Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
15.4 kcal/mol
Protein clashes
2
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.62, H-bond role recall 0.80
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.200 kcal/mol/HA)
✓ Good fit quality (FQ -11.05)
✓ Deep burial (98% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (15.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (9)
Score
-31.197
kcal/mol
LE
-1.200
kcal/mol/HA
Fit Quality
-11.05
FQ (Leeson)
HAC
26
heavy atoms
MW
351
Da
LogP
0.96
cLogP
Final rank
0.1533
rank score
Inter norm
-1.283
normalised
Contacts
20
H-bonds 11
Interaction summary
HBD 1
HBA 1
HY 9
PI 2
CLASH 1
Interaction summary
HBD 1
HBA 1
HY 9
PI 2
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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: strict.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
SER207
SER95
TRP221
TYR174
TYR98
VAL206
| ||
| Current overlap | 15 | Native recall | 0.79 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 5 | HB residue recall | 1.00 |
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| Residue summary | LEU: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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 246 | 0.05212297211422521 | -1.26728 | -31.9198 | 9 | 20 | 15 | 0.79 | 0.80 | - | no | Open |
| 245 | 0.15333775693127674 | -1.28287 | -31.1967 | 11 | 20 | 15 | 0.79 | 0.80 | - | no | Current |
| 251 | 0.375190949082224 | -1.10388 | -27.2108 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 269 | 2.030229846488461 | -0.847474 | -16.4266 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 263 | 2.036323288363696 | -1.19848 | -25.4194 | 11 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 239 | 3.0498119327730224 | -1.07349 | -27.244 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.197kcal/mol
Ligand efficiency (LE)
-1.1999kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.055
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
351.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.96
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.79kcal/mol
Minimised FF energy
71.39kcal/mol
SASA & burial
✓ computed
SASA (unbound)
596.0Ų
Total solvent-accessible surface area of free ligand
BSA total
586.4Ų
Buried surface area upon binding
BSA apolar
469.0Ų
Hydrophobic contacts buried
BSA polar
117.4Ų
Polar contacts buried
Fraction buried
98.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1603.4Ų
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
921.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)