XED/Cosmic Atom Types - their definitions with hints on their allocation
'nat' | 'ityp' | type | Special Description | Valence | Hints on Allocation |
6 | 1 | C sp3 | tetrahedral | 4 | |
6 | 2 | C sp2 | trigonal | 3 | Non-aromatic or heterocycle |
6 | 3 | C aromatic | trigonal | 3 | |
6 | 4 | C sp | linear | 2 | |
7 | 5 | N sp3+ | tetrahedral | 4 | N cation |
7 | 6 | N sp3 | tetrahedral | 3 | N-pyramidal only |
7 | 7 | N azide | trigonal | 2 | Azide only |
7 | 8 | N sp2 | digonal | 2 | Always 2 valent =bond |
7 | 9 | N trig | trigonal planar | 3 | Flat- peptide, amide |
8 | 10 | Osp3 | digonal | 2 | |
8 | 11 | O sp2 | trigonal | 1 | Carbonyl only |
16 | 12 | S sp3 | tetrahedral | 6 | |
16 | 13 | S sp2 | trigonal | 1 | 1 valent only (cf. carbonyl) |
5 | 14 | P | tetrahedral | 6 | |
1 | 15 | H | single | 1 | |
9 | 16 | F | single | 1 | |
17 | 17 | CL | single | 1 | |
35 | 18 | BR | single | 1 | |
53 | 19 | I | single | 1 | |
xx | 20 | Metal | User defined | x | |
0 | 21 | Dummy | single | 1 | |
8 | 22 | O (NO2,NO3-,etc) | 1.5 | 1 | Uncharged O see special |
7 | 23 | N sp(CN) | triple | 1 | Nitrile only |
8 | 24 | O (PO &SO) | double | 2 & > | Uncharged O see special |
7 | 25 | Nsp2+ | trigonal | 3 | Cation guanidinium, pyridinium etc |
8 | 26 | Osp3 | single | 1 | Anion only- carboxylate |
8 | 27 | Notional Anion | |||
8 | 28 | Notional Cation | |||
-5 | 29 | -ve Field points | |||
-6 | 29 | +ve Field points | |||
-7 | 29 | Surface Field points | |||
-2 | 30 | lp ("rabbits ear" & tetrahedra) | Not used | ||
-1 | 31 | pz pi (PI points) | XED | ||
-2 | 32 | py lp (90degs to pi - single valence) | XED | ||
-3 | 33 | px1 lp (linear to sigma/pi bond- inner) | XED | ||
-3 | 34 | px2 lp (linear to sigma/pi bond- outer) | XED | ||
-4 | 35 | px3 lp (bond point) | XED | ||
-4 | 36 | hpt (Hydrogen bond point) | Not used |