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
17.7 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.59, Jaccard 0.45, H-bond role recall 0.33
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.087 kcal/mol/HA)
✓ Good fit quality (FQ -10.27)
✓ Good H-bonds (5 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Moderate strain (17.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-30.450
kcal/mol
LE
-1.087
kcal/mol/HA
Fit Quality
-10.27
FQ (Leeson)
HAC
28
heavy atoms
MW
401
Da
LogP
2.23
cLogP
Final rank
2.2093
rank score
Inter norm
-1.105
normalised
Contacts
15
H-bonds 7
Interaction summary
HBD 2
HBA 3
HY 4
PI 2
CLASH 3
Interaction summary
HBD 2
HBA 3
HY 4
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 10 | Native recall | 0.59 |
| Jaccard | 0.45 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 548 | 0.6067675643089019 | -0.91307 | -10.311 | 5 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 556 | 1.728252009536883 | -1.22489 | -21.6697 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 549 | 2.20929891941585 | -1.10472 | -30.4504 | 7 | 15 | 10 | 0.59 | 0.33 | - | no | Current |
| 574 | 3.200521320066378 | -0.853064 | -13.3418 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 558 | 3.460830310890564 | -0.973641 | -25.0281 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 4.136553907887692 | -1.13429 | -23.1701 | 16 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 582 | 4.298262327047228 | -0.796914 | -17.889 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 556 | 4.83223480932776 | -1.07236 | -21.1171 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 560 | 5.628665404275403 | -0.846398 | -11.7793 | 13 | 17 | 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
-30.450kcal/mol
Ligand efficiency (LE)
-1.0875kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.266
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
401.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.23
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-55.80kcal/mol
Minimised FF energy
-73.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
669.4Ų
Total solvent-accessible surface area of free ligand
BSA total
525.8Ų
Buried surface area upon binding
BSA apolar
369.2Ų
Hydrophobic contacts buried
BSA polar
156.6Ų
Polar contacts buried
Fraction buried
78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1647.0Ų
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
1041.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)