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
36.8 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.65, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.321 kcal/mol/HA)
✓ Good fit quality (FQ -12.61)
✓ Good H-bonds (5 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Very high strain energy (36.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-38.300
kcal/mol
LE
-1.321
kcal/mol/HA
Fit Quality
-12.61
FQ (Leeson)
HAC
29
heavy atoms
MW
384
Da
LogP
3.08
cLogP
Interaction summary
HB 5
HY 23
PI 4
CLASH 3
Interaction summary
HB 5
HY 23
PI 4
CLASH 3
| Final rank | 3.371 | Score | -38.300 |
|---|---|---|---|
| Inter norm | -1.159 | Intra norm | -0.161 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 14 clashes; 2 protein clashes; 3 cofactor-context clashes; high strain Δ 36.8 | ||
| Residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
MET183
MET233
NDP302
PHE113
SER227
TYR194
VAL228
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 490 | 1.7537992888862641 | -1.02991 | -31.929 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 510 | 2.7776297499552585 | -0.913277 | -24.5256 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 490 | 3.0102673198467875 | -1.09437 | -36.7781 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 476 | 3.201813221844428 | -1.11372 | -39.2841 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 463 | 3.371347263661328 | -1.15929 | -38.3001 | 5 | 16 | 13 | 0.76 | 0.33 | - | no | Current |
| 492 | 3.58544371075322 | -1.07046 | -34.4741 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 495 | 3.7879791106918894 | -0.807385 | -24.528 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 526 | 4.210215324924119 | -0.780771 | -24.0519 | 4 | 18 | 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
-38.300kcal/mol
Ligand efficiency (LE)
-1.3207kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.607
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
384.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
128.03kcal/mol
Minimised FF energy
91.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
603.2Ų
Total solvent-accessible surface area of free ligand
BSA total
557.0Ų
Buried surface area upon binding
BSA apolar
425.9Ų
Hydrophobic contacts buried
BSA polar
131.0Ų
Polar contacts buried
Fraction buried
92.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1626.6Ų
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
1020.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)