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 high
Native strong
SASA done
Strain ΔE
20.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.76, Jaccard 0.65, H-bond role recall 0.33
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.982 kcal/mol/HA)
✓ Good fit quality (FQ -9.27)
✓ Good H-bonds (4 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (20.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-27.507
kcal/mol
LE
-0.982
kcal/mol/HA
Fit Quality
-9.27
FQ (Leeson)
HAC
28
heavy atoms
MW
384
Da
LogP
4.16
cLogP
Interaction summary
HB 4
HY 24
PI 4
CLASH 2
Interaction summary
HB 4
HY 24
PI 4
CLASH 2
| Final rank | 3.092 | Score | -27.507 |
|---|---|---|---|
| Inter norm | -1.036 | Intra norm | 0.054 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes | ||
| Residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
MET183
MET233
NDP302
PHE113
TYR191
TYR194
TYR283
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 | 13 | Native recall | 0.76 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 483 | 1.0853100332132994 | -1.15783 | -26.9741 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 1.3030885157662433 | -0.984884 | -24.6447 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 539 | 1.3153312150478562 | -0.956507 | -24.115 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 1.4983376621522455 | -1.21454 | -29.8472 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 487 | 1.829623080713065 | -0.906153 | -22.6394 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 522 | 1.886285713477351 | -0.843689 | -17.4728 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 527 | 2.9175440723674373 | -1.05324 | -24.3241 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 456 | 3.0916468248736995 | -1.03596 | -27.5073 | 4 | 16 | 13 | 0.76 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.507kcal/mol
Ligand efficiency (LE)
-0.9824kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.274
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
384.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.16
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
98.67kcal/mol
Minimised FF energy
78.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
620.2Ų
Total solvent-accessible surface area of free ligand
BSA total
557.0Ų
Buried surface area upon binding
BSA apolar
435.5Ų
Hydrophobic contacts buried
BSA polar
121.4Ų
Polar contacts buried
Fraction buried
89.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1642.9Ų
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
1034.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)