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* \\\\ CHARMM27 All-Hydrogen Nucleic Acid Parameter File ////
* \\\\\\\\\\\\\\\\\\ Developmental ////////////////////////
* Alexander D. MacKerell Jr. and Nicolas Foloppe
* December, 2003
* All comments to ADM jr. via the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
!
!references
!
!NUCLEIC ACIDS
!
!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and
!Condensed Phase Macromolecular Target Data. 2000, 21: 86-104.
!
!and
!
!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
!and RNA in Solution. 2000, 21: 105-120.
!
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
!2-(aminobutyl)-1,3-propandiol terms
CN8 NN6 200.000 1.480 ! methylammonium
NN6 HN1 403.000 1.040 ! methylammonium
!abasic deoxynucleoside
ON6 CN8B 260.0 1.420 ! susil
CN8 CN8B 222.50 1.528 ! Alkanes, sacred
!
!NICH parameters to maintain back compatibility following
!atom type switch from HN3 to HN6
CN3C HN6 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95
CN3 HN6 350.0 1.09 !nadh, adm jr., 8/98
!
CN1 CN3 302.0 1.409 !U, adm jr. 11/97
CN1 CN3T 302.0 1.403 !T, adm jr. 11/97
CN1A CN3 302.0 1.480 !nad/ppi, jjp1/adm jr. 7/95
CN1 CN5G 302.0 1.360 !G, adm jr. 11/97
CN1A NN1 560.0 1.360 !nad/ppi, jjp1/adm jr. 7/95
CN1 NN2 380.0 1.367 !C, adm jr. 11/97
CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97
CN1 NN2G 340.0 1.396 !G, adm jr. 11/97
CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97
CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97
CN1 NN3 350.0 1.335 !C, adm jr. 11/97
CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91
CN1A ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95
CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95
CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91
CN2 CN3 320.0 1.406 !C, adm jr. 11/97
CN2 CN3D 260.0 1.405 !5mc, adm jr. 9/9/93, from cn2 cn3
CN2 CN5 360.0 1.358 !A, adm jr. 11/97
CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91
CN2 NN2G 400.0 1.392 !G
CN2 NN3 450.0 1.343 !C
CN2 NN3A 400.0 1.342 !A, adm jr. 11/97
CN2 NN3G 320.0 1.326 !G, adm jr. 11/97
CN3 CN3 500.0 1.326 !C,U adm jr. 11/97
CN3 CN3T 560.0 1.320 !T, adm jr. 11/97
CN3A CN3 450.0 1.360 !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3 420.0 1.350 !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3 420.0 1.320 !nadh/ppi, jjp1/adm jr. 7/95
CN3D CN3 560.0 1.335 !5mc, adm jr. 9/9/93, from cn3 cn3
CN3 CN8 222.5 1.490 !nadh/ppi, jjp1/adm jr. 7/95
CN3D CN9 230.0 1.480 !5mc, adm jr. 9/9/93, from cn3 cn9
CN3T CN9 230.0 1.478 !T, adm jr. 11/97
CN3 HN3 350.0 1.09 !C,U, JWK
CN3T HN3 350.0 1.09 !T, JWK
CN3 HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95
CN3A HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95
CN3B HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95
CN3C HN3 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95
CN3 NN2 302.0 1.343 !C, adm jr. 11/97
CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97
CN3B NN2 420.0 1.315 !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2 420.0 1.355 !nadh/ppi, jjp1/adm jr. 7/95
CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91
CN4 NN2 320.0 1.374 !A, adm jr. 11/97
CN4 NN2B 300.0 1.378 !G, adm jr. 11/97
CN4 NN2G 350.0 1.365 !Inosine, adm jr. 2/94
CN4 NN3A 420.0 1.322 !A, adm jr. 11/97
CN4 NN3I 450.0 1.295 !Inosine, adm jr. 2/94
CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97
CN5 CN5 310.0 1.361 !A, adm jr. 11/97
CN5 CN5G 320.0 1.350 !G, adm jr. 11/97
CN5 NN2 300.0 1.375 !A, adm jr. 11/97
CN5 NN2B 302.0 1.375 !G, adm jr. 11/97
CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91
CN5 NN3G 350.0 1.315 !G, adm jr. 11/97
CN5 NN3I 350.0 1.332 !Inosine, adm jr. 9/98
CN5 NN4 310.0 1.355 !A, adm jr. 11/97
CN5G NN4 310.0 1.365 !G, adm jr. 11/97
CN8 CN8 222.50 1.528 !Alkanes, sacred
CN8 CN9 222.50 1.528 !Alkanes, sacred
CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR.
CN8 ON5 428.0 1.42 !RIBOSE, MeOH
CN9 HN9 322.0 1.111 !alkanes
CN9 ON2 340.0 1.43 !DMP, ADM Jr.
HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91
HN2 NN2 474.0 1.01 !C,U, JWK
HN2 NN2B 474.0 1.01 !G, adm jr. 11/97
HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91
HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91
HN4 ON4 545.0 0.960 !MP_1, ADM Jr.
HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM)
HT OT 450.0 0.9572 ! from TIPS3P geometry
ON2 P 270.0 1.60 !DMP, ADM Jr.
ON3 P 580.0 1.48 !DMP, ADM Jr.
ON4 P 237.0 1.58 !MP_1, ADM Jr.
ON2 P2 300.0 1.68 !nad/ppi, jjp1/adm jr. 7/95
ON3 P2 480.0 1.53 !nad/ppi, jjp1/adm jr. 7/95
ON2 P3 300.0 1.68 !PPI2, from nad/ppi, adm jr. 7/01
ON3 P3 480.0 1.53 !PPI2, from nad/ppi, adm jr. 7/01
ON4 P3 237.0 1.58 !PPI2, from MP_1, ADM Jr.
NN5 HN1 460.0 1.01 !sugar model, adm jr.
!@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@
CN7B ON6 260.0 1.420 ! From exp
CN7B CN8 200.0 1.518 ! From exp
CN7 ON6 240.0 1.446 ! Fom exp.
CN7 CN7 222.5 1.529 ! From exp
CN7 CN8 222.5 1.516 ! From exp.
CN7 CN9 222.5 1.516 ! for 5MET, From alkanes
CN7 HN7 309.0 1.111 !Alkanes, sacred
CN8 HN8 309.0 1.111 !Alkanes, sacred
CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF)
!@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@
!@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@
CN7B ON6B 260.0 1.420 ! From CN7B ON6
CN7 ON6B 240.0 1.480 ! From CN7 ON6
CN7B CN7B 200.0 1.450 !
CN7 CN7B 222.5 1.460 ! Specific to RNA
!@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@
!@@@@@@@@@ Begining of endocyclic bonds for arabinose @@@@@@@@@
! Transfered from DNA
CN7B CN7C 200.0 1.518 ! For arabinose, from CN7B CN8
CN7 CN7C 222.5 1.516 ! For arabinose, from CN7 CN8
CN7C HN7 309.0 1.111 ! From CN8 HN7
!@@@@@@@@@ End of endocyclic bonds for arabinose @@@@@@@@@
!@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@
CN7 CN8B 222.5 1.512 ! From exp.
CN8B ON2 320.0 1.44 ! From exp
!CN8B ON5 250.0 1.44 ! From CN8B ON2
CN8B ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
CN7 ON2 310.0 1.433 ! From exp
CN7B ON2 310.0 1.433 ! From exp, for NADPH etc.
!CN7 ON5 250.0 1.420 ! ALLOW ALI ALC ARO
CN7 ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
! C1'-N9 (purines)/C1'-N1 (pyrimidines)
CN9 NN2 400.0 1.456 !9-M-A/C, adm jr.
CN8 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
CN9 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
CN7B NN2 220.0 1.456 !A/C
CN7B NN2B 220.0 1.458 !G/T/U
! C5'-H in model compounds and DNA
CN8B HN8 309.0 1.111 !Alkanes, sacred
ON5 HN5 545.0 0.960 !RIBOSE, MeOH
!@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@
!@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@
!CN7B ON5 250.0 1.400 ! From CN7 ON5
CN7B ON5 428.0 1.400 ! check adm jr.,
!FC should be 428.000 based on Meoh
!@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@
!@@@@@@@@@ Begining of exocyclic bonds for arabinose @@@@@@@@@
!CN7C ON5 250.0 1.400 ! From CN7 ON5
CN7C ON5 428.0 1.400 ! check adm jr.,
!FC should be 428.000 based on Meoh
!@@@@@@@@@ End of exocyclic bonds for arabinose @@@@@@@@@
!@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@
CN8 ON2 340.0 1.44 !
!@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@
! C1'-ND1 in imidazole model compound
CN7B NR1 220.000 1.4620 ! From crystal nucleosides A/G (NF)
NR1 CPH1 400.000 1.3800 ! From imidazole (NF)
NR1 CPH2 400.000 1.3600 ! From imidazole (NF)
NR2 CPH1 400.000 1.3800 ! From imidazole (NF)
NR2 CPH2 400.000 1.3200 ! From imidazole (NF)
CPH1 CPH1 410.000 1.3600 ! From imidazole (NF)
HR1 CPH2 340.000 1.0900 ! From imidazole (NF)
HR3 CPH1 365.000 1.0830 ! From imidazole (NF)
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
! angle parameters have been rearranged based on model
! compounds and functional groups. Additional angle
! parameters follow sorted based on the central atom
!
!2-(aminobutyl)-1,3-propandiol terms
CN7 CN8 CN8 58.35 113.60 11.16 2.561 !alkane
CN8 CN7 CN8 58.35 113.60 11.16 2.561 !alkane
CN8 CN8 CN8 58.35 113.60 11.16 2.561 !alkane
HN1 NN6 CN8 30.00 109.50 20.00 2.074 !methylammonium
NN6 CN8 HN8 45.00 107.50 35.00 2.101 !methylammonium
CN7 CN8 ON2 115.00 109.70 !DNA exocyclic angles
NN6 CN8 CN8 67.70 110.00 !methylammonium
HN1 NN6 HN1 44.00 109.50 !methylammonium
!abasic propyl linkage
ON2 CN8 CN8 115.0 109.7 !DNA exocyclic angles
!abasic deoxynucleoside
CN7 ON6 CN8B 110.0 109.0
ON6 CN8B CN8 90.0 106.0
CN8B CN8 CN7 80.0 106.0
ON6 CN8B HN8 45.2 107.24 !
HN8 CN8B CN8 34.53 110.10 22.53 2.179 ! alkane
HN8 CN8 CN8B 34.53 110.10 22.53 2.179 ! alkane
!NICH parameters to maintain back compatibility following
!atom type switch from HN3 to HN6
NN2 CN3C HN6 42.0 119.0 !nad/ppi, jjp1/adm jr. 7/95
HN6 CN3C CN3 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95
HN6 CN3 CN8 30.0 116.0 !nadh/ppi, jjp1/adm jr. 7/95
CN3C CN3 HN6 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95
! pyrmidines
!@@@@@@@@ Adenine
! ade 6-mem ring
CN2 NN3A CN4 90.0 117.8 !6R) adm jr. 11/97
NN3A CN4 NN3A 60.0 133.0 !6R)
CN4 NN3A CN5 90.0 110.1 !6R)
CN5 CN5 NN3A 60.0 127.4 !6R) bridgeC4
CN2 CN5 CN5 60.0 121.0 !6R) bridgeC5
CN5 CN2 NN3A 60.0 110.7 !6R)
CN5 CN5 NN2 100.0 105.7 !5R) bridgeC4
CN5 CN5 NN4 100.0 110.0 !5R) bridgeC5
CN4 NN4 CN5 120.0 104.6 !5R)
NN2 CN4 NN4 100.0 113.4 !5R)
CN4 NN2 CN5 100.0 106.3 !5R)
NN2 CN5 NN3A 100.0 126.9 !bridgeC4
CN2 CN5 NN4 100.0 129.0 !bridgeC5
HN3 CN4 NN3A 38.0 113.5 !h2
NN3A CN2 NN1 50.0 130.7 !n6
CN5 CN2 NN1 50.0 118.6 !
CN2 NN1 HN1 40.0 121.5 !h61,h62, C,A,G
HN1 NN1 HN1 31.0 117.0 !C,A,G
NN4 CN4 HN3 39.0 124.8 !h8, G,A
NN2 CN4 HN3 39.0 121.8 !
CN5 NN2 HN2 30.0 129.4 !h9
CN4 NN2 HN2 30.0 125.0 !
!@@@@@@@@ Guanine
! gua 6-mem ring
CN1 NN2G CN2 70.0 131.1 !6R)G, adm jr. 11/97
NN2G CN2 NN3G 70.0 122.2 !6R)
CN2 NN3G CN5 90.0 109.4 !6R)
CN5G CN5 NN3G 70.0 129.9 !6R) bridgeC4
CN1 CN5G CN5 70.0 119.6 !6R) bridgeC5
CN5G CN1 NN2G 70.0 107.8 !6R)
CN5G CN5 NN2B 100.0 104.6 !5R) bridgeC4
CN5 CN5G NN4 100.0 111.4 !5R) bridgeC5
CN4 NN4 CN5G 120.0 103.8 !5R)
NN2B CN4 NN4 100.0 113.0 !5R)
CN4 NN2B CN5 100.0 107.2 !5R)
NN2B CN5 NN3G 140.0 125.5 ! bridgeC4
CN1 CN5G NN4 125.0 129.0 ! bridgeC5
CN1 NN2G HN2 45.0 113.3 ! h1
CN2 NN2G HN2 45.0 115.6 !
NN1 CN2 NN2G 95.0 115.4 ! n2
NN1 CN2 NN3G 95.0 122.4 !
NN2G CN1 ON1 50.0 127.5 ! o6
CN5G CN1 ON1 50.0 124.7 !
HN3 CN4 NN2B 40.0 122.2 ! h8 (NN4 CN4 HN3 124.8)
CN4 NN2B HN2 30.0 124.6 ! h9
CN5 NN2B HN2 30.0 129.3 !
!@@@@@@@@ Cytosine
! cyt 6-mem ring
CN1 NN2 CN3 50.0 124.1 !C, adm jr. 11/97
NN2 CN1 NN3 50.0 116.8 !C
CN1 NN3 CN2 85.0 119.1 !C
CN3 CN2 NN3 85.0 119.3 !C
CN2 CN3 CN3 85.0 117.8 !C
CN3 CN3 NN2 85.0 122.9 !C
CN1 NN2 HN2 37.0 121.2 !C, h1
CN3 NN2 HN2 37.0 114.7 !C
NN2 CN1 ON1C 130.0 119.4 !C, o2
NN3 CN1 ON1C 130.0 123.8 !C
NN3 CN2 NN1 81.0 122.3 !C, n4
CN3 CN2 NN1 81.0 118.4 !C
CN2 CN3 HN3 38.0 120.1 !C h5
CN3 CN3 HN3 38.0 122.1 !C,U
HN3 CN3 NN2 44.0 115.0 !C, h6
!@@@@@@@@ Uracil
! ura 6-mem ring
CN1T NN2B CN3 70.0 122.0 !U, adm jr. 11/97
NN2B CN1T NN2U 50.0 114.0 !U
CN1T NN2U CN1 50.0 130.2 !U
NN2U CN1 CN3 70.0 112.6 !U
CN1 CN3 CN3 100.0 117.6 !U
CN3 CN3 NN2B 100.0 123.6 !U
CN1T NN2B HN2 40.5 122.0 !U, h1
CN3 NN2B HN2 32.0 116.0 !U
NN2B CN1T ON1 100.0 121.6 !U, o2
NN2U CN1T ON1 100.0 124.4 !U
CN1T NN2U HN2 40.5 114.4 !U, h3
CN1 NN2U HN2 40.5 115.4 !U
NN2U CN1 ON1 100.0 121.9 !U, o4
CN3 CN1 ON1 100.0 125.5 !U,
CN1 CN3 HN3 30.0 120.3 !U, h5
HN3 CN3 NN2B 30.0 114.3 !U, h6
! thymine 6-mem ring (unique from ura)
CN3T CN1 NN2U 70.0 113.5 !T, adm jr. 11/97
CN1 CN3T CN3 120.0 116.7 !T
CN3T CN3 NN2B 120.0 123.6 !125.3 !T
CN3T CN1 ON1 100.0 124.6 !T, o4
CN1 CN3T CN9 38.0 118.7 !T, c5 methyl
CN3 CN3T CN9 38.0 124.6 !T
CN3T CN3 HN3 30.0 122.1 !T, h6
! Inosine, adm jr., 9/98 update
HN3 CN4 NN3I 35.0 116.75 !c2
HN3 CN4 NN2G 35.0 115.75 !c2
NN3I CN4 NN2G 80.0 127.5 !c2
CN5G CN5 NN3I 100.0 127.0 !c4, r6
NN2B CN5 NN3I 140.0 128.4 !c4, r5
CN1 NN2G CN4 125.0 129.7 !n1
CN4 NN2G HN2 40.5 117.0 !n1
CN4 NN3I CN5 90.0 108.4 !n3
! base to methyl connection
CN1T NN2B CN9 70.0 116.0 !1-M-T/U, adm jr.
CN3 NN2B CN9 70.0 122.0 !1-M-T/U, adm jr. 7/24/91
CN1 NN2 CN9 70.0 115.4 !1-M-C, adm jr.
CN3 NN2 CN9 70.0 120.5 !1-M-C, adm jr. 7/24/91
CN5 NN2 CN9 70.0 125.9 !9-M-A, adm jr.
CN4 NN2 CN9 70.0 127.8 !9-M-A, adm jr.
CN5 NN2B CN9 70.0 125.9 !9-M-G, adm jr.
CN4 NN2B CN9 70.0 126.9 !9-M-G, adm jr.
CN5 NN2B CN8 70.0 125.9 !9-E-G, adm jr.
CN4 NN2B CN8 70.0 126.9 !9-E-G, adm jr.
NN2B CN8 CN9 70.0 113.7 !9-E-G, adm jr.
!===== For glycosydic linkage, base to c1'
CN1T NN2B CN7B 45.0 118.4 !U/T, FC from A
CN3 NN2B CN7B 45.0 119.6 !U/T
CN1 NN2 CN7B 45.0 120.0 !C, FC from A
CN3 NN2 CN7B 45.0 115.9 !C
CN5 NN2 CN7B 45.0 126.1 !A
CN4 NN2 CN7B 45.0 127.6 !A
CN5 NN2B CN7B 45.0 126.5 !G
CN4 NN2B CN7B 45.0 126.3 !G
ON6 CN7B NN2 110.0 108.0 !C/A DNA
ON6B CN7B NN2 110.0 112.0 !C/A RNA
CN8 CN7B NN2 110.0 113.7 !C/A
CN7 CN7B NN2 110.0 111.0 !C/A, RNA, 25P1
CN7B CN7B NN2 110.0 111.0 !C/A, RNA
CN7C CN7B NN2 110.0 111.0 !C/A, Arabinose (NF)
ON6 CN7B NN2B 110.0 108.0 !T/U/G (DNA) FC from A
ON6B CN7B NN2B 110.0 112.0 !T/U/G (RNA) FC from A
CN8 CN7B NN2B 110.0 113.7 !T/U/G
CN7 CN7B NN2B 110.0 111.0 !T/U/G, RNA, 25P1
CN7B CN7B NN2B 110.0 111.0 !T/U/G, RNA
CN7C CN7B NN2B 110.0 111.0 !T/U/G, Arabinose (NF)
HN7 CN7B NN2 43.0 111.0 !
HN7 CN7B NN2B 43.0 111.0 !From HN7 CN7B NN2
!===== End of glycosydic linkage
! remaining terms ordered based on central atom
CN3 CN1A NN1 85.0 113.0 80.0 2.46 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN1A ON1 85.0 118.5 20.0 2.43 !nad/ppi, jjp1/adm jr. 7/95
NN1 CN1A ON1 85.0 128.5 20.0 2.17 !nad/ppi, jjp1/adm jr. 7/95
CN3D CN2 NN1 110.0 116.4 !5mc, adm jr. 9/9/93
CN3D CN2 NN3 30.0 121.3 !5mc, adm jr. 9/9/93
CN1A CN3 CN3C 5.0 107.8 !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3 CN8 125.0 124.2 !nadh/ppi, jjp1/adm jr. 7/95
CN2 CN3D CN3 100.0 117.8 !5mc, adm jr. 9/9/93
CN2 CN3D CN9 40.0 118.0 !5mc, adm jr. 9/9/93
CN3A CN3 CN1A 40.0 110.2 !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3 CN1A 10.0 131.8 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3A CN3 50.0 118.0 !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3 CN3B 40.0 118.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3 CN8 53.5 108.5 !nadh/ppi, jjp1/adm jr. 7/95
CN3B CN3 CN8 53.5 108.5 !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3 CN8 43.5 128.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3D CN9 40.0 124.2 !5mc, adm jr. 9/9/93
CN3D CN3 HN3 30.0 122.0 !5mc, adm jr. 9/9/93
CN3B CN3 HN3B 30.0 122.0 !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3 HN3B 30.0 119.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3C HN3 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95
CN3C CN3 HN3 42.0 116.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3A HN3B 80.0 121.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3B HN3B 80.0 120.5 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3B NN2 120.0 122.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3C NN2 60.0 122.0 !nadh/ppi, jjp1/adm jr. 7/95
CN3D CN3 NN2 100.0 124.2 !5mc, adm jr. 9/9/93
CN8 CN3 HN3 30.0 116.0 !nadh/ppi, jjp1/adm jr. 7/95
HN3B CN3B NN2 80.0 117.5 !nad/ppi, jjp1/adm jr. 7/95
HN3 CN3C NN2 42.0 119.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN8 CN3 125.0 108.0 !nadh/ppi, jjp1/adm jr. 7/95
CN3 CN8 HN8 55.0 110.10 !nadh/ppi, jjp1/adm jr. 7/95
CN9 CN8 HN8 34.6 110.10 22.53 2.179 ! Alkanes, sacred
CN9 CN7 HN7 34.6 110.10 22.53 2.179 ! Alkanes, sacred
HN8 CN8 NN2 33.43 110.1 !FOR 9-M-ADE(THY), ADM
HN8 CN8 ON5 45.9 108.89 !RIBOSE, Adm Jr. MeOH
CN3 CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred
CN3T CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred
CN3D CN9 HN9 33.43 110.10 22.53 2.179 ! Alkanes, sacred
CN8 CN9 HN9 34.60 110.10 22.53 2.179 ! Alkanes, sacred
HN9 CN9 CN7 33.43 110.1 22.53 2.179 ! Alkanes, sacred
HN9 CN9 NN2 33.43 110.1 !FOR 9-M-A(T), adm jr.
HN9 CN9 NN2B 33.43 110.1 !FOR 9-M-G(C), adm jr.
HN8 CN8 NN2B 33.43 110.1 !FOR 9-E-G, adm jr.
HN9 CN9 ON2 60.0 109.5 !DMP, ADM Jr.
CN1A NN1 HN1 35.0 120.0 !nad/ppi, jjp1/adm jr. 7/95
CN3B NN2 CN3B 30.0 120.0 !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2 CN3C 20.0 114.0 !nadh/ppi, jjp1/adm jr. 7/95
CN3B NN2 CN7B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2 CN7B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95
CN3B NN2 HN2 32.0 117.4 !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2 HN2 39.0 123.0 !nad/ppi, jjp1/adm jr. 7/95
HN1 NN5 HN1 39.0 106.0 ! sugar model, adm jr.
CN9 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM Jr.
CN9 ON2 P2 20.0 120.0 35. 2.33 !nad/ppi, jjp1/adm jr. 7/95
P ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95
P2 ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95
P3 ON2 P 45.0 140.0 40.0 3.15 !PPI2, from nad/ppi, adm jr., 7/01
P2 ON2 P2 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95
HN4 ON4 P 30.0 115.0 40.0 2.35 !MP_1, ADM Jr.
HN4 ON4 P3 30.0 120.0 40.0 2.35 !PPI2, from MP_1, adm jr., 7/01
HN5 ON5 CN8 57.5 106.0 !RIBOSE, Adm Jr. MeOH
HN5 ON5 CN9 57.5 106.0 !RIBOSE, Adm Jr. MeOH
ON2 P ON2 80.0 104.3 !DMP, ADM Jr.
ON2 P ON4 48.1 108.0 !MP_1, ADM Jr.
ON2 P3 ON4 48.1 100.0 !PPI2, from MP_1, adm jr., 7/01
ON3 P ON4 98.9 108.23 !MP_1, ADM Jr.
ON3 P3 ON4 98.9 108.23 !PPI2, from MP_1, adm jr., 7/01
ON4 P ON4 98.9 104.0 !MP_0, ADM Jr.
ON2 P2 ON2 80.0 104.3 !nad/ppi, jjp1/adm jr. 7/95
ON2 P2 ON3 88.9 111.6 !nad/ppi, jjp1/adm jr. 7/95
ON2 P3 ON3 88.9 105.0 !PPI2, from nad/ppi, adm jr., 7/01
ON3 P2 ON3 104.0 120.0 !nad/ppi, jjp1/adm jr. 7/95
ON3 P3 ON3 104.0 120.0 !PPI2, from nad/ppi, adm jr., 7/01
CN7 CN8 ON5 75.7 110.10 !RIBOSE, adm jr. MeOH
HN9 CN9 HN9 35.500 108.40 5.40 1.802 !alkane update, adm jr. 3/2/92
!@@@@@@@@@ Beginning of endocyclic valence angles for regular DNA @@@@@@@
CN7 ON6 CN7B 110.0 108.0 ! NF, 11/97, C4'O4'C1'
ON6 CN7B CN8 90.0 102.0 ! NF, 11/97, C4'O4'C1'
CN7B CN8 CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3'
CN8 CN7 CN7 60.00 102.0 8.0 2.561 !NF, 11/97, C2'C3'C4'
CN9 CN7 CN7 60.00 102.0 8.0 2.561 !for 5MET, adm jr.
CN7 CN7 ON6 100.0 104.0 ! NF, 11/97, C3'C4'O4'
CN8 CN7 ON6 100.0 104.0 ! NF, 11/97, C3'C4'O4', 25P1
HN7 CN7 ON6 45.2 107.24 !
HN7 CN7B ON6 45.2 107.24 !
HN7 CN7 CN7 40.0 108.00 !
CN7B CN8 HN8 33.4 110.10 22.53 2.179 ! following terms directly
CN8 CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes
HN7 CN7 CN8 34.5 110.1 22.53 2.179 !
HN8 CN8 CN7 34.53 110.10 22.53 2.179 !
HN8 CN8 CN8 34.53 110.10 22.53 2.179 !
HN8 CN8 HN8 35.5 109.00 5.40 1.802 !
HN7 CN7 HN7 35.5 109.00 5.40 1.802 !
!@@@@@@@@@ End of endocyclic valence angles for regular DNA @@@@@@@
!@@@@@@@@@ Beginning of endocyclic valence angles for regular RNA @@@@@@@
CN7 ON6B CN7B 110.0 115.0 ! From CN7 ON6 CN7B
CN7 CN7 ON6B 100.0 110.0 ! From CN7 CN7 ON6
CN8 CN7 ON6B 100.0 110.0 ! From CN7 CN7 ON6, 25P1
ON6B CN7B CN7B 90.0 106.0 ! 030998
CN7B CN7B CN7 110.0 96.0 !
CN7B CN7B CN8 110.0 96.0 ! 25P1
CN7B CN7 CN7 60.0 100.0 8.00 2.561 !NF, 11/97, C2'C3'C4'
!CN7 CN8 CN7 60.0 100.0 8.00 2.561 !NF, 11/97, C2'C3'C4', 25P1
HN7 CN7 ON6B 45.2 107.24 !
HN7 CN7B ON6B 45.2 107.24 !
CN7B CN7B HN7 33.4 110.10 22.53 2.179 ! following terms directly
HN7 CN7B HN7 35.5 109.00 5.40 1.802 !
!@@@@@@@@@ End of endocyclic valence angles for regular RNA @@@@@@@
!@@@@@@@@@ Beginning of endocyclic valence angles for arabinose @@@@@@@
ON6 CN7B CN7C 90.0 102.0 ! NF, 11/97, C4'O4'C1'
CN7B CN7C CN7 80.00 100.0 ! NF, 11/97, C1'C2'C3'
CN7C CN7 CN7 60.00 102.0 8.00 2.561 !NF, 11/97, C2'C3'C4'
CN7B CN7C HN7 33.4 110.10 22.53 2.179 ! following terms directly
CN7C CN7B HN7 33.4 110.10 22.53 2.179 ! from alkanes
HN7 CN7 CN7C 34.5 110.1 22.53 2.179 !
HN7 CN7C CN7 34.53 110.10 22.53 2.179 !
HN7 CN7C HN7 35.5 109.00 5.40 1.802 !
!@@@@@@@@@ End of endocyclic valence angles for arabinose @@@@@@@
!@@@@@@@@@ Beginning of exocyclic valence angles for regular DNA @@@@@@@
ON6 CN7 CN8B 90.0 108.2 !NF, 11/97, O4'C4'C5'
ON6 CN7 CN9 90.0 108.2 !for 5MET, adm jr.
CN7 CN7 CN8B 45.0 110.0 !NF, 11/97, C3'C4'C5'
CN8 CN7 CN8B 58.35 113.60 11.16 2.561 ! from alkane, 25P1
CN7 CN8B ON2 70.0 108.4 !NF, 11/97, C4'C5'O5'
CN7 CN7 ON2 115.0 109.7 !NF, 11/97, C4'C3'O3'
CN7 CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH
CN7B CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3' for NADPH
CN8 CN7B ON2 115.0 109.7 !NF, 11/97, C4'C3'O3', 25P1
CN8 CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3'
CN8B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C5'O5'P
CN7 ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P
CN7B ON2 P 20.0 120.0 35.00 2.33 !NF, 11/97, C3'O3'P, for NADPH
! sugar
HN7 CN7 CN8B 34.5 110.1 22.53 2.179 ! From HN7 CN7 CN8
HN8 CN8B ON2 60.0 109.5 ! From HN7 CN8 ON2
HN5 ON5 CN8B 57.5 106.0 ! From HN5 ON5 CN8
HN8 CN8B HN8 35.5 109.0 5.40 1.802 ! Alkanes, sacred
HN8 CN8B CN7 34.53 110.1 22.53 2.179 ! Alkanes, sacred
HN7 CN7 ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2
HN7 CN7B ON2 60.0 109.5 !DMP, adm jr. from HN7 CN8 ON2, for NADPH
!===== For 5ter patch:
CN7 CN8B ON5 75.7 110.10 ! From CN7 CN8B ON5
CN8B CN7 ON5 90.0 108.2 ! phosphoramidate, carbocyclic
HN8 CN8B ON5 45.9 108.89 ! From HN7 CN8 ON5
!===== For 3ter patch:
ON5 CN7 CN8 75.7 110.0 ! from CHARMM22
ON5 CN7 CN7 75.7 110.1 !
HN7 CN7 ON5 60.0 109.5 !
HN5 ON5 CN7 57.5 109.0 !
!@@@@@@@@@ End of exocyclic valence angles for regular DNA @@@@@@@
!@@@@@@@@@ Beginning of exocyclic valence angles for regular RNA @@@@@@@
!O4'-C4'-C5'
ON6B CN7 CN8B 90.0 108.2 !
ON6B CN7 CN9 90.0 108.2 ! for 5MET patch, adm jr.
!O3'-C3'-C2'
ON2 CN7 CN7B 90.0 110.0 !
ON5 CN7 CN7B 90.0 110.0 ! From ON5 CN7 CN8
!O2'-C2'-C1'
ON5 CN7B CN7B 80.0 108.4 !
!O2'-C2'-C3'
ON5 CN7B CN7 90.0 108.0 !
HN7 CN7B ON5 60.0 109.5 !
HN5 ON5 CN7B 57.5 109.0 !
HN7 CN7B CN7 34.53 110.10 22.53 2.179
HN7 CN7 CN7B 34.53 110.10 22.53 2.179
!@@@@@@@@@ End of exocyclic valence angles for regular RNA @@@@@@@
CN7C CN7 ON2 115.0 109.7 !NF, 11/97, C2'C3'O3'
!===== For 3ter patch:
!From DNA:
ON5 CN7 CN7C 75.7 110.0 ! from CHARMM22
!From RNA:
ON5 CN7C CN7B 80.0 108.4 ! From ON5 CN7B CN7B
!O2'-C2'-C3'
ON5 CN7C CN7 90.0 108.0 ! From ON5 CN7B CN7
HN7 CN7C ON5 60.0 109.5 !
HN5 ON5 CN7C 57.5 109.0 ! 032598
!@@@@@@@@@ Beginning of exocyclic valence angles for arabinose @@@@@@@
!@@@@@@@@@ End of exocyclic valence angles for arabinose @@@@@@@
!@@@@@@@@@ Beginning of angles for the nucleotide analogue @@@@@@@
CN8 ON2 P 20.0 120.0 35. 2.33 !DMP, adm jr.
!@@@@@@@@@ End of angles for the nucleotide analogue @@@@@@@
ON2 P ON3 98.9 111.6 !DMP, adm jr.
ON3 P ON3 120.0 120.0 !DMP, adm jr.
HN8 CN8 ON2 60.0 109.5 !DMP, adm jr.
ON5 P ON3 98.9 111.6 ! From ON2 P ON3
!-- For imidazole, from imidazole alone:
!-- and for link between sugar and imidazole
ON6 CN7B NR1 140.0 108.00 ! k guessed, theta from ribo./desox. xtal (NF)
ON6B CN7B NR1 140.0 108.00 ! RNUS
CN8 CN7B NR1 140.0 113.70 ! k guessed, theta from ribo./desox. xtal (NF)
CN7B CN7B NR1 140.0 113.70 ! RNUS
CN7B NR1 CPH2 130.0 127.00 ! k guessed, theta from A/G xtal (NF)
CN7B NR1 CPH1 130.0 126.00 ! k guessed, theta from A/G xtal (NF)
HN7 CN7B NR1 30.0 106.3 ! k guessed, theta from ai (NF)
CPH2 NR1 CPH1 130.0 107.0000 ! From imidazole (NF), modified for 360 deg. condition
CPH2 NR2 CPH1 130.0 104.0000 ! From imidazole (NF)
NR1 CPH1 CPH1 130.0 106.0000 ! From imidazole (NF)
NR1 CPH2 NR2 130.0 112.5000 ! From imidazole
NR2 CPH1 CPH1 130.0 110.0000 ! From imidazole (NF)
NR1 CPH2 HR1 25.0 122.50 20.00 2.14000 ! From imidazole (NF)
NR2 CPH2 HR1 25.0 125.00 20.00 2.12000 ! From imidazole (NF)
HR3 CPH1 CPH1 25.0 130.00 20.00 2.20000 ! From imidazole (NF)
NR1 CPH1 HR3 25.0 124.00 20.00 2.14000 ! From imidazole (NF)
NR2 CPH1 HR3 25.0 120.00 20.00 2.14000 ! From imidazole (NF)
!------------------------ For water -------------------
HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY
!------------------------ added for arao -----------------------
!------------------------ added for araim ----------------------
ON6 CN7B CN7 120.0 106.25 !
CN7B CN7 CN8 58.35 113.6 11.16 2.561 !
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
!2-(aminobutyl)-1,3-propandiol terms
X CN8 ON2 X -0.10 3 0.0 ! phosphate ester
X CN7 CN8 X 0.20 3 0.0 ! alkane
X CN8 NN6 X 0.10 3 0.0 ! methylammonium
!abasic nucleoside terms - susil
CN7 ON6 CN8B HN8 0.195 1 0.0
ON6 CN8B CN8 HN8 0.195 1 0.0
HN7 CN7 ON6 CN8B 0.195 3 0.0
CN8B CN8 CN7 HN7 0.195 3 0.0
HN8 CN8B CN8 HN8 0.195 3 0.0
HN8 CN8B CN8 CN7 0.195 3 0.0
! c5'-c4'-o4'-c1', exo
CN8B CN7 ON6 CN8B 0.5 5 0.0 ! min at 150 310 max at 25 200
CN8B CN7 ON6 CN8B 0.1 3 180.0
CN8B CN7 ON6 CN8B 0.5 1 0.0
! c1'-c2'-c3'-o3', exo
CN8B CN8 CN7 ON5 0.4 5 0.0
CN8B CN8 CN7 ON5 0.4 3 0.0
CN8B CN8 CN7 ON5 0.7 2 0.0 !elevates energy at 0 (c3'endo), adm
CN8B CN8 CN7 ON5 0.5 1 180.0 !elevates energy at 0 (c3'endo), adm
CN8B CN8 CN7 ON2 0.4 5 0.0 !terms for oligonuclotide
CN8B CN8 CN7 ON2 0.4 3 0.0
CN8B CN8 CN7 ON2 0.7 2 0.0
CN8B CN8 CN7 ON2 0.5 1 180.0
! c4'-o4'-c1'-c2', tau0
CN7 ON6 CN8B CN8 0.6 6 180.0
CN7 ON6 CN8B CN8 0.6 3 0.0
! o4'-c1'-c2'-c3', tau1
ON6 CN8B CN8 CN7 0.7 5 180.0 !lowers 90, shifts c2endo minimum towards 200
ON6 CN8B CN8 CN7 0.4 4 0.0 !lowers 90, shifts c2endo minimum towards 200
ON6 CN8B CN8 CN7 0.4 3 180.0 !lowers 90, shifts c2endo minimum towards 200
! c4'-c3'-c2'-c1', tau2
CN7 CN7 CN8 CN8B 0.5 4 0.0
CN7 CN7 CN8 CN8B 0.1 3 0.0 !lowers energy in 150 to 250 range
! c1'-o4'-c4'-c3', tau4
CN8B ON6 CN7 CN7 0.5 3 0.0 !effects surface in 200-360 region
! PHOSPHATE
ON2 P ON2 CN7 1.20 1 180.0 !10/97, DMP, adm jr.
ON2 P ON2 CN7 0.10 2 180.0 !10/97, DMP, adm jr.
ON2 P ON2 CN7 0.10 3 180.0 !10/97, DMP, adm jr.
ON2 P ON2 CN7 0.00 6 0.0 !10/97, DMP, adm jr.
ON2 P ON2 CN7B 1.20 1 180.0 !10/97, DMP, adm jr., 25P1
ON2 P ON2 CN7B 0.10 2 180.0 !10/97, DMP, adm jr., 25P1
ON2 P ON2 CN7B 0.10 3 180.0 !10/97, DMP, adm jr., 25P1
ON2 P ON2 CN7B 0.00 6 0.0 !10/97, DMP, adm jr., 25P1
ON2 P ON2 CN8 1.20 1 180.0 !10/97, DMP, adm jr.
ON2 P ON2 CN8 0.10 2 180.0 !10/97, DMP, adm jr.
ON2 P ON2 CN8 0.10 3 180.0 !10/97, DMP, adm jr.
ON2 P ON2 CN8 0.00 6 0.0 !10/97, DMP, adm jr.
! Added when C5' defined as CN8B (NF 041497):
ON2 P ON2 CN8B 1.20 1 180.0 !10/97, DMP, adm jr.
ON2 P ON2 CN8B 0.10 2 180.0 !10/97, DMP, adm jr.
ON2 P ON2 CN8B 0.10 3 180.0 !10/97, DMP, adm jr.
ON2 P ON2 CN8B 0.00 6 0.0 !10/97, DMP, adm jr.
ON2 P ON2 CN9 1.20 1 180.0 !dmp
ON2 P ON2 CN9 0.10 2 180.0 !dmp
ON2 P ON2 CN9 0.10 3 180.0 !dmp
ON2 P ON2 CN9 0.00 6 0.0 !dmp
!
ON3 P ON2 CN7 0.10 3 0.0 !dmp,eps, O1P-P-O3'-C3'
ON3 P ON2 CN7B 0.10 3 0.0 !for NADPH
ON3 P ON2 CN8 0.10 3 0.0 !dmp
ON3 P ON2 CN8B 0.10 3 0.0 !dmp,bet, O1P-P-O5'-C5'
ON3 P ON2 CN9 0.10 3 0.0 !dmp
! terminal phosphate terms, adm jr.
ON4 P ON2 CN7 0.95 2 0.0 !MP_1, adm jr.
ON4 P ON2 CN7 0.50 3 0.0 !MP_1, adm jr.
ON4 P ON2 CN7B 0.95 2 0.0 !for NADPH
ON4 P ON2 CN7B 0.50 3 0.0 !for NADPH
ON4 P ON2 CN8 0.95 2 0.0 !MP_1, adm jr.
ON4 P ON2 CN8 0.50 3 0.0 !MP_1, adm jr.
ON4 P ON2 CN8B 0.95 2 0.0 !MP_1, adm jr.
ON4 P ON2 CN8B 0.50 3 0.0 !MP_1, adm jr.
ON4 P ON2 CN9 0.95 2 0.0 !MP_1, adm jr.
ON4 P ON2 CN9 0.50 3 0.0 !MP_1, adm jr.
X ON4 P X 0.30 3 0.0 !MP_1, adm jr.
! When O5' is ON2 (phosphodiester linkage):
P ON2 CN7 HN7 0.000 3 0.0 !dmp,eps, H-C3'-O3'-P
P ON2 CN7B HN7 0.000 3 0.0 !for NADPH
P ON2 CN8B HN8 0.000 3 0.0 !dmp,beta, H-C5'-O5'-P
P ON2 CN8 HN8 0.000 3 0.0 !dmp
P ON2 CN9 HN9 0.000 3 0.0 !dmp
! butane gauche terms
cn9 cn8 cn8 cn9 0.15 1 0.0
cn9 cn8 cn8 cn8 0.15 1 0.0
! BASES
! Uracil
NN2B CN1T NN2U CN1 1.5 2 180.0 ! adm jr. 11/97
CN1T NN2U CN1 CN3 1.5 2 180.0 ! adm jr. 11/97
NN2U CN1 CN3 CN3 1.5 2 180.0 ! adm jr. 11/97
CN1 CN3 CN3 NN2B 6.0 2 180.0 ! adm jr. 11/97
CN3 CN3 NN2B CN1T 1.5 2 180.0 ! adm jr. 11/97
CN3 NN2B CN1T NN2U 1.5 2 180.0 ! adm jr. 11/97
HN3 CN3 CN3 HN3 3.0 2 180.0 ! adm jr. 11/97
HN3 CN3 CN1 ON1 6.0 2 180.0 ! adm jr. 11/97
ON1 CN1T NN2B HN2 0.0 2 180.0 ! adm jr. 11/97
ON1 CN1 NN2U HN2 0.0 2 180.0 ! adm jr. 11/97
ON1 CN1T NN2U HN2 0.0 2 180.0 ! adm jr. 11/97
HN2 NN2B CN3 HN3 1.5 2 180.0 ! adm jr. 11/97
NN2B CN1T NN2U HN2 3.8 2 180.0 ! adm jr. 11/97
CN3 CN1 NN2U HN2 3.8 2 180.0 ! adm jr. 11/97
CN3 CN3 NN2B HN2 1.6 2 180.0 ! adm jr. 11/97
NN2U CN1T NN2B HN2 1.6 2 180.0 ! adm jr. 11/97
!Thymine
CN1T NN2B CN3 CN3T 1.8 2 180.0 ! adm jr. 11/97
NN2U CN1 CN3T CN3 1.8 2 180.0 ! adm jr. 11/97
CN1 CN3T CN3 NN2B 3.0 2 180.0 ! adm jr. 11/97
NN2B CN1 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97
NN2B CN3 CN3T CN9 5.6 2 180.0 ! adm jr. 11/97
CN1 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97
CN3 CN3T CN9 HN9 0.46 3 0.0 ! adm jr. 11/97
CN3T CN1 NN2U HN2 4.8 2 180.0 ! adm jr. 11/97
! Cytosine
CN3 NN2 CN1 NN3 0.6 2 180.0 ! adm jr. 11/97
NN2 CN1 NN3 CN2 0.6 2 180.0 ! adm jr. 11/97
CN1 NN3 CN2 CN3 6.0 2 180.0 ! adm jr. 11/97
NN3 CN2 CN3 CN3 0.6 2 180.0 ! adm jr. 11/97
CN2 CN3 CN3 NN2 6.0 2 180.0 ! adm jr. 11/97
CN3 CN3 NN2 CN1 0.6 2 180.0 ! adm jr. 11/97
NN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97
CN3 CN2 NN1 HN1 1.0 2 180.0 ! adm jr. 11/97
NN1 CN2 NN3 CN1 2.0 2 180.0 ! adm jr. 11/97
NN1 CN2 CN3 CN3 2.0 2 180.0 ! adm jr. 11/97
NN1 CN2 CN3 HN3 2.0 2 180.0 ! adm jr. 11/97
ON1C CN1 NN2 HN2 3.0 2 180.0 ! adm jr. 11/97
ON1C CN1 NN3 CN2 1.6 2 180.0 ! adm jr. 11/97
ON1C CN1 NN2 CN3 1.6 2 180.0 ! adm jr. 11/97
NN3 CN2 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97
NN2 CN3 CN3 HN3 3.4 2 180.0 ! adm jr. 11/97
CN2 CN3 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97
CN1 NN2 CN3 HN3 4.6 2 180.0 ! adm jr. 11/97
X CN2 NN3 X 2.0 2 180.0 ! adm jr. 11/97
! 5-methylcytosine
NN2 CN3 CN3D CN2 3.0 2 180.0 !5mc, adm jr. 9/9/93
CN3 CN3D CN2 NN3 1.0 2 180.0 !5mc, adm jr. 9/9/93
CN3D CN2 NN3 CN1 10.0 2 180.0 !5mc, adm jr. 9/9/93
CN3D CN3 NN2 CN1 1.0 2 180.0 !5mc, adm jr. 9/9/93
CN3D CN2 NN1 HN1 2.0 2 180.0 !5mc, adm jr. 9/9/93
NN1 CN2 CN3D CN3 0.0 2 180.0 !5mc, adm jr. 9/9/93
NN1 CN2 CN3D CN9 0.0 2 180.0 !5mc, adm jr. 9/9/93
NN2 CN3 CN3D CN9 4.0 2 180.0 !5mc, adm jr. 9/9/93
NN3 CN2 CN3D CN9 0.0 2 180.0 !5mc, adm jr. 9/9/93
CN3 CN3D CN9 HN9 0.0 3 0.0 !5mc, adm jr. 9/9/93
CN2 CN3D CN9 HN9 0.35 3 0.0 !5mc, adm jr. 9/9/93
CN2 CN3D CN3 HN3 4.0 2 180.0 !5mc, adm jr. 9/9/93
CN9 CN3D CN3 HN3 4.0 2 180.0 !5mc, adm jr. 9/9/93
! Adenine
CN2 NN3A CN4 NN3A 1.8 2 180.0 ! adm jr. 11/97, 6-mem
NN3A CN4 NN3A CN5 2.0 2 180.0 !
CN4 NN3A CN5 CN5 1.8 2 180.0 !
NN3A CN5 CN5 CN2 2.0 2 180.0 ! treated 2x
CN5 CN5 CN2 NN3A 1.8 2 180.0 !
CN5 CN2 NN3A CN4 10.0 2 180.0 !
CN5 CN5 NN4 CN4 6.0 2 180.0 ! 5-mem
CN5 NN4 CN4 NN2 14.0 2 180.0 !
NN4 CN4 NN2 CN5 6.0 2 180.0 !
CN4 NN2 CN5 CN5 6.0 2 180.0 !
NN2 CN5 CN5 NN4 14.0 2 180.0 ! treated 2x
CN2 NN3A CN4 HN3 8.5 2 180.0 ! H2
CN5 NN3A CN4 HN3 8.5 2 180.0 ! H2
CN5 NN4 CN4 HN3 5.2 2 180.0 ! H8
CN5 NN2 CN4 HN3 5.2 2 180.0 ! H8
CN5 CN5 NN2 HN2 1.2 2 180.0 ! H9
NN4 CN4 NN2 HN2 1.2 2 180.0 ! H9
HN2 NN2 CN4 HN3 0.0 2 180.0 ! H8-C-N-H9
CN4 NN3A CN2 NN1 4.0 2 180.0 ! N6
CN5 CN5 CN2 NN1 4.0 2 180.0 ! N6
NN4 CN5 CN2 NN1 0.0 2 180.0 ! N6
CN5 CN2 NN1 HN1 0.5 2 180.0 ! 6-NH2
NN3A CN2 NN1 HN1 0.5 2 180.0 !
! Butterfly motion
NN3A CN5 CN5 NN4 7.0 2 180.0 !A, adm jr. 11/97
CN2 CN5 CN5 NN2 7.0 2 180.0 !A
NN3A CN2 CN5 NN4 2.0 2 180.0 !A
CN2 CN5 NN4 CN4 2.0 2 180.0 !A
CN4 NN3A CN5 NN2 2.0 2 180.0 !A
NN3A CN5 NN2 CN4 2.0 2 180.0 !A
! Guanine
CN1 NN2G CN2 NN3G 0.2 2 180.0 !adm jr. 11/97, 6-mem
NN2G CN2 NN3G CN5 2.0 2 180.0 !
CN2 NN3G CN5 CN5G 0.2 2 180.0 !
NN3G CN5 CN5G CN1 2.0 2 180.0 !
CN5 CN5G CN1 NN2G 0.2 2 180.0 !
CN5G CN1 NN2G CN2 0.2 2 180.0 !
CN5 CN5G NN4 CN4 6.0 2 180.0 !5-mem
CN5G NN4 CN4 NN2B 16.0 2 180.0 !
NN4 CN4 NN2B CN5 6.0 2 180.0 !
CN4 NN2B CN5 CN5G 6.0 2 180.0 !
NN2B CN5 CN5G NN4 10.0 2 180.0 !
! substitutents
ON1 CN1 CN5G CN5 14.0 2 180.0 !G, O6
ON1 CN1 CN5G NN4 0.0 2 180.0 !
ON1 CN1 NN2G CN2 14.0 2 180.0 !
ON1 CN1 NN2G HN2 0.0 2 180.0 !
NN1 CN2 NN2G CN1 4.0 2 180.0 !G, N2
NN1 CN2 NN3G CN5 4.0 2 180.0 !
NN1 CN2 NN2G HN2 0.0 2 180.0 !
NN2G CN2 NN1 HN1 1.2 2 180.0 !
NN3G CN2 NN1 HN1 1.2 2 180.0 !
HN2 NN2G CN1 CN5G 3.6 2 180.0 !G, H1
HN2 NN2G CN2 NN3G 3.6 2 180.0 !
HN3 CN4 NN4 CN5G 5.6 2 180.0 !G, H8
HN3 CN4 NN2B CN5 5.6 2 180.0 !
HN3 CN4 NN2B HN2 0.0 2 180.0 !
HN2 NN2B CN5 CN5G 1.2 2 180.0 !G, H9
HN2 NN2B CN5 NN3G 1.2 2 180.0 !
HN2 NN2B CN4 NN4 1.2 2 180.0 !
! Butterfly motion
NN3G CN5 CN5G NN4 10.0 2 180.0 !adm jr. 11/97
CN1 CN5G CN5 NN2 10.0 2 180.0 !
NN2G CN1 CN5G NN4 2.0 2 180.0 !
CN1 CN5G NN4 CN4 2.0 2 180.0 !
CN2 NN3G CN5 NN2B 2.0 2 180.0 !
NN3G CN5 NN2B CN4 2.0 2 180.0 !
! inosine, adm jr. 2/94
CN5 CN5 NN3I CN4 6.0 2 180.0
NN2G CN4 NN3I CN5 6.0 2 180.0
NN3I CN4 NN2G HN2 1.5 2 180.0
NN3I CN4 NN2G CN1 1.5 2 180.0
HN3 CN4 NN2G HN2 1.5 2 180.0
HN3 CN4 NN2G CN1 1.5 2 180.0
! Wild cards for inosine
X CN4 NN3I X 3.5 2 180.0
X CN5 NN3I X 1.0 2 180.0
! Wild cards for uracil, thymine and cytosine
X CN1 NN3 X 1.0 2 180.0 ! c22
X CN1 NN2 X 0.9 2 180.0 ! c22
X CN1T NN2B X 0.9 2 180.0 ! From X CN1 NN2 X, for thymines
X CN1 NN2G X 0.9 2 180.0 ! c22
X CN1 NN2U X 0.9 2 180.0 ! c22
X CN1T NN2U X 0.9 2 180.0 ! c22
X CN3 NN2 X 1.0 2 180.0 ! c22
X CN3 NN2B X 1.0 2 180.0 ! From X CN3 NN2 X, for thymines
X CN3 CN3 X 1.0 2 180.0 ! c22
X CN3 CN3T X 1.0 2 180.0 !T, adm jr. 11/97
X CN1 CN3 X 1.0 2 180.0 ! c22
X CN1 CN3T X 1.0 2 180.0 !T, adm jr. 11/97
X CN2 CN3 X 0.8 2 180.0 ! c22
! Wild cards for adenine and guanine
X CN1 CN5G X 1.0 2 180.0 ! adm jr. 11/97
X CN2 NN2G X 1.0 2 180.0 !
X CN2 CN5 X 1.0 2 180.0 !
X CN4 NN2 X 1.5 2 180.0 !
X CN4 NN2B X 1.5 2 180.0 ! From X CN4 NN2 X
X CN4 NN3A X 3.5 2 180.0 !
X CN4 NN4 X 2.0 2 180.0 ! A,G
X CN5 CN5 X 0.0 2 180.0 !
X CN5G CN5 X 0.0 2 180.0 ! adm jr. 11/97
X CN5 NN2 X 1.5 2 180.0 !
X CN5 NN2B X 1.5 2 180.0 ! From X CN5 NN2 X
X CN5 NN3A X 1.0 2 180.0 !
X CN5 NN3G X 1.0 2 180.0 ! adm jr. 11/97
X CN5 NN4 X 1.0 2 180.0 !
X CN5G NN4 X 1.0 2 180.0 ! adm jr. 11/97
X CN2 NN3A X 1.0 2 180.0 !
X CN2 NN3G X 1.0 2 180.0 ! adm jr. 11/97
! MISC.
CN1 NN2 CN9 HN9 0.19 3 0.0 ! 1-M-C
CN3 NN2 CN9 HN9 0.00 3 0.0 ! 1-M-C
CN4 NN2 CN9 HN9 0.00 3 0.0 ! 9-M-A
CN5 NN2 CN9 HN9 0.19 3 0.0 ! 9-M-A
CN1 NN2B CN9 HN9 0.19 3 0.0 ! 1-M-U
CN1T NN2B CN9 HN9 0.19 3 0.0 ! 1-M-T
CN3 NN2B CN9 HN9 0.00 3 0.0 ! 1-M-T/U
CN4 NN2B CN9 HN9 0.00 3 0.0 ! 9-M-G
CN5 NN2B CN9 HN9 0.19 3 0.0 ! 9-M-G
CN4 NN2B CN8 HN8 0.00 3 0.0 ! 9-E-G
CN5 NN2B CN8 HN8 0.19 3 0.0 ! 9-E-G
CN4 NN2B CN8 CN9 0.00 3 0.0 ! 9-E-G
CN5 NN2B CN8 CN9 0.19 3 0.0 ! 9-E-G
X CN8 CN8 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15)
X CN8 CN9 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15)
! nicotinamide adenine dinucleotide
CN3 NN2 CN3B HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
HN2 NN2 CN3B HN3B 3.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
HN3B CN3 CN3A HN3B 2.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
HN3B CN3 CN3B HN3B 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
NN2 CN3B CN3 HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN1A CN3 HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3 CN3B HN3B 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3 CN3A HN3B 5.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN1A CN3 HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3 CN3 HN3 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3 CN1A ON1 2.38 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3 CN1A ON1 2.38 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3 CN1A NN1 0.35 1 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3 CN1A NN1 0.62 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3 CN1A NN1 0.35 1 0.0 !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3 CN1A NN1 0.62 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3A CN3 CN1A 3.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 CN3A CN3 CN3B 6.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
NN2 CN3B CN3 CN3A 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3B NN2 CN3B CN3 4.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
X CN3 CN3A X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
X CN3 CN3B X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
X CN3 CN8 X 1.0 3 180.0 !nad/ppi, jjp1/adm jr. 7/95
X NN1 CN1A X 2.5 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
X NN2 CN3B X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
! nicotinamide adenine dinucleotide hydride, nadh
CN8 CN3 CN1A ON1 1.00 2 180.0 !nadh, jjp1,adm jr. 4/95
CN8 CN3 CN1A ON1 1.00 3 0.0 !nadh, jjp1,adm jr. 4/95
CN8 CN3 CN1A ON1 0.40 6 0.0 !nadh, jjp1,adm jr. 4/95
CN8 CN3 CN1A NN1 0.50 2 180.0 !nadh, jjp1,adm jr. 4/95
CN8 CN3 CN1A NN1 0.35 3 180.0 !nadh, jjp1,adm jr. 4/95
CN8 CN3 CN1A NN1 0.40 6 0.0 !nadh, jjp1,adm jr. 4/95
CN3C CN3 CN1A ON1 0.30 1 0.0 !nadh, jjp1,adm jr. 4/95
CN3C CN3 CN1A ON1 1.95 2 180.0 !nadh, jjp1,adm jr. 4/95
CN3C CN3 CN1A NN1 1.10 1 180.0 !nadh, jjp1,adm jr. 4/95
CN3C CN3 CN1A NN1 1.95 2 180.0 !nadh, jjp1,adm jr. 4/95
HN2 NN2 CN3C HN3 4.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3 NN2 CN3C HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
NN2 CN3C CN3 HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN8 CN3 CN3C NN2 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3 CN8 CN3 4.0 3 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3 CN3C NN2 2.5 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
X CN3 CN3C X 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
X NN2 CN3C X 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2 CN3C CN3 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95
! pyrophosphate (ppi)
P2 ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
P2 ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
P ON2 P2 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
P ON2 P2 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
P2 ON2 P2 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
P2 ON2 P2 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
P ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
P ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
P ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
P ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
P ON2 P2 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
P ON2 P2 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
P2 ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
P2 ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
P2 ON2 P2 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95
P2 ON2 P2 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95
! protonated pyrophosphate (ppi2)
P ON2 P3 ON2 0.03 2 0.0 !from P ON2 P2 ON2, adm jr. 7/01
P ON2 P3 ON2 0.03 3 0.0 !from P ON2 P2 ON2, adm jr. 7/01
P3 ON2 P ON2 0.03 2 0.0 !from P ON2 P2 ON2, adm jr. 7/01
P3 ON2 P ON2 0.03 3 0.0 !from P ON2 P2 ON2, adm jr. 7/01
P ON2 P3 ON3 0.10 2 0.0 !from P ON2 P2 ON3, adm jr. 7/01
P ON2 P3 ON3 0.03 3 0.0 !from P ON2 P2 ON3, adm jr. 7/01
P3 ON2 P ON3 0.10 2 0.0 !from P ON2 P2 ON3, adm jr. 7/01
P3 ON2 P ON3 0.03 3 0.0 !from P ON2 P2 ON3, adm jr. 7/01
P ON2 P3 ON4 0.10 2 0.0 !from P ON2 P2 ON4, adm jr. 7/01
P ON2 P3 ON4 0.03 3 0.0 !from P ON2 P2 ON4, adm jr. 7/01
X ON4 P3 X 0.30 3 0.0 !from MP_1, adm jr.
!for nadp/nadph, adm jr.
HN7 CN7 CN7B ON5 0.195 3 0.0
HN8 CN8B CN7 ON5 0.195 1 0.0 ! phosphoramidate and carbocyclic sugars
HN7 CN7 CN7 CN7 0.195 3 0.0
HN7 CN7 CN7 CN7B 0.195 3 0.0
HN7 CN7B CN7 CN7 0.195 3 0.0
HN7 CN7B NN2 CN3B 0.195 3 0.0
HN7 CN7B NN2 CN3C 0.195 3 0.0
HN7 CN7 CN7B HN7 0.195 3 0.0
HN7 CN7 CN7B ON6 0.195 3 0.0
HN7 CN7 CN7B ON2 0.195 3 0.0
HN8 CN8 CN7B ON2 0.195 3 0.0 ! 25P1
HN7 CN7B CN7B ON2 0.195 3 0.0
HN7 CN7 CN7B NN2 0.195 3 0.0
!
ON6 CN7B CN7 ON5 3.4 1 180.0 !gam
CN7 CN7B NN2 CN3B 0.0 3 0.0
CN8 CN7B NN2 CN3B 0.0 3 0.0 ! 25P1
CN7B CN7B NN2 CN3B 0.0 3 0.0 ! for NADPH
ON6 CN7B NN2 CN3B 0.0 3 0.0 !
ON6B CN7B NN2 CN3B 0.0 3 0.0 ! for NADPH
CN7 CN7B NN2 CN3C 0.0 3 0.0
CN7B CN7B NN2 CN3C 0.0 3 0.0 ! for NADPH
ON6 CN7B NN2 CN3C 0.0 3 0.0 !
ON6B CN7B NN2 CN3C 0.0 3 0.0 ! for NADPH
CN7 CN7 CN7B NN2 0.0 3 0.0
CN8 CN7 CN7B NN2 0.0 3 0.0 ! 25P1
CN7 CN7B NN2 CN5 0.3 3 0.0 ! NF
CN7 CN7B NN2 CN4 0.0 3 180.0 ! NF
ON2 CN7 CN7B NN2 0.0 3 0.0
ON2 CN7B CN7B NN2 0.0 3 0.0 !for NADPH
ON2 CN7B CN7B NN2B 0.0 3 0.0 ! 25P1
ON5 CN7 CN7B NN2 0.0 3 0.0
! sugar, replace with ribose terms 021998
CN7 CN7B ON6 CN7 0.6 6 180.0
CN7B CN7 CN7 CN7 0.4 6 0.0 ! good for amplitudes
CN7B CN7 CN7 CN9 0.4 6 0.0 ! good for amplitudes, 5MET
CN7 CN7 CN7 ON6 0.6 6 0.0
CN7 CN7 CN7B ON6 0.6 6 0.0
CN8 CN7 CN7B ON6 0.6 6 0.0 ! 25P1
ON2 CN7 CN7 CN7 0.8 6 0.0 !
ON2 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right
ON2 CN7 CN7 CN7 2.0 3 180.0 !
! for ndph
ON2 CN7B CN7 CN7 0.8 6 0.0 !
ON2 CN7B CN7 CN7 0.4 5 0.0 ! Moves the barrier right
ON2 CN7B CN7 CN7 2.0 3 180.0 !
! 25P1
ON2 CN7B CN8 CN7 0.8 6 0.0 !
ON2 CN7B CN8 CN7 0.4 5 0.0 ! Moves the barrier right
ON2 CN7B CN8 CN7 2.0 3 180.0 !
!
ON5 CN7 CN7 CN7 0.8 6 0.0 !
ON5 CN7 CN7 CN7 0.4 5 0.0 ! Moves the barrier right
ON5 CN7 CN7 CN7 2.0 3 180.0 !
ON5 CN7 CN7 ON5 0.0 3 0.0 !
ON5 CN7 CN7 ON2 0.0 3 0.0 !
ON2 CN7 CN7B ON6 0.5 6 0.0 !good for amplitudes
ON2 CN7 CN7B ON6 0.3 5 0.0 !impact on amplitudes
ON2 CN7 CN7B ON6 0.6 4 180.0 !increases c2'endo
ON2 CN7 CN7B ON6 0.2 3 0.0 !
CN7 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg.
!============ new parameters for sugar model compounds ===============
!---------------- added for thf-imidazole ------------------
!-- For link between base and sugar:
CN7B NR1 CPH1 HR3 0.0 2 180.0 !NF
CN7B NR1 CPH1 CPH1 0.0 1 0.0 !
CN7B NR1 CPH2 HR1 0.0 2 180.0 !
CN7B NR1 CPH2 NR2 0.0 2 180.0 !
!-- For chi:
ON6 CN7B NR1 CPH1 0.2 3 0.0 !
ON6 CN7B NR1 CPH1 0.5 2 -70.0 !
ON6 CN7B NR1 CPH1 0.6 1 180.0 !
ON6 CN7B NR1 CPH2 0.3 1 0.0 !
ON6B CN7B NR1 CPH1 0.2 3 0.0 ! RNUS
ON6B CN7B NR1 CPH1 0.5 2 -70.0 ! RNUS
ON6B CN7B NR1 CPH1 0.6 1 180.0 ! RNUS
ON6B CN7B NR1 CPH2 0.3 1 0.0 ! RNUS
CN8 CN7B NR1 CPH1 0.2 4 0.0 !
CN8 CN7B NR1 CPH2 0.1 3 180.0 !
CN8 CN7B NR1 CPH2 0.3 2 0.0 !
CN8 CN7B NR1 CPH2 0.0 1 180.0 !
CN7B CN7B NR1 CPH1 0.2 4 0.0 ! RNUS
CN7B CN7B NR1 CPH2 0.1 3 180.0 ! RNUS
CN7B CN7B NR1 CPH2 0.3 2 0.0 ! RNUS
CN7B CN7B NR1 CPH2 0.0 1 180.0 ! RNUS
HN7 CN7B NR1 CPH1 0.0 3 0.0 !
HN7 CN7B NR1 CPH2 0.195 3 0.0 !
CN8 CN8 CN7B NR1 0.0 3 0.0
CN7 CN7B CN7B NR1 0.0 3 0.0 ! RNUS
CN8 ON6 CN7B NR1 0.0 3 0.0
HN8 CN8 CN7B NR1 0.0 3 0.0
HN7 CN7B CN7B NR1 0.0 3 0.0 ! RNUS
NR1 CN7B CN7B ON5 0.0 3 0.0 ! RNUS
!-- For imidazole, transferred from imidazole alone:
CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! From imidazole (NF)
CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! From imidazole (NF)
NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! From imidazole (NF)
NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! From imidazole (NF)
NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! From imidazole (NF)
NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! From imidazole (NF)
HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! From imidazole (NF)
HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! From imidazole (NF)
HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! From imidazole (NF)
HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! From imidazole (NF)
HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! From imidazole (NF)
NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! From imidazole (NF)
!------------------- added for thf-oh-ch3-im ---------------------
CN7B ON6 CN7 CN8 0.0 3 0.0 ! 25P1
CN7B ON6 CN7 CN9 0.0 3 0.0
CN7 ON6 CN7B NR1 0.0 3 0.0
CN7 ON6B CN7B NR1 0.0 3 0.0 ! RNUS
NR1 CN7B CN8 CN7 0.0 3 0.0
!%%%%%%% new terms for dna and the deoxyribose-based model compounds %%%%%%
! The following is for: THF3P (model for espilon), THFM3P (model for puckering),
! THF5P (model for gamma and beta), THFCH3IM (model for chi), nucleotide analogue
!@@@@@@ Begining of chi
!============= added for torsion about chi in adenine ============
!For link from sugar to base:
CN7B NN2 CN4 HN3 0.3 2 180.0 ! NF
CN7B NN2 CN5 CN5 11.0 2 180.0 ! adm jr.
CN7B NN2 CN4 NN4 11.0 2 180.0 ! adm jr.
CN7B NN2 CN4 NN3A 11.0 2 180.0 ! adm jr.
!For chi itself:
!DNA:
ON6 CN7B NN2 CN5 1.1 1 180.0 !
ON6 CN7B NN2 CN4 1.1 1 0.0 ! NF
!RNA:
ON6B CN7B NN2 CN5 1.1 1 180.0 !
ON6B CN7B NN2 CN4 1.1 1 0.0 !
!DNA:
CN8 CN7B NN2 CN5 0.3 3 0.0 ! NF
CN8 CN7B NN2 CN4 0.0 3 180.0 ! NF
!RNA:
CN7B CN7B NN2 CN5 0.3 3 0.0 ! NF
CN7B CN7B NN2 CN4 0.0 3 180.0 ! NF
!Arabinose:
CN7C CN7B NN2 CN5 0.3 3 0.0 !
CN7C CN7B NN2 CN4 0.0 3 180.0 !
HN7 CN7B NN2 CN5 0.0 3 0.0 ! NF
HN7 CN7B NN2 CN4 0.195 3 0.0 ! NF
!@@@@@@ End of chi in adenines
!============== terms for torsion about chi in cytosines ===========
CN7B NN2 CN3 HN3 0.3 2 180.0 ! NF
CN7B NN2 CN1 ON1C 11.0 2 180.0 ! adm jr. from A
CN7B NN2 CN1 NN3 11.0 2 180.0 ! adm jr.
CN7B NN2 CN3 CN3 11.0 2 180.0 ! adm jr.
!DNA:
ON6 CN7B NN2 CN1 0.0 3 0.0 !
ON6 CN7B NN2 CN3 1.0 1 0.0 ! NF
!RNA:
ON6B CN7B NN2 CN1 0.0 3 0.0 !
ON6B CN7B NN2 CN3 1.0 1 0.0 !
!DNA:
CN7 CN7B NN2 CN1 1.0 3 0.0 ! 25P1
CN8 CN7B NN2 CN1 1.0 3 0.0 !
CN7 CN7B NN2 CN3 0.0 3 180.0 ! NF 030697, 25P1
CN8 CN7B NN2 CN3 0.0 3 180.0 ! NF 030697
!RNA:
CN7B CN7B NN2 CN1 1.0 3 0.0 !
CN7B CN7B NN2 CN3 0.0 3 180.0 !
!Arabinose:
CN7C CN7B NN2 CN1 1.0 3 0.0 !
CN7C CN7B NN2 CN3 0.0 3 180.0 !
HN7 CN7B NN2 CN1 0.0 3 0.0 ! NF
HN7 CN7B NN2 CN3 0.195 3 0.0 ! NF
!@@@@@@ End of chi in cytosines
!=========== terms for torsion about chi in uracils/thymines ===========
CN7B NN2B CN3 HN3 0.3 2 180.0 ! NF
CN7B NN2B CN1T ON1 11.0 2 180.0 ! adm jr. from A
CN7B NN2B CN1T NN2U 11.0 2 180.0 ! adm jr.
CN7B NN2B CN3 CN3T 11.0 2 180.0 ! adm jr.
!DNA:
ON6 CN7B NN2B CN1 0.0 3 0.0 !
ON6 CN7B NN2B CN1T 0.7 3 0.0 !
ON6 CN7B NN2B CN1T 0.8 1 180.0 !
ON6 CN7B NN2B CN3 0.9 1 0.0 ! NF
!RNA:
ON6B CN7B NN2B CN1 0.0 3 0.0 !
ON6B CN7B NN2B CN1T 0.7 3 0.0 !
ON6B CN7B NN2B CN1T 0.8 1 180.0 !
ON6B CN7B NN2B CN3 0.9 1 0.0 !
!DNA:
CN8 CN7B NN2B CN1T 0.2 3 180.0 !
CN8 CN7B NN2B CN3 0.0 3 180.0 ! NF
!RNA:
CN7B CN7B NN2B CN1T 0.2 3 180.0 !
CN7B CN7B NN2B CN3 0.0 3 180.0 !
!Arabinose:
CN7C CN7B NN2B CN1T 0.2 3 180.0 !
CN7C CN7B NN2B CN3 0.0 3 180.0 !
HN7 CN7B NN2B CN1T 0.0 3 0.0 ! NF
HN7 CN7B NN2B CN3 0.195 3 0.0 ! NF
!@@@@@@ End of chi in thymines
!============= added for torsion about chi in guanine ============
CN7B NN2B CN4 HN3 0.3 2 180.0 ! NF
CN7B NN2B CN4 NN4 11.0 2 180.0 ! adm jr.
CN7B NN2B CN5 CN5G 11.0 2 180.0 ! adm jr. from U
CN7B NN2B CN5 NN3G 11.0 2 180.0 ! adm jr.
!DNA:
ON6 CN7B NN2B CN5 0.2 3 0.0 !
ON6 CN7B NN2B CN5 1.1 1 180.0 !
ON6 CN7B NN2B CN4 1.4 1 0.0 ! NF
!RNA:
ON6B CN7B NN2B CN5 0.2 3 0.0 !
ON6B CN7B NN2B CN5 1.1 1 180.0 !
ON6B CN7B NN2B CN4 1.4 1 0.0 !
!DNA:
CN8 CN7B NN2B CN5 0.0 3 0.0 ! NF
CN8 CN7B NN2B CN4 0.0 3 180.0 ! NF 030697
!RNA:
CN7B CN7B NN2B CN5 0.0 3 0.0 ! NF
CN7B CN7B NN2B CN4 0.0 3 180.0 !
!Arabinose:
CN7C CN7B NN2B CN5 0.0 3 0.0 !
CN7C CN7B NN2B CN4 0.0 3 180.0 !
HN7 CN7B NN2B CN5 0.0 3 0.0 ! NF
HN7 CN7B NN2B CN4 0.195 3 0.0 ! NF
!@@@@@@ End of chi in guanines
!@@@@@@ link (not chi) between base and sugar for both purines and pyrimidines:
!DNA:
CN7 ON6 CN7B NN2 0.0 3 0.0
CN7 ON6 CN7B NN2B 0.0 3 0.0
!RNA:
CN7 ON6B CN7B NN2 0.0 3 0.0
CN7 ON6B CN7B NN2B 0.0 3 0.0
!DNA:
CN7 CN8 CN7B NN2 0.0 3 0.0
CN7 CN8 CN7B NN2B 0.0 3 0.0
HN8 CN8 CN7B NN2 0.0 3 0.0
HN8 CN8 CN7B NN2B 0.0 3 0.0
!RNA:
CN7 CN7B CN7B NN2 0.0 3 0.0
CN8 CN7B CN7B NN2 0.0 3 0.0 ! 25P1
CN7 CN7B CN7B NN2B 0.0 3 0.0
CN8 CN7B CN7B NN2B 0.0 3 0.0 ! 25P1
!Arabinose:
CN7 CN7C CN7B NN2 0.0 3 0.0
CN7 CN7C CN7B NN2B 0.0 3 0.0
!RNA
HN7 CN7B CN7B NN2 0.0 3 0.0
HN7 CN7B CN7B NN2B 0.0 3 0.0
!Arabinose:
HN7 CN7C CN7B NN2 0.0 3 0.0
HN7 CN7C CN7B NN2B 0.0 3 0.0
!@@@@@@ Begining of torsions involving exocyclic sugar atoms:
!======= CN7 CN8B ON2 P = C4'-C5'-O5'-P
CN7 CN8B ON2 P 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr.
! the following differ significantly from the alcohols
! in the protein (based on ethanol), they also differ from other
! NA C-C-OH-H parameters (see below)
! The two following terms have been replaced by their ethanol
! counterpart (NF, 083098)
CN7 CN8B ON5 HN5 1.3300 1 0.00
CN7 CN8B ON5 HN5 0.1800 2 0.00
CN7 CN8B ON5 HN5 0.3200 3 0.00
!======= HN8 CN8B ON2 P = H-C5'-O5'-P )beta
HN8 CN8B ON5 HN5 0.0 3 0.0 !bet
!======== CN7 CN7 CN8B ON2 = C3'-C4'-C5'-O5'
! When O5' is ON2 (phosphodiester linkage):
CN7 CN7 CN8B ON2 0.20 4 180.0 !gam adm jr.
CN7 CN7 CN8B ON2 0.80 3 180.0 !gam C3'-C4'-C5'-O5'
CN7 CN7 CN8B ON2 0.40 2 0.0 !gam
CN7 CN7 CN8B ON2 2.50 1 180.0 !gam
!
CN8 CN7 CN8B ON2 0.2 3 180.0 ! from gam, carbocyclic and 25P1
! When O5' is ON5 (5TER patch):
CN7 CN7 CN8B ON5 0.20 4 180.0 !gam adm jr.
CN7 CN7 CN8B ON5 0.80 3 180.0 !gam C3'-C4'-C5'-O5'
CN7 CN7 CN8B ON5 0.40 2 0.0 !gam
CN7 CN7 CN8B ON5 2.50 1 180.0 !gam
!======== ON6 CN7 CN8B ON2 = O4'-C4'-C5'-O5'
! When O5' is ON2 (3'-5' phosphodiester linkage)
ON6 CN7 CN8B ON2 3.4 1 180.0 !gam O4'-C4'-C5'-O5',influences +60
ON6B CN7 CN8B ON2 3.4 1 180.0 !gam, RNA
! When O5' is ON5 (5TER patch):
ON6 CN7 CN8B ON5 3.4 1 180.0 !gam
ON6B CN7 CN8B ON5 3.4 1 180.0 !gam, RNA
!======== HN8 CN8B CN7 CN7 = H-C5'-C4'-H
HN8 CN8B CN7 CN7 0.195 3 0.0 !gam,H-C5'-C4'-H
HN8 CN8B CN7 CN8 0.195 1 0.0 !gam, carbocylic, 25P1
!======== HN7 CN8B CN7 ON6 = H-C5'-C4'-O4'
HN8 CN8B CN7 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4'
HN8 CN8B CN7 ON6B 0.195 1 0.0 !gam, RNA
!======== HN7 CN7 CN8B ON2 = H-C4'-C5'-O5'
! When O5' is ON2 (phosphodiester linkage):
HN7 CN7 CN8B ON2 0.195 3 0.0 !gam H-C4'-C5'-O5'
! When O5' is ON5 (5TER patch):
HN7 CN7 CN8B ON5 0.195 3 0.0 !gam
HN8 CN8 CN8 ON6 0.195 1 0.0 !gam,H-C5'-C4'-O4'
! terms for 5MET patch
CN9 CN7 CN7 CN8B 0.5 4 180.0 !cn8 -> cn9
HN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9
CN7 CN7 CN9 HN9 0.195 3 0.0 !cn8 -> cn9
ON6 CN7 CN9 HN9 0.195 3 0.0 !cn7 -> cn9
HN7 CN7B CN7 CN8 0.195 3 0.0 !cn8 -> cn9, 25P1
HN7 CN7 CN7 CN9 0.195 3 0.0 !cn8 -> cn9
ON2 CN7 CN7 CN9 0.2 4 0.0 !cn8b -> cn9
ON2 CN7 CN7 CN9 0.8 3 180.0 !cn8b -> cn9
CN8 CN7 CN7 CN9 0.5 4 180.0 !cn8b -> cn9
!======== CN8 CN7 CN7 CN8B = C2'-C3'-C4'-C5'
! This term is well suited to modify the puckering surfaces, in
! particular because it is present in THF5P
CN8 CN7 CN7 CN8B 0.5 4 180.0 !del lowers 180 deg.
CN7B CN7 CN7 CN8B 0.2 4 180.0 !del, RNA
CN7C CN7 CN7 CN8B 0.5 4 180.0 !del, arabinose
!======== CN8B CN7 CN7 ON2 = C5'-C4'-C3'-O3'
! These terms affect the c2endo/c3endo energy difference
! When O3' is ON2 (3'-5' phosphodiester linkage)
ON2 CN7 CN7 CN8B 0.2 4 0.0 !del
! the following term controls the location of the barrier at ~75 deg.
ON2 CN7 CN7 CN8B 0.8 3 180.0 !del,decreases P [100,250]
! When O3' is ON5 (patch 3TER)
ON5 CN7 CN7 CN8B 0.2 4 0.0 !
ON5 CN7 CN7 CN8B 0.8 3 180.0 !
!======== ON6 CN7 CN7 ON2 = O4'-C4'-C3'-O3'
! These terms contribute to delta
! These terms are present in THF3P and THFM3P but not in THF5P
! When O3' is ON2 (3'-5' phosphodiester linkage)
ON2 CN7 CN7 ON6 0.5 6 0.0 !del, good for amplitudes
ON2 CN7 CN7 ON6 0.3 5 0.0 !del, impact on amplitudes
ON2 CN7 CN7 ON6 0.6 4 180.0 !del, increases c2'endo
ON2 CN7 CN7 ON6 0.2 3 0.0 !
ON2 CN7 CN7 ON6B 0.4 6 0.0 !del, RNA, good for amplitudes
ON2 CN7 CN7 ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes
ON2 CN7 CN7 ON6B 0.0 4 180.0 !del, RNA, increases c2'endo
ON2 CN7 CN7 ON6B 1.6 3 0.0 !del, RNA, increases C2'endo
! for ndph: make identical to ON2 CN7 CN7 ON6B
ON2 CN7B CN7B ON6B 0.4 6 0.0 !del, RNA, good for amplitudes
ON2 CN7B CN7B ON6B 0.0 5 0.0 !del, RNA, impact on amplitudes
ON2 CN7B CN7B ON6B 0.0 4 180.0 !del, RNA, increases c2'endo
ON2 CN7B CN7B ON6B 1.6 3 0.0 !del, RNA, increases C2'endo
! When O3' is ON5 (patch 3TER)
ON5 CN7 CN7 ON6 0.5 6 0.0 !
ON5 CN7 CN7 ON6 0.3 5 0.0 !
ON5 CN7 CN7 ON6 0.6 4 180.0 !
ON5 CN7 CN7 ON6 0.2 3 0.0 !
ON5 CN7 CN7 ON6B 0.4 6 0.0 !RNA
ON5 CN7 CN7 ON6B 0.0 5 0.0 !RNA
ON5 CN7 CN7 ON6B 0.0 4 180.0 !RNA
ON5 CN7 CN7 ON6B 1.6 3 0.0 !RNA. increases c2'endo
!======== CN8B CN7 ON6 CN7B = C5'-C4'-O4'-C1'
! This term can be used to adjust the c2'endo/c3'endo
! energy difference in THF5P
CN7B ON6 CN7 CN8B 0.8 3 0.0 ! P [30,80]
CN7B ON6B CN7 CN8B 2.0 3 0.0 ! To lower barrier in RNA
CN7B ON6B CN7 CN8 2.0 3 0.0 ! To lower barrier in RNA, 25P1
CN7B ON6B CN7 CN9 2.0 3 0.0 ! To lower barrier in RNA, 5MET
!======== ON2 CN7 CN8 CN7B = O3'-C3'-C2'-C1'
! This term can be used to adjust the c2'endo/c3'endo
! When O3' is ON2
ON2 CN7 CN8 CN7B 0.8 6 0.0 !
ON2 CN7 CN8 CN7B 0.4 5 0.0 ! Moves the barrier right
ON2 CN7 CN8 CN7B 2.0 3 180.0 !
ON2 CN7 CN7B CN7B 0.6 6 0.0 ! RNA
ON2 CN7 CN7B CN7B 0.0 5 0.0 ! RNA c2/c3 endo in RNA
ON2 CN7 CN7B CN7B 1.6 3 180.0 !
ON2 CN7 CN7C CN7B 0.8 6 0.0 ! Arabinose (from DNA)
ON2 CN7 CN7C CN7B 0.4 5 0.0 !
ON2 CN7 CN7C CN7B 2.0 3 180.0 !
!When O3' is ON5 (patch 3TER)
ON5 CN7 CN8 CN7B 0.8 6 0.0 !
ON5 CN7 CN8 CN7B 0.4 5 0.0 !
ON5 CN7 CN8 CN7B 2.0 3 180.0 !
ON5 CN7 CN7B CN7B 0.6 6 0.0 ! RNA, c2/c3 endo
ON5 CN7 CN7B CN7B 0.0 5 0.0 ! RNA
ON5 CN7 CN7B CN7B 1.6 3 180.0 ! RNA
ON5 CN7 CN7C CN7B 0.8 6 0.0 ! Arabinose (from DNA)
ON5 CN7 CN7C CN7B 0.4 5 0.0 ! Arabinose (from DNA)
ON5 CN7 CN7C CN7B 2.0 3 180.0 ! Arabinose (from DNA)
!======== ON2 CN7 CN8 HN8 = O3'-C3'-C2'-H
ON2 CN7 CN8 HN8 0.195 3 0.0 !
ON5 CN7 CN8 HN8 0.195 3 180.0 !
ON2 CN7 CN7B HN7 0.195 3 0.0 ! RNA
ON5 CN7 CN7B HN7 0.195 3 180.0 ! RNA
ON2 CN7 CN7C HN7 0.195 3 0.0 ! Arabinose (from DNA)
ON5 CN7 CN7C HN7 0.195 3 180.0 ! Arabinose (from DNA)
!======== HN7 CN7 CN7 ON2 = H-C4'-C3'-O3'
HN7 CN7 CN7 ON2 0.195 3 0.0
HN7 CN7 CN7 ON5 0.195 3 0.0
!======== CN7 CN7 ON2 P = C4'-C3'-O3'-P
CN7 CN7 ON2 P 0.6 5 0.0 !eps
CN7 CN7 ON2 P 0.2 4 0.0 !eps, locat of 200 mimima
CN7 CN7 ON2 P 0.0 3 180.0 !eps, barE beteen minima
CN7 CN7 ON2 P 0.4 2 0.0 !eps, relE of 200 vs 275 min
CN7 CN7 ON2 P 1.9 1 180.0 !eps
!======== CN8 CN7 ON2 P = C2'-C3'-O3'-P
! This term is involved in epsilon
CN8 CN7 ON2 P 2.5 1 180.0 !eps
CN7B CN7 ON2 P 2.5 1 180.0 !eps, RNA
CN7B CN7B ON2 P 2.5 1 180.0 !eps, NADPH
CN7 CN7B ON2 P 2.5 1 180.0 !eps, NADPH
CN8 CN7B ON2 P 2.5 1 180.0 !eps, 25P1
CN7C CN7 ON2 P 2.5 1 180.0 !eps, Arabinose (from DNA)
! base on thfalloh
! the following differ significantly from the protein based
! alcohol parameters (based on ethanol, see above)
CN7 CN7 ON5 HN5 0.5 3 0.0
CN7 CN7 ON5 HN5 0.3 2 180.0
CN7 CN7 ON5 HN5 1.5 1 0.0
CN8 CN7 ON5 HN5 0.5 3 0.0
CN8 CN7 ON5 HN5 1.0 2 180.0
CN8 CN7 ON5 HN5 0.3 1 0.0
CN7B CN7 ON5 HN5 0.8 3 0.0 ! RNA
CN7B CN7 ON5 HN5 0.5 1 0.0 ! RNA
CN7C CN7 ON5 HN5 0.8 3 0.0 ! Arabinose (from DNA)
CN7C CN7 ON5 HN5 0.5 1 0.0 ! Arabinose (from DNA)
! Was simply transfered from HN7 CN7 ON2 P
! adm jr. should convert to alcohol term (see ribose etc)
HN7 CN7 ON5 HN5 0.0 3 0.0
HN7 CN7 CN8B HN8 0.195 3 0.0 !gam H-C4'-C5'-H
HN7 CN7 CN7 CN8B 0.195 3 0.0 !gam H-C3'-C4'-C5'
!@@@@@@ End of torsions involving exocyclic atoms:
!@@@@@@ Begining of torsions for endocyclic atoms only:
CN8 CN7B ON6 CN7 0.6 6 180.0 !C2'-C1'-O4'-C4'
CN8 CN7 CN7 ON6 0.0 3 0.0 !C2'-C3'-C4'-O4'
CN7B CN7B ON6B CN7 0.0 6 0.0 ! RNA, Lowers barrier
CN7B CN7 CN7 ON6B 0.0 3 0.0 ! RNA
CN7C CN7B ON6 CN7 0.6 6 180.0 ! Arabinose (from DNA)
CN7C CN7 CN7 ON6 0.0 3 0.0 ! Arabinose (from DNA)
!======== CN7 CN8 CN7B ON6 for nucleosides, transfered from =========
!======== CN7 CN8 CN8 ON6 from thfoh ==============================
CN7 CN8 CN7B ON6 0.6 6 0.0 ! C3'-C2'-C1'-O4', adjust barrier
CN7 CN7B CN7B ON6B 0.4 6 0.0 ! RNA
CN8 CN7B CN7B ON6B 0.4 6 0.0 ! RNA, 25P1
CN7 CN7C CN7B ON6 0.6 6 0.0 ! Arabinose (from DNA)
!======== C1'-C2'-C3'-C4' ========
CN7B CN8 CN7 CN7 0.4 6 0.0 ! good for amplitudes
CN7B CN7B CN7 CN7 0.0 6 0.0 ! RNA
CN7B CN7B CN8 CN7 0.0 6 0.0 ! RNA, 25P1
CN7B CN7C CN7 CN7 0.4 6 0.0 ! Arabinose (from DNA)
!======== CN7 CN7 ON6 CN7B for nucleosides, transfered from ========
!======== CN7 CN7 ON6 CN8 from thfohch3 ============================
CN7 CN7 ON6 CN7B 0.6 6 180.0 ! C3'-C4'-O4'-C1'
CN7 CN7 ON6B CN7B 0.0 6 180.0 ! RNA
!======== Directly adjusted with TM3P
HN7 CN7 CN7 CN8 0.0 3 0.0 !puc,H-C3'-C4'-C5'
HN7 CN7 CN7 CN7C 0.0 3 0.0 ! Arabinose (from DNA)
!======== HN7 CN7 CN7 ON6 = H-C2'-C3'-O4'
HN7 CN7 CN8 CN7B 0.195 3 0.0 !H-C3'-C2'-C1'
HN7 CN7B CN8 CN7 0.195 3 0.0 !H-C1'-C2'-C3'
HN7 CN7 CN7 ON6 0.195 3 180.0 ! useful
HN8 CN8 CN7B ON6 0.195 3 0.0 !H-C2'-C1'-O4'
HN7 CN7 CN7 HN7 0.195 3 0.0 !H-C4'-C3'-H
HN7 CN7B CN8 HN8 0.195 3 0.0 !H-C1'-C2'-H
HN7 CN7 CN8 HN8 0.195 3 0.0 !H-C3'-C2'-H
HN8 CN8 CN7 CN7 0.195 3 0.0 ! useful *cccc*
HN7 CN7 ON6 CN7B 0.195 3 0.0 !H-C3'-C2'-C1'
HN7 CN7B ON6 CN7 0.000 3 0.0 !H-C1'-O4'-C4'
HN7 CN7 CN7 ON6B 0.195 3 180.0 ! RNA
HN9 CN9 CN7 ON6B 0.195 3 180.0 ! RNA, 5MET
HN8 CN8 CN7B ON6B 0.195 3 0.0 ! RNA
HN7 CN7B ON6B CN7 0.000 3 0.0 ! RNA
HN7 CN7 ON6B CN7B 0.195 3 0.0 ! RNA
HN7 CN7 CN7B CN7B 0.195 3 0.0 ! RNA, H-C3'-C2'-C1'
HN8 CN8 CN7B CN7B 0.195 3 0.0 ! RNA, H-C3'-C2'-C1', 25P1
HN7 CN7B CN7B CN7 0.195 3 0.0 ! RNA, H-C1'-C2'-C3'
HN7 CN7B CN7B CN8 0.195 3 0.0 ! RNA, H-C1'-C2'-C3', 25P1
HN7 CN7B CN7B ON6B 0.195 3 0.0 ! RNA, H-C2'-C1'-O4'
HN7 CN7 CN7C CN7B 0.195 3 0.0 !Arabinose (from DNA), H-C3'-C2'-C1'
HN7 CN7B CN7C CN7 0.195 3 0.0 !Arabinose (from DNA), H-C1'-C2'-C3'
HN7 CN7C CN7B ON6 0.195 3 0.0 !Arabinose (from DNA), H-C2'-C1'-O4'
HN7 CN7B CN7C HN7 0.195 3 0.0 !Arabinose (from DNA), H-C1'-C2'-H
HN7 CN7 CN7C HN7 0.195 3 0.0 !Arabinose (from DNA), H-C3'-C2'-H
HN7 CN7C CN7 CN7 0.195 3 0.0 !Arabinose (from DNA), useful *cccc*
!@@@@@@ End of torsions for endocyclic atoms only
!@@@@@@ Begining of torsions specifically defined for RNA @@@@@@
! N9-C1'-C2'-O2':
NN2 CN7B CN7B ON5 0.000 3 0.0 ! Adenine and cytosine
NN2B CN7B CN7B ON5 0.000 3 0.0 ! Guanine and uracil
ON5 CN7B CN7B HN7 0.000 3 0.0 !
HN7 CN7B CN7B HN7 0.000 3 0.0 !
CN7 CN7 CN7B ON5 0.000 3 0.0
ON6B CN7B CN7B ON5 0.000 3 0.0
ON5 CN7B CN7 ON2 0.000 3 0.0
! for ndph
ON5 CN7 CN7B ON2 0.000 3 0.0
ON5 CN7B CN7 ON5 0.000 3 0.0
HN7 CN7B ON5 HN5 0.000 3 0.0
! the following differ significantly from the protein based
! alcohol parameters (based on ethanol, see above)
HN5 ON5 CN7B CN7B 0.000 6 180.0 !
HN5 ON5 CN7B CN7B 0.800 3 0.0 !
HN5 ON5 CN7B CN7B 0.000 2 180.0 !
HN5 ON5 CN7B CN7B 0.000 1 180.0 !
HN5 ON5 CN7B CN7 0.300 3 0.0 ! 030298
HN5 ON5 CN7B CN7 0.000 1 0.0 ! 030298
!@@@@@@ End of torsions specifically defined for RNA @@@@@@
!@@@@@@ Begining of torsions specifically defined for arabinose @@@@@@
ON6 CN7B CN7C ON5 0.000 3 0.0
! the following differ significantly from the protein based
! alcohol parameters (based on ethanol, see above)
CN7B CN7C ON5 HN5 0.000 3 0.0
CN7 CN7C ON5 HN5 0.000 3 0.0
HN7 CN7B CN7C ON5 0.000 3 0.0
CN7 CN7 CN7C ON5 0.000 3 0.0
HN7 CN7C ON5 HN5 0.000 3 0.0
ON5 CN7C CN7 HN7 0.000 3 0.0
ON5 CN7C CN7 ON2 0.000 3 0.0
!@@@@@@ End of torsions specifically defined for arabinose @@@@@@
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
!
HN2 X X NN2 1.0 0 0.0 !C, adm jr. 11/97
NN2B CN4 CN5 HN2 7.0 0 0.0 !G, adm jr. 11/97
NN2G CN4 CN1 HN2 0.8 0 0.0 !Inosine, adm jr. 2/94
HN1 X X NN1 4.0 0 0.0 !G, adm jr. 11/97
NN1 CN2 HN1 HN1 6.0 0 0.0 !A,C adm jr. 11/97
CN1 X X ON1 90.0 0 0.0 !U
CN1T X X ON1 90.0 0 0.0 !U
CN1 NN2G CN5G ON1 90.0 0 0.0 !G
CN1T NN2B NN2U ON1 110.0 0 0.0 !T/O2, adm jr. 11/97
CN1 NN2U CN3T ON1 90.0 0 0.0 !T/O4, adm jr. 11/97
CN1 X X ON1C 80.0 0 0.0 !C, par_32, adm jr. 10/2/91
CN2 X X NN1 90.0 0 0.0 !C,
CN2 NN3G NN2G NN1 40.0 0 0.0 !G
CN2 NN3A CN5 NN1 40.0 0 0.0 !A
CN2 NN3 CN3 NN1 60.0 0 0.0 !C,
CN4 NN2G NN3I HN3 39.0 0 0.0 !Inosine, adm jr. 2/94
CN9 X X CN3T 14.0 0 0.0 !T, adm jr. 11/97
! nicotinamide adenine dinucleotide
CN3 CN3C CN8 HN6 15.0 0 0.0 !nich, jjp1/adm jr.
HN3B X X CN3 15.0 0 0.0 !nad/ppi, jjp1/adm jr.
HN3B X X CN3A 13.0 0 0.0 !nad/ppi, jjp1/adm jr.
HN3B X X CN3B 13.0 0 0.0 !nad/ppi, jjp1/adm jr.
HN2 CN3 CN3B NN2 50.0 0 0.0 !nad/ppi, jjp1/adm jr.
HN1 HN1 CN1A NN1 -5.0 0 0.0 !nad/ppi, jjp1/adm jr.
ON1 X X CN1A 40.0 0 0.0 !nad/ppi, jjp1/adm jr.
HN3 X X CN3C 53.0 0 0.0 !nad/ppi, jjp1/adm jr.
HN6 X X CN3C 53.0 0 0.0 !nich, adm jr.
HN8 CN3 CN3 CN8 18.0 0 0.0 !nad/ppi, jjp1/adm jr.
!================== new terms added for sugar model compounds =========
!----------------------- Added for imidazole --------------------
HR1 NR1 NR2 CPH2 0.50 0 0.00 ! From imidazole (NF)
HR1 NR2 NR1 CPH2 0.50 0 0.00 ! From imidazole (NF)
HR3 CPH1 NR1 CPH1 0.50 0 0.00 ! From imidazole (NF)
HR3 CPH1 NR2 CPH1 0.50 0 0.00 ! From imidazole (NF)
HR3 NR1 CPH1 CPH1 0.50 0 0.00 ! From imidazole (NF)
HR3 NR2 CPH1 CPH1 0.50 0 0.00 ! From imidazole (NF)
NR1 CPH1 CPH2 CN7B 0.60 0 0.00 ! From imidazole (NF), k increased
NR1 CPH2 CPH1 CN7B 0.60 0 0.00 ! From imidazole (NF), k increased
! Wildcards used to minimize memory requirements
NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH -
CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
HT 0.0 -0.0460 0.2245 ! TIP3P
HN1 0.0 -0.0460 0.2245
HN2 0.0 -0.0460 0.2245
HN3 0.0 -0.046 1.1000 !adm jr. aromatic Hvdw
HNP 0.0 -0.03 1.3582 !JES 8/25/89 values from Jorgensen fit to hydration energy
HN3B 0.0 -0.046 0.9000 !nad/ppi, jjp1/adm jr.
HN3C 0.0 -0.03 1.3582 !check
HN4 0.0 -0.0460 0.2245
HN5 0.0 -0.0460 0.2245
HN6 0.0 -0.0220 1.3200
HN7 0.0 -0.0220 1.3200
HN8 0.0 -0.0280 1.3400 ! Hydrogen bound to CN8
HN9 0.0 -0.0240 1.3400 ! Hydrogen bound to CN9
HNE1 0.0 -0.031 1.25 ! alkene, yin,adm jr., 12/95
HNE2 0.0 -0.026 1.26 ! alkene, yin,adm jr., 12/95
!
NN1 0.0 -0.20 1.85
NN1C 0.0 -0.20 1.85
NN2 0.0 -0.20 1.85
NN2B 0.0 -0.20 1.85 ! From NN2, for N9 in guanines
NN2C 0.0 -0.20 1.85 !
NN2G 0.0 -0.20 1.85
NN2U 0.0 -0.20 1.85
NN3 0.0 -0.20 1.85
NN3A 0.0 -0.20 1.85
NN3G 0.0 -0.20 1.85
NN3I 0.0 -0.20 1.85
NN4 0.0 -0.20 1.85
NN5 0.0 -0.20 1.85
NN6 0.0 -0.20 1.85
!
ON1 0.0 -0.1200 1.70
ON1C 0.0 -0.1200 1.70
ON2 0.0 -0.1521 1.77
ON2B 0.0 -0.1521 1.77 !(see toppar_tyr_ser_thr_phosphate.str)
ON3 0.0 -0.1200 1.70
ON4 0.0 -0.1521 1.77
ON5 0.0 -0.1521 1.77
ON6 0.0 -0.1521 1.77
ON6B 0.0 -0.1521 1.77
OT 0.0 -0.1521 1.7682 ! TIP3P
!
! base ring C vdw param, 11/14/97, adm jr
CN1 0.0 -0.10 1.9000
CN1A 0.0 -0.07 2.0000 ! nad/ppi, jjp1/adm jr. (protein CC)
CN1T 0.0 -0.10 1.9000
CN2 0.0 -0.10 1.9000
CN3 0.0 -0.09 1.9000
CN3A 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr.
CN3B 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr.
CN3C 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr.
CN3D 0.0 -0.09 1.9000 ! 5mc, adm jr.
CN3T 0.0 -0.09 1.9000 ! T, adm jr.
CN4 0.0 -0.075 1.9000
CN5 0.0 -0.075 1.9000
CN5G 0.0 -0.075 1.9000
CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
CN7C 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
CN7D 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
! alkane optimized terms below, Yin and MacKerell, 1998, JCC, In press
CN8 0.0 -0.0560 2.010 0.0 -0.01 1.90 !
CN8B 0.0 -0.0560 2.010 0.0 -0.01 1.90 !
CN9 0.0 -0.0780 2.040 0.0 -0.01 1.90 !
!
CNE1 0.0 -0.068 2.09 ! alkene, yin,adm jr., 12/95
CNE2 0.0 -0.064 2.08 ! alkene, yin,adm jr., 12/95
CNA 0.0 -0.07 1.9924 !benzene (JES)
CNA2 0.0 -0.07 1.90 !dft, adm jr.
!
!carbocyclic sugars (see toppar_all27_na_carbocyclic.str)
CN6 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
CN7E 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
!
FN1 0.0 -0.09 1.70 !aliphatic F preliminary from Yin Thesis
!see toppar_all22_prot_fluoro_alkane.str for better parameters
FNA 0.0 -0.12 1.70 !aromatic F, 1,3-difluorobenzene pure solvent
!
P 0.0 -0.585 2.15
P2 0.0 -0.585 2.15 ! nad/ppi, jjp1/adm jr. (see toppar_all27_na_nad_ppi.str)
P3 0.0 -0.585 2.15 ! for PPI2, adm jr. (see toppar_all27_na_nad_ppi.str)
!
!-------------- for imidazole --------------
CPH1 0.000000 -0.050000 1.800000 ! From imidazole (NF)
CPH2 0.000000 -0.050000 1.800000 ! From imidazole (NF)
NR1 0.000000 -0.200000 1.850000 ! From imidazole (NF)
NR2 0.000000 -0.200000 1.850000 ! From imidazole (NF)
HR3 0.000000 -0.007800 1.468000 ! From imidazole (NF)
HR1 0.000000 -0.046000 0.900000 ! From imidazole (NF)
!
! ions
SOD 0.0 -0.0469 1.36375 ! sodium
! D. Beglovd and B. Roux, dA=-100.8 kcal/mol
POT 0.0 -0.0870 1.76375 ! potassium
! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
CLA 0.0 -0.150 2.27 ! chloride
! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
CAL 0.0 -0.120 1.367 ! Calcium
! S. Marchand and B. Roux, dA = -384.8 kcal/mol
MG 0.0 -0.0150 1.18500 ! Magnesium
! B. Roux dA = -441.65
CES 0.0 -0.1900 2.100
! Cesium, so far untested.
ZN 0.0 -0.250000 1.090000 !
! RHS March 18, 1990
DUM 0.0 -0.000 1.00 ! dummy atom
NBFIX
! Emin Rmin
! (kcal/mol) (A)
!
HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
! READ PARAM APPEND CARD
! to append hbond parameters from the file: par_hbond.inp
END
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