FAIRMol

NMT-TY0920

Pose ID 5731 Compound 544 Pose 313

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 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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
29.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.00
Burial
89%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.001 kcal/mol/HA) ✓ Good fit quality (FQ -9.45) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ High strain energy (29.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-28.020
kcal/mol
LE
-1.001
kcal/mol/HA
Fit Quality
-9.45
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.48
cLogP
Strain ΔE
29.3 kcal/mol
SASA buried
89%
Lipo contact
76% BSA apolar/total
SASA unbound
626 Ų
Apolar buried
421 Ų

Interaction summary

HB 7 HY 24 PI 2 CLASH 3

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
Final rank2.736Score-28.020
Inter norm-0.946Intra norm-0.055
Top1000noExcludedno
Contacts18H-bonds7
Artifact reasongeometry warning; 12 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 29.3
Residues
NDP301 ALA32 ARG48 ASP52 ILE45 MET53 PHE56 PRO88 SER44 SER86 THR83 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49 VAL87

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 overlap14Native recall0.67
Jaccard0.56RMSD-
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
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 14 0.67 0.00 - no Current
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 0 0.00 0.00 - no Open
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 -28.020kcal/mol
Ligand efficiency (LE) -1.0007kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.447
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.48
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -26.00kcal/mol
Minimised FF energy -55.26kcal/mol

SASA & burial

✓ computed
SASA (unbound) 625.8Ų
Total solvent-accessible surface area of free ligand
BSA total 554.6Ų
Buried surface area upon binding
BSA apolar 420.9Ų
Hydrophobic contacts buried
BSA polar 133.7Ų
Polar contacts buried
Fraction buried 88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3229.9Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1667.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)