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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
18.1 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.973 kcal/mol/HA)
✓ Good fit quality (FQ -9.19)
✓ Good H-bonds (4 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Moderate strain (18.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-27.247
kcal/mol
LE
-0.973
kcal/mol/HA
Fit Quality
-9.19
FQ (Leeson)
HAC
28
heavy atoms
MW
419
Da
LogP
3.01
cLogP
Final rank
4.2253
rank score
Inter norm
-1.073
normalised
Contacts
13
H-bonds 7
Interaction summary
HBA 4
PC 2
HY 4
PI 3
CLASH 3
Interaction summary
HBA 4
PC 2
HY 4
PI 3
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 11 | Native recall | 0.65 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 391 | 0.8112587710984578 | -0.883156 | -21.7804 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 1.761457712336876 | -1.18388 | -28.0949 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 484 | 2.388298171391906 | -0.868572 | -20.6754 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 101 | 2.911216982679596 | -0.879119 | -20.3872 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 95 | 2.970006987126121 | -1.08769 | -25.015 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 379 | 3.450130273935065 | -0.998633 | -22.0405 | 14 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 423 | 3.7405836219795368 | -1.00578 | -24.1953 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 160 | 3.885655564123343 | -0.784425 | -18.1914 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 100 | 4.225272845749715 | -1.07342 | -27.2468 | 7 | 13 | 11 | 0.65 | 0.33 | - | no | Current |
| 73 | 5.143261743022093 | -1.07475 | -24.8662 | 12 | 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
-27.247kcal/mol
Ligand efficiency (LE)
-0.9731kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.186
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
419.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.01
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-21.99kcal/mol
Minimised FF energy
-40.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
652.8Ų
Total solvent-accessible surface area of free ligand
BSA total
532.2Ų
Buried surface area upon binding
BSA apolar
327.4Ų
Hydrophobic contacts buried
BSA polar
204.8Ų
Polar contacts buried
Fraction buried
81.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1591.9Ų
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
1029.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)