FAIRMol

Z56900576

Pose ID 3121 Compound 915 Pose 411

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
T05
L. major PTR1 L. major
Ligand Z56900576
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
51.2 kcal/mol
Protein clashes
4
Internal clashes
7
Native overlap
contact recall 0.82, Jaccard 0.74, H-bond role recall 0.33
Burial
92%
Hydrophobic fit
73%
Reason: 7 internal clashes, strain 51.2 kcal/mol
strain ΔE 51.2 kcal/mol 4 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.944 kcal/mol/HA) ✓ Good fit quality (FQ -8.58) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Extreme strain energy (51.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-23.596
kcal/mol
LE
-0.944
kcal/mol/HA
Fit Quality
-8.58
FQ (Leeson)
HAC
25
heavy atoms
MW
357
Da
LogP
2.90
cLogP
Final rank
3.5501
rank score
Inter norm
-1.139
normalised
Contacts
16
H-bonds 15
Strain ΔE
51.2 kcal/mol
SASA buried
92%
Lipo contact
73% BSA apolar/total
SASA unbound
557 Ų
Apolar buried
375 Ų

Interaction summary

HBD 4 HBA 3 HY 6 PI 3 CLASH 7

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap14Native recall0.82
Jaccard0.74RMSD-
HB strict3Strict recall0.43
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.40

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
454 0.30756688115420167 -1.2819 -34.2305 9 17 0 0.00 0.00 - no Open
498 2.275973682627344 -1.22007 -29.2064 5 18 0 0.00 0.00 - no Open
411 3.5501330490652308 -1.13882 -23.5963 15 16 14 0.82 0.33 - 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 -23.596kcal/mol
Ligand efficiency (LE) -0.9439kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.580
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 357.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.90
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 51.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 100.21kcal/mol
Minimised FF energy 49.01kcal/mol

SASA & burial

✓ computed
SASA (unbound) 557.4Ų
Total solvent-accessible surface area of free ligand
BSA total 513.6Ų
Buried surface area upon binding
BSA apolar 375.2Ų
Hydrophobic contacts buried
BSA polar 138.4Ų
Polar contacts buried
Fraction buried 92.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1567.2Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1028.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)