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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
9.7 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.36, H-bond role recall 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.173 kcal/mol/HA)
✓ Good fit quality (FQ -10.52)
✓ Good H-bonds (3 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (9.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-28.161
kcal/mol
LE
-1.173
kcal/mol/HA
Fit Quality
-10.52
FQ (Leeson)
HAC
24
heavy atoms
MW
337
Da
LogP
2.83
cLogP
Final rank
1.7316
rank score
Inter norm
-1.261
normalised
Contacts
13
H-bonds 6
Interaction summary
HBD 1
HBA 2
PC 1
HY 3
PI 2
CLASH 2
Interaction summary
HBD 1
HBA 2
PC 1
HY 3
PI 2
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 8 | Native recall | 0.47 |
| Jaccard | 0.36 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 102 | 1.7316048619282671 | -1.26112 | -28.1611 | 6 | 13 | 8 | 0.47 | 0.50 | - | no | Current |
| 409 | 3.8792717208930334 | -1.17631 | -25.4259 | 13 | 14 | 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
-28.161kcal/mol
Ligand efficiency (LE)
-1.1734kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.516
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.83
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
80.78kcal/mol
Minimised FF energy
71.04kcal/mol
SASA & burial
✓ computed
SASA (unbound)
593.9Ų
Total solvent-accessible surface area of free ligand
BSA total
507.4Ų
Buried surface area upon binding
BSA apolar
382.9Ų
Hydrophobic contacts buried
BSA polar
124.4Ų
Polar contacts buried
Fraction buried
85.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1596.2Ų
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
1041.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)