FAIRMol

KB_chagas_16

Pose ID 4193 Compound 1371 Pose 130

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 KB_chagas_16
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
20.4 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.75, H-bond role recall 0.60
Burial
93%
Hydrophobic fit
86%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.232 kcal/mol/HA) ✓ Good fit quality (FQ -11.20) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ High strain energy (20.4 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (13)
Score
-30.812
kcal/mol
LE
-1.232
kcal/mol/HA
Fit Quality
-11.20
FQ (Leeson)
HAC
25
heavy atoms
MW
344
Da
LogP
1.35
cLogP
Strain ΔE
20.4 kcal/mol
SASA buried
93%
Lipo contact
86% BSA apolar/total
SASA unbound
589 Ų
Apolar buried
475 Ų

Interaction summary

HB 10 HY 24 PI 4 CLASH 2

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 rank1.003Score-30.812
Inter norm-1.228Intra norm-0.004
Top1000noExcludedno
Contacts16H-bonds10
Artifact reasongeometry warning; 13 clashes; 4 protein contact clashes; 4 cofactor-context clashes; moderate strain Δ 20.4
Residues
ARG14 ASP161 CYS168 GLU217 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE97 PRO210 SER95 TRP221 TYR174 VAL206

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 overlap15Native recall0.79
Jaccard0.75RMSD-
HB strict4Strict recall0.67
HB same residue+role3HB role recall0.60
HB same residue4HB residue recall0.80

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
130 1.0027683112845442 -1.22842 -30.8121 10 16 15 0.79 0.60 - no Current
139 1.357070151489854 -0.905977 -15.7844 6 18 0 0.00 0.00 - no Open
155 3.106656649132985 -1.08871 -24.2879 9 18 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 -30.812kcal/mol
Ligand efficiency (LE) -1.2325kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.204
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.35
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -131.95kcal/mol
Minimised FF energy -152.31kcal/mol

SASA & burial

✓ computed
SASA (unbound) 589.0Ų
Total solvent-accessible surface area of free ligand
BSA total 550.3Ų
Buried surface area upon binding
BSA apolar 475.3Ų
Hydrophobic contacts buried
BSA polar 75.0Ų
Polar contacts buried
Fraction buried 93.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1648.5Ų
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 914.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)