C_beta = Atom('CH2')
C_delta_1 = Atom('CH')
C_delta_2 = Atom('C')
C_epsilon_2 = Atom('C')
C_epsilon_3 = Atom('CH')
C_eta_2 = Atom('CH')
C_gamma = Atom('C')
C_zeta_2 = Atom('CH')
C_zeta_3 = Atom('CH')
H_epsilon_1 = Atom('H')
N_epsilon_1 = Atom('N')
bonds = [Bond(C_gamma, C_beta), Bond(C_delta_1, C_gamma), Bond(N_epsilon_1, C_delta_1), Bond(H_epsilon_1, N_epsilon_1), Bond(C_epsilon_2, N_epsilon_1), Bond(C_zeta_2, C_epsilon_2), Bond(C_eta_2, C_zeta_2), Bond(C_zeta_3, C_eta_2), Bond(C_epsilon_3, C_zeta_3), Bond(C_delta_2, C_epsilon_3), Bond(C_gamma, C_delta_2), Bond(C_epsilon_2, C_delta_2), ]
opls_atom_type = {C_gamma: 'C*', H_epsilon_1: 'H', C_eta_2: 'CD', C_zeta_3: 'CD', C_epsilon_2: 'CN', N_epsilon_1: 'NA', C_zeta_2: 'CD', C_delta_2: 'CB', C_delta_1: 'CG', C_epsilon_3: 'CD', C_beta: 'C2', }
opls_charge = {C_gamma: -.055, H_epsilon_1: .42, C_eta_2: 0.0, C_zeta_3: .0, C_epsilon_2: .13, N_epsilon_1: -.57, C_zeta_2: 0., C_delta_2: -.055, C_delta_1: .13, C_epsilon_3: 0.0, C_beta: 0.0, }
name = 'tru_sidechain'
pdbmap = [('TRU', {'NE1': N_epsilon_1, '1HE': H_epsilon_1, 'CD2': C_delta_2, 'CD1': C_delta_1, 'CE3': C_epsilon_3, 'CH2': C_eta_2, 'CZ3': C_zeta_3, 'CG': C_gamma, 'CB': C_beta, 'CZ2': C_zeta_2, 'CE2': C_epsilon_2, }, ), ]
pdb_alternative = {'HE1': '1HE', 'HB1': '3HB', }






