;----------------------------TITLE ----------------------------------------------------------------------------------------- ; Bistriflimide ; ; This file was generated at 03:36 on 2021-02-13 by ; ; Automatic Topology Builder ; ; REVISION 2021-02-02 11:21:59 ;--------------------------------------------------------------------------------------------------------------------------- ; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark ; ; Institute : Molecular Dynamics group, ; School of Chemistry and Molecular Biosciences (SCMB), ; The University of Queensland, QLD 4072, Australia ; URL : https://atb.uq.edu.au ; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. ; An Automated force field Topology Builder (ATB) and repository: version 1.0. ; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037. ; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE. ; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane. ; DOI:10.1021/acs.jctc.8b00768 ; ; Disclaimer : ; While every effort has been made to ensure the accuracy and validity of parameters provided below ; the assignment of parameters is being based on an automated procedure combining data provided by a ; given user as well as calculations performed using third party software. They are provided as a guide. ; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided ; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion ; and to perform additional validation tests for their specific application if required. Neither the authors ; of the ATB or The University of Queensland except any responsibly for how the parameters may be used. ; ; Release notes and warnings: ; (1) The topology is based on a set of atomic coordinates and other data provided by the user after ; after quantum mechanical optimization of the structure using different levels of theory depending on ; the nature of the molecule. ; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous. ; In these cases alternative type codes are provided at the end of the line. ; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral ; type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard" ; or "uncertain" in comments. ; (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder ; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually ; before the file can be used. ;--------------------------------------------------------------------------------------------------------------------------- ; Input Structure : UYKS ; Output : UNITED ATOM topology ; Use in conjunction with the corresponding united atom PDB file. ;--------------------------------------------------------------------------------------------------------------------------- ; Citing this topology file ; ATB molid: 348621 ; ATB Topology Hash: bd0ae ;--------------------------------------------------------------------------------------------------------------------------- ; Final Topology Generation was performed using: ; A B3LYP/6-31G* optimized geometry. ; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set. ; Initial charges were estimated using the ESP method of Merz-Kollman. ; Final charges and charge groups were generated by method described in the ATB paper. ; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory. ;--------------------------------------------------------------------------------------------------------------------------- ; ; [ UYKS ] [ moleculetype ] ; Name nrexcl UYKS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 F 1 UYKS F6 1 -0.106 18.9984 2 C 1 UYKS C2 2 0.336 12.0110 3 F 1 UYKS F4 3 -0.106 18.9984 4 F 1 UYKS F5 4 -0.106 18.9984 5 SDmso 1 UYKS S1 5 0.774 32.0600 6 OM 1 UYKS O3 6 -0.489 15.9994 7 OM 1 UYKS O4 7 -0.489 15.9994 8 NOpt 1 UYKS N1 8 -0.628 14.0067 9 SDmso 1 UYKS S2 9 0.774 32.0600 10 OM 1 UYKS O1 10 -0.489 15.9994 11 OM 1 UYKS O2 11 -0.489 15.9994 12 C 1 UYKS C1 12 0.336 12.0110 13 F 1 UYKS F1 13 -0.106 18.9984 14 F 1 UYKS F2 14 -0.106 18.9984 15 F 1 UYKS F3 15 -0.106 18.9984 ; total charge of the molecule: -1.000 [ bonds ] ; ai aj funct c0 c1 1 2 2 0.1340 1.0500e+07 2 3 2 0.1340 1.0500e+07 2 4 2 0.1340 1.0500e+07 2 5 2 0.1870 3.5900e+06 5 6 2 0.1470 8.7100e+06 5 7 2 0.1470 8.7100e+06 5 8 2 0.1610 4.8400e+06 8 9 2 0.1610 4.8400e+06 9 10 2 0.1470 8.7100e+06 9 11 2 0.1470 8.7100e+06 9 12 2 0.1870 3.5900e+06 12 13 2 0.1340 1.0500e+07 12 14 2 0.1340 1.0500e+07 12 15 2 0.1340 1.0500e+07 [ pairs ] ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 1 6 1 1 7 1 1 8 1 2 9 1 3 6 1 3 7 1 3 8 1 4 6 1 4 7 1 4 8 1 5 10 1 5 11 1 5 12 1 6 9 1 7 9 1 8 13 1 8 14 1 8 15 1 10 13 1 10 14 1 10 15 1 11 13 1 11 14 1 11 15 1 [ angles ] ; ai aj ak funct angle fc 1 2 3 2 109.00 1680.51 1 2 4 2 109.00 1680.51 1 2 5 2 110.30 524.00 3 2 4 2 109.00 1680.51 3 2 5 2 110.30 524.00 4 2 5 2 110.30 524.00 2 5 6 2 104.00 490.00 2 5 7 2 104.00 490.00 2 5 8 2 106.00 1733.55 6 5 7 2 119.00 2211.40 6 5 8 2 109.00 1680.51 7 5 8 2 109.00 1680.51 5 8 9 2 124.00 3074.03 8 9 10 2 109.00 1680.51 8 9 11 2 109.00 1680.51 8 9 12 2 106.00 1733.55 10 9 11 2 119.00 2211.40 10 9 12 2 104.00 490.00 11 9 12 2 104.00 490.00 9 12 13 2 110.30 524.00 9 12 14 2 110.30 524.00 9 12 15 2 110.30 524.00 13 12 14 2 109.00 1680.51 13 12 15 2 109.00 1680.51 14 12 15 2 109.00 1680.51 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc [ dihedrals ] ; ai aj ak al funct ph0 cp mult 3 2 5 8 1 0.00 2.93 3 5 8 9 10 1 180.00 1.00 3 6 5 8 9 1 180.00 1.00 3 8 9 12 13 1 0.00 2.93 3 [ exclusions ] ; ai aj funct ; GROMOS 1-4 exclusions