FAIRMol

Z2009870667

Pose ID 1936 Compound 1213 Pose 581

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
T03
L. major DHFR L. major
Ligand Z2009870667

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
25.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.80, Jaccard 0.64, H-bond role recall 0.20
Burial
85%
Hydrophobic fit
89%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.570 kcal/mol/HA) ✓ Good fit quality (FQ -5.99) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ High strain energy (25.9 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (15)
Score
-23.378
kcal/mol
LE
-0.570
kcal/mol/HA
Fit Quality
-5.99
FQ (Leeson)
HAC
41
heavy atoms
MW
586
Da
LogP
8.95
cLogP
Strain ΔE
25.9 kcal/mol
SASA buried
85%
Lipo contact
89% BSA apolar/total
SASA unbound
923 Ų
Apolar buried
696 Ų

Interaction summary

HB 2 HY 24 PI 1 CLASH 4

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 rank1.924Score-23.378
Inter norm-0.707Intra norm0.137
Top1000noExcludedno
Contacts21H-bonds2
Artifact reasongeometry warning; 15 clashes; 6 protein contact clashes; moderate strain Δ 25.7
Residues
ALA32 ARG48 ARG97 GLU216 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO50 PRO88 THR83 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49 VAL87

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
Jaccard0.64RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
581 1.9238030268576571 -0.706909 -23.3781 2 21 16 0.80 0.20 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -23.378kcal/mol
Ligand efficiency (LE) -0.5702kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.991
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 41HA

Physicochemical properties
Molecular weight 586.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) 8.95
Lipinski: ≤ 5
Rotatable bonds 13

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 67.00kcal/mol
Minimised FF energy 41.13kcal/mol

SASA & burial

✓ computed
SASA (unbound) 923.0Ų
Total solvent-accessible surface area of free ligand
BSA total 783.2Ų
Buried surface area upon binding
BSA apolar 696.4Ų
Hydrophobic contacts buried
BSA polar 86.8Ų
Polar contacts buried
Fraction buried 84.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1801.6Ų
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 848.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)