FAIRMol

NMT-TY0957

Pose ID 1734 Compound 264 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
T03
L. major DHFR L. major
Ligand NMT-TY0957

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
29.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.80, Jaccard 0.70, H-bond role recall 0.20
Burial
91%
Hydrophobic fit
78%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.136 kcal/mol/HA) ✓ Good fit quality (FQ -10.72) ✓ Good H-bonds (5 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (29.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-31.797
kcal/mol
LE
-1.136
kcal/mol/HA
Fit Quality
-10.72
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.07
cLogP
Strain ΔE
29.7 kcal/mol
SASA buried
91%
Lipo contact
78% BSA apolar/total
SASA unbound
679 Ų
Apolar buried
482 Ų

Interaction summary

HB 5 HY 24 PI 2 CLASH 2
Final rank3.325Score-31.797
Inter norm-1.074Intra norm-0.061
Top1000noExcludedno
Contacts19H-bonds5
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; moderate strain Δ 29.7
Residues
ALA32 ARG92 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 PRO88 PRO93 THR54 TYR162 VAL30 VAL31 VAL87

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap16Native recall0.80
Jaccard0.70RMSD-
HB strict2Strict recall0.29
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
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 1 0.05 0.00 - no Open
403 1.7481430375200544 -0.991243 -27.3069 7 18 0 0.00 0.00 - no Open
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 0 0.00 0.00 - 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 16 0.80 0.20 - no Current
414 3.598164167482077 -0.922403 -23.4985 9 14 1 0.05 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 -31.797kcal/mol
Ligand efficiency (LE) -1.1356kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.720
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.07
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -79.18kcal/mol
Minimised FF energy -108.91kcal/mol

SASA & burial

✓ computed
SASA (unbound) 679.2Ų
Total solvent-accessible surface area of free ligand
BSA total 620.7Ų
Buried surface area upon binding
BSA apolar 481.8Ų
Hydrophobic contacts buried
BSA polar 138.9Ų
Polar contacts buried
Fraction buried 91.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1539.8Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 802.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)