FAIRMol

Z45614063

Pose ID 6054 Compound 2187 Pose 636

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
T09
L. major DHFR-TS L. major
Ligand Z45614063

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
22.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Burial
96%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.037 kcal/mol/HA) ✓ Good fit quality (FQ -9.29) ✓ Good H-bonds (3 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (22.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-24.881
kcal/mol
LE
-1.037
kcal/mol/HA
Fit Quality
-9.29
FQ (Leeson)
HAC
24
heavy atoms
MW
368
Da
LogP
2.43
cLogP
Final rank
3.1869
rank score
Inter norm
-1.059
normalised
Contacts
18
H-bonds 5
Strain ΔE
22.1 kcal/mol
SASA buried
96%
Lipo contact
71% BSA apolar/total
SASA unbound
604 Ų
Apolar buried
408 Ų

Interaction summary

HBD 1 HBA 2 HY 9 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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.
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 overlap13Native recall0.62
Jaccard0.50RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
663 1.8318066994046442 -1.12484 -23.824 10 15 0 0.00 0.00 - no Open
654 2.6135148345167436 -1.15722 -26.2556 8 17 0 0.00 0.00 - no Open
654 3.1427476690832297 -1.13387 -23.6503 5 19 0 0.00 0.00 - no Open
636 3.186904029274852 -1.05913 -24.8813 5 18 13 0.62 0.00 - no Current
657 3.9843393634997644 -1.39289 -29.5256 8 20 0 0.00 0.00 - no Open
659 5.110545450686871 -1.20698 -24.3241 10 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 -24.881kcal/mol
Ligand efficiency (LE) -1.0367kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.291
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 368.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.43
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -105.92kcal/mol
Minimised FF energy -128.00kcal/mol

SASA & burial

✓ computed
SASA (unbound) 603.9Ų
Total solvent-accessible surface area of free ligand
BSA total 576.5Ų
Buried surface area upon binding
BSA apolar 408.4Ų
Hydrophobic contacts buried
BSA polar 168.1Ų
Polar contacts buried
Fraction buried 95.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3188.8Ų
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 1666.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)