Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
No SASA yet
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA missing
Strain ΔE
25.4 kcal/mol
Protein clashes
4
Internal clashes
16
Native overlap
contact recall 0.79, Jaccard 0.79, H-bond role recall 0.40
Reason: 16 internal clashes
4 protein-contact clashes
16 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.986 kcal/mol/HA)
✓ Good fit quality (FQ -9.08)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (25.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (16)
ℹ SASA not computed
Score
-25.625
kcal/mol
LE
-0.986
kcal/mol/HA
Fit Quality
-9.08
FQ (Leeson)
HAC
26
heavy atoms
MW
344
Da
LogP
3.80
cLogP
Interaction summary
HB 6
HY 24
PI 4
CLASH 0
Interaction summary
HB 6
HY 24
PI 4
CLASH 0
| Final rank | 4.580 | Score | -25.625 |
|---|---|---|---|
| Inter norm | -1.158 | Intra norm | 0.172 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 16 clashes; 4 protein contact clashes; high strain Δ 30.1 | ||
| Residues |
ARG14
CYS168
GLY205
LEU208
LEU209
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
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: 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 | 15 | Native recall | 0.79 |
| Jaccard | 0.79 | 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: 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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1875 | 4.005010205162219 | -1.10519 | -33.5954 | 6 | 16 | 15 | 0.79 | 0.60 | - | no | Open |
| 1800 | 4.579950957861197 | -1.15778 | -25.6248 | 6 | 15 | 15 | 0.79 | 0.40 | - | no | Current |
| 2137 | 5.175713990098788 | -0.778723 | -24.3097 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2285 | 5.413840730423675 | -0.616645 | -22.9547 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2279 | 5.608687471503549 | -0.905999 | -23.6184 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2287 | 5.62603529737203 | -0.805143 | -22.6726 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2136 | 5.8594678624747125 | -0.686705 | -11.1597 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2082 | 6.265619274534258 | -1.02397 | -29.3524 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1878 | 6.314171543143123 | -1.09987 | -22.3095 | 4 | 11 | 11 | 0.58 | 0.20 | - | no | Open |
| 1873 | 6.4742569799604315 | -0.961402 | -23.547 | 6 | 12 | 11 | 0.58 | 0.40 | - | no | Open |
| 2128 | 6.478286035222596 | -0.862834 | -11.4604 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1809 | 6.349388050975404 | -1.19864 | -34.7516 | 9 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1876 | 6.370747318105377 | -1.05228 | -32.4574 | 7 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 2289 | 6.382718590238487 | -0.668159 | -24.9053 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2133 | 6.403156955567874 | -0.924532 | -30.2379 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2132 | 6.487674164538864 | -0.707499 | -16.7846 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2130 | 6.660079205153325 | -0.91826 | -27.6552 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1877 | 6.943840658804206 | -1.03606 | -28.0983 | 7 | 12 | 10 | 0.53 | 0.40 | - | yes | Open |
| 2138 | 7.132952034146429 | -0.927428 | -20.207 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2290 | 7.358397424682779 | -0.735679 | -25.1192 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2131 | 7.422677892927867 | -0.75223 | -19.3819 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1872 | 7.442795289828515 | -1.33625 | -37.8164 | 6 | 16 | 15 | 0.79 | 0.40 | - | yes | Open |
| 1805 | 7.620462880213802 | -1.13753 | -32.5841 | 7 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2281 | 7.690083894668603 | -0.851882 | -22.0735 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2129 | 7.693534801033937 | -1.01471 | -29.5295 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1880 | 7.950175890596021 | -1.0379 | -33.817 | 6 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 2280 | 7.967391662969672 | -0.873227 | -14.061 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1802 | 8.340433953348079 | -0.95898 | -20.8017 | 3 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2284 | 8.405079920854117 | -0.667415 | -13.8648 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1871 | 8.410201104023038 | -1.18693 | -28.6175 | 9 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2090 | 8.463972881538385 | -1.09673 | -34.3822 | 9 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2286 | 8.536398528162913 | -0.7634 | -20.3568 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2086 | 8.801721033381781 | -0.983084 | -28.6774 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1808 | 8.821916418896157 | -1.05223 | -27.9979 | 5 | 17 | 15 | 0.79 | 0.40 | - | yes | Open |
| 2083 | 8.923860818051242 | -1.09581 | -30.981 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2089 | 9.438997680416733 | -1.02562 | -24.302 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2091 | 9.637617412222545 | -0.920638 | -28.1327 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1799 | 9.870318631957277 | -1.29621 | -20.0353 | 8 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1870 | 10.00424550788779 | -1.19358 | -17.1893 | 8 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2087 | 10.470296388657033 | -1.02366 | -31.1566 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2085 | 10.5464537209453 | -1.04811 | -23.883 | 8 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1801 | 11.215176828446877 | -1.37104 | -39.8358 | 7 | 17 | 15 | 0.79 | 0.40 | - | yes | Open |
| 2081 | 11.358717644467015 | -1.16406 | -23.7428 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1807 | 11.835549837269522 | -1.01756 | -13.0578 | 10 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1803 | 13.172001498321126 | -1.14124 | -18.8764 | 10 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 2288 | 56.89487213969281 | -0.767611 | -14.9201 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2135 | 57.02539108215842 | -0.695221 | -24.5633 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2127 | 57.036530618020976 | -0.801382 | -24.999 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1879 | 57.61135575650444 | -1.0829 | -33.0707 | 5 | 15 | 13 | 0.68 | 0.20 | - | yes | Open |
| 2088 | 58.79282235496613 | -0.934604 | -23.972 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2283 | 58.96960884209247 | -0.645202 | -17.476 | 7 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2282 | 59.16780939151691 | -0.883292 | -26.5827 | 4 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2134 | 59.42719437372133 | -0.82137 | -24.0088 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1869 | 59.86138065279036 | -1.05915 | -25.4059 | 4 | 20 | 14 | 0.74 | 0.00 | - | yes | Open |
| 1806 | 60.065836640858414 | -0.989907 | -24.4348 | 8 | 17 | 15 | 0.79 | 0.40 | - | yes | Open |
| 2080 | 60.63339298634609 | -1.14069 | -32.7101 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1798 | 60.82440334568592 | -1.06704 | -25.4959 | 7 | 13 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1874 | 60.92815914247352 | -1.07815 | -25.4793 | 7 | 16 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1804 | 61.74434928709139 | -1.11474 | -31.9766 | 4 | 14 | 10 | 0.53 | 0.00 | - | yes | Open |
| 2084 | 67.53690889968402 | -1.04113 | -24.4538 | 8 | 23 | 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
-25.625kcal/mol
Ligand efficiency (LE)
-0.9856kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.080
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
118.58kcal/mol
Minimised FF energy
93.20kcal/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.