FAIRMol

Z55694322

Pose ID 14879 Compound 256 Pose 641

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 Z55694322

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
45.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.86, Jaccard 0.78, H-bond role recall 0.45
Burial
83%
Hydrophobic fit
80%
Reason: strain 45.0 kcal/mol
strain ΔE 45.0 kcal/mol 4 protein-contact clashes 4 intramolecular clashes 60% of hydrophobic surface is solvent-exposed (15/25 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.026 kcal/mol/HA) ✓ Good fit quality (FQ -10.18) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (45.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-33.859
kcal/mol
LE
-1.026
kcal/mol/HA
Fit Quality
-10.18
FQ (Leeson)
HAC
33
heavy atoms
MW
460
Da
LogP
5.10
cLogP
Strain ΔE
45.0 kcal/mol
SASA buried
83%
Lipo contact
80% BSA apolar/total
SASA unbound
706 Ų
Apolar buried
467 Ų

Interaction summary

HB 9 HY 6 PI 1 CLASH 4 ⚠ Exposure 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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (15/25 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 25 Buried (contacted) 10 Exposed 15 LogP 5.1 H-bonds 9
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank5.605Score-33.859
Inter norm-1.113Intra norm0.087
Top1000noExcludedno
Contacts20H-bonds9
Artifact reasongeometry warning; 16 clashes; 3 protein clashes; high strain Δ 45.0
Residues
ALA158 ALA24 ASN126 ASN41 ASP129 GLN42 GLU21 GLU43 GLU73 GLY23 GLY25 LEU130 LYS127 LYS159 LYS26 PHE38 SER22 SER27 SER28 THR44

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 overlap18Native recall0.86
Jaccard0.78RMSD-
HB strict7Strict recall0.47
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
620 0.9124878828115518 -0.742763 -23.1308 0 15 0 0.00 0.00 - no Open
616 1.5903297613763936 -0.695296 -20.3004 1 17 0 0.00 0.00 - no Open
617 1.6999776302048877 -0.781972 -26.1696 4 14 0 0.00 0.00 - no Open
606 2.1579267805035065 -0.935582 -30.0151 4 17 0 0.00 0.00 - no Open
619 2.321598553519423 -0.843726 -27.1331 2 17 0 0.00 0.00 - no Open
611 2.3721997365242466 -0.744991 -19.006 2 19 0 0.00 0.00 - no Open
632 2.5845937659195366 -0.808096 -24.1504 9 17 0 0.00 0.00 - no Open
628 3.0667722052197655 -0.693175 -22.2941 6 15 0 0.00 0.00 - no Open
615 3.648743788972634 -0.72495 -21.5538 6 19 0 0.00 0.00 - no Open
629 4.069678458429272 -0.67542 -22.0358 6 19 0 0.00 0.00 - no Open
630 4.138721914791422 -0.806706 -25.3439 5 18 1 0.05 0.00 - no Open
616 5.015225112007658 -0.909212 -28.7073 9 17 0 0.00 0.00 - no Open
641 5.605204418092712 -1.11254 -33.8589 9 20 18 0.86 0.45 - no Current
631 5.82846986775583 -0.854024 -26.3807 7 19 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 -33.859kcal/mol
Ligand efficiency (LE) -1.0260kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.180
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 459.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.10
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 45.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 62.78kcal/mol
Minimised FF energy 17.73kcal/mol

SASA & burial

✓ computed
SASA (unbound) 706.4Ų
Total solvent-accessible surface area of free ligand
BSA total 585.1Ų
Buried surface area upon binding
BSA apolar 466.9Ų
Hydrophobic contacts buried
BSA polar 118.2Ų
Polar contacts buried
Fraction buried 82.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1449.4Ų
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 501.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)