CRITERIA FOR RNA :
1. Atoms nomenclature: (Since RNA can form bonds between bases, backbone, sugar etc.)
Base atoms : N1,N3,N4,N6,N7,N9,O2,O4,O6,C5,C6,C2,C8 (in terms of atoms which will participate in hbonding in A,G,C,U nucleotides)
Sugar atoms : C1', C2', O2',O4'
Backbone atoms: OP1, OP2, O5',C5',C4',C3',O3'
Donor atoms: O of HOH,O2',C1',C2',C3',C4',C5', (O3',O5' -> Only if present in terminal/end residues)
Adenine (A) -> C2,N6, N9, C8
Guanine (G) -> N1, N2, C8, N9
Cytosine (C) -> N1,N4,C5,C6
Uracil (U) -> N1,N3, C5,C6
Acceptor atoms: O of HOH,OP1,OP2, O2', O3', O4' , O5'
Adenine (A) -> N1, N3, N7,N6,N9
Guanine (G) -> N3, O6, N7,N1,N2,N9
Cytosine (C) -> O2, N3,N1,N4
Uracil (U) -> O2,O4,N1,N3
If bond is base-base , then we have to sub classify those atoms are from which edge i.e. Watson -crick (WC), Hoogsteen (H) or Sugar (S)
WC -> A -> N6, N1, C2
G -> O6, N1, N2
C-> N4, N3, O2
U-> O4, N3, O2
H-> A-> N6, N7, [ A(N6) can be of both WC or H type]
G-> O6, N7
C-> N4, C5
U-> O4, C5
S-> A-> C2, N3, O2'
G-> N2,N3, O2'
C-> O2, O2' (ribose sugar's Oxygen)
U->O2, O2'
2. All types of strong and weak hbonds is required.
3. Kindly include Water (HOH, DOD) in the donor. We would like to study what bonds water forms with other nucleotides .
4. Also, in nomenclature of donor/acceptor atoms, kindly mention if atoms is not from a nucleotide but from a HETATOM -> HOH, Metal ligands, peptides.
5. Proper annotation in HBAT hbond list of RNA atoms- eg. atoms involved in hbond are from a Base/Backbone/Sugar. (Please add more details on the same)
