FAIRMol

Z56787095

Pose ID 14681 Compound 820 Pose 443

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 Z56787095

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
75.0 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.95, Jaccard 0.80, H-bond role recall 0.55
Burial
85%
Hydrophobic fit
72%
Reason: 6 internal clashes, strain 75.0 kcal/mol
strain ΔE 75.0 kcal/mol 6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.672 kcal/mol/HA) ✓ Good fit quality (FQ -6.98) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Extreme strain energy (75.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-26.218
kcal/mol
LE
-0.672
kcal/mol/HA
Fit Quality
-6.98
FQ (Leeson)
HAC
39
heavy atoms
MW
570
Da
LogP
4.15
cLogP
Final rank
4.6939
rank score
Inter norm
-0.811
normalised
Contacts
24
H-bonds 12
Strain ΔE
75.0 kcal/mol
SASA buried
85%
Lipo contact
72% BSA apolar/total
SASA unbound
814 Ų
Apolar buried
498 Ų

Interaction summary

HBD 3 HBA 3 HY 3 PI 1 CLASH 6

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

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 overlap20Native recall0.95
Jaccard0.80RMSD-
HB strict5Strict recall0.33
HB same residue+role6HB role recall0.55
HB same residue6HB residue recall0.55

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
488 1.672200773331258 -0.719774 -22.9505 3 19 0 0.00 0.00 - no Open
447 1.9322741281478826 -0.717572 -28.5262 3 21 0 0.00 0.00 - no Open
480 1.992766089379955 -0.587649 -23.5693 5 21 0 0.00 0.00 - no Open
462 3.0789642120118357 -0.8542 -33.1254 4 21 0 0.00 0.00 - no Open
440 3.7496370630942577 -0.624881 -21.4116 9 14 0 0.00 0.00 - no Open
509 3.921737239173272 -0.684945 -27.1972 5 13 0 0.00 0.00 - no Open
423 4.448396986697342 -0.829802 -27.9931 13 23 0 0.00 0.00 - no Open
450 4.44869914518263 -0.509693 -17.2386 7 12 0 0.00 0.00 - no Open
443 4.693852668046735 -0.811438 -26.2177 12 24 20 0.95 0.55 - no Current
420 5.195508061932922 -0.713708 -25.239 7 16 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 -26.218kcal/mol
Ligand efficiency (LE) -0.6722kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.977
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 39HA

Physicochemical properties
Molecular weight 569.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.15
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 75.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 19.70kcal/mol
Minimised FF energy -55.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 813.8Ų
Total solvent-accessible surface area of free ligand
BSA total 689.9Ų
Buried surface area upon binding
BSA apolar 497.6Ų
Hydrophobic contacts buried
BSA polar 192.3Ų
Polar contacts buried
Fraction buried 84.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1435.7Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 520.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)