FAIRMol

GemmaOHDUnisi_41

Pose ID 14578 Compound 1416 Pose 340

DB SELECTIONDocking 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 GemmaOHDUnisi_41

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
15.0 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.81, Jaccard 0.61, H-bond role recall 0.36
Burial
84%
Hydrophobic fit
83%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 80% of hydrophobic surface is solvent-exposed (24/30 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 (-0.963 kcal/mol/HA) ✓ Good fit quality (FQ -9.71) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (15.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-33.709
kcal/mol
LE
-0.963
kcal/mol/HA
Fit Quality
-9.71
FQ (Leeson)
HAC
35
heavy atoms
MW
462
Da
LogP
6.37
cLogP
Strain ΔE
15.0 kcal/mol
SASA buried
84%
Lipo contact
83% BSA apolar/total
SASA unbound
755 Ų
Apolar buried
528 Ų

Interaction summary

HB 11 HY 4 PI 1 CLASH 6 ⚠ Exposure 80%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
80% of hydrophobic surface is solvent-exposed (24/30 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 30 Buried (contacted) 6 Exposed 24 LogP 6.37 H-bonds 11
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank4.601Score-33.709
Inter norm-0.941Intra norm-0.022
Top1000noExcludedno
Contacts24H-bonds11
Artifact reasongeometry warning; 15 clashes; 2 protein clashes
Residues
ALA156 ALA158 ALA70 ASN126 ASN41 ASP129 ASP68 GLN42 GLU73 GLY23 GLY25 GLY71 LEU130 LYS127 LYS128 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28 THR44 THR69

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

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 overlap17Native recall0.81
Jaccard0.61RMSD-
HB strict4Strict recall0.27
HB same residue+role4HB role recall0.36
HB same residue5HB residue recall0.45

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
360 1.9858794448475394 -0.60587 -22.5384 8 15 0 0.00 0.00 - no Open
310 2.215876786266132 -0.810312 -26.2423 7 20 0 0.00 0.00 - no Open
296 2.3735761215630813 -0.974129 -31.9318 5 22 0 0.00 0.00 - no Open
304 2.4109016880892273 -0.837854 -29.8668 7 13 0 0.00 0.00 - no Open
350 2.5106836985505296 -0.819328 -29.6374 5 17 0 0.00 0.00 - no Open
350 2.9414702362290113 -0.751309 -27.9819 5 17 0 0.00 0.00 - no Open
358 3.175808622050242 -0.595751 -15.5491 3 17 0 0.00 0.00 - no Open
421 3.3117905327030788 -0.65678 -23.4933 3 16 0 0.00 0.00 - no Open
340 3.408980607340969 -0.695149 -24.1764 7 10 0 0.00 0.00 - no Open
387 3.5593066442778185 -0.749818 -29.818 7 21 0 0.00 0.00 - no Open
384 3.6360066859245648 -0.841444 -26.102 8 16 0 0.00 0.00 - no Open
458 3.684952783737684 -0.836742 -25.2904 4 18 0 0.00 0.00 - no Open
341 4.458291848249892 -0.632747 -19.3542 9 19 0 0.00 0.00 - no Open
340 4.6006376252543095 -0.940685 -33.7094 11 24 17 0.81 0.36 - no Current
312 5.204738389636102 -0.790161 -23.6613 11 20 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 -33.709kcal/mol
Ligand efficiency (LE) -0.9631kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.715
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.37
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 99.04kcal/mol
Minimised FF energy 84.03kcal/mol

SASA & burial

✓ computed
SASA (unbound) 755.3Ų
Total solvent-accessible surface area of free ligand
BSA total 633.3Ų
Buried surface area upon binding
BSA apolar 528.2Ų
Hydrophobic contacts buried
BSA polar 105.1Ų
Polar contacts buried
Fraction buried 83.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1483.3Ų
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 509.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)