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
17.4 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.82, Jaccard 0.67, H-bond role recall 0.33
Reason: no major geometry red flags detected
3 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.827 kcal/mol/HA)
✓ Good fit quality (FQ -8.21)
✓ Good H-bonds (5 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (17.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-27.301
kcal/mol
LE
-0.827
kcal/mol/HA
Fit Quality
-8.21
FQ (Leeson)
HAC
33
heavy atoms
MW
434
Da
LogP
4.80
cLogP
Interaction summary
HB 5
HY 24
PI 4
CLASH 4
Interaction summary
HB 5
HY 24
PI 4
CLASH 4
| Final rank | 2.397 | Score | -27.301 |
|---|---|---|---|
| Inter norm | -0.886 | Intra norm | 0.058 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
ARG17
ASP181
GLY225
LEU188
LEU226
LEU229
MET183
MET233
NDP302
PHE113
PRO115
SER111
TYR114
TYR191
TYR194
VAL228
VAL230
ARG287
| ||
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
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 | 14 | Native recall | 0.82 |
| Jaccard | 0.67 | 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 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 625 | 0.7633810195800521 | -0.929769 | -26.8898 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 620 | 0.9612587282449622 | -0.813433 | -27.1209 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 629 | 1.4412018690246926 | -0.85665 | -25.1232 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 1.5629610996764716 | -0.869106 | -21.8212 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 621 | 2.0695638733844843 | -0.677901 | -18.7342 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 618 | 2.3966992058634435 | -0.885772 | -27.3014 | 5 | 18 | 14 | 0.82 | 0.33 | - | no | Current |
| 612 | 3.0264509688115697 | -0.976286 | -31.1583 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 634 | 3.100681749180362 | -0.601271 | -18.9765 | 5 | 12 | 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
-27.301kcal/mol
Ligand efficiency (LE)
-0.8273kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.208
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
173.47kcal/mol
Minimised FF energy
156.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
712.7Ų
Total solvent-accessible surface area of free ligand
BSA total
575.1Ų
Buried surface area upon binding
BSA apolar
483.5Ų
Hydrophobic contacts buried
BSA polar
91.7Ų
Polar contacts buried
Fraction buried
80.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1725.2Ų
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
1068.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)