10.4. Local Geometry and Stereochemistry

10.4.1. Stereospecific Aconitase

Modelling of the reaction performed by the aconitase enzyme in the citric acid cycle: citrate to D-isocitrate. The rule implements the stereo-specificity of the reaction.

Explore in the playground.

 1water = smiles("O", "H_2O")
 2cit = smiles("C(C(=O)O)C(CC(=O)O)(C(=O)O)O", name="Cit")
 3d_icit = smiles("C([C@@H]([C@H](C(=O)O)O)C(=O)O)C(=O)O", name="D-ICit")
 4
 5aconitase = ruleGMLString("""rule [
 6   ruleID "Aconitase"
 7   left [
 8      # the dehydrated water
 9      edge [ source 1 target 100 label "-" ]
10      edge [ source 2 target 102 label "-" ]
11      # the hydrated water
12      edge [ source 200 target 202 label "-" ]
13   ]
14   context [
15      node [ id 1 label "C" ]
16      edge [ source 1 target 2 label "-" ] # goes from - to = to -
17      node [ id 2 label "C" ]
18      # the dehydrated water
19      node [ id 100 label "O" ]
20      edge [ source 100 target 101 label "-" ]
21      node [ id 101 label "H" ]
22      node [ id 102 label "H" ]
23      # the hydrated water
24      node [ id 200 label "O" ]
25      edge [ source 200 target 201 label "-" ]
26      node [ id 201 label "H" ]
27      node [ id 202 label "H" ]
28      # dehydrated C neighbours
29      node [ id 1000 label "C" ]
30      edge [ source 1 target 1000 label "-" ]
31      node [ id 1010 label "O" ]
32      edge [ source 1000 target 1010 label "-" ]
33      node [ id 1001 label "C" ]
34      edge [ source 1 target 1001 label "-" ]
35      # hydrated C neighbours
36      node [ id 2000 label "C" ]
37      edge [ source 2 target 2000 label "-" ]
38      node [ id 2001 label "H" ]
39      edge [ source 2 target 2001 label "-" ]
40   ]
41   right [
42      # The '!' in the end changes it from TetrahedralSym to
43      # TetrahedralFixed
44      node [ id 1 stereo "tetrahedral[1000, 1001, 202, 2]!" ]
45      node [ id 2 stereo "tetrahedral[200, 1, 2000, 2001]!" ]
46      # the dehydrated water
47      edge [ source 100 target 102 label "-" ]
48      # the hydrated water
49      edge [ source 1 target 202 label "-" ]
50      edge [ source 2 target 200 label "-" ]
51   ]
52]""")
53
54dg = DG(graphDatabase=inputGraphs,
55      labelSettings=LabelSettings(
56         LabelType.Term,
57         LabelRelation.Specialisation,
58         LabelRelation.Specialisation))
59dg.build().execute(addSubset(cit, water) >> aconitase)
60for e in dg.edges:
61   p = GraphPrinter()
62   p.withColour = True
63   e.print(p, matchColour="Maroon")

10.4.2. Stereoisomers of Tartaric Acid

Generation of stereoisomers of tartaric acid, starting from a model without stereo-information and fixating each tetrahedral embedding.

Explore in the playground.

 1smiles("C(C(C(=O)O)O)(C(=O)O)O", name="Tartaric acid")
 2smiles("[C@@H]([C@H](C(=O)O)O)(C(=O)O)O", name="L-tartaric acid")
 3smiles("[C@H]([C@@H](C(=O)O)O)(C(=O)O)O", name="D-tartaric acid")
 4smiles("[C@@H]([C@@H](C(=O)O)O)(C(=O)O)O", name="Meso-tartaric acid")
 5change = ruleGMLString("""rule [
 6   ruleID "Change"
 7   left [
 8      node [ id 0 stereo "tetrahedral" ]
 9   ]
10   context [
11      node [ id 0 label "*" ]
12      node [ id 1 label "*" ]
13      node [ id 2 label "*" ]
14      node [ id 3 label "*" ]
15      node [ id 4 label "*" ]
16      edge [ source 0 target 1 label "-" ]
17      edge [ source 0 target 2 label "-" ]
18      edge [ source 0 target 3 label "-" ]
19      edge [ source 0 target 4 label "-" ]
20   ]
21   right [
22      node [ id 0 stereo "tetrahedral[1, 2, 3, 4]!" ]
23   ]
24]""")
25
26dg = DG(graphDatabase=inputGraphs,
27      labelSettings=LabelSettings(
28         LabelType.Term,
29         LabelRelation.Specialisation,
30         LabelRelation.Specialisation))
31dg.build().execute(addSubset(inputGraphs) >> repeat(change))
32
33p = GraphPrinter()
34p.setMolDefault()
35p.withPrettyStereo = True
36change.print(p)
37p = DGPrinter()
38p.withRuleName = True
39p.withRuleId = False
40dg.print(p)

10.4.3. Non-trivial Stereoisomers

Generation of stereoisomers in a non-trivial molecule.

Explore in the playground.

 1g = smiles("N[C@](O)([C@](S)(P)(O))([C@](S)(P)(O))")
 2change = ruleGMLString("""rule [
 3   ruleID "Change"
 4   left [
 5      node [ id 0 stereo "tetrahedral" ]
 6   ]
 7   context [
 8      node [ id 0 label "*" ]
 9      node [ id 1 label "*" ]
10      node [ id 2 label "*" ]
11      node [ id 3 label "*" ]
12      node [ id 4 label "*" ]
13      edge [ source 0 target 1 label "-" ]
14      edge [ source 0 target 2 label "-" ]
15      edge [ source 0 target 3 label "-" ]
16      edge [ source 0 target 4 label "-" ]
17   ]
18   right [
19      node [ id 0 stereo "tetrahedral[1, 2, 3, 4]!" ]
20   ]
21]""")
22
23dg = DG(graphDatabase=inputGraphs,
24      labelSettings=LabelSettings(
25         LabelType.Term,
26         LabelRelation.Specialisation,
27         LabelRelation.Specialisation))
28dg.build().execute(addSubset(inputGraphs) >> repeat(change))
29
30p = GraphPrinter()
31p.setMolDefault()
32p.withPrettyStereo = True
33change.print(p)
34p = DGPrinter()
35p.withRuleName = True
36p.withRuleId = False
37dg.print(p)