Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
26.5 kcal/mol
Protein clashes
11
Internal clashes
11
Native overlap
contact recall 0.68, Jaccard 0.52, H-bond role recall 0.20
Reason: 11 protein-contact clashes, 11 internal clashes
11 protein-contact clashes
11 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.001 kcal/mol/HA)
✓ Good fit quality (FQ -9.55)
✓ Good H-bonds (3 bonds)
✓ Deep burial (98% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (26.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-29.022
kcal/mol
LE
-1.001
kcal/mol/HA
Fit Quality
-9.55
FQ (Leeson)
HAC
29
heavy atoms
MW
406
Da
LogP
3.74
cLogP
Final rank
3.9467
rank score
Inter norm
-1.134
normalised
Contacts
19
H-bonds 5
Interaction summary
HBA 3
HY 10
PI 4
CLASH 11
Interaction summary
HBA 3
HY 10
PI 4
CLASH 11
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.
| 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 | 13 | Native recall | 0.68 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 127 | 3.127858519265289 | -0.653635 | -14.5608 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 122 | 3.471987782665667 | -1.11657 | -28.4331 | 5 | 19 | 13 | 0.68 | 0.20 | - | no | Open |
| 96 | 3.9466631181326814 | -1.13422 | -29.022 | 5 | 19 | 13 | 0.68 | 0.20 | - | no | Current |
| 137 | 4.20025134010485 | -0.854363 | -22.8507 | 10 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 70 | 5.716832078836834 | -0.961696 | -23.7608 | 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
-29.022kcal/mol
Ligand efficiency (LE)
-1.0008kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.553
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
406.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.74
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
47.22kcal/mol
Minimised FF energy
20.74kcal/mol
SASA & burial
✓ computed
SASA (unbound)
652.5Ų
Total solvent-accessible surface area of free ligand
BSA total
643.0Ų
Buried surface area upon binding
BSA apolar
478.6Ų
Hydrophobic contacts buried
BSA polar
164.4Ų
Polar contacts buried
Fraction buried
98.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1614.0Ų
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
922.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)