J. Am. Chem. Soc., 1996, 118(45), , DOI: /ja

Transcription

1 J. Am. Chem. Soc., 1996, 118(45), , DOI: /ja Terms & Conditions Electronic Supporting Information files are available without a subscription to ACS Web Editions. The American Chemical Society holds a copyright ownership interest in any copyrightable Supporting Information. Files available from the ACS website may be downloaded for personal use only. Users are not otherwise permitted to reproduce, republish, redistribute, or sell any Supporting Information from the ACS website, either in whole or in part, in either machinereadable form or any other form without permission from the American Chemical Society. For permission to reproduce, republish and redistribute this material, requesters must process their own requests via the RightsLink permission system. Information about how to use the RightsLink permission system can be found at Copyright 1996 American Chemical Society

2 IYYUMir~1llud1 % L1Ud1 13UU~r'LY J. MIII. '.ki~i.3ul. V 110 ra~ LJJUIgU~irII 31tPJIUMIIIILaI radgr I Supporting Information Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids William L. Jorgensen,* David S. Maxwell, and Julian Tirado-Rives Department of Chemistry, Yale University,New Haven, Connecticut The following tables contain the available non-bonded and torsional parameters for the OPLS-AA force field. These and the bond-stretching and angle-bending parameters are available by ftp after contacting W. L. Jorgensen by at bill@adrik.chem.yale.edu. Form of the Force Field Bond stretching: Angle bending: Ebnd Kr - rq ) 2 bonds Ea,,g, = Y KO (- 0eq)2 angles Torsion: E(0) + cos( + f 1)] + -- cos(20 + f 2)] + 1+ cos(30 + f 3)] Non-bonded: ona onb Eab i j (c 2 r/ 2 _/+4 r 6 f! = 0.5 if i, j are 1,4; otherwise, f, = 1.0 1

3 . I I -Xxx x X Uxx U X Uy J. -xxx- xx xxx- u - v x x - x "E, x x uffx xxx -L"x x "E, - Table 1. OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols atom or group q, e- Y, A., kcal mol-1 C, CH C, RCH C, R 2 CH C, R 3 CH C, R 4 C H, RH, alkanes C, Benzene H, Benzene C, CH 3 of toluene C, CH 2 of ethyl benzene C, R 2 C= C, RHC= C, H 2 C= H, HC= , ROH H(0), ROH H(C), CH 3 0H C, CH 3 0H and RCH 2 0H C, R 2 CHOH C, R 3 COH C, COH phenol , phenol H, phenol

4 '"i iryyul %M111r1Rd11a '1111d1 3uulrLy J. MIII. %-.I11i11. oulu. V 1 10 r-agri IZLLJ JUlgrl11ir11 31tPJIUMIIIILaI radgr J Table 2. OPLS-AA Non-Bonded Parameters for Sulfur Compounds and Amines atom or group g, e- a, A 6, kcal mol- 1 S, RSH H(S), RSH C, CH 3 SH C, RCH 2 SH C, R 2 CHSH C, R 3 CSH S, RSR C, CH 3 SR C, RCH 2 SR C, R 2 CHSR C, R 3 CSR S, RSSR C, CH 3 SSR C, RCH 2 SSR C, R 2 CHSSR C, R 3 CSSR N, RNH H, RNH C, CH 3 NH C, RCH 2 NH C, R 2 CHNH C, R 3 CNH

5 ' U IY -IIluaII % L1Ud1 OULY J. MIII. a.~iii ulu. V 1 10 rag~i ILLJ- JUIgr,1irllI 31tPJIUMIIILaI Fr '-t Table 3. OPLS-AA Non-Bonded Parameters for Ammonium Ions, Imidazoles, and Carboxylate Ionsa atom or group, e- N, RNH H, RNH C, CH 3 NH C, RCH 2 NH C, R 2 CHN{ C, R 3 CNH C, Cs 1 in HID, HIE C, C8 2 in HID, Cy in HIE C, Cy in HD, C 8 2 in HE C, Csj in HIP C, Cy, C82 in HIP H, Hon C5 or Cs in HID, HIE, HIP N, N5 in HID or Ns in HIE H, H(N8) in HID or H(Ns) in HIE N, Ns in ID or N in HIE N, in HIP H(N), in HIP C, CH 3 - in 5-methylimidazole C, RCH 2 - in 5-ethylimidazole C, RCOO , RCOO C, CH 3 COO C, RCH 2 COO C, R 2 CHCOO C, R 3 CCOO_ a HID, HIE, and HIP refer to unprotonated histidine Ns, and protonated histidine (imidazole), respectively. a, A s, kcal mol-i (imidazole) with hydrogens on N8 or 4

6 vi o American onemicai zociety J. Am. k-nem. oc. v 116 ragei izlz jorgensen 3uppiementai rage D Table 4. OPLS-AA Non-Bonded Parameters for Guanidinium Ions, Tryptophan, and Amidesa atom or group N, NH 2 in guanidinium H, NH 2 in guanidinium C, guanidinium N, NHR in alkylguanidinium H, NHR in alkylguanidinium C, CH 3 in methylguanidinium C, CH 3 in ethylguanidinium (EG) C, CH 2 (5) in Arg, EG C, CH 2 (y) in Arg N, Ns in Trp H, He(N) in Trp C, Cy in Trp C, CHS,s,,j in Trp H, Ha,,C (C) in Trp C, C6 in Trp C, C, in Trp C, C=O in amide 0, C=0 in amide H, HCONRR' N, 10 amide N, 20 amide N, 30 amide H(N), 20 amide H(N), 20 amide C, CH 3 N- 20 amide C, CH3N- 30 amide C, R CH2N - 30 amide (C5 in Pro) C, R 2CHN - 30 amide (Ca in Pro) C, CH2(c) in Gly C, CHR(oc) in Ala q, e a, A s, kcal mol

7 . I I -Xxx x X Uxx U X Uy J. -xxx- xx xxx- u - v x x - x "E, x x uffx xxx -L"x x "E, " C, CRR'(a) in Aib a R in RCONR'R" is neutral and uses alkane parameters. 6

8 ' U~rlul 'Y %L-V1111Rd11 '1111d1 3UU~r'LY J. MIII. a.~11 ulu. V 1 10 rag~i IZLLJ JU~gr11 ir11 31tPJIUMIIILaI Fr / Table 5. OPLS-AA Non-Bonded Parameters for Ethers, Acetals, Aldehydes, Ketones, and Carboxylic Acids. 0, ROR C, CH 3 0R C, RCH 2 0R C, R 2 CHOR C, R 3 COR H, CHnOR 0, acetal C, ROCH 2 0R H, ROCH 2 0R C, ROCHROR H, ROCHROR C, ROCR 2 0R C, RCHO O, RCHO H, RCHO C, R 2 CO 0, R 2 CO H, CHnCORa C, RCOOH O(C), RCOOH O(H), RCOOH Atom or group H, RCOOH a H on alpha C of aldehyde and ketone. g, e a, A s, kcal mol Alpha C uses alkyl C parameters (Ta ble 1). 7

9 '- M11l11Llua1 llrlul %YYU '.111c1 3uulrLy J. MIII. %-.I11i11. aulu. V 1 10 r-agri IZLLJ JUlgr11ir11 31tPJIUMIIIILaI Fr 0 Table 6. Bond Stretching and Angle Bending Parameters AMBER Typea req or Geq K CT-CT HC-CT HC-CT-HC HC-CT-CT CT-CT-CT a The AMBER atom types are from reference 3. req or 0 eg CHARMM/ K

10 vi o American onemicai zociety J. Am. Linem. oc. v 116 ragei izlz jorgensen 3uppiementai rage! Table 7. OPLS-AA Fourier Coefficients (kcal/mol) for Torsional Energy Functionsa System Dihedral V 1 V 2 V 3 alkane H-C-C-H H-C-C-C C-C-C-C alkene H-C-C=C ethylbenzene H-C-Car-Car C-C-Car-Car H-C-C-Car alcohol H-C-O-H C-C-O-H H-C-C-O C-C-C-O phenol H-O-Car-Car thiol H-C-S-H C-C-S-H H-C-C-S C-C-C-S sulfide H-C-S-C C-C-C-S C-C-S-C disulfide C-S-S-C H-C-S-S C-C-S-S o amine H-C-N-H H-C-C-N C-C-N-H C-C-C-N ammonium ion H-C-N-H C-C-N-H H-C-C-N C-C-C-N a Those listed with VI=V 2 =V 3 =0 are shown for completeness. 9

11 '- iliyyu %M111r11Lld '.111Ld1 3uulrLy J. MIII. a.~ii ulu. V 1 10 r-agri IZLL)J Uigrlirlli 31tPJIUMIIIILaI fr IV Table 8. OPLS-AA Fourier Coefficients (kcal/mol) for Torsional Energy Functionsa System ether acetal carboxylate ion carboxylic acid aldehyde/ketone aldehyde ketone aldehyde/ketone aldehyde ketone aldehyde/ketone aldehyde/ketone amide Dihedral H-C-O-C C-C-O-C C-O-C-O H-C-C-O C-C-C-O H-C-C-C(O) C-C-C-C(O) O-C-O-H C-C-O-H H-C-C-O H-C-C(O)-H H-C-C(O)-C C-C-C-O C-C-C(O)-H C-C-C(O)-C H-C-C-C(O) C-C-C-C(O) C(O)-N-C-H C(O)-N-C-C H-N-C-H H-N-C-C N-C-C-H N-C-C-C H-C-C(O)-N H-C-C(O)-O C-C-C(O)-N C-C-C(O)-O H-C-C-C(O) C-C-C-C(O) H-C-N3 0 -C H,C-C(O)-N-H VI V V

12 1Y "um1r1llui11 '..I11111III1 3uulrLy J. MIII. '..,11r111. k3ul. V 110 ra~ ZJJU~gr11ir11 31tPP1U111~ Ld1 radgr 11 H,C-C(O)-N-C O-C(O)-N-H O-C(O)-N-C a Those listed with V1=V2=V3=0 are shown for completeness. 11

13 '-'I U M11~1lluI1 % luaI13UU~r'LY J. MIII. a.~iii ulu. V 1 10 rag~i IZZ- JU~gr11 ir11 31tPP1U111~Ld1 rager I/- Table 9. OPLS-AA Fourier Coefficients (kcal/mol) for Torsional Energy Functionsa System peptidea (p peptide (p' peptide 9" peptide peptide xy peptide y'i peptide y" peptide peptide XI peptide X1 peptide X1 peptide XIb X1, Ser & Thr Ser & Thr X1, Cys Cys 5-ethylimidazole 3-ethylindole guanidinium ion Dihedral C(O)-N-C-C(O) C(O)-N-C-C C(O)-N-C-H H-N-Ca-X N-C-C(O)-N C-C-C(O)-N H-C-C(O)-N X-Cc-C(O)-O N-C-C-C N-C-C-H C(O)-C-C-H C(O)-C-C-C N-C-C-O C(O)-C-C-O N-C-C-S C(O)-C-C-S H-C-C-N C-C-C-N H-C-C3-C2 H-C-C3-C C-C-C3-C2 C-C-C3-C H-N-C-N C-N-C-N C-C-N-C H-C-C-N H-C-N-H a The 0 and Vt are used in the standard way. The " and ' denote dihedrals which extend to the Ca hydrogen and Cp carbon, respectively. b The remaining dihedral parameters for XI with the Ca hydrogen are the same as for alkanes, alcohols, and thiols. VI V V