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 medium
Native strong
SASA done
Strain ΔE
19.9 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.42, H-bond role recall 0.60
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.220 kcal/mol/HA)
✓ Good fit quality (FQ -11.09)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Moderate strain (19.9 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (6)
Score
-30.498
kcal/mol
LE
-1.220
kcal/mol/HA
Fit Quality
-11.09
FQ (Leeson)
HAC
25
heavy atoms
MW
354
Da
LogP
2.02
cLogP
Interaction summary
HB 6
HY 24
PI 4
CLASH 3
Interaction summary
HB 6
HY 24
PI 4
CLASH 3
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 rank | 0.005 | Score | -30.498 |
|---|---|---|---|
| Inter norm | -1.379 | Intra norm | 0.159 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 6 clashes; 4 protein contact clashes; 1 severe cofactor-context clash | ||
| Residues |
ARG14
ASP161
CYS168
GLY205
LEU263
LYS224
MET163
NAP301
PHE97
PRO210
TRP221
TYR174
VAL206
ALA268
HIS267
| ||
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.42 | RMSD | - |
| HB strict | 4 | Strict recall | 0.67 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 37 | 0.004767659810388354 | -1.37861 | -30.4982 | 6 | 15 | 10 | 0.53 | 0.60 | - | no | Current |
| 30 | 2.6969487096829448 | -1.26117 | -31.2387 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 26 | 3.0481352297410775 | -0.910607 | -17.2426 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 3.230473428426704 | -0.987778 | -23.9638 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 3.8545254112429492 | -1.1403 | -20.7475 | 6 | 13 | 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
-30.498kcal/mol
Ligand efficiency (LE)
-1.2199kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.090
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
353.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.02
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-120.37kcal/mol
Minimised FF energy
-140.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
606.9Ų
Total solvent-accessible surface area of free ligand
BSA total
572.8Ų
Buried surface area upon binding
BSA apolar
485.5Ų
Hydrophobic contacts buried
BSA polar
87.3Ų
Polar contacts buried
Fraction buried
94.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1643.3Ų
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
921.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)