FAIRMol

GemmaOHDUnisi_30

Pose ID 5765 Compound 2870 Pose 347

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
T09
L. major DHFR-TS L. major
Ligand GemmaOHDUnisi_30

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
10.3 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.17
Burial
85%
Hydrophobic fit
83%
Reason: 8 internal clashes
8 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.192 kcal/mol/HA) ✓ Good fit quality (FQ -10.16) ✓ Good H-bonds (5 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Moderate strain (10.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-25.023
kcal/mol
LE
-1.192
kcal/mol/HA
Fit Quality
-10.16
FQ (Leeson)
HAC
21
heavy atoms
MW
279
Da
LogP
3.48
cLogP
Strain ΔE
10.3 kcal/mol
SASA buried
85%
Lipo contact
83% BSA apolar/total
SASA unbound
515 Ų
Apolar buried
363 Ų

Interaction summary

HB 5 HY 24 PI 2 CLASH 0

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
No clash · clashes detected for this pose.
Final rank1.568Score-25.023
Inter norm-1.237Intra norm0.046
Top1000noExcludedno
Contacts15H-bonds5
Artifact reasongeometry warning; 8 clashes; 1 protein clash
Residues
NDP301 ALA32 ARG48 ASP52 GLY157 ILE45 MET53 PHE56 PRO50 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap11Native recall0.52
Jaccard0.44RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.17

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
320 0.25828970369132925 -1.52526 -28.4236 4 14 0 0.00 0.00 - no Open
347 1.5679916420256366 -1.23715 -25.0233 5 15 11 0.52 0.17 - no Current
312 1.7818278313920717 -1.4367 -27.5687 6 13 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 -25.023kcal/mol
Ligand efficiency (LE) -1.1916kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.164
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 279.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.48
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 62.75kcal/mol
Minimised FF energy 52.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 514.7Ų
Total solvent-accessible surface area of free ligand
BSA total 438.7Ų
Buried surface area upon binding
BSA apolar 363.3Ų
Hydrophobic contacts buried
BSA polar 75.4Ų
Polar contacts buried
Fraction buried 85.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3163.4Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1678.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)