name ='ribose_5ter_3ter'

H_5_terminal = Atom('H')
O_5 = Atom('O')
C_5 = Atom('C')
H_51 = Atom('H')
H_52 = Atom('H')
C_4 = Atom('C')
H_4 = Atom('H')
O_4 = Atom('O')
C_1 = Atom('C')
H_1 = Atom('H')
C_3 = Atom('C')
H_3 = Atom('H')
C_2 = Atom('C')
H_21 = Atom('H')
O_2 = Atom('O')
H_O2 = Atom('H')
O_3 = Atom('O')
H_3_terminal = Atom('H')

bonds = [Bond(O_5, H_5_terminal), Bond(C_5, O_5), Bond(H_51, C_5), Bond(H_52, C_5), Bond(C_4, C_5), Bond(H_4, C_4), Bond(O_4, C_4), Bond(C_1, O_4), Bond(H_1, C_1), Bond(C_3, C_4), Bond(H_3, C_3), Bond(C_2, C_3), Bond(H_21, C_2), Bond(O_2, C_2), Bond(H_O2, O_2), Bond(O_3, C_3), Bond(H_3_terminal, O_3), Bond(C_1, C_2), ]

pdbmap = [('R', {"2HO*": H_O2, "2H5*": H_52, "1H5*": H_51, "C5*": C_5, "C2*": C_2, "C3*": C_3, "C1*": C_1, "H5T": H_5_terminal, "O2*": O_2, "C4*": C_4, "1H2*": H_21, "H1*": H_1, "O3*": O_3, "H3*": H_3, "H3T": H_3_terminal, "H4*": H_4, "O4*": O_4, "O5*": O_5, })]
pdb_alternative = {"H2'": "2HO*", "2HO'": "2HO*", "2H5'": "2H5*", "1H5'": "1H5*", "C5'": "C5*", "C2'": "C2*", "C3'": "C3*", "C1'": "C1*", "O2'": "O2*", "C4'": "C4*", "H1'": "H1*", "O3'": "O3*", "H3'": "H3*", "H4'": "H4*", "O4'": "O4*", "O5'": "O5*"}

amber_atom_type = {H_O2: 'HO', H_52: 'H1', H_51: 'H1', C_5: 'CT', C_2: 'CT', C_3: 'CT', C_1: 'CT', H_5_terminal: 'HO', O_2: 'OH', C_4: 'CT', H_21: 'H1', H_1: 'H2', O_3: 'OH', H_3: 'H1', H_3_terminal: 'HO', H_4: 'H1', O_4: 'OS', O_5: 'OH', }
