FAIRMol

TC491

Pose ID 1648 Compound 552 Pose 293

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
T03
L. major DHFR L. major
Ligand TC491

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
38.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.60, Jaccard 0.48, H-bond role recall 0.00
Burial
90%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.661 kcal/mol/HA) ✓ Good fit quality (FQ -6.77) ✓ Good H-bonds (4 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Very high strain energy (38.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (18)
Score
-24.460
kcal/mol
LE
-0.661
kcal/mol/HA
Fit Quality
-6.77
FQ (Leeson)
HAC
37
heavy atoms
MW
501
Da
LogP
4.88
cLogP
Final rank
3.3208
rank score
Inter norm
-0.781
normalised
Contacts
17
H-bonds 6
Strain ΔE
38.0 kcal/mol
SASA buried
90%
Lipo contact
85% BSA apolar/total
SASA unbound
813 Ų
Apolar buried
622 Ų

Interaction summary

HBD 2 HBA 2 HY 8 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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: permissive.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap12Native recall0.60
Jaccard0.48RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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
294 1.245508240700725 -0.728849 -25.9836 5 20 0 0.00 0.00 - no Open
346 1.930187225320806 -0.655486 -21.8232 3 17 0 0.00 0.00 - no Open
313 3.2272343925835325 -0.816086 -23.0339 7 22 0 0.00 0.00 - no Open
293 3.3208224858699698 -0.781481 -24.4604 6 17 12 0.60 0.00 - no Current
290 3.749228973927113 -0.629948 -20.9201 5 12 0 0.00 0.00 - no Open
194 3.909806676956081 -0.745338 -25.6544 8 15 0 0.00 0.00 - no Open
374 4.34931664373597 -0.650967 -19.125 6 15 0 0.00 0.00 - no Open
179 5.697827032796828 -0.75975 -24.0093 14 18 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 -24.460kcal/mol
Ligand efficiency (LE) -0.6611kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.768
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 37HA

Physicochemical properties
Molecular weight 500.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.88
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 135.73kcal/mol
Minimised FF energy 97.69kcal/mol

SASA & burial

✓ computed
SASA (unbound) 812.6Ų
Total solvent-accessible surface area of free ligand
BSA total 732.4Ų
Buried surface area upon binding
BSA apolar 622.2Ų
Hydrophobic contacts buried
BSA polar 110.2Ų
Polar contacts buried
Fraction buried 90.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1704.9Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 800.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)