Self-consistent fast ion distributions are usually obtained using a code that solves the guiding-centre equations, with an appropriate fast ion source (e.g. NBI pinis) and sink (e.g. collision operators). Straight field-line coordinate systems, such as Boozer coordinates, are ordinarily convenient due to the simple separation of longitudinal and cross-field motion, and the simple expression of magnetic differential operators. However, these coordinates are found to be near-singular at the boundary of the internal helical region associated with an n = m = 1 infernal mode. These important configurations are associated with many tokamak phenomena, including snakes and long-lived modes [1] in spherical or more conventional devices. Such internal helical states occur when there is a radially extended region where the safety factor is close to unity. Recent calculations predict the possibility of helical equilibria in ITER hybrid scenarios [2]. The ANIMEC code [3] conveniently produces an equilibrium helical state despite choosing for example an axisymmetric fixed boundary. The corresponding magnetic field in these coordinates can now be fed to the newly devised Particle-In-Cell (PIC) code VENUS-LEVIS, which has been upgraded with phase-space Lagrangian guiding-centre orbit equations [4], embodying full 3D anisotropic electromagnetic fields and a formulation that is independent of coordinate choice, despite retaining intrinsic Hamiltonian properties. The simulations are applied to MAST experiments where the presence of along-lived mode can effect confinement of neutral beam ions, potentially affecting NBI heating and current drive [1]. Neighbouring equilibria from ANIMEC, one helical in the core and the other axisymmetic, permits a precise means of identifying the effect of 3D geometry on the simulated confinement properties of MAST's neutral beam fast ion population. In agreement with the compared experimental data from MAST neutron camera, a significant fraction of particles are pushed out of the helical core region affecting both the measured radial neutron distribution and the heating and current drive properties of the neutral beam population.