Status

Success

 

User

16606

Elapsed Time

00:00:02

Start

09/24/22 10:38:30

Finish

09/24/22 10:38:32

Server Name

DS Version

19.1.0.18287

PP Version

19.1.0.1963

DS Client Version

19.1.0.18287

Server Ports

9944 (9943)

OS Distribution

Windows

OS Version

10.0.22000

Memory Total

23.85 GB

Memory Free

12.51 GB

Protocol Settings

Input Ligands

NonStandard Name Property

False

Name Property

Change Ionization

True

Ionization Method

pH Based

pH Based

Minimum pH

7.4

Maximum pH

7.4

Rule Based

Acid Ionization

Carboxylate

Base Ionization

Ionization Enumeration

One Protomer

Filter SMARTS

Remove Charges

Generate Tautomers

False

Enumerate What

AllTautomers

Maximum Number of Tautomers

10

ConsiderCarbonAsDonor

Never

MakeAllSp2AtomsAcceptors

False

Perceive Charge Tautomerization

False

Amides Tautomerization

Tautomerize Only Diamides

Preserve Aromaticity

False

Generate Isomers

False

EnumerateWhat

SkipStereoAtomsAtBridgeHeads

True

AcceptInputStereoAsMarked

True

 

Fix Bad Valencies

True

Generate Coordinates

3D

Rearrange Hydrogens

True

Parallel Processing

False

Batch Size

25

Server

localhost

Server Processes

2

Preserve Order

True

Advanced

Duplicate Structures

Remove

SMIRKS Acid Templates

# ACIDS [#6:1][SX4:2](=[O:3])(=[O:4])[OH:6]>>[#6:1][SX4:2](=[O:3])(=[O:4])[O-:6] Sulfonate [#6:1][OX2:2][PX4:3](=[O:4])([O+0:5][#1,#6:6])[OH:7]>>[#6:1][OX2:2][PX4:3](=[O:4])([O+0:5][#1,#6:6])[O-:7] Phosphate (1st ionization) [#6:1][OX2:2][PX4:3](=[O:4])([OH,O-:5])[OH:7]>>[#6:1][OX2:2][PX4:3](=[O:4])([O-:5])[O-:7] Phosphate (2nd ionization) [#6:1][C:2](=[O:3])[OH:4]>>[#6:1][C:2](=[O:3])[O-:4] Carboxylate [#6:1][OX2:2][SX4:3](=[O:4])(=[O:5])[OH:6]>>[#6:1][OX2:2][SX4:3](=[O:4])(=[O:5])[O-:6] Sulfate [#6:1][SX3:2](=[O:3])[OH:4]>>[#6:1][SX3:2](=[O:3])[O-:4] Sulfinic Acid [#6:1][PX4:2](=[O:3])([OH:4])[OX2:5][#6,#1:6]>>[#6:1][PX4:2](=[O:3])([O-:4])[OX2:5][#6,#1:6] Phosphonates (1st ionization) [#6:1][PX4:2](=[O:3])([OH:4])[OH:5]>>[#6:1][PX4:2](=[O:3])([O-:4])[O-:5] Phosphonates (2nd ionization) [#6:1][PX4:2](=[O:3])([OH:4])[#6:5]>>[#6:1][PX4:2](=[O:3])([O-:4])[#6:5] Phosphinates [c:1][SX2H:2]>>[c:1][S-:2] Thiol (aryl) [C:1][SX2:2][H]>>[C:1][S-1:2] Thiol (aliphatic) [*:1][c:2]1[n:3][n:4][nH:5][n:6]1>>[*:1][c:2]1[n:3][n:4][n-:5][n:6]1 Tetrazolates 1 [*:1][c:2]1[n:3][n:4][n:5][nH:6]1>>[*:1][c:2]1[n:3][n:4][n:5][n-:6]1 Tetrazolates 2 [#6,H:1][CX3:2](=[O:3])[SH:4]>>[#6,H:1][CX3:2](=[O:3])[S-:4] Thiocarboxylates [#6,H:1][CX3:2](=[S:3])[SH:4]>>[#6,H:1][CX3:2](=[S:3])[S-:4] Dithiocarboxylates [c:1][SX4:2]([NH2:3])(=[OX1:4])(=[OX1:5])>>[c:1][SX4:2]([NH-:3])(=[OX1:4])(=[OX1:5]) Sulfonamides (aryl) [#6:1][CX3:2](=[O:3])[NH:4][CX3:5](=[O:6])[#6:7]>>[#6:1][CX3:2](=[O:3])[N-1:4][CX3:5](=[O:6])[#6:7] N-Acyl Amide [c:1][OX2H:2]>>[c:1][O-:2] Phenol [CX4:1][SX4:2]([NH2])(=[OX1:3])(=[OX1:4])>>[CX4:1][SX4:2]([N-1])(=[OX1:3])(=[OX1:4]) Sulfonamide (alkyl) [#6:4][NHX3:2][CX3:1](=[OX1:3])[#6:5]>>[#6:4][N-1:2][CX3:1](=[OX1:3])[#6:5] Amides [#6,H:1][CX3:2](=[O:3])[NX3:4]([OH:5])>>[#6,H:1][CX3:2](=[O:3])[NX3:4]([O-1:5]) Hydroxamates

SMIRKS Base Templates

# BASES ['$'([N+0X3]([H])([H])[CX4]):1]>>[N+1:1]([H]) Amine (primary) ['$'([N+0X3]([H])([CX4])[CX4]):1]>>[N+1:1]([H]) Amine (secondary) ['$'([N+0X3]([CX4])([CX4])[CX4]):1]>>[N+1:1]([H]) Amine (tertiary) [c:1][N+0:2]([CX4,H:3])[CX4,H:4]>>[c:1][N+1:2]([H])([CX4,H:3])[CX4,H:4] Amine (aryl) [#6,H:1][N+0X3:2]([#6,H:3])[C:4](=[N+0X2:5][CX4,H:6])[N+0X3:7]([#6,H:8])[#6,H:9]>>[#6,H:1][N+0:2]([#6,H:3])[C:4](=[N+1:5]([H])[#6,H:6])[N+0:7]([#6,H:8])[#6,H:9] Guanidine [#6,H:1][N+0X3:2]([#6,H:3])[C:4](=[N+0X2:5][#6,H:6])[#6,H:7]>>[#6,H:1][N+0:2]([#6,H:3])[C:4](=[N+1:5]([H])[#6,H:6])[#6,H:7] Amidine [CX4:1][N+0X3:2]([#6,H:3])[N:4]([#6,H:5])[#6,H:6]>>[CX4:1][N+1:2]([H])([#6,H:3])[N:4]([#6,H:5])[#6,H:6] Hydrazine (alkyl) [CX4,H:1][#6:2]1:[#6:3]([CX4,H:4])[#7+0:5][#6:6]([CX4,H:7]):[#7X2+0:8]1>>[CX4,H:1][#6:2]1:[#6:3]([CX4,H:4])[#7+0:5][#6:6]([CX4,H:7]):[#7+1:8]1[H] Imidazole [c:1][N+0X3:2]([CX4,H:3])[N:4]([CX4,H:5])[CX4,H:6]>>[c:1][N+1:2]([H])([CX4,H:3])[N:4]([CX4,H:5])[CX4,H:6] Hydrazine (aryl) [C,H:1][C:2](=[O:3])[N+0X3:4]([CX4,H:5])[N+0X3:6]([CX4,H:7])[CX4,H:8]>>[C,H:1][C:2](=[O:3])[N+0:4]([CX4,H:5])[N+1:6]([H])([CX4,H:7])[CX4,H:8] Hydrazide

SMARTS Charge Templates

# SMARTS Rules for filtering molecules with charges # positive charges separated by 1 bond length [+,+2,+3,+4,+5,+6,+7;!'$'([+,+2,+3,+4,+5,+6,+7]~[-,-2,-3,-4,-5,-6,-7])]~[+,+2,+3,+4,+5,+6,+7;!'$'([+,+2,+3,+4,+5,+6,+7]~[-,-2,-3,-4,-5,-6,-7])] Positive 1-Bond # positive charges separated by 2 bond length [+,+2,+3,+4,+5,+6,+7;!'$'([+,+2,+3,+4,+5,+6,+7]~[-,-2,-3,-4,-5,-6,-7])]~[*]~[+,+2,+3,+4,+5,+6,+7;!'$'([+,+2,+3,+4,+5,+6,+7]~[-,-2,-3,-4,-5,-6,-7])] Positive 2-Bonds # positive charges separated by 3 bond length [+,+2,+3,+4,+5,+6,+7;!'$'([+,+2,+3,+4,+5,+6,+7]~[-,-2,-3,-4,-5,-6,-7])]~[*]~[*]~[+,+2,+3,+4,+5,+6,+7;!'$'([+,+2,+3,+4,+5,+6,+7]~[-,-2,-3,-4,-5,-6,-7])] Positive 3-Bonds # negative charges separated by 1 bond length [-,-2,-3,-4,-5,-6,-7;!'$'([-,-2,-3,-4,-5,-6,-7]~[+,+2,+3,+4,+5,+6,+7])]~[-,-2,-3,-4,-5,-6,-7;!'$'([-,-2,-3,-4,-5,-6,-7]~[+,+2,+3,+4,+5,+6,+7])] Negative 1-Bonds # negative charges separated by 2 bond length [-,-2,-3,-4,-5,-6,-7;!'$'([-,-2,-3,-4,-5,-6,-7]~[+,+2,+3,+4,+5,+6,+7])]~[*]~[-,-2,-3,-4,-5,-6,-7;!'$'([-,-2,-3,-4,-5,-6,-7]~[+,+2,+3,+4,+5,+6,+7])] Negative 2-Bonds # negative charges separated by 3 bond length [-,-2,-3,-4,-5,-6,-7;!'$'([-,-2,-3,-4,-5,-6,-7]~[+,+2,+3,+4,+5,+6,+7])]~[*]~[*]~[-,-2,-3,-4,-5,-6,-7;!'$'([-,-2,-3,-4,-5,-6,-7]~[+,+2,+3,+4,+5,+6,+7])] Negative 3-Bonds