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
25.5 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.82, Jaccard 0.67, H-bond role recall 0.67
Reason: no major geometry red flags detected
4 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.675 kcal/mol/HA)
✓ Good fit quality (FQ -6.91)
✓ Good H-bonds (4 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (25.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-24.970
kcal/mol
LE
-0.675
kcal/mol/HA
Fit Quality
-6.91
FQ (Leeson)
HAC
37
heavy atoms
MW
495
Da
LogP
3.17
cLogP
Interaction summary
HB 4
HY 24
PI 6
CLASH 5
Interaction summary
HB 4
HY 24
PI 6
CLASH 5
| Final rank | 3.235 | Score | -24.970 |
|---|---|---|---|
| Inter norm | -0.785 | Intra norm | 0.110 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | geometry warning; 18 clashes; 1 protein clash; 2 cofactor-context clashes; moderate strain Δ 24.1 | ||
| Residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU189
LEU226
LEU229
LYS198
MET183
NDP302
PHE113
SER111
SER112
TYR191
TYR194
VAL230
ARG287
| ||
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| 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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 14 | Native recall | 0.82 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 4 | Strict recall | 0.57 |
| HB same residue+role | 4 | HB role recall | 0.67 |
| HB same residue | 4 | HB residue recall | 0.80 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 70 | 0.9441837428913401 | -1.14683 | -33.4245 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 60 | 1.353649379244449 | -1.14596 | -33.7036 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 53 | 2.955680988621583 | -0.717527 | -22.2933 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 56 | 3.0450219135992884 | -0.711971 | -23.6267 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 68 | 3.157440750940877 | -0.734977 | -22.3917 | 9 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 52 | 3.2354079941176104 | -0.785109 | -24.9697 | 4 | 18 | 14 | 0.82 | 0.67 | - | no | Current |
| 78 | 4.087075192168423 | -0.776562 | -24.1835 | 11 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 70 | 4.300072111504438 | -0.965604 | -29.7543 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 47 | 4.4701940342157265 | -0.737164 | -25.0202 | 11 | 19 | 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
-24.970kcal/mol
Ligand efficiency (LE)
-0.6749kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.909
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
494.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.17
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
17.30kcal/mol
Minimised FF energy
-8.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
812.8Ų
Total solvent-accessible surface area of free ligand
BSA total
625.9Ų
Buried surface area upon binding
BSA apolar
526.4Ų
Hydrophobic contacts buried
BSA polar
99.5Ų
Polar contacts buried
Fraction buried
77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1825.9Ų
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
1052.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)