Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
19.0 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.41, Jaccard 0.37, H-bond role recall 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
45% of hydrophobic surface appears solvent-exposed (9/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.192 kcal/mol/HA)
✓ Good fit quality (FQ -10.84)
✓ Good H-bonds (5 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Moderate strain (19.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-29.803
kcal/mol
LE
-1.192
kcal/mol/HA
Fit Quality
-10.84
FQ (Leeson)
HAC
25
heavy atoms
MW
333
Da
LogP
2.66
cLogP
Interaction summary
HB 5
HY 11
PI 2
CLASH 3
⚠ Exposure 45%
Interaction summary
HB 5
HY 11
PI 2
CLASH 3
⚠ Exposure 45%
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
Partial hydrophobic solvent exposure
45% of hydrophobic surface appears solvent-exposed (9/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 11
Exposed 9
LogP 2.66
H-bonds 5
Exposed fragments:
phenyl (5/5 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 2.687 | Score | -29.803 |
|---|---|---|---|
| Inter norm | -1.244 | Intra norm | 0.052 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 5 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; 2 severe cofactor-context clashes | ||
| Residues |
ARG17
LEU229
LYS16
NDP302
PHE113
SER111
SER112
TYR194
VAL230
| ||
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 | 7 | Native recall | 0.41 |
| Jaccard | 0.37 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 585 | 1.8262933247315551 | -1.10505 | -21.9069 | 2 | 12 | 11 | 0.65 | 0.17 | - | no | Open |
| 572 | 2.0439671731543423 | -1.10015 | -26.0693 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 562 | 2.6867018007655448 | -1.24434 | -29.8034 | 5 | 9 | 7 | 0.41 | 0.50 | - | no | Current |
| 576 | 4.064891135826998 | -1.10482 | -21.3976 | 7 | 15 | 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
-29.803kcal/mol
Ligand efficiency (LE)
-1.1921kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.838
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
333.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-12.13kcal/mol
Minimised FF energy
-31.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
568.4Ų
Total solvent-accessible surface area of free ligand
BSA total
482.5Ų
Buried surface area upon binding
BSA apolar
409.8Ų
Hydrophobic contacts buried
BSA polar
72.7Ų
Polar contacts buried
Fraction buried
84.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1624.7Ų
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
1047.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)