Rename the functional element N2d to N1d 

- to be consistent with the definition of N3 and N5
- N1d is a nitrogen atom that has one single bond and provides one
electron to bonding

e.g.: H2NN

1 H 0 0 {3,S}
2 H 0 0 {3,S}
3 N5d 0 0 {1,S} {2,S} {4,D}
4 N1d 0 2 {3,D}
Correct adjacency list of He in molecule.py