FAIRMol

KB_HAT_25

Pose ID 1464 Compound 108 Pose 109

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 KB_HAT_25

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 strong SASA done
Strain ΔE
27.0 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.55, Jaccard 0.44, H-bond role recall 0.20
Burial
83%
Hydrophobic fit
76%
Reason: 13 internal clashes
13 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.665 kcal/mol/HA) ✓ Good fit quality (FQ -6.66) ✓ Good H-bonds (5 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ High strain energy (27.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-22.615
kcal/mol
LE
-0.665
kcal/mol/HA
Fit Quality
-6.66
FQ (Leeson)
HAC
34
heavy atoms
MW
476
Da
LogP
2.21
cLogP
Strain ΔE
27.0 kcal/mol
SASA buried
83%
Lipo contact
76% BSA apolar/total
SASA unbound
799 Ų
Apolar buried
507 Ų

Interaction summary

HB 5 HY 24 PI 2 CLASH 0
Final rank3.266Score-22.615
Inter norm-0.810Intra norm0.145
Top1000noExcludedno
Contacts16H-bonds5
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; moderate strain Δ 26.4
Residues
ARG48 ARG97 ASP52 ILE45 LEU94 LYS57 LYS95 MET53 PHE56 PHE91 PRO88 SER44 SER86 TRP47 VAL49 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 overlap11Native recall0.55
Jaccard0.44RMSD-
HB strict1Strict recall0.14
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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
116 0.9967124239667426 -0.835107 -24.9422 1 19 0 0.00 0.00 - no Open
145 1.3995751921199313 -0.88415 -27.5642 3 16 0 0.00 0.00 - no Open
182 1.4861130235883124 -0.855269 -26.7745 4 22 0 0.00 0.00 - no Open
140 1.615020829250697 -0.925503 -28.3157 6 17 1 0.05 0.00 - no Open
161 2.662027008092362 -0.751934 -23.4535 3 14 0 0.00 0.00 - no Open
149 3.0092960382301914 -0.757482 -21.0618 2 22 1 0.05 0.00 - no Open
117 3.133913752613804 -0.893126 -27.6382 10 20 0 0.00 0.00 - no Open
92 3.1897154297188073 -0.7343 -24.0617 7 15 0 0.00 0.00 - no Open
109 3.266242765469782 -0.81009 -22.6151 5 16 11 0.55 0.20 - no Current
95 3.6098926606982675 -0.795677 -23.8078 8 16 0 0.00 0.00 - no Open
150 3.6690791561020983 -0.768661 -24.4817 6 18 0 0.00 0.00 - no Open
91 3.8086261390469938 -0.740979 -20.0503 5 21 0 0.00 0.00 - no Open
124 4.692634237226219 -0.64544 -22.9491 7 15 0 0.00 0.00 - no Open
103 4.725842136853786 -0.76159 -22.4824 5 18 0 0.00 0.00 - no Open
118 4.790784883872673 -0.731769 -21.8142 8 17 0 0.00 0.00 - no Open
73 4.7962875837914805 -1.009 -30.2636 11 20 0 0.00 0.00 - no Open
46 5.044122438992116 -0.80531 -23.3978 7 15 0 0.00 0.00 - no Open
87 5.0598912182116695 -0.712441 -22.3133 4 21 1 0.05 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 -22.615kcal/mol
Ligand efficiency (LE) -0.6652kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.655
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 475.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 100.99kcal/mol
Minimised FF energy 74.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 798.8Ų
Total solvent-accessible surface area of free ligand
BSA total 665.4Ų
Buried surface area upon binding
BSA apolar 507.5Ų
Hydrophobic contacts buried
BSA polar 157.9Ų
Polar contacts buried
Fraction buried 83.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1623.1Ų
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 836.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)