FAIRMol

NMT-TY0920

Pose ID 1721 Compound 544 Pose 366

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 NMT-TY0920

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 mixed SASA done
Strain ΔE
39.3 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.40, Jaccard 0.30, H-bond role recall 0.20
Burial
83%
Hydrophobic fit
74%
Reason: 12 internal clashes
12 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.174 kcal/mol/HA) ✓ Good fit quality (FQ -11.08) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (39.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-32.862
kcal/mol
LE
-1.174
kcal/mol/HA
Fit Quality
-11.08
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Final rank
3.3335
rank score
Inter norm
-1.043
normalised
Contacts
15
H-bonds 6
Strain ΔE
39.3 kcal/mol
SASA buried
83%
Lipo contact
74% BSA apolar/total
SASA unbound
669 Ų
Apolar buried
413 Ų

Interaction summary

HBD 2 HBA 4 HY 4 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
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 overlap8Native recall0.40
Jaccard0.30RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
302 0.5239567590025211 -1.18433 -30.604 9 13 0 0.00 0.00 - no Open
319 0.9940520654587742 -0.944043 -25.3008 5 13 0 0.00 0.00 - no Open
320 1.0669444827431311 -0.878088 -31.4505 3 16 1 0.05 0.00 - no Open
345 1.1134646347622539 -0.877657 -23.1229 3 15 0 0.00 0.00 - no Open
369 1.570299553280359 -0.935163 -25.1037 6 14 0 0.00 0.00 - no Open
285 1.846962516011115 -1.10054 -35.0271 11 16 0 0.00 0.00 - no Open
333 2.430240854014312 -0.961348 -34.1213 11 17 0 0.00 0.00 - no Open
313 2.7355217655896267 -0.945999 -28.0195 7 18 1 0.05 0.00 - no Open
388 3.1357764599548372 -1.01979 -35.0482 6 16 0 0.00 0.00 - no Open
366 3.33349022232488 -1.04252 -32.8619 6 15 8 0.40 0.20 - no Current
313 3.427850034969361 -1.24397 -30.3675 11 26 0 0.00 0.00 - no Open
342 3.492057571577017 -0.785111 -22.7794 9 15 0 0.00 0.00 - no Open
295 3.616137840018539 -0.981468 -32.0097 7 17 0 0.00 0.00 - no Open
437 3.855523120955258 -0.937716 -27.4849 10 13 0 0.00 0.00 - no Open
349 4.8296015227220686 -0.681525 -25.7042 8 9 0 0.00 0.00 - no Open
361 5.231781681702861 -0.899682 -33.3801 11 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 -32.862kcal/mol
Ligand efficiency (LE) -1.1736kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.080
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.31
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -23.02kcal/mol
Minimised FF energy -62.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 668.8Ų
Total solvent-accessible surface area of free ligand
BSA total 557.5Ų
Buried surface area upon binding
BSA apolar 412.8Ų
Hydrophobic contacts buried
BSA polar 144.8Ų
Polar contacts buried
Fraction buried 83.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1518.8Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 809.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)