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 mixed
SASA done
Strain ΔE
6.2 kcal/mol
Protein clashes
1
Internal clashes
4
Native overlap
contact recall 0.47, Jaccard 0.43, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (6.2 kcal/mol)
✓ Excellent LE (-1.502 kcal/mol/HA)
✓ Good fit quality (FQ -12.56)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-30.030
kcal/mol
LE
-1.502
kcal/mol/HA
Fit Quality
-12.56
FQ (Leeson)
HAC
20
heavy atoms
MW
271
Da
LogP
2.23
cLogP
Interaction summary
HB 7
HY 16
PI 1
CLASH 4
Interaction summary
HB 7
HY 16
PI 1
CLASH 4
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 | 0.800 | Score | -30.030 |
|---|---|---|---|
| Inter norm | -1.683 | Intra norm | 0.182 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 7 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; 1 severe cofactor-context clash | ||
| Residues |
ARG14
ASP161
LEU208
LEU209
LYS13
NAP301
PHE97
PRO210
SER95
TYR174
VAL211
| ||
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 | 0.43 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 521 | -0.07895923437601685 | -1.64823 | -27.6509 | 6 | 17 | 15 | 0.79 | 0.40 | - | no | Open |
| 521 | 0.6898490708952878 | -1.39958 | -22.7449 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 528 | 0.7995282429380937 | -1.68304 | -30.0302 | 7 | 11 | 9 | 0.47 | 0.40 | - | no | Current |
| 537 | 0.9000688127635621 | -1.5798 | -28.6387 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 555 | 1.898156266383085 | -1.19422 | -20.9939 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 2.174966198704028 | -1.36094 | -22.3096 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 537 | 3.7603426496280146 | -1.12156 | -19.3209 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 3.9775243006343235 | -1.42387 | -26.5144 | 9 | 19 | 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
-30.030kcal/mol
Ligand efficiency (LE)
-1.5015kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.565
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
271.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.23
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
6.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
70.19kcal/mol
Minimised FF energy
64.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
495.3Ų
Total solvent-accessible surface area of free ligand
BSA total
426.7Ų
Buried surface area upon binding
BSA apolar
338.7Ų
Hydrophobic contacts buried
BSA polar
88.0Ų
Polar contacts buried
Fraction buried
86.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1498.1Ų
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
952.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)