FAIRMol

NMT-TY0959

Pose ID 405 Compound 527 Pose 405

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-TY0959
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
29.1 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.40
Burial
80%
Hydrophobic fit
73%
Reason: 11 internal clashes
11 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.106 kcal/mol/HA) ✓ Good fit quality (FQ -10.32) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (29.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-29.865
kcal/mol
LE
-1.106
kcal/mol/HA
Fit Quality
-10.32
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
29.1 kcal/mol
SASA buried
80%
Lipo contact
73% BSA apolar/total
SASA unbound
650 Ų
Apolar buried
379 Ų

Interaction summary

HB 6 HY 24 PI 3 CLASH 0
Final rank2.981Score-29.865
Inter norm-1.183Intra norm0.077
Top1000noExcludedno
Contacts15H-bonds6
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 29.1
Residues
ALA10 ARG29 ASN65 GLU31 ILE8 LEU23 LEU28 NAP201 PHE32 PHE35 PRO27 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 overlap11Native recall0.52
Jaccard0.44RMSD-
HB strict1Strict recall0.20
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
350 0.3629211958252925 -0.926251 -24.8853 2 13 0 0.00 0.00 - no Open
308 0.8712687604222177 -1.14475 -30.9484 7 15 0 0.00 0.00 - no Open
313 1.3142726160638258 -1.30957 -33.6603 12 15 0 0.00 0.00 - no Open
337 1.7652358533706136 -0.983958 -24.6706 6 21 0 0.00 0.00 - no Open
326 1.9773175739360493 -1.1336 -31.1195 10 21 0 0.00 0.00 - no Open
291 2.165473959343045 -1.26034 -34.3636 9 22 0 0.00 0.00 - no Open
301 2.480529293523874 -1.03512 -28.7525 9 12 0 0.00 0.00 - no Open
391 2.9008417563283935 -1.06217 -28.0759 7 15 11 0.52 0.80 - no Open
405 2.9806369013586718 -1.18262 -29.8648 6 15 11 0.52 0.40 - no Current
381 3.0321874169205607 -1.08611 -28.6887 6 16 0 0.00 0.00 - no Open
379 3.2808649478445537 -0.969429 -25.6956 10 17 0 0.00 0.00 - no Open
332 3.3588118370115048 -1.08116 -27.9486 7 17 0 0.00 0.00 - no Open
416 3.387046221950613 -0.924839 -25.7132 8 13 0 0.00 0.00 - no Open
334 3.429500560915679 -1.04914 -24.4852 8 15 0 0.00 0.00 - no Open
349 3.654496302035269 -0.850128 -21.98 8 14 0 0.00 0.00 - no Open
302 3.8731875216797746 -1.1408 -30.4082 8 22 0 0.00 0.00 - no Open
286 4.0813402406540185 -0.908062 -25.3939 13 15 0 0.00 0.00 - no Open
358 4.09740218547716 -0.710564 -18.8071 6 10 0 0.00 0.00 - no Open
336 4.132326379777683 -0.942975 -24.3804 7 17 0 0.00 0.00 - no Open
453 4.769829786717276 -1.02855 -27.026 8 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 -29.865kcal/mol
Ligand efficiency (LE) -1.1061kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.320
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) 29.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -55.26kcal/mol
Minimised FF energy -84.36kcal/mol

SASA & burial

✓ computed
SASA (unbound) 649.9Ų
Total solvent-accessible surface area of free ligand
BSA total 516.9Ų
Buried surface area upon binding
BSA apolar 378.9Ų
Hydrophobic contacts buried
BSA polar 138.1Ų
Polar contacts buried
Fraction buried 79.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1541.2Ų
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 625.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)