FAIRMol

OHD_MAC_3

Pose ID 14579 Compound 394 Pose 341

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 OHD_MAC_3

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
43.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.36
Burial
76%
Hydrophobic fit
79%
Reason: strain 43.9 kcal/mol
strain ΔE 43.9 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 52% of hydrophobic surface appears solvent-exposed (13/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.828 kcal/mol/HA) ✓ Good fit quality (FQ -8.47) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Extreme strain energy (43.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (18)
Score
-30.616
kcal/mol
LE
-0.828
kcal/mol/HA
Fit Quality
-8.47
FQ (Leeson)
HAC
37
heavy atoms
MW
496
Da
LogP
3.70
cLogP
Final rank
3.9446
rank score
Inter norm
-0.823
normalised
Contacts
19
H-bonds 13
Strain ΔE
43.9 kcal/mol
SASA buried
76%
Lipo contact
79% BSA apolar/total
SASA unbound
790 Ų
Apolar buried
478 Ų

Interaction summary

HBD 3 HBA 4 HY 3 PI 1 CLASH 3

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

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: 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 overlap14Native recall0.67
Jaccard0.54RMSD-
HB strict4Strict recall0.27
HB same residue+role4HB role recall0.36
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
316 1.8123558888823286 -0.914971 -21.5319 11 16 0 0.00 0.00 - no Open
297 1.9627077011111906 -0.856269 -30.9159 7 17 0 0.00 0.00 - no Open
418 2.3141715410362105 -0.726701 -18.6058 6 19 0 0.00 0.00 - no Open
355 2.726833739982142 -0.713638 -21.039 6 16 0 0.00 0.00 - no Open
424 3.1850901586862492 -0.660276 -18.3491 3 15 0 0.00 0.00 - no Open
343 3.3671400095098463 -0.659786 -18.405 6 13 0 0.00 0.00 - no Open
403 3.4226305072552163 -0.802117 -22.9256 6 20 0 0.00 0.00 - no Open
341 3.944633688462524 -0.82259 -30.6165 13 19 14 0.67 0.36 - no Current
361 4.005889507463297 -0.627719 -10.5556 4 17 0 0.00 0.00 - no Open
297 5.174209118778855 -0.756161 -20.4707 15 17 0 0.00 0.00 - no Open
461 5.260205083426885 -0.657307 -17.5204 7 19 0 0.00 0.00 - no Open
390 5.533655050515578 -0.807189 -28.3864 11 22 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 -30.616kcal/mol
Ligand efficiency (LE) -0.8275kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.472
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 37HA

Physicochemical properties
Molecular weight 496.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.70
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 141.41kcal/mol
Minimised FF energy 97.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 790.3Ų
Total solvent-accessible surface area of free ligand
BSA total 604.3Ų
Buried surface area upon binding
BSA apolar 477.8Ų
Hydrophobic contacts buried
BSA polar 126.5Ų
Polar contacts buried
Fraction buried 76.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1439.2Ų
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 527.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)