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
17.3 kcal/mol
Protein clashes
1
Internal clashes
4
Native overlap
contact recall 0.65, Jaccard 0.52, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.074 kcal/mol/HA)
✓ Good fit quality (FQ -9.62)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (17.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.767
kcal/mol
LE
-1.074
kcal/mol/HA
Fit Quality
-9.62
FQ (Leeson)
HAC
24
heavy atoms
MW
368
Da
LogP
2.43
cLogP
Interaction summary
HB 9
HY 18
PI 2
CLASH 4
Interaction summary
HB 9
HY 18
PI 2
CLASH 4
| Final rank | 3.222 | Score | -25.767 |
|---|---|---|---|
| Inter norm | -1.165 | Intra norm | 0.091 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 9 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; 4 cofactor-context clashes | ||
| Residues |
ALA182
ARG17
ASP181
GLY225
LEU188
LEU226
LEU229
MET183
NDP302
PHE113
SER227
TYR114
TYR194
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 | 11 | Native recall | 0.65 |
| Jaccard | 0.52 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 641 | 0.996170229026272 | -1.32395 | -28.1168 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 635 | 1.5521669381048986 | -1.09042 | -23.7226 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 647 | 2.5350330653132933 | -1.18347 | -26.7149 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 662 | 2.5760465111665063 | -1.18521 | -25.9775 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 643 | 2.859482682481522 | -0.983196 | -22.5121 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 653 | 2.912148041490271 | -1.31011 | -29.0433 | 12 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 651 | 3.165601413469841 | -0.982393 | -21.7643 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 653 | 3.221699438426105 | -1.16465 | -25.7672 | 9 | 15 | 11 | 0.65 | 0.33 | - | no | Current |
| 658 | 5.142005379099134 | -1.15028 | -26.4406 | 13 | 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
-25.767kcal/mol
Ligand efficiency (LE)
-1.0736kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.622
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
368.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.43
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-111.51kcal/mol
Minimised FF energy
-128.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
611.5Ų
Total solvent-accessible surface area of free ligand
BSA total
497.1Ų
Buried surface area upon binding
BSA apolar
329.5Ų
Hydrophobic contacts buried
BSA polar
167.6Ų
Polar contacts buried
Fraction buried
81.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1595.2Ų
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
1027.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)