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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
19.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.43, H-bond role recall 0.60
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.607 kcal/mol/HA)
✓ Good fit quality (FQ -13.18)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (88% SASA buried)
✗ Moderate strain (19.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-30.541
kcal/mol
LE
-1.607
kcal/mol/HA
Fit Quality
-13.18
FQ (Leeson)
HAC
19
heavy atoms
MW
292
Da
LogP
2.64
cLogP
Interaction summary
HB 8
HY 15
PI 1
CLASH 2
Interaction summary
HB 8
HY 15
PI 1
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 | 0.860 | Score | -30.541 |
|---|---|---|---|
| Inter norm | -1.840 | Intra norm | 0.233 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 8 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash; 1 severe cofactor-context clash | ||
| Residues |
ARG14
ASP161
LEU208
LEU209
LYS13
LYS178
NAP301
PHE97
PRO210
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 | 1 | Strict recall | 0.17 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 637 | -0.12491101091613598 | -1.50432 | -29.0327 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 0.859553254517949 | -1.84028 | -30.5415 | 8 | 11 | 9 | 0.47 | 0.60 | - | no | Current |
| 645 | 1.3544903360149785 | -1.49695 | -26.5081 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 644 | 1.6425695927885842 | -1.20951 | -21.2053 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 638 | 2.036705655377867 | -1.58228 | -28.5129 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 644 | 2.4572488566700317 | -1.44642 | -26.4617 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 632 | 2.5202235143508624 | -1.84946 | -32.4157 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 641 | 5.406612215688473 | -1.36205 | -24.0266 | 14 | 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
-30.541kcal/mol
Ligand efficiency (LE)
-1.6074kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.176
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
292.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.64
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.19kcal/mol
Minimised FF energy
28.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
478.7Ų
Total solvent-accessible surface area of free ligand
BSA total
423.8Ų
Buried surface area upon binding
BSA apolar
237.4Ų
Hydrophobic contacts buried
BSA polar
186.3Ų
Polar contacts buried
Fraction buried
88.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
56.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1365.1Ų
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
937.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)