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
30.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.40, Jaccard 0.29, H-bond role recall 0.60
Reason: no major geometry red flags detected
2 protein-contact clashes
46% of hydrophobic surface appears solvent-exposed (6/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.019 kcal/mol/HA)
✓ Good fit quality (FQ -9.00)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Very high strain energy (30.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-23.444
kcal/mol
LE
-1.019
kcal/mol/HA
Fit Quality
-9.00
FQ (Leeson)
HAC
23
heavy atoms
MW
353
Da
LogP
1.26
cLogP
Interaction summary
HB 11
HY 5
PI 0
CLASH 2
⚠ Exposure 46%
Interaction summary
HB 11
HY 5
PI 0
CLASH 2
⚠ Exposure 46%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
46% of hydrophobic surface appears solvent-exposed (6/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 13
Buried (contacted) 7
Exposed 6
LogP 1.26
H-bonds 11
Exposed fragments:
phenyl (4/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.349 | Score | -23.444 |
|---|---|---|---|
| Inter norm | -0.991 | Intra norm | -0.029 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 11 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes; high strain Δ 30.7 | ||
| Residues |
ALA244
ARG337
ASP243
ASP385
GLU384
LEU339
MET386
PHE383
PRO338
THR241
VAL335
VAL336
| ||
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 | 6 | Native recall | 0.40 |
| Jaccard | 0.29 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 316 | 1.9160126527138646 | -0.936024 | -21.449 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 278 | 1.9632061033636858 | -1.23187 | -29.5802 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 335 | 2.279560783148469 | -0.836864 | -20.633 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 298 | 2.4959341423803725 | -1.18433 | -27.7045 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 350 | 2.8871935436214495 | -1.13026 | -23.8892 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 328 | 3.34922510797409 | -0.990588 | -23.4443 | 11 | 12 | 6 | 0.40 | 0.60 | - | no | Current |
| 385 | 3.5748823696267844 | -1.1536 | -27.6164 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 347 | 3.741128851709964 | -1.38593 | -32.0766 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 3.895818972211368 | -1.29627 | -28.5384 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 4.420406439957224 | -0.972962 | -25.0114 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 248 | 4.628592872571314 | -1.0994 | -24.8798 | 15 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 5.3707651519523365 | -1.31364 | -29.8849 | 16 | 21 | 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
-23.444kcal/mol
Ligand efficiency (LE)
-1.0193kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.996
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.26
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-74.30kcal/mol
Minimised FF energy
-104.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
567.4Ų
Total solvent-accessible surface area of free ligand
BSA total
429.1Ų
Buried surface area upon binding
BSA apolar
280.3Ų
Hydrophobic contacts buried
BSA polar
148.7Ų
Polar contacts buried
Fraction buried
75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2368.3Ų
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
1381.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)