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
12.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.62, H-bond role recall 0.17
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.627 kcal/mol/HA)
✓ Good fit quality (FQ -13.34)
✓ Good H-bonds (5 bonds)
✓ Deep burial (98% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Moderate strain (12.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-30.910
kcal/mol
LE
-1.627
kcal/mol/HA
Fit Quality
-13.34
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
0.02
cLogP
Interaction summary
HB 5
HY 12
PI 3
CLASH 3
Interaction summary
HB 5
HY 12
PI 3
CLASH 3
| Final rank | 3.366 | Score | -30.910 |
|---|---|---|---|
| Inter norm | -1.634 | Intra norm | 0.008 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 5 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes; 1 severe cofactor-context clash | ||
| Residues |
ALA182
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
MET183
NDP302
PHE113
PRO224
SER111
SER227
TYR191
TYR194
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 | 13 | Native recall | 0.76 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 312 | -0.12698051497752788 | -1.4099 | -25.1999 | 5 | 13 | 13 | 0.76 | 0.67 | - | no | Open |
| 409 | 1.5618486583435398 | -1.25392 | -19.5039 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 329 | 1.810958723850599 | -1.17778 | -21.5875 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 267 | 3.3656450884601203 | -1.63439 | -30.9104 | 5 | 17 | 13 | 0.76 | 0.17 | - | no | Current |
| 265 | 3.3810319513898386 | -1.35166 | -24.7621 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 341 | 3.5339212025300557 | -1.51737 | -27.3765 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 382 | 3.8196564752012465 | -1.26937 | -21.4516 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 4.003072569334565 | -1.34735 | -23.6626 | 10 | 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
-30.910kcal/mol
Ligand efficiency (LE)
-1.6269kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.335
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.02
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-127.05kcal/mol
Minimised FF energy
-139.53kcal/mol
SASA & burial
✓ computed
SASA (unbound)
477.6Ų
Total solvent-accessible surface area of free ligand
BSA total
465.8Ų
Buried surface area upon binding
BSA apolar
314.1Ų
Hydrophobic contacts buried
BSA polar
151.6Ų
Polar contacts buried
Fraction buried
97.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1476.4Ų
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
1024.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)