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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
10.5 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.74, Jaccard 0.67, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.052 kcal/mol/HA)
✓ Good fit quality (FQ -10.15)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Moderate strain (10.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (10)
Score
-31.574
kcal/mol
LE
-1.052
kcal/mol/HA
Fit Quality
-10.15
FQ (Leeson)
HAC
30
heavy atoms
MW
432
Da
LogP
5.94
cLogP
Final rank
0.5342
rank score
Inter norm
-1.021
normalised
Contacts
16
H-bonds 1
Interaction summary
HBD 1
HY 11
PI 6
CLASH 5
Interaction summary
HBD 1
HY 11
PI 6
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 380 | 0.5342419513750902 | -1.0207 | -31.5737 | 1 | 16 | 14 | 0.74 | 0.20 | - | no | Current |
| 411 | 0.6743617837883694 | -1.11254 | -34.3361 | 4 | 18 | 14 | 0.74 | 0.40 | - | no | Open |
| 438 | 0.896731816131236 | -0.79585 | -23.8324 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 458 | 1.9526431378011986 | -0.766456 | -24.4438 | 2 | 16 | 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
-31.574kcal/mol
Ligand efficiency (LE)
-1.0525kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.152
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
431.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.94
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.38kcal/mol
Minimised FF energy
88.90kcal/mol
SASA & burial
✓ computed
SASA (unbound)
677.5Ų
Total solvent-accessible surface area of free ligand
BSA total
621.2Ų
Buried surface area upon binding
BSA apolar
555.5Ų
Hydrophobic contacts buried
BSA polar
65.6Ų
Polar contacts buried
Fraction buried
91.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1746.0Ų
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
917.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)