FAIRMol

NMT-TY0929

Pose ID 392 Compound 484 Pose 392

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
T01
Human DHFR Human
Ligand NMT-TY0929
PDB5SD8↗

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
29.7 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.48, Jaccard 0.38, H-bond role recall 0.20
Burial
76%
Hydrophobic fit
74%
Reason: 11 internal clashes
11 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.152 kcal/mol/HA) ✓ Good fit quality (FQ -10.75) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (29.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-31.102
kcal/mol
LE
-1.152
kcal/mol/HA
Fit Quality
-10.75
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
29.7 kcal/mol
SASA buried
76%
Lipo contact
74% BSA apolar/total
SASA unbound
635 Ų
Apolar buried
360 Ų

Interaction summary

HB 6 HY 24 PI 2 CLASH 0
Final rank2.769Score-31.102
Inter norm-1.122Intra norm-0.029
Top1000noExcludedno
Contacts15H-bonds6
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 29.7
Residues
ALA10 ARG29 GLU31 ILE8 LEU23 LEU28 NAP201 PHE32 PHE35 PRO27 THR137 TRP25 TYR122 TYR34 VAL9

Protein summary

200 residues
Protein targetT01Atoms3128
Residues200Chains2
Residue summaryLYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

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:NAP201

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5SD8Contacts21
PoseOpen native poseHB0
IFP residues
ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap10Native recall0.48
Jaccard0.38RMSD-
HB strict1Strict recall0.20
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
346 0.35538722495997677 -0.978913 -25.6036 2 13 0 0.00 0.00 - no Open
293 1.274900942951345 -1.03583 -28.5719 7 12 0 0.00 0.00 - no Open
323 1.3627403067812827 -0.906394 -18.7308 3 16 0 0.00 0.00 - no Open
375 2.0500114754417558 -1.04631 -29.6312 5 15 11 0.52 0.20 - no Open
318 2.0823117440239103 -1.13317 -28.9361 12 15 0 0.00 0.00 - no Open
322 2.294639162656896 -0.986167 -29.4161 5 20 0 0.00 0.00 - no Open
441 2.5220455662358785 -0.89302 -25.8372 8 15 0 0.00 0.00 - no Open
338 2.659289984590069 -0.997905 -24.9728 12 15 0 0.00 0.00 - no Open
392 2.7685730244744846 -1.12247 -31.1016 6 15 10 0.48 0.20 - no Current
333 3.6903577688505305 -0.859379 -21.1312 9 16 0 0.00 0.00 - no Open
343 3.8983164634663794 -0.849572 -21.6991 9 14 0 0.00 0.00 - no Open
372 3.9624227153920875 -1.10356 -28.0126 4 18 0 0.00 0.00 - no Open
282 4.021294943242523 -1.239 -35.8435 9 17 0 0.00 0.00 - no Open
316 4.705477255827921 -1.17836 -28.5533 9 21 0 0.00 0.00 - no Open
287 4.830955251729373 -1.16188 -25.6924 10 15 0 0.00 0.00 - no Open
353 5.092204702816937 -0.795238 -22.7627 7 12 0 0.00 0.00 - no Open
272 5.40909853377186 -0.937498 -19.6641 16 12 0 0.00 0.00 - no Open
409 5.703467463727863 -0.909529 -26.8524 10 16 0 0.00 0.00 - no Open
296 6.199766084150915 -1.0563 -30.5291 13 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 -31.102kcal/mol
Ligand efficiency (LE) -1.1519kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.747
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -31.61kcal/mol
Minimised FF energy -61.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 635.4Ų
Total solvent-accessible surface area of free ligand
BSA total 484.2Ų
Buried surface area upon binding
BSA apolar 360.4Ų
Hydrophobic contacts buried
BSA polar 123.8Ų
Polar contacts buried
Fraction buried 76.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1527.5Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 619.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)