FAIRMol

OHD_TB2020_48

Pose ID 4106 Compound 2887 Pose 43

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
T07
T. brucei PTR1 T. brucei
Ligand OHD_TB2020_48
PDB6RX6↗

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
63.6 kcal/mol
Protein clashes
3
Internal clashes
6
Native overlap
contact recall 0.84, Jaccard 0.64, H-bond role recall 0.60
Burial
73%
Hydrophobic fit
94%
Reason: 6 internal clashes, strain 63.6 kcal/mol
strain ΔE 63.6 kcal/mol 3 protein-contact clashes 6 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 -6.09) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (94%) ✗ Extreme strain energy (63.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (16)
Score
-25.088
kcal/mol
LE
-0.570
kcal/mol/HA
Fit Quality
-6.09
FQ (Leeson)
HAC
44
heavy atoms
MW
610
Da
LogP
0.40
cLogP
Strain ΔE
63.6 kcal/mol
SASA buried
73%
Lipo contact
94% BSA apolar/total
SASA unbound
955 Ų
Apolar buried
650 Ų

Interaction summary

HB 8 HY 24 PI 0 CLASH 6

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.105Score-25.088
Inter norm-0.696Intra norm0.126
Top1000noExcludedno
Contacts22H-bonds8
Artifact reasongeometry warning; 16 clashes; 6 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 63.4
Residues
ALA96 ARG14 ASN127 CYS168 GLU217 LEU208 LEU209 LYS178 LYS220 MET169 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER95 TRP221 TYR174 TYR98 VAL206 HIS267

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap16Native recall0.84
Jaccard0.64RMSD-
HB strict3Strict recall0.50
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
43 2.104977277935008 -0.696189 -25.0881 8 22 16 0.84 0.60 - no Current
57 3.0319147779755555 -0.733475 -27.4455 10 22 14 0.74 0.60 - no Open
38 4.2301654787057075 -0.557948 -22.6725 6 17 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 -25.088kcal/mol
Ligand efficiency (LE) -0.5702kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.092
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 44HA

Physicochemical properties
Molecular weight 609.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.40
Lipinski: ≤ 5
Rotatable bonds 11

Conformational strain (MMFF94s)
Strain energy (ΔE) 63.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -49.72kcal/mol
Minimised FF energy -113.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 955.0Ų
Total solvent-accessible surface area of free ligand
BSA total 694.8Ų
Buried surface area upon binding
BSA apolar 649.5Ų
Hydrophobic contacts buried
BSA polar 45.3Ų
Polar contacts buried
Fraction buried 72.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 93.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2019.6Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 941.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)