Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.078 kcal/mol/HA)
✓ Good fit quality (FQ -10.29)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (21.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-31.259
kcal/mol
LE
-1.078
kcal/mol/HA
Fit Quality
-10.29
FQ (Leeson)
HAC
29
heavy atoms
MW
408
Da
LogP
3.67
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 21.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 22
π–π 3
Clashes 8
Severe clashes 0
| Final rank | 5.890348814034777 | Score | -31.2595 |
|---|---|---|---|
| Inter norm | -1.11901 | Intra norm | 0.041094 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 15 clashes; 8 protein contact clashes; high strain Δ 33.1 | ||
| Residues | A:ALA212;A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:TYR174;A:VAL206;A:VAL211 | ||
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 | ||
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 | H-bonds | 6 |
| IFP residues | A:ARG14; A:ASP161; A:CYS168; A:GLY205; A:LEU208; A:LEU209; A:LYS178; A:MET213; A:NAP301; A:PHE171; A:PHE97; A:PRO210; A:PRO99; A:SER207; A:SER95; A:TRP221; A:TYR174; A:TYR98; A:VAL206 | ||
| Current overlap | 11 | Native recall | 0.58 |
| Jaccard | 0.50 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2335 | 4.061691886301118 | -0.851656 | -21.6169 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1100 | 4.787372003350519 | -1.05697 | -30.0887 | 9 | 15 | 12 | 0.63 | 0.40 | - | no | Open |
| 1097 | 5.040820345346657 | -1.00871 | -25.7342 | 12 | 17 | 13 | 0.68 | 0.40 | - | no | Open |
| 2334 | 5.111765077331845 | -0.841432 | -19.3789 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2337 | 5.325863711702867 | -0.910995 | -22.2244 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 854 | 5.465550579216255 | -0.723193 | -15.9659 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1552 | 5.493229889405914 | -0.71564 | -14.3851 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3184 | 5.641098129243347 | -0.581167 | -11.0742 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1099 | 5.890348814034777 | -1.11901 | -31.2595 | 5 | 14 | 11 | 0.58 | 0.40 | - | no | Current |
| 1751 | 5.903512446961664 | -0.519993 | -10.8087 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 910 | 5.916354618205191 | -0.954098 | -23.5257 | 9 | 16 | 15 | 0.79 | 0.60 | - | no | Open |
| 1554 | 6.075633683155976 | -0.934369 | -21.9795 | 13 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1646 | 6.18429495912932 | -0.669379 | -20.913 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1556 | 6.202913238606168 | -0.969893 | -23.4259 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1551 | 6.206566096358066 | -1.0099 | -21.3506 | 14 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1094 | 6.208528558579416 | -1.21234 | -31.4355 | 8 | 14 | 11 | 0.58 | 0.40 | - | no | Open |
| 826 | 6.512700177451733 | -1.07635 | -21.6753 | 9 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 1400 | 6.561249648586537 | -0.698939 | -21.4668 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3057 | 6.800833490420674 | -0.790188 | -17.565 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1143 | 7.184623093561577 | -0.924357 | -24.2096 | 13 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1144 | 7.47073863284113 | -0.955531 | -22.4266 | 13 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 3183 | 7.489694201151503 | -0.738402 | -16.9141 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1750 | 5.906464004859652 | -0.5977 | -17.705 | 5 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1745 | 5.912714459289429 | -0.563951 | -10.4169 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1749 | 6.189196127535265 | -0.488662 | -11.6095 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 853 | 6.43236420017673 | -0.755214 | -22.6037 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2338 | 6.816656703617586 | -0.734912 | -17.2989 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1641 | 6.946643423704989 | -0.719578 | -20.925 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1644 | 7.090749593549192 | -0.711076 | -22.0214 | 2 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 852 | 7.121958352734343 | -0.781796 | -18.784 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3055 | 7.191585062457597 | -0.804998 | -18.1009 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3058 | 7.219399448670644 | -0.790405 | -20.3102 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1401 | 7.700993314468961 | -0.706171 | -22.0719 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1747 | 7.721357163690497 | -0.567698 | -12.3005 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1643 | 7.769245109776122 | -0.601527 | -14.2677 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 857 | 7.857888168724932 | -0.773364 | -18.8903 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3054 | 8.117329032973123 | -0.748175 | -17.0971 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1399 | 8.326418734691467 | -0.70725 | -13.3254 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1748 | 8.488221073084768 | -0.659172 | -19.2452 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1645 | 8.523077427400766 | -0.689741 | -9.41437 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3059 | 8.52620357326094 | -0.822251 | -21.0851 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 908 | 8.567233341973703 | -1.06167 | -19.4935 | 10 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 2340 | 8.628421890063638 | -0.796578 | -22.4143 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3056 | 8.692178434366078 | -0.720026 | -16.7971 | 11 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 855 | 8.739527255499087 | -0.804502 | -18.9329 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 829 | 8.766276799513033 | -1.04606 | -27.7476 | 6 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1640 | 8.824542025725556 | -0.718002 | -15.2142 | 11 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1550 | 8.865635211433716 | -0.890175 | -19.4052 | 16 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 828 | 8.898772839392837 | -1.05323 | -17.7058 | 12 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 909 | 8.95226542074102 | -0.998231 | -30.497 | 10 | 16 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1397 | 9.001546049883952 | -0.738534 | -19.1012 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1140 | 9.050619723848104 | -0.890188 | -19.8728 | 10 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3180 | 9.070660468841533 | -0.701388 | -16.422 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1557 | 9.188623497517309 | -0.905479 | -22.8267 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1398 | 9.233282745004523 | -0.714702 | -12.8115 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1553 | 9.274058312586602 | -0.83401 | -20.8551 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 913 | 9.329335045315279 | -0.874451 | -19.9329 | 9 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2336 | 9.354355392031085 | -0.832597 | -21.29 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1642 | 9.390223575957444 | -0.615723 | -13.1479 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 827 | 9.422313060682622 | -1.03518 | -30.1795 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 912 | 9.766845572498044 | -0.875211 | -26.7895 | 10 | 16 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1095 | 9.801854792726894 | -0.970957 | -23.2559 | 11 | 10 | 7 | 0.37 | 0.60 | - | yes | Open |
| 1746 | 9.804331283282977 | -0.566719 | -12.9342 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 856 | 10.345843372891043 | -0.771962 | -17.1066 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3186 | 10.48970283990753 | -0.79702 | -20.9316 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1093 | 10.58106081382148 | -1.1374 | -29.4091 | 6 | 17 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1141 | 10.699200376784797 | -1.01193 | -17.5375 | 11 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1096 | 10.768142647700412 | -1.46947 | -36.7122 | 10 | 16 | 10 | 0.53 | 0.60 | - | yes | Open |
| 3182 | 10.800286294974278 | -0.700001 | -15.7401 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1139 | 10.825142231120754 | -0.97529 | -25.1222 | 11 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 911 | 10.85555511236051 | -0.916335 | -16.9478 | 9 | 14 | 11 | 0.58 | 0.40 | - | yes | Open |
| 831 | 11.22784922029668 | -1.03841 | -30.025 | 5 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2339 | 11.289780436374649 | -0.931014 | -26.9895 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1142 | 11.315790398458073 | -1.03535 | -26.8687 | 11 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1396 | 11.475425302794196 | -0.762705 | -16.3168 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 832 | 11.511455744899113 | -0.988372 | -28.313 | 5 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1138 | 11.68155466549761 | -1.0998 | -19.4414 | 9 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1098 | 11.722351927577938 | -1.45362 | -36.2268 | 9 | 16 | 10 | 0.53 | 0.80 | - | yes | Open |
| 3185 | 12.179057401875244 | -0.91643 | -18.9903 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1555 | 12.434305863018238 | -0.883876 | -18.737 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3181 | 12.839363861920049 | -0.802946 | -20.4131 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 830 | 14.923940542284125 | -0.942156 | -15.9988 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.259kcal/mol
Ligand efficiency (LE)
-1.0779kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.289
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
407.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.67
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.62kcal/mol
Minimised FF energy
64.95kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.