FAIRMol

NMT-TY0957

Pose ID 403 Compound 264 Pose 403

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-TY0957
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
27.6 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.60
Burial
84%
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 (-0.975 kcal/mol/HA) ✓ Good fit quality (FQ -9.21) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (27.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-27.307
kcal/mol
LE
-0.975
kcal/mol/HA
Fit Quality
-9.21
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Strain ΔE
27.6 kcal/mol
SASA buried
84%
Lipo contact
74% BSA apolar/total
SASA unbound
660 Ų
Apolar buried
406 Ų

Interaction summary

HB 7 HY 24 PI 1 CLASH 2
Final rank1.748Score-27.307
Inter norm-0.991Intra norm0.016
Top1000noExcludedno
Contacts18H-bonds7
Artifact reasongeometry warning; 10 clashes; 1 protein clash; 4 cofactor-context clashes; moderate strain Δ 27.3
Residues
ALA10 ASP22 GLU31 GLY117 GLY21 ILE8 LEU23 NAP201 PHE32 PHE35 PRO26 PRO27 PRO62 SER60 TRP25 TYR122 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 overlap15Native recall0.71
Jaccard0.62RMSD-
HB strict3Strict recall0.60
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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
349 0.7278409086070636 -0.881455 -21.5148 2 14 0 0.00 0.00 - no Open
311 1.3229509224018154 -1.16017 -29.6884 9 15 0 0.00 0.00 - no Open
334 1.51730203346956 -0.851135 -24.9989 8 16 0 0.00 0.00 - no Open
335 1.7260732089299 -0.999198 -26.3291 6 21 0 0.00 0.00 - no Open
403 1.7481430375200544 -0.991243 -27.3069 7 18 15 0.71 0.60 - no Current
347 2.3447902198011827 -0.753436 -19.3121 7 15 0 0.00 0.00 - no Open
389 2.786111419208295 -1.0956 -28.7016 6 16 12 0.57 0.40 - no Open
289 3.0086401503696756 -1.24814 -30.9089 9 21 0 0.00 0.00 - no Open
301 3.1451083125642456 -1.02377 -27.2511 8 23 0 0.00 0.00 - no Open
357 3.2475516904388395 -0.897972 -24.0584 9 11 0 0.00 0.00 - no Open
377 3.304488419434868 -0.914277 -26.47 6 16 0 0.00 0.00 - no Open
379 3.3253823915120413 -1.07446 -31.7967 5 19 0 0.00 0.00 - no Open
414 3.598164167482077 -0.922403 -23.4985 9 14 0 0.00 0.00 - no Open
332 3.624289409705216 -0.937648 -25.3511 7 11 0 0.00 0.00 - no Open
330 4.212597954691834 -0.897031 -24.2894 4 14 0 0.00 0.00 - no Open
451 4.456710646262987 -0.898418 -22.7057 8 16 0 0.00 0.00 - no Open
324 5.157273396991818 -1.11879 -29.0355 13 26 0 0.00 0.00 - no Open
284 5.171548217517241 -0.94018 -23.463 14 15 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 -27.307kcal/mol
Ligand efficiency (LE) -0.9752kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.207
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.31
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -59.84kcal/mol
Minimised FF energy -87.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 659.8Ų
Total solvent-accessible surface area of free ligand
BSA total 551.8Ų
Buried surface area upon binding
BSA apolar 406.4Ų
Hydrophobic contacts buried
BSA polar 145.4Ų
Polar contacts buried
Fraction buried 83.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1552.2Ų
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 623.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)