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 high
Native mixed
SASA done
Strain ΔE
18.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.33, Jaccard 0.22, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.229 kcal/mol/HA)
✓ Good fit quality (FQ -10.28)
✓ Good H-bonds (5 bonds)
✓ Deep burial (78% SASA buried)
✗ Moderate strain (18.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.578
kcal/mol
LE
-1.229
kcal/mol/HA
Fit Quality
-10.28
FQ (Leeson)
HAC
20
heavy atoms
MW
313
Da
LogP
0.81
cLogP
Interaction summary
HB 5
HY 15
PI 1
CLASH 1
Interaction summary
HB 5
HY 15
PI 1
CLASH 1
| Final rank | 2.806 | Score | -24.578 |
|---|---|---|---|
| Inter norm | -1.143 | Intra norm | -0.086 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ARG337
ARG342
GLU343
GLU348
LEU339
LEU350
LEU372
PRO338
PRO340
PRO344
PRO373
TYR370
TYR371
| ||
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
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:ORX602
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 5 | Native recall | 0.33 |
| Jaccard | 0.22 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 336 | 0.4844925064188378 | -1.39656 | -27.4507 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 349 | 1.1863918513579474 | -1.5105 | -29.9063 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 337 | 1.381328489051882 | -1.29645 | -28.1728 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 278 | 1.3816063438262176 | -1.23041 | -24.2745 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 402 | 1.6036568051311582 | -1.42934 | -28.6624 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 231 | 2.233432618713564 | -1.2498 | -24.5852 | 15 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 257 | 2.3622034295832517 | -1.46745 | -28.4593 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 297 | 2.3754379684594595 | -1.21827 | -20.0212 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 322 | 2.806279579150012 | -1.14305 | -24.5776 | 5 | 13 | 5 | 0.33 | 0.20 | - | no | Current |
| 321 | 3.1266169303527573 | -1.22396 | -25.01 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 327 | 3.316554828658691 | -0.968003 | -19.9316 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 374 | 3.55323396923254 | -1.61668 | -32.5631 | 12 | 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
-24.578kcal/mol
Ligand efficiency (LE)
-1.2289kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.284
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
313.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.81
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-85.97kcal/mol
Minimised FF energy
-104.72kcal/mol
SASA & burial
✓ computed
SASA (unbound)
501.1Ų
Total solvent-accessible surface area of free ligand
BSA total
393.6Ų
Buried surface area upon binding
BSA apolar
203.6Ų
Hydrophobic contacts buried
BSA polar
190.0Ų
Polar contacts buried
Fraction buried
78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
51.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2270.3Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1373.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)