FAIRMol

NMT-TY0621

Pose ID 14533 Compound 518 Pose 295

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-TY0621

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
29.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.57, Jaccard 0.40, H-bond role recall 0.36
Burial
91%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 61% of hydrophobic surface is solvent-exposed (11/18 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 (-1.100 kcal/mol/HA) ✓ Good fit quality (FQ -10.50) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (29.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-31.896
kcal/mol
LE
-1.100
kcal/mol/HA
Fit Quality
-10.50
FQ (Leeson)
HAC
29
heavy atoms
MW
438
Da
LogP
2.95
cLogP
Final rank
2.7968
rank score
Inter norm
-1.111
normalised
Contacts
21
H-bonds 15
Strain ΔE
29.9 kcal/mol
SASA buried
91%
Lipo contact
72% BSA apolar/total
SASA unbound
640 Ų
Apolar buried
417 Ų

Interaction summary

HBD 2 HBA 5 HY 4 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 7.

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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 overlap12Native recall0.57
Jaccard0.40RMSD-
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
321 0.4312888916095546 -0.855947 -25.5191 1 14 0 0.00 0.00 - no Open
307 1.303464687200235 -0.78987 -18.3238 4 19 0 0.00 0.00 - no Open
289 1.76930837462521 -1.29932 -35.9638 10 15 0 0.00 0.00 - no Open
422 2.7545848910139727 -0.868419 -24.2502 5 17 0 0.00 0.00 - no Open
295 2.796755929845018 -1.11058 -31.8963 15 21 12 0.57 0.36 - no Current
377 2.9388887475161027 -0.975895 -27.6065 6 15 0 0.00 0.00 - no Open
360 3.268268659000955 -0.926537 -24.8747 6 16 0 0.00 0.00 - no Open
346 3.7743481783884123 -0.840004 -25.3743 9 18 0 0.00 0.00 - no Open
267 4.280322512603641 -0.963547 -25.3705 10 15 0 0.00 0.00 - no Open
326 4.289068608505349 -0.759293 -21.2289 7 14 0 0.00 0.00 - no Open
340 4.374513372828821 -0.659938 -21.0777 6 12 0 0.00 0.00 - no Open
268 4.513993838828387 -1.00962 -28.398 9 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 -31.896kcal/mol
Ligand efficiency (LE) -1.0999kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.499
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 437.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.95
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -71.08kcal/mol
Minimised FF energy -101.00kcal/mol

SASA & burial

✓ computed
SASA (unbound) 639.6Ų
Total solvent-accessible surface area of free ligand
BSA total 581.5Ų
Buried surface area upon binding
BSA apolar 417.0Ų
Hydrophobic contacts buried
BSA polar 164.5Ų
Polar contacts buried
Fraction buried 90.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1331.9Ų
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 491.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)