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
15.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.80
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.416 kcal/mol/HA)
✓ Good fit quality (FQ -12.69)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (15.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-33.976
kcal/mol
LE
-1.416
kcal/mol/HA
Fit Quality
-12.69
FQ (Leeson)
HAC
24
heavy atoms
MW
324
Da
LogP
3.45
cLogP
Interaction summary
HB 10
HY 24
PI 5
CLASH 2
Interaction summary
HB 10
HY 24
PI 5
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 | 1.891 | Score | -33.976 |
|---|---|---|---|
| Inter norm | -1.358 | Intra norm | -0.058 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 10 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; 1 severe cofactor-context clash | ||
| Residues |
ARG14
ASP161
CYS168
GLU217
LEU208
LEU209
MET163
MET213
NAP301
PHE171
PHE97
PRO210
TRP221
TYR174
| ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 4 | Strict recall | 0.67 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 387 | 0.36051882321163314 | -1.34004 | -29.2797 | 9 | 15 | 14 | 0.74 | 0.80 | - | no | Open |
| 417 | 1.8908796334170939 | -1.35793 | -33.9757 | 10 | 14 | 12 | 0.63 | 0.80 | - | no | Current |
| 435 | 1.9004749194382002 | -1.02058 | -25.9903 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 2.807878564222623 | -1.0264 | -24.6204 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 403 | 3.0441745044344053 | -1.17278 | -25.3923 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 3.272585015045708 | -1.014 | -21.3315 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 496 | 4.171712409869473 | -0.992234 | -24.6771 | 8 | 13 | 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
-33.976kcal/mol
Ligand efficiency (LE)
-1.4157kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.687
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
324.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.45
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.56kcal/mol
Minimised FF energy
50.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
519.4Ų
Total solvent-accessible surface area of free ligand
BSA total
485.2Ų
Buried surface area upon binding
BSA apolar
365.5Ų
Hydrophobic contacts buried
BSA polar
119.7Ų
Polar contacts buried
Fraction buried
93.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1535.0Ų
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
912.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)