
-9.89
FQ (Leeson)
HAC
31
heavy atoms
MW
460
Da
LogP
2.45
cLogP
Strain ΔE
32.3 kcal/mol
SASA buried
89%
Lipo contact
72% BSA apolar/total
SASA unbound
694 Ų
Apolar buried
446 Ų

Interaction summary

HB 14 HY 10 PI 0 CLASH 2 ⚠ Exposure 65%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (13/20 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 20 Buried (contacted) 7 Exposed 13 LogP 2.45 H-bonds 14
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.040Score-31.475
Inter norm-0.988Intra norm-0.027
Top1000noExcludedno
Contacts24H-bonds14
Artifact reasongeometry warning; 12 clashes; 1 protein clash; high strain Δ 32.3
Residues
ALA24 ALA48 ALA70 ASP68 GLN42 GLU21 GLU43 GLU73 GLY23 GLY25 GLY47 GLY71 ILE46 LEU31 LEU39 LEU51 LYS127 LYS26 PHE38 SER22 SER27 SER28 THR44 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 overlap13Native recall0.62
Jaccard0.41RMSD-
HB strict5Strict recall0.33
HB same residue+role4HB role recall0.36
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
302 0.8971350997771225 -0.807855 -20.869 4 21 0 0.00 0.00 - no Open
370 0.9210647889777489 -0.875749 -27.0837 6 20 0 0.00 0.00 - no Open
340 1.252813065356264 -0.77723 -24.1077 3 20 0 0.00 0.00 - no Open
329 1.522074512203647 -0.723208 -21.4941 6 12 0 0.00 0.00 - no Open
353 2.2704929493478354 -0.823986 -23.5041 4 19 0 0.00 0.00 - no Open
282 2.3565383036457663 -0.839266 -25.1335 6 19 0 0.00 0.00 - no Open
289 3.040071703780371 -0.988061 -31.4748 14 24 13 0.62 0.36 - no Current
285 3.1293627715196166 -1.09642 -30.3765 10 15 0 0.00 0.00 - no Open
418 3.533831568613022 -0.797244 -23.8892 10 16 0 0.00 0.00 - no Open
388 3.6343383937469538 -0.749265 -22.332 7 13 0 0.00 0.00 - no Open
262 4.143948027164196 -0.952432 -27.504 10 22 0 0.00 0.00 - no Open
322 4.563724517232619 -0.858686 -25.0504 13 18 0 0.00 0.00 - no Open
319 4.877370290226992 -0.746215 -21.9956 8 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 -31.475kcal/mol
Ligand efficiency (LE) -1.0153kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.892
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 459.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.45
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -67.99kcal/mol
Minimised FF energy -100.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 694.1Ų
Total solvent-accessible surface area of free ligand
BSA total 616.1Ų
Buried surface area upon binding
BSA apolar 445.9Ų
Hydrophobic contacts buried
BSA polar 170.2Ų
Polar contacts buried
Fraction buried 88.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1377.4Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 492.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)