FAIRMol

NMT-TY0623

Pose ID 379 Compound 343 Pose 379

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-TY0623
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
24.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.57, Jaccard 0.50, H-bond role recall 0.20
Burial
85%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.067 kcal/mol/HA) ✓ Good fit quality (FQ -10.19) ✓ Good H-bonds (5 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (24.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-30.952
kcal/mol
LE
-1.067
kcal/mol/HA
Fit Quality
-10.19
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
2.54
cLogP
Strain ΔE
24.5 kcal/mol
SASA buried
85%
Lipo contact
74% BSA apolar/total
SASA unbound
691 Ų
Apolar buried
430 Ų

Interaction summary

HB 5 HY 23 PI 3 CLASH 1
Final rank2.058Score-30.952
Inter norm-1.048Intra norm-0.019
Top1000noExcludedno
Contacts15H-bonds5
Artifact reasongeometry warning; 11 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 24.5
Residues
ALA10 ARG29 GLU31 GLY21 ILE8 LEU23 LEU28 NAP201 PHE32 PHE35 PRO27 SER60 THR57 VAL116 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 overlap12Native recall0.57
Jaccard0.50RMSD-
HB strict0Strict recall0.00
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
290 -0.07584312586851832 -1.13056 -32.0626 7 15 0 0.00 0.00 - no Open
322 0.30845358684249946 -0.891961 -22.9586 1 16 0 0.00 0.00 - no Open
277 0.7836269283764385 -0.966102 -28.607 8 17 0 0.00 0.00 - no Open
393 1.7697479735872257 -0.888141 -25.7806 6 15 0 0.00 0.00 - no Open
379 2.0583001140760584 -1.04849 -30.952 5 15 12 0.57 0.20 - no Current
424 2.557044498817305 -0.988533 -28.1895 8 17 0 0.00 0.00 - no Open
342 2.7977411127516505 -0.78462 -22.2614 10 10 0 0.00 0.00 - no Open
328 2.9974190872298045 -0.816997 -22.4353 4 15 0 0.00 0.00 - no Open
309 3.050671063739145 -0.980479 -28.998 6 18 0 0.00 0.00 - no Open
331 3.103020756997463 -0.788626 -21.3481 8 19 0 0.00 0.00 - no Open
353 3.2612201780631067 -1.05701 -30.407 7 17 0 0.00 0.00 - no Open
362 3.7208953487922924 -0.983933 -23.2803 7 17 13 0.62 0.80 - no Open
348 3.795992434048253 -0.864899 -26.6158 8 20 0 0.00 0.00 - no Open
289 3.87862843107247 -0.963867 -29.2468 8 19 0 0.00 0.00 - no Open
328 4.137080334224266 -0.976406 -27.277 12 18 0 0.00 0.00 - no Open
309 4.286815840501966 -0.801912 -23.8944 5 20 0 0.00 0.00 - no Open
269 4.88188196770325 -1.1395 -32.34 11 17 0 0.00 0.00 - no Open
255 5.815034729044303 -0.891682 -22.7371 13 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 -30.952kcal/mol
Ligand efficiency (LE) -1.0673kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.188
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.54
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -56.16kcal/mol
Minimised FF energy -80.63kcal/mol

SASA & burial

✓ computed
SASA (unbound) 690.8Ų
Total solvent-accessible surface area of free ligand
BSA total 584.7Ų
Buried surface area upon binding
BSA apolar 430.3Ų
Hydrophobic contacts buried
BSA polar 154.4Ų
Polar contacts buried
Fraction buried 84.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1576.5Ų
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 618.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)