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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
30.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.63, Jaccard 0.60, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.563 kcal/mol/HA)
✓ Good fit quality (FQ -5.25)
✓ Good H-bonds (5 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (30.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-15.192
kcal/mol
LE
-0.563
kcal/mol/HA
Fit Quality
-5.25
FQ (Leeson)
HAC
27
heavy atoms
MW
367
Da
LogP
1.06
cLogP
Interaction summary
HB 5
HY 16
PI 3
CLASH 2
Interaction summary
HB 5
HY 16
PI 3
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 | 2.205 | Score | -15.192 |
|---|---|---|---|
| Inter norm | -0.987 | Intra norm | 0.424 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; moderate strain Δ 29.9 | ||
| Residues |
ARG17
ASP232
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
SER111
TYR191
TYR194
VAL230
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 12 | Native recall | 0.63 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.80 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 237 | 1.4290717238990738 | -0.953072 | -24.1167 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 215 | 2.0171944907376305 | -1.06213 | -16.1562 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 252 | 2.2051864699877384 | -0.986889 | -15.1919 | 5 | 13 | 12 | 0.63 | 0.40 | - | no | Current |
| 172 | 3.0439487765845445 | -1.02531 | -26.2453 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 233 | 3.1278106641215495 | -0.876137 | -19.5221 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 292 | 4.3181297952992415 | -0.767501 | -8.35862 | 6 | 8 | 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
-15.192kcal/mol
Ligand efficiency (LE)
-0.5627kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.249
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
367.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.06
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
143.44kcal/mol
Minimised FF energy
112.88kcal/mol
SASA & burial
✓ computed
SASA (unbound)
660.8Ų
Total solvent-accessible surface area of free ligand
BSA total
499.1Ų
Buried surface area upon binding
BSA apolar
366.2Ų
Hydrophobic contacts buried
BSA polar
132.9Ų
Polar contacts buried
Fraction buried
75.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1647.8Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1048.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)