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 mixed
SASA done
Strain ΔE
18.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.39, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.536 kcal/mol/HA)
✓ Good fit quality (FQ -12.59)
✓ Good H-bonds (4 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (18.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
Score
-29.174
kcal/mol
LE
-1.536
kcal/mol/HA
Fit Quality
-12.59
FQ (Leeson)
HAC
19
heavy atoms
MW
308
Da
LogP
3.86
cLogP
Interaction summary
HB 4
HY 24
PI 4
CLASH 2
Interaction summary
HB 4
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 rank | -0.879 | Score | -29.174 |
|---|---|---|---|
| Inter norm | -1.594 | Intra norm | 0.059 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | geometry warning; 3 clashes; 2 protein contact clashes | ||
| Residues |
ARG14
ASN175
ASP161
CYS168
LYS178
MET163
NAP301
PHE171
PHE97
PRO167
SER95
TYR174
VAL164
| ||
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 | 9 | Native recall | 0.47 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 666 | -0.8794313331773516 | -1.59413 | -29.1739 | 4 | 13 | 9 | 0.47 | 0.00 | - | no | Current |
| 661 | 0.41553730051275123 | -1.39667 | -25.7584 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 663 | 0.6103829203165203 | -1.17145 | -22.0213 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 663 | 1.2061701241431626 | -1.35954 | -25.9347 | 6 | 15 | 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
-29.174kcal/mol
Ligand efficiency (LE)
-1.5355kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.586
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
308.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.71kcal/mol
Minimised FF energy
16.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
520.8Ų
Total solvent-accessible surface area of free ligand
BSA total
503.9Ų
Buried surface area upon binding
BSA apolar
341.9Ų
Hydrophobic contacts buried
BSA polar
161.9Ų
Polar contacts buried
Fraction buried
96.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1465.8Ų
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
929.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)