Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
No SASA yet
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA missing
Strain ΔE
14.3 kcal/mol
Protein clashes
6
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.74, H-bond role recall 0.40
Reason: no major geometry red flags detected
6 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.219 kcal/mol/HA)
✓ Good fit quality (FQ -10.93)
✓ Strong H-bond network (13 bonds)
✗ Moderate strain (14.3 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (12)
ℹ SASA not computed
Score
-29.266
kcal/mol
LE
-1.219
kcal/mol/HA
Fit Quality
-10.93
FQ (Leeson)
HAC
24
heavy atoms
MW
365
Da
LogP
2.51
cLogP
Interaction summary
HB 13
HY 24
PI 4
CLASH 1
Interaction summary
HB 13
HY 24
PI 4
CLASH 1
| Final rank | 3.304 | Score | -29.266 |
|---|---|---|---|
| Inter norm | -1.190 | Intra norm | -0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 12 clashes; 6 protein contact clashes; moderate strain Δ 13.5 | ||
| Residues |
ARG14
ASP161
CYS168
LEU208
LEU209
MET213
NAP301
PHE171
PHE97
PRO210
SER95
TRP221
TYR174
VAL206
| ||
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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 14 | Native recall | 0.74 |
| Jaccard | 0.74 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
HB · H-bonds
Mode: permissive. 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 172 | 2.9583132347911665 | -1.20346 | -25.7588 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 119 | 3.0411416082296214 | -1.18879 | -29.0207 | 6 | 14 | 14 | 0.74 | 0.40 | - | no | Open |
| 117 | 3.3037872853401975 | -1.18971 | -29.2661 | 6 | 14 | 14 | 0.74 | 0.40 | - | no | Current |
| 170 | 4.451495078205778 | -1.16923 | -25.0891 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 118 | 5.18116131436111 | -1.15484 | -25.0514 | 7 | 12 | 12 | 0.63 | 0.40 | - | no | Open |
| 122 | 5.471817934988997 | -0.743153 | -15.0498 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 120 | 5.6539743183894 | -1.12904 | -24.6433 | 7 | 12 | 12 | 0.63 | 0.40 | - | no | Open |
| 171 | 4.618794082020386 | -1.18707 | -21.4229 | 11 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 173 | 54.02556249294625 | -1.20338 | -22.2631 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 123 | 59.382537021470505 | -0.878394 | -19.1316 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.266kcal/mol
Ligand efficiency (LE)
-1.2194kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.928
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
365.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.51
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-135.83kcal/mol
Minimised FF energy
-150.14kcal/mol
SASA & burial
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate SASA burial metrics without blocking the page.