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 high
Native mixed
SASA done
Strain ΔE
8.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.47, Jaccard 0.38, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.327 kcal/mol/HA)
✓ Good fit quality (FQ -11.32)
✓ Good H-bonds (3 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ Moderate strain (8.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-27.860
kcal/mol
LE
-1.327
kcal/mol/HA
Fit Quality
-11.32
FQ (Leeson)
HAC
21
heavy atoms
MW
294
Da
LogP
3.30
cLogP
Final rank
2.2302
rank score
Inter norm
-1.414
normalised
Contacts
12
H-bonds 6
Interaction summary
HBA 3
PC 2
HY 4
PI 3
CLASH 1
Interaction summary
HBA 3
PC 2
HY 4
PI 3
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | 0.38 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 494 | 1.3391484112069343 | -1.21365 | -23.16 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 2.0118790855175046 | -1.27636 | -26.3833 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 2.2302149066875736 | -1.41383 | -27.8598 | 6 | 12 | 8 | 0.47 | 0.33 | - | no | Current |
| 488 | 4.480625061862758 | -1.28514 | -26.7794 | 11 | 16 | 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
-27.860kcal/mol
Ligand efficiency (LE)
-1.3267kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.316
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
294.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.30
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
19.50kcal/mol
Minimised FF energy
10.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
528.0Ų
Total solvent-accessible surface area of free ligand
BSA total
445.8Ų
Buried surface area upon binding
BSA apolar
281.6Ų
Hydrophobic contacts buried
BSA polar
164.2Ų
Polar contacts buried
Fraction buried
84.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1488.3Ų
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
1043.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)