Macrocycle Threading

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Distance

DD, DIS, MDIS, MDISG, ODIS, OPOS, OPOS2, ORAD, ORAD2, POS, RAD

Angle

ANG, ANG2, AXANG, AXANG2, DIH, DIH2, PANG, PVANG

Coordination

CNFF, CNGFF, CNSW, CNGSW, CNRF, CNGRF

Shape

ACYL, ASPH, EVEC, PMGTD, PMOGT, PLANE, RGYR, RMSDT, SANIS

Nucleic Acids

NALBPP, NASBPP, NASBPPOLD, NALSTP, NASSTP, NASSTPOLD, NASBO, NAPBO, NABEND

Puckering

PUCK6Q, PUCK6P, PUCK6T, PUCK5Q, PUCK5P

Special

WORMPOS, WORMANG

Energy

POT, EGAP

Algebra

ADD, SUB, MULT, DIV, FSWITCH, RSWITCH

Macrocycle Threading

PMFLib offers two collective variables, WORMPOS and WORMANG, for the description of the mutual position of a macrocycle (host) and an axle (guest) in a complex. Their mathematical definition is rather intricate. Therefore, we will here provide only their setup and geometrical meaning.

The collective variable WORMPOS aims to determine the parametric position of the guest towards the host. The position is defined by the intersection between the guest worm-like representation and the plane representing the host. The guest can be discretized by control points corresponding to centers of masses (COMs) of selected guest fragments. The plane is obtained by the root-mean-square fit to selected atoms of the host. Since the guest can be naturally bent, there might be more intersections. Thus, the intersection is searched only within a selector zone represented by a sphere centered on the host COM. The parameters of the selector zone (seldist and steepness parameters) ensure that only the intersection occurring in the host cavity is considered.

The supplementary collective variable WORMANG is defined as an angle between the normal vector of the plane and a worm segment within the selector zone.

References

• Kulkarni, S. G.; Jelinkova, K.; Necas, M.; Pruckova, Z.; Rouchal, M.; Dastychova, L.; Kulhanek, P.; Vicha, R. A Photochemical/Thermal Switch Based on 4,4 ’-Bis(Benzimidazolio)Stilbene: Synthesis and Supramolecular Properties. ChemPhysChem 2020, 21 (18), 2084–2095. https://doi.org/10.1002/cphc.202000472.

Examples

[WORMPOS]
name        tau
nsegs       6
totlen      19.339
alpha_a     0.0000
alpha_b     0.1993
alpha_c     0.3983
alpha_d     0.6019
alpha_e     0.8009
alpha_f     1.0000

group_a     :1-7 & (!@H=)
x_direction :1@O4
y_direction :3@O4
seldist       1.968
steepness     2.334

segment_a   :8@C4,C5,C6,C7,C8,C9
segment_b   :8@C11
segment_c   :8@C14,C16,C17
segment_d   :8@C20,C21,C23
segment_e   :8@C26
segment_f   :8@C29,C30,C31,C32,C33,C34

[WORMANG]
name        chi
nsegs       6

group_a     :1-7 & (!@H=)
x_direction :1@O4
y_direction :3@O4
seldist       1.968
steepness     2.334
wmode       com

segment_a   :8@C4,C5,C6,C7,C8,C9
segment_b   :8@C11
segment_c   :8@C14,C16,C17
segment_d   :8@C20,C21,C23
segment_e   :8@C26
segment_f   :8@C29,C30,C31,C32,C33,C34