List of possible Atoms
PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs BR 79.90 ! bromine C 12.01 sp2 C carbonyl group CA 12.01 sp2 C pure aromatic (benzene) CB 12.01 sp2 aromatic C, 5&6 membered ring junction CC 12.01 sp2 aromatic C, 5 memb. ring HIS CK 12.01 sp2 C 5 memb.ring in purines CM 12.01 sp2 C pyrimidines in pos. 5 & 6 CN 12.01 sp2 C aromatic 5&6 memb.ring junct.(TRP) CQ 12.01 sp2 C in 5 mem.ring of purines between 2 N CR 12.01 sp2 arom as CQ but in HIS CT 12.01 sp3 aliphatic C CV 12.01 sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) CW 12.01 sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) C* 12.01 sp2 arom. 5 memb.ring w/1 subst. (TRP) C0 40.08 calcium F 19.00 fluorine H 1.008 H bonded to nitrogen atoms HC 1.008 H aliph. bond. to C without electrwd.group H1 1.008 H aliph. bond. to C with 1 electrwd. group H2 1.008 H aliph. bond. to C with 2 electrwd.groups H3 1.008 H aliph. bond. to C with 3 eletrwd.groups HA 1.008 H arom. bond. to C without elctrwd. groups H4 1.008 H arom. bond. to C with 1 electrwd. group H5 1.008 H arom. bond. to C with 2 electrwd. groups HO 1.008 hydroxyl group HS 1.008 hydrogen bonded to sulphur HW 1.008 H in TIP3P water HP 1.008 H bonded to C next to positively charged gr I 126.9 iodine IM 35.45 assumed to be Cl- IP 22.99 assumed to be Na+ MG 24.305 magnesium N 14.01 sp2 nitrogen in amide groups NA 14.01 sp2 N in 5 memb.ring w/H atom (HIS) NB 14.01 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) NC 14.01 sp2 N in 6 memb.ring w/LP (ADE,GUA) N2 14.01 sp2 N in amino groups N3 14.01 sp3 N for charged amino groups (Lys, etc) N* 14.01 sp2 N O 16.00 carbonyl group oxygen OW 16.00 oxygen in TIP3P water OH 16.00 oxygen in hydroxyl group OS 16.00 ether and ester oxygen O2 16.00 carboxyl and phosphate group oxygen P 30.97 phosphate S 32.06 sulphur in disulfide linkage SH 32.06 sulphur in cystine CU 63.55 copper FE 55.00 iron Li 6.94 lithium K 39.10 potassium Rb 85.47 rubidium Cs 132.91 cesium C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2 OW-HW 553.0 0.9572 ! TIP3P water HW-HW 553.0 1.5136 TIP3P water C -CA 469.0 1.409 JCC,7,(1986),230; TYR C -CB 447.0 1.419 JCC,7,(1986),230; GUA C -CM 410.0 1.444 JCC,7,(1986),230; THY,URA C -CT 317.0 1.522 JCC,7,(1986),230; AA C -N* 424.0 1.383 JCC,7,(1986),230; CYT,URA C -NA 418.0 1.388 JCC,7,(1986),230; GUA.URA C -NC 457.0 1.358 JCC,7,(1986),230; CYT C -O 570.0 1.229 JCC,7,(1986),230; AA,CYT,GUA,THY,URA C -O2 656.0 1.250 JCC,7,(1986),230; GLU,ASP C -OH 450.0 1.364 JCC,7,(1986),230; TYR CA-CA 469.0 1.400 JCC,7,(1986),230; BENZENE,PHE,TRP,TYR CA-CB 469.0 1.404 JCC,7,(1986),230; ADE,TRP CA-CM 427.0 1.433 JCC,7,(1986),230; CYT CA-CT 317.0 1.510 JCC,7,(1986),230; PHE,TYR CA-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR CA-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; no assigned CA-N2 481.0 1.340 JCC,7,(1986),230; ARG,CYT,GUA CA-NA 427.0 1.381 JCC,7,(1986),230; GUA CA-NC 483.0 1.339 JCC,7,(1986),230; ADE,CYT,GUA CB-CB 520.0 1.370 JCC,7,(1986),230; ADE,GUA CB-N* 436.0 1.374 JCC,7,(1986),230; ADE,GUA CB-NB 414.0 1.391 JCC,7,(1986),230; ADE,GUA CB-NC 461.0 1.354 JCC,7,(1986),230; ADE,GUA CK-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE,GUA CK-N* 440.0 1.371 JCC,7,(1986),230; ADE,GUA CK-NB 529.0 1.304 JCC,7,(1986),230; ADE,GUA CM-CM 549.0 1.350 JCC,7,(1986),230; CYT,THY,URA CM-CT 317.0 1.510 JCC,7,(1986),230; THY CM-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA CM-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA CM-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; not assigned CM-N* 448.0 1.365 JCC,7,(1986),230; CYT,THY,URA CQ-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE CQ-NC 502.0 1.324 JCC,7,(1986),230; ADE CT-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS CT-HC 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, SUGARS CT-H1 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, RIBOSE CT-H2 340.0 1.090 changed from 331 bsd on NMA nmodes; SUGARS CT-H3 340.0 1.090 changed from 331 bsd on NMA nmodes; not assigned CT-HP 340.0 1.090 changed from 331; AA-lysine, methyl ammonium cation CT-N* 337.0 1.475 JCC,7,(1986),230; ADE,CYT,GUA,THY,URA CT-N2 337.0 1.463 JCC,7,(1986),230; ARG CT-OH 320.0 1.410 JCC,7,(1986),230; SUGARS CT-OS 320.0 1.410 JCC,7,(1986),230; NUCLEIC ACIDS H -N2 434.0 1.010 JCC,7,(1986),230; ADE,CYT,GUA,ARG H -N* 434.0 1.010 for plain unmethylated bases ADE,CYT,GUA,ARG H -NA 434.0 1.010 JCC,7,(1986),230; GUA,URA,HIS HO-OH 553.0 0.960 JCC,7,(1986),230; SUGARS,SER,TYR HO-OS 553.0 0.960 JCC,7,(1986),230; NUCLEOTIDE ENDS O2-P 525.0 1.480 JCC,7,(1986),230; NA PHOSPHATES OH-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES OS-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES C*-HC 367.0 1.080 changed from 340. bsd on C6H6 nmodes, not needed AA C -N 490.0 1.335 JCC,7,(1986),230; AA C*-CB 388.0 1.459 JCC,7,(1986),230; TRP C*-CT 317.0 1.495 JCC,7,(1986),230; TRP C*-CW 546.0 1.352 JCC,7,(1986),230; TRP CA-CN 469.0 1.400 JCC,7,(1986),230; TRP CB-CN 447.0 1.419 JCC,7,(1986),230; TRP CC-CT 317.0 1.504 JCC,7,(1986),230; HIS CC-CV 512.0 1.375 JCC,7,(1986),230; HIS(delta) CC-CW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon) CC-NA 422.0 1.385 JCC,7,(1986),230; HIS CC-NB 410.0 1.394 JCC,7,(1986),230; HIS CN-NA 428.0 1.380 JCC,7,(1986),230; TRP CR-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS CR-NA 477.0 1.343 JCC,7,(1986),230; HIS CR-NB 488.0 1.335 JCC,7,(1986),230; HIS CT-N 337.0 1.449 JCC,7,(1986),230; AA CT-N3 367.0 1.471 JCC,7,(1986),230; LYS CT-S 227.0 1.810 changed from 222.0 based on dimethylS nmodes CT-SH 237.0 1.810 changed from 222.0 based on methanethiol nmodes CV-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; HIS CV-NB 410.0 1.394 JCC,7,(1986),230; HIS CW-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) CW-NA 427.0 1.381 JCC,7,(1986),230; HIS,TRP H -N 434.0 1.010 JCC,7,(1986),230; AA H -N3 434.0 1.010 JCC,7,(1986),230; LYS HS-SH 274.0 1.336 JCC,7,(1986),230; CYS S -S 166.0 2.038 JCC,7,(1986),230; CYX (SCHERAGA) CT-F 367.0 1.380 JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 HW-OW-HW 100. 104.52 TIP3P water HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds) CB-C -NA 70.0 111.30 NA CB-C -O 80.0 128.80 CM-C -NA 70.0 114.10 CM-C -O 80.0 125.30 CT-C -O 80.0 120.40 CT-C -O2 70.0 117.00 N*-C -NA 70.0 115.40 N*-C -NC 70.0 118.60 N*-C -O 80.0 120.90 NA-C -O 80.0 120.60 NC-C -O 80.0 122.50 CT-C -N 70.0 116.60 AA general N -C -O 80.0 122.90 AA general O -C -O 80.0 126.00 AA COO- terminal residues O2-C -O2 80.0 126.00 AA GLU (SCH JPC 79,2379) CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA tyr CA-C -OH 70.0 120.00 AA tyr C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes CA-CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes CA-CA-CB 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes CA-CA-CT 70.0 120.00 CA-CA-HA 35.0 120.00 CA-CA-H4 35.0 120.00 CB-CA-HA 35.0 120.00 CB-CA-H4 35.0 120.00 CB-CA-N2 70.0 123.50 CB-CA-NC 70.0 117.30 CM-CA-N2 70.0 120.10 CM-CA-NC 70.0 121.50 N2-CA-NA 70.0 116.00 N2-CA-NC 70.0 119.30 NA-CA-NC 70.0 123.30 C -CA-HA 35.0 120.00 AA tyr N2-CA-N2 70.0 120.00 AA arg CN-CA-HA 35.0 120.00 AA trp CA-CA-CN 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA trp C -CB-CB 63.0 119.20 changed from 85.0 bsd on C6H6 nmodes; NA gua C -CB-NB 70.0 130.00 CA-CB-CB 63.0 117.30 changed from 85.0 bsd on C6H6 nmodes; NA ade CA-CB-NB 70.0 132.40 CB-CB-N* 70.0 106.20 CB-CB-NB 70.0 110.40 CB-CB-NC 70.0 127.70 N*-CB-NC 70.0 126.20 C*-CB-CA 63.0 134.90 changed from 85.0 bsd on C6H6 nmodes; AA trp C*-CB-CN 63.0 108.80 changed from 85.0 bsd on C6H6 nmodes; AA trp CA-CB-CN 63.0 116.20 changed from 85.0 bsd on C6H6 nmodes; AA trp H5-CK-N* 35.0 123.05 H5-CK-NB 35.0 123.05 N*-CK-NB 70.0 113.90 C -CM-CM 63.0 120.70 changed from 85.0 bsd on C6H6 nmodes; NA thy C -CM-CT 70.0 119.70 C -CM-HA 35.0 119.70 C -CM-H4 35.0 119.70 CA-CM-CM 63.0 117.00 changed from 85.0 bsd on C6H6 nmodes; NA cyt CA-CM-HA 35.0 123.30 CA-CM-H4 35.0 123.30 CM-CM-CT 70.0 119.70 CM-CM-HA 35.0 119.70 CM-CM-H4 35.0 119.70 CM-CM-N* 70.0 121.20 H4-CM-N* 35.0 119.10 H5-CQ-NC 35.0 115.45 NC-CQ-NC 70.0 129.10 CM-CT-HC 50.0 109.50 changed based on NMA nmodes CT-CT-CT 40.0 109.50 CT-CT-HC 50.0 109.50 changed based on NMA nmodes CT-CT-H1 50.0 109.50 changed based on NMA nmodes CT-CT-H2 50.0 109.50 changed based on NMA nmodes CT-CT-HP 50.0 109.50 changed based on NMA nmodes CT-CT-N* 50.0 109.50 CT-CT-OH 50.0 109.50 CT-CT-OS 50.0 109.50 HC-CT-HC 35.0 109.50 H1-CT-H1 35.0 109.50 HP-CT-HP 35.0 109.50 AA lys, ch3nh4+ H2-CT-N* 50.0 109.50 changed based on NMA nmodes H1-CT-N* 50.0 109.50 changed based on NMA nmodes H1-CT-OH 50.0 109.50 changed based on NMA nmodes H1-CT-OS 50.0 109.50 changed based on NMA nmodes H2-CT-OS 50.0 109.50 changed based on NMA nmodes N*-CT-OS 50.0 109.50 H1-CT-N 50.0 109.50 AA general changed based on NMA nmodes C -CT-H1 50.0 109.50 AA general changed based on NMA nmodes C -CT-HP 50.0 109.50 AA zwitterion changed based on NMA nmodes H1-CT-S 50.0 109.50 AA cys changed based on NMA nmodes H1-CT-SH 50.0 109.50 AA cyx changed based on NMA nmodes CT-CT-S 50.0 114.70 AA cyx (SCHERAGA JPC 79,1428) CT-CT-SH 50.0 108.60 AA cys H2-CT-H2 35.0 109.50 AA lys H1-CT-N2 50.0 109.50 AA arg changed based on NMA nmodes HP-CT-N3 50.0 109.50 AA lys, ch3nh3+, changed based on NMA nmodes CA-CT-CT 63.0 114.00 AA phe tyr (SCH JPC 79,2379) C -CT-HC 50.0 109.50 AA gln changed based on NMA nmodes C -CT-N 63.0 110.10 AA general CT-CT-N2 80.0 111.20 AA arg (JCP 76, 1439) CT-CT-N 80.0 109.70 AA ala, general (JACS 94, 2657) C -CT-CT 63.0 111.10 AA general CA-CT-HC 50.0 109.50 AA tyr changed based on NMA nmodes CT-CT-N3 80.0 111.20 AA lys (JCP 76, 1439) CC-CT-CT 63.0 113.10 AA his CC-CT-HC 50.0 109.50 AA his changed based on NMA nmodes C -CT-N3 80.0 111.20 AA amino terminal residues C*-CT-CT 63.0 115.60 AA trp C*-CT-HC 50.0 109.50 AA trp changed based on NMA nmodes CT-CC-NA 70.0 120.00 AA his CT-CC-CV 70.0 120.00 AA his CT-CC-NB 70.0 120.00 AA his CV-CC-NA 70.0 120.00 AA his CW-CC-NA 70.0 120.00 AA his CW-CC-NB 70.0 120.00 AA his CT-CC-CW 70.0 120.00 AA his H5-CR-NA 35.0 120.00 AA his H5-CR-NB 35.0 120.00 AA his NA-CR-NA 70.0 120.00 AA his NA-CR-NB 70.0 120.00 AA his CC-CV-H4 35.0 120.00 AA his CC-CV-NB 70.0 120.00 AA his H4-CV-NB 35.0 120.00 AA his CC-CW-H4 35.0 120.00 AA his CC-CW-NA 70.0 120.00 AA his H4-CW-NA 35.0 120.00 AA his C*-CW-H4 35.0 120.00 AA trp C*-CW-NA 70.0 108.70 AA trp CT-C*-CW 70.0 125.00 AA trp CB-C*-CT 70.0 128.60 AA trp CB-C*-CW 63.0 106.40 changed from 85.0 bsd on C6H6 nmodes; AA trp CA-CN-NA 70.0 132.80 AA trp CB-CN-NA 70.0 104.40 AA trp CA-CN-CB 63.0 122.70 changed from 85.0 bsd on C6H6 nmodes; AA trp C -N -CT 50.0 121.90 AA general C -N -H 30.0 120.00 AA general, gln, asn,changed based on NMA nmodes CT-N -H 30.0 118.04 AA general, changed based on NMA nmodes CT-N -CT 50.0 118.00 AA pro (DETAR JACS 99,1232) H -N -H 35.0 120.00 ade,cyt,gua,gln,asn ** C -N*-CM 70.0 121.60 C -N*-CT 70.0 117.60 C -N*-H 30.0 119.20 changed based on NMA nmodes CB-N*-CK 70.0 105.40 CB-N*-CT 70.0 125.80 CB-N*-H 30.0 125.80 for unmethylated n.a. bases,chngd bsd NMA nmodes CK-N*-CT 70.0 128.80 CK-N*-H 30.0 128.80 for unmethylated n.a. bases,chngd bsd NMA nmodes CM-N*-CT 70.0 121.20 CM-N*-H 30.0 121.20 for unmethylated n.a. bases,chngd bsd NMA nmodes CA-N2-H 35.0 120.00 H -N2-H 35.0 120.00 CT-N2-H 35.0 118.40 AA arg CA-N2-CT 50.0 123.20 AA arg CT-N3-H 50.0 109.50 AA lys, changed based on NMA nmodes H -N3-H 35.0 109.50 AA lys, AA(end) C -NA-C 70.0 126.40 C -NA-CA 70.0 125.20 C -NA-H 30.0 116.80 changed based on NMA nmodes CA-NA-H 30.0 118.00 changed based on NMA nmodes CC-NA-CR 70.0 120.00 AA his CC-NA-H 30.0 120.00 AA his, changed based on NMA nmodes CR-NA-CW 70.0 120.00 AA his CR-NA-H 30.0 120.00 AA his, changed based on NMA nmodes CW-NA-H 30.0 120.00 AA his, changed based on NMA nmodes CN-NA-CW 70.0 111.60 AA trp CN-NA-H 30.0 123.10 AA trp, changed based on NMA nmodes CB-NB-CK 70.0 103.80 CC-NB-CR 70.0 117.00 AA his CR-NB-CV 70.0 117.00 AA his C -NC-CA 70.0 120.50 CA-NC-CB 70.0 112.20 CA-NC-CQ 70.0 118.60 CB-NC-CQ 70.0 111.00 C -OH-HO 35.0 113.00 CT-OH-HO 55.0 108.50 HO-OH-P 45.0 108.50 CT-OS-CT 60.0 109.50 CT-OS-P 100.0 120.50 P -OS-P 100.0 120.50 O2-P -OH 45.0 108.23 O2-P -O2 140.0 119.90 O2-P -OS 100.0 108.23 OH-P -OS 45.0 102.60 OS-P -OS 45.0 102.60 CT-S -CT 62.0 98.90 AA met CT-S -S 68.0 103.70 AA cyx (SCHERAGA JPC 79,1428) CT-SH-HS 43.0 96.00 changed from 44.0 based on methanethiol nmodes HS-SH-HS 35.0 92.07 AA cys F -CT-F 77.0 109.10 JCC,13,(1992),963; F -CT-H1 35.0 109.50 JCC,13,(1992),963; X -C -CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 X -C -CB-X 4 12.00 180.0 2. intrpol.bsd.on C6H6 X -C -CM-X 4 8.70 180.0 2. intrpol.bsd.on C6H6 X -C -N*-X 4 5.80 180.0 2. JCC,7,(1986),230 X -C -NA-X 4 5.40 180.0 2. JCC,7,(1986),230 X -C -NC-X 2 8.00 180.0 2. JCC,7,(1986),230 X -C -OH-X 2 1.80 180.0 2. JCC,7,(1986),230 X -C -CT-X 4 0.00 0.0 2. JCC,7,(1986),230 X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 X -CA-CB-X 4 14.00 180.0 2. intrpol.bsd.on C6H6 X -CA-CM-X 4 10.20 180.0 2. intrpol.bsd.on C6H6 X -CA-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -CA-N2-X 4 9.60 180.0 2. reinterpolated 93' X -CA-NA-X 4 6.00 180.0 2. JCC,7,(1986),230 X -CA-NC-X 2 9.60 180.0 2. JCC,7,(1986),230 X -CB-CB-X 4 21.80 180.0 2. intrpol.bsd.on C6H6 X -CB-N*-X 4 6.60 180.0 2. JCC,7,(1986),230 X -CB-NB-X 2 5.10 180.0 2. JCC,7,(1986),230 X -CB-NC-X 2 8.30 180.0 2. JCC,7,(1986),230 X -CK-N*-X 4 6.80 180.0 2. JCC,7,(1986),230 X -CK-NB-X 2 20.00 180.0 2. JCC,7,(1986),230 X -CM-CM-X 4 26.60 180.0 2. intrpol.bsd.on C6H6 X -CM-CT-X 6 0.00 0.0 3. JCC,7,(1986),230 X -CM-N*-X 4 7.40 180.0 2. JCC,7,(1986),230 X -CQ-NC-X 2 13.60 180.0 2. JCC,7,(1986),230 X -CT-CT-X 9 1.40 0.0 3. JCC,7,(1986),230 X -CT-N -X 6 0.00 0.0 2. JCC,7,(1986),230 X -CT-N*-X 6 0.00 0.0 2. JCC,7,(1986),230 X -CT-N2-X 6 0.00 0.0 3. JCC,7,(1986),230 X -CT-OH-X 3 0.50 0.0 3. JCC,7,(1986),230 X -CT-OS-X 3 1.15 0.0 3. JCC,7,(1986),230 X -OH-P -X 3 0.75 0.0 3. JCC,7,(1986),230 X -OS-P -X 3 0.75 0.0 3. JCC,7,(1986),230 X -C -N -X 4 10.00 180.0 2. AA|check Wendy?&NMA X -CT-N3-X 9 1.40 0.0 3. JCC,7,(1986),230 X -CT-S -X 3 1.00 0.0 3. JCC,7,(1986),230 X -CT-SH-X 3 0.75 0.0 3. JCC,7,(1986),230 X -C*-CB-X 4 6.70 180.0 2. intrpol.bsd.onC6H6aa X -C*-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -C*-CW-X 4 26.10 180.0 2. intrpol.bsd.on C6H6 X -CA-CN-X 4 14.50 180.0 2. reinterpolated 93' X -CB-CN-X 4 12.00 180.0 2. reinterpolated 93' X -CC-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -CC-CV-X 4 20.60 180.0 2. intrpol.bsd.on C6H6 X -CC-CW-X 4 21.50 180.0 2. intrpol.bsd.on C6H6 X -CC-NA-X 4 5.60 180.0 2. JCC,7,(1986),230 X -CC-NB-X 2 4.80 180.0 2. JCC,7,(1986),230 X -CN-NA-X 4 6.10 180.0 2. reinterpolated 93' X -CR-NA-X 4 9.30 180.0 2. JCC,7,(1986),230 X -CR-NB-X 2 10.00 180.0 2. JCC,7,(1986),230 X -CV-NB-X 2 4.80 180.0 2. JCC,7,(1986),230 X -CW-NA-X 4 6.00 180.0 2. JCC,7,(1986),230 CT-CT-OS-CT 1 0.383 0.0 -3. CT-CT-OS-CT 1 0.1 180.0 2. C -N -CT-C 1 0.30 180.0 -2. C -N -CT-C 1 0.85 000.0 1. N -CT-C -N 1 0.30 180.0 -2. N -CT-C -N 1 0.85 000.0 1. CT-CT-N -C 1 0.50 180.0 -4. CT-CT-N -C 1 0.15 180.0 -3. CT-CT-N -C 1 0.00 180.0 -2. CT-CT-N -C 1 0.53 0.0 1. CT-CT-C -N 1 0.100 0.0 -4. CT-CT-C -N 1 0.000 0.0 -3. CT-CT-C -N 1 0.07 0.0 -2. CT-CT-C -N 1 0.000 180.0 1. H -N -C -O 1 2.50 180.0 -2. JCC,7,(1986),230 H -N -C -O 1 2.00 0.0 1. J.C.cistrans-NMA DE CT-S -S -CT 1 3.50 0.0 -2. JCC,7,(1986),230 CT-S -S -CT 1 0.60 0.0 3. JCC,7,(1986),230 OS-CT-CT-OS 1 0.144 0.0 -3. JCC,7,(1986),230 OS-CT-CT-OS 1 1.00 0.0 2. pucker anal (93') OS-CT-CT-OH 1 0.144 0.0 -3. JCC,7,(1986),230 OS-CT-CT-OH 1 1.00 0.0 2. pucker anal (93') OH-CT-CT-OH 1 0.144 0.0 -3. JCC,7,(1986),230 OH-CT-CT-OH 1 1.00 0.0 2. check glicolWC? puc OH-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230 OH-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2 OS-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230 OS-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2 OS-CT-N*-CK 1 0.50 180.0 -2. sugar frag calc (PC) OS-CT-N*-CK 1 2.50 0.0 1. sugar frag calc (PC) OS-CT-N*-CM 1 0.50 180.0 -2. sugar frag calc (PC) OS-CT-N*-CM 1 2.50 0.0 1. sugar frag calc (PC) X -X -C -O 10.5 180. 2. JCC,7,(1986),230 X -O2-C -O2 10.5 180. 2. JCC,7,(1986),230 X -X -N -H 1.0 180. 2. JCC,7,(1986),230 X -X -N2-H 1.0 180. 2. JCC,7,(1986),230 X -X -NA-H 1.0 180. 2. JCC,7,(1986),230 X -N2-CA-N2 10.5 180. 2. JCC,7,(1986),230 X -CT-N -CT 1.0 180. 2. JCC,7,(1986),230 X -X -CA-HA 1.1 180. 2. bsd.on C6H6 nmodes X -X -CW-H4 1.1 180. 2. X -X -CR-H5 1.1 180. 2. X -X -CV-H4 1.1 180. 2. X -X -CQ-H5 1.1 180. 2. X -X -CK-H5 1.1 180. 2. X -X -CM-H4 1.1 180. 2. X -X -CM-HA 1.1 180. 2. X -X -CA-H4 1.1 180. 2. bsd.on C6H6 nmodes X -X -CA-H5 1.1 180. 2. bsd.on C6H6 nmodes CK-CB-N*-CT 1.0 180. 2. CM-C -N*-CT 1.0 180. 2. dac guess, 9/94 CM-C -CM-CT 1.1 180. 2. NA-CV-CC-CT 1.1 180. 2. NB-CW-CC-CT 1.1 180. 2. NA-CW-CC-CT 1.1 180. 2. CW-CB-C*-CT 1.1 180. 2. CA-CA-CA-CT 1.1 180. 2. N2-CA-CM-NC 1.1 180. 2. dac guess, 9/94 CB-NC-CA-N2 1.1 180. 2. aeh from dac, 10/94 NA-NC-CA-N2 1.1 180. 2. aeh from dac, 10/94 CT-CM-CM-C 1.1 180. 2. dac guess, 9/94 CA-CA-C -OH 1.1 180. 2. HW OW 0000. 0000. 4. N NA N2 N* NC NB N3 NP NO C C* CA CB CC CN CM CK CQ CW CV CR CA CX CY CD MOD4 RE H 0.6000 0.0157 !Ferguson base pair geom. HO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657 HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP HC 1.4870 0.0157 OPLS H1 1.3870 0.0157 VEENSTRA et al JCC,8,(1992),963 H2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963 H3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963 HA 1.4590 0.0150 Spellmeyer H4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor H5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor HW 0.0000 0.0000 TIP3P water model HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 O 1.6612 0.2100 OPLS O2 1.6612 0.2100 OPLS OW 1.7683 0.1520 TIP3P water model OH 1.7210 0.2104 OPLS OS 1.6837 0.1700 OPLS ether CT 1.9080 0.1094 Spellmeyer CA 1.9080 0.0860 Spellmeyer CM 1.9080 0.0860 Spellmeyer C 1.9080 0.0860 OPLS N 1.8240 0.1700 OPLS S 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's SH 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's P 2.1000 0.2000 JCC,7,(1986),230; IM 0.0 0.0 Cl- ion (?) Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. IP 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. I 2.35 0.40 JCC,7,(1986),230; F 1.75 0.061 Gough et al. J.C.C.13,(1992),963. END END