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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
29.2 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.47, Jaccard 0.47, H-bond role recall 0.60
Reason: no major geometry red flags detected
2 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-2.354 kcal/mol/HA)
✓ Good fit quality (FQ -16.23)
✓ Good H-bonds (5 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ High strain energy (29.2 kcal/mol)
✗ Geometry warnings
Score
-30.604
kcal/mol
LE
-2.354
kcal/mol/HA
Fit Quality
-16.23
FQ (Leeson)
HAC
13
heavy atoms
MW
180
Da
LogP
-1.30
cLogP
Final rank
0.1010
rank score
Inter norm
-2.313
normalised
Contacts
9
H-bonds 11
Interaction summary
HBD 4
HBA 1
HY 1
PI 2
CLASH 4
Interaction summary
HBD 4
HBA 1
HY 1
PI 2
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 9 | Native recall | 0.47 |
| Jaccard | 0.47 | RMSD | - |
| HB strict | 4 | Strict recall | 0.67 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 159 | -0.1527119339673711 | -2.50492 | -32.8805 | 16 | 10 | 8 | 0.42 | 0.60 | - | no | Open |
| 130 | 0.10104388636201347 | -2.31252 | -30.6044 | 11 | 9 | 9 | 0.47 | 0.60 | - | no | Current |
| 321 | 1.8593922176772624 | -1.82257 | -24.1499 | 14 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 175 | 3.643192275056469 | -2.33744 | -31.0332 | 16 | 18 | 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
-30.604kcal/mol
Ligand efficiency (LE)
-2.3542kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-16.227
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
13HA
Physicochemical properties
Molecular weight
180.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.30
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
158.40kcal/mol
Minimised FF energy
129.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
367.0Ų
Total solvent-accessible surface area of free ligand
BSA total
348.4Ų
Buried surface area upon binding
BSA apolar
229.3Ų
Hydrophobic contacts buried
BSA polar
119.1Ų
Polar contacts buried
Fraction buried
94.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1393.1Ų
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
1026.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)