FAIRMol

NMT-TY0931

Pose ID 5738 Compound 813 Pose 320

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-TY0931

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
44.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.17
Burial
89%
Hydrophobic fit
69%
Reason: strain 44.1 kcal/mol
strain ΔE 44.1 kcal/mol 5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.605 kcal/mol/HA) ✓ Good fit quality (FQ -14.38) ✓ Good H-bonds (5 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Extreme strain energy (44.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-38.523
kcal/mol
LE
-1.605
kcal/mol/HA
Fit Quality
-14.38
FQ (Leeson)
HAC
24
heavy atoms
MW
369
Da
LogP
1.63
cLogP
Final rank
3.2778
rank score
Inter norm
-1.326
normalised
Contacts
16
H-bonds 13
Strain ΔE
44.1 kcal/mol
SASA buried
89%
Lipo contact
69% BSA apolar/total
SASA unbound
566 Ų
Apolar buried
349 Ų

Interaction summary

HBD 2 HBA 3 HY 9 PI 2 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

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.
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 overlap11Native recall0.52
Jaccard0.42RMSD-
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
377 1.5996512594301042 -1.11817 -30.6457 6 14 0 0.00 0.00 - no Open
320 3.2777637337523795 -1.32557 -38.5235 13 16 11 0.52 0.17 - no Current
368 3.633649594796415 -0.947283 -24.2083 9 19 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 -38.523kcal/mol
Ligand efficiency (LE) -1.6051kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.385
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 369.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.63
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 44.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -57.75kcal/mol
Minimised FF energy -101.84kcal/mol

SASA & burial

✓ computed
SASA (unbound) 566.2Ų
Total solvent-accessible surface area of free ligand
BSA total 503.4Ų
Buried surface area upon binding
BSA apolar 348.8Ų
Hydrophobic contacts buried
BSA polar 154.6Ų
Polar contacts buried
Fraction buried 88.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3146.8Ų
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 1681.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)