FAIRMol

Z19456272

Pose ID 1184 Compound 100 Pose 506

DB fairmolDocking 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
T02
Human DHFR Human
Ligand Z19456272
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 medium Native strong SASA done
Strain ΔE
19.5 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.00
Burial
83%
Hydrophobic fit
63%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.659 kcal/mol/HA) ✓ Good fit quality (FQ -6.42) ✓ Good H-bonds (3 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Moderate strain (19.5 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Internal clashes (9)
Score
-20.440
kcal/mol
LE
-0.659
kcal/mol/HA
Fit Quality
-6.42
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Strain ΔE
19.5 kcal/mol
SASA buried
83%
Lipo contact
63% BSA apolar/total
SASA unbound
716 Ų
Apolar buried
375 Ų

Interaction summary

HB 3 HY 24 PI 3 CLASH 3

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
Final rank1.374Score-20.440
Inter norm-0.848Intra norm0.189
Top1000noExcludedno
Contacts19H-bonds3
Artifact reasongeometry warning; 9 clashes; 7 protein contact clashes; 1 cofactor-context clash
Residues
ALA10 ARG29 GLU31 ILE61 ILE8 LEU23 LEU28 LEU68 NAP201 PHE32 PHE35 PRO27 THR137 THR57 TRP25 TYR122 TYR34 VAL116 VAL9

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 overlap14Native recall0.67
Jaccard0.54RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

200 residues
Protein targetT02Atoms3128
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
458 0.27097943228209714 -0.811185 -19.6635 2 14 0 0.00 0.00 - no Open
513 0.9544730494110983 -0.848599 -22.718 5 16 13 0.62 0.00 - no Open
139 1.2196504051403532 -0.732121 -21.3242 5 16 0 0.00 0.00 - no Open
506 1.3741049807450607 -0.848148 -20.44 3 19 14 0.67 0.00 - no Current
114 1.8007768117229013 -0.767307 -20.1444 8 15 0 0.00 0.00 - no Open
131 1.8058017168282356 -0.940039 -24.6674 6 14 0 0.00 0.00 - no Open
117 2.0182178879377184 -0.829303 -24.0955 5 14 0 0.00 0.00 - no Open
485 2.0994881049338083 -0.856427 -22.7639 4 13 0 0.00 0.00 - no Open
105 2.2832214801183897 -0.874039 -22.0808 4 17 0 0.00 0.00 - no Open
453 2.83121549954444 -0.908661 -22.7336 12 15 0 0.00 0.00 - no Open
447 2.8591163001678837 -0.882026 -22.5359 9 16 0 0.00 0.00 - no Open
525 2.939096492500812 -0.773608 -21.4384 5 12 0 0.00 0.00 - no Open
64 2.9866007130431282 -0.949521 -25.285 13 16 0 0.00 0.00 - no Open
450 3.435617077931159 -1.00835 -28.0542 9 19 0 0.00 0.00 - no Open
91 3.5725886357035477 -0.950541 -26.1853 11 15 0 0.00 0.00 - no Open
89 3.588860201862459 -0.897555 -24.8412 10 10 0 0.00 0.00 - no Open
425 4.484716716621432 -0.989791 -28.8598 6 13 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 -20.440kcal/mol
Ligand efficiency (LE) -0.6594kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.424
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 28.89kcal/mol
Minimised FF energy 9.43kcal/mol

SASA & burial

✓ computed
SASA (unbound) 716.4Ų
Total solvent-accessible surface area of free ligand
BSA total 595.0Ų
Buried surface area upon binding
BSA apolar 374.9Ų
Hydrophobic contacts buried
BSA polar 220.1Ų
Polar contacts buried
Fraction buried 83.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1555.2Ų
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 602.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)