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)
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)
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