FAIRMol

OHD_TbNat_126

Pose ID 96 Compound 432 Pose 96

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 OHD_TbNat_126
PDB5SD8↗

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
26.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.81, Jaccard 0.71, H-bond role recall 0.00
Burial
87%
Hydrophobic fit
91%
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 (-0.519 kcal/mol/HA) ✓ Good fit quality (FQ -5.61) ✓ Good H-bonds (3 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ High strain energy (26.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (21)
Score
-23.898
kcal/mol
LE
-0.519
kcal/mol/HA
Fit Quality
-5.61
FQ (Leeson)
HAC
46
heavy atoms
MW
623
Da
LogP
4.24
cLogP
Strain ΔE
26.0 kcal/mol
SASA buried
87%
Lipo contact
91% BSA apolar/total
SASA unbound
843 Ų
Apolar buried
669 Ų

Interaction summary

HB 3 HY 24 PI 3 CLASH 4
Final rank2.490Score-23.898
Inter norm-0.560Intra norm0.041
Top1000noExcludedno
Contacts20H-bonds3
Artifact reasongeometry warning; 21 clashes; 5 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 26.0
Residues
ALA10 ARG29 ASN65 ASP22 GLU31 ILE61 ILE8 LEU23 LEU28 LEU68 NAP201 PHE32 PHE35 PRO27 PRO62 SER60 THR57 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 overlap17Native recall0.81
Jaccard0.71RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
88 2.107196163600904 -0.570982 -14.5556 0 18 16 0.76 0.00 - no Open
84 2.3322273296990996 -0.415063 -18.7308 3 12 0 0.00 0.00 - no Open
96 2.4902473371946754 -0.560498 -23.8982 3 20 17 0.81 0.00 - 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 -23.898kcal/mol
Ligand efficiency (LE) -0.5195kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.607
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 46HA

Physicochemical properties
Molecular weight 622.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.24
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 227.51kcal/mol
Minimised FF energy 201.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 843.2Ų
Total solvent-accessible surface area of free ligand
BSA total 734.1Ų
Buried surface area upon binding
BSA apolar 669.1Ų
Hydrophobic contacts buried
BSA polar 65.0Ų
Polar contacts buried
Fraction buried 87.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1868.9Ų
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 586.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)