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 strong
SASA done
Strain ΔE
17.0 kcal/mol
Protein clashes
0
Internal clashes
2
Native overlap
contact recall 0.68, Jaccard 0.68, H-bond role recall 0.40
Reason: no major geometry red flags detected
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.839 kcal/mol/HA)
✓ Good fit quality (FQ -14.73)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (96% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (17.0 kcal/mol)
✗ Geometry warnings
Score
-33.096
kcal/mol
LE
-1.839
kcal/mol/HA
Fit Quality
-14.73
FQ (Leeson)
HAC
18
heavy atoms
MW
250
Da
LogP
-0.28
cLogP
Interaction summary
HB 9
HY 11
PI 2
CLASH 2
Interaction summary
HB 9
HY 11
PI 2
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 | 0.359 | Score | -33.096 |
|---|---|---|---|
| Inter norm | -1.803 | Intra norm | -0.036 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 9 |
| Artifact reason | geometry warning; 3 clashes; 1 protein clash; 6 cofactor-context clashes | ||
| Residues |
ARG14
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE97
PRO210
SER207
SER95
TYR174
VAL206
| ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 51 | -0.03183588600961795 | -1.36389 | -23.1567 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 45 | 0.256907533078594 | -1.87501 | -34.3019 | 9 | 14 | 14 | 0.74 | 0.40 | - | no | Open |
| 58 | 0.358531789347295 | -1.80264 | -33.0958 | 9 | 13 | 13 | 0.68 | 0.40 | - | no | Current |
| 32 | 0.4809538120366504 | -1.47485 | -24.884 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 42 | 1.96128924357558 | -1.59674 | -26.8495 | 11 | 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
-33.096kcal/mol
Ligand efficiency (LE)
-1.8387kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-14.735
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
250.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.28
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-19.79kcal/mol
Minimised FF energy
-36.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
442.1Ų
Total solvent-accessible surface area of free ligand
BSA total
424.7Ų
Buried surface area upon binding
BSA apolar
315.9Ų
Hydrophobic contacts buried
BSA polar
108.8Ų
Polar contacts buried
Fraction buried
96.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1467.5Ų
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
917.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)