FAIRMol

NMT-TY0606

Pose ID 5695 Compound 2583 Pose 277

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 NMT-TY0606

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
40.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.48, Jaccard 0.38, H-bond role recall 0.17
Burial
85%
Hydrophobic fit
64%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.127 kcal/mol/HA) ✓ Good fit quality (FQ -10.24) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Extreme strain energy (40.2 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Internal clashes (9)
Score
-28.166
kcal/mol
LE
-1.127
kcal/mol/HA
Fit Quality
-10.24
FQ (Leeson)
HAC
25
heavy atoms
MW
383
Da
LogP
1.22
cLogP
Strain ΔE
40.2 kcal/mol
SASA buried
85%
Lipo contact
64% BSA apolar/total
SASA unbound
609 Ų
Apolar buried
330 Ų

Interaction summary

HB 10 HY 23 PI 2 CLASH 1

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 rank1.194Score-28.166
Inter norm-1.111Intra norm-0.016
Top1000noExcludedno
Contacts15H-bonds10
Artifact reasongeometry warning; 9 clashes; 7 protein contact clashes; high strain Δ 40.2
Residues
NDP301 ALA32 ARG48 ASP52 ILE182 ILE45 MET53 PHE56 SER44 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 overlap10Native recall0.48
Jaccard0.38RMSD-
HB strict0Strict recall0.00
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
277 1.1936033222892555 -1.11099 -28.1665 10 15 10 0.48 0.17 - no Current
300 1.8320490045581734 -0.9401 -25.4603 2 19 1 0.05 0.00 - no Open
287 2.8232451920098742 -1.2636 -31.8054 14 17 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 -28.166kcal/mol
Ligand efficiency (LE) -1.1267kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.242
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 383.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.22
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -67.59kcal/mol
Minimised FF energy -107.77kcal/mol

SASA & burial

✓ computed
SASA (unbound) 609.4Ų
Total solvent-accessible surface area of free ligand
BSA total 516.5Ų
Buried surface area upon binding
BSA apolar 330.3Ų
Hydrophobic contacts buried
BSA polar 186.1Ų
Polar contacts buried
Fraction buried 84.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3144.7Ų
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 1687.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)