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 mixed
SASA done
Strain ΔE
27.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.42, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.109 kcal/mol/HA)
✓ Good fit quality (FQ -10.08)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (27.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-27.725
kcal/mol
LE
-1.109
kcal/mol/HA
Fit Quality
-10.08
FQ (Leeson)
HAC
25
heavy atoms
MW
356
Da
LogP
2.23
cLogP
Interaction summary
HB 10
HY 2
PI 0
CLASH 3
⚠ Exposure 64%
Interaction summary
HB 10
HY 2
PI 0
CLASH 3
⚠ Exposure 64%
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17
Buried (contacted) 6
Exposed 11
LogP 2.23
H-bonds 10
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.866 | Score | -27.725 |
|---|---|---|---|
| Inter norm | -1.121 | Intra norm | 0.012 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 10 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes; moderate strain Δ 27.1 | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
LEU382
MET386
PHE383
PRO338
THR241
VAL336
| ||
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.42 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 613 | 0.3306519453204769 | -1.08162 | -26.4832 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 0.36934626421649913 | -1.02585 | -20.7811 | 11 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 0.3731963767257122 | -0.923569 | -24.115 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 1.6316030669638548 | -1.1021 | -24.3015 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 619 | 1.8963284840180428 | -0.922081 | -17.5343 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 603 | 2.445716149633084 | -1.02364 | -24.9584 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 625 | 2.904649738910798 | -1.08342 | -24.739 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 628 | 2.926952741865505 | -1.0052 | -20.509 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 615 | 3.336867848722131 | -0.959593 | -23.3189 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 607 | 3.6933906595283736 | -1.0718 | -26.3483 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 601 | 3.8658657511488674 | -1.1213 | -27.725 | 10 | 12 | 8 | 0.53 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.725kcal/mol
Ligand efficiency (LE)
-1.1090kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.082
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
356.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.23
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
77.20kcal/mol
Minimised FF energy
50.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
603.7Ų
Total solvent-accessible surface area of free ligand
BSA total
413.1Ų
Buried surface area upon binding
BSA apolar
323.1Ų
Hydrophobic contacts buried
BSA polar
90.0Ų
Polar contacts buried
Fraction buried
68.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2415.8Ų
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
1387.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)