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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
12.6 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.528 kcal/mol/HA)
✓ Good fit quality (FQ -12.53)
✓ Deep burial (86% SASA buried)
✗ Moderate strain (12.6 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (6)
Score
-29.033
kcal/mol
LE
-1.528
kcal/mol/HA
Fit Quality
-12.53
FQ (Leeson)
HAC
19
heavy atoms
MW
292
Da
LogP
2.64
cLogP
Interaction summary
HB 2
HY 19
PI 4
CLASH 4
Interaction summary
HB 2
HY 19
PI 4
CLASH 4
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
| Final rank | -0.125 | Score | -29.033 |
|---|---|---|---|
| Inter norm | -1.504 | Intra norm | -0.024 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 2 |
| Artifact reason | geometry warning; 6 clashes; 4 protein contact clashes; 3 cofactor-context clashes | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
NDP302
PHE113
TYR194
VAL230
ARG287
| ||
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 637 | -0.12491101091613598 | -1.50432 | -29.0327 | 2 | 10 | 10 | 0.53 | 0.20 | - | no | Current |
| 624 | 0.859553254517949 | -1.84028 | -30.5415 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 645 | 1.3544903360149785 | -1.49695 | -26.5081 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 644 | 1.6425695927885842 | -1.20951 | -21.2053 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 638 | 2.036705655377867 | -1.58228 | -28.5129 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 644 | 2.4572488566700317 | -1.44642 | -26.4617 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 632 | 2.5202235143508624 | -1.84946 | -32.4157 | 10 | 14 | 12 | 0.63 | 0.60 | - | no | Open |
| 641 | 5.406612215688473 | -1.36205 | -24.0266 | 14 | 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
-29.033kcal/mol
Ligand efficiency (LE)
-1.5280kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.525
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
292.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.64
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
41.85kcal/mol
Minimised FF energy
29.29kcal/mol
SASA & burial
✓ computed
SASA (unbound)
461.9Ų
Total solvent-accessible surface area of free ligand
BSA total
398.0Ų
Buried surface area upon binding
BSA apolar
220.3Ų
Hydrophobic contacts buried
BSA polar
177.6Ų
Polar contacts buried
Fraction buried
86.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
55.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1409.7Ų
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
1012.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)