BONDS OSP CSP 750.0 1.220 !Residue SPA - force constant and equilibrium bond length taken with !analogy from ester bond in fatty acid. - AS 05/05 OP CSP 150.0 1.334 !Residue SPA - force constant and equilibrium bond length taken with !analogy from ester bond in fatty acid. - AS 05/05 CSP CT1 250.000 1.4900 !Residue SPA - force constant and equilibrium bond length taken with !analogy from C CT1 bond in Serine. - AS 05/05 OP CN7 340.0 1.43 !Residue SPA - force constant and equilibrium bond length taken with !analogy from ester bond in fatty acid. - AS 05/05 !AOS for ophosphoserine Patrick O'Donoghue, 4/14/2005 C ON2 150.000 1.322 ! pod By analogy with "OS CT3" (1.3340) and QM CT2 ON2 320.0 1.44 ! pod analogy from "CN8B ON2", From exp ANGLES CT2 CT1 CSP 52.0 108.00 !Residue SPA - force constant and equilibrium bond length taken with !analogy from ester bond in fatty acid. - AS 05/05 HB CT1 CSP 50.000 109.50 !Residue SPA - force constant and equilibrium bond length taken with !analogy from serine - AS 05/05 NH1 CT1 CSP 50.000 107.00 !Residue SPA - force constant and equilibrium bond length taken with !analogy from serine - AS 05/05 OSP CSP CT1 70.0 125.0 20.0 2.442 !Residue SPA - force constant and equilibrium bond length taken with !analogy from ester bond in fatty acid - AS 05/05 OP CSP CT1 55.0 109.0 20.00 2.3260 !Residue SPA - force constant and equilibrium bond length taken with !analogy from ester bond in fatty acid - AS 05/05 OSP CSP OP 90.0 125.9 160.0 2.2576 !Residue SPA - force constant and equilibrium bond length taken with !analogy from ester bond in fatty acid - AS 05/05 CSP OP CN7 40.0 109.6 30.0 2.2651 !Residue SPA - force constant and equilibrium bond length taken with !analogy from ester bond in fatty acid - AS 05/05 OP CN7 CN7 115.0 109.7 !Residue SPA - force constant and equilibrium bond length taken with !analogy from cytosine - AS 05/05 OP CN7 HN7 60.0 109.5 !Residue SPA - force constant and equilibrium bond length taken with !analogy from cytosine - AS 05/05 OP CN7 CN7B 90.0 110.0 !Residue SPA - force constant and equilibrium bond length taken with !analogy from cytosine - AS 05/05 NH3 CT1 CSP 43.700 110.0000 !Residue SPA - force constant and equilibrium length taken with !analogy from NH3 CT1 C from amino acid patch - AS 05/05 CT1 C ON2 55.000 117.20 ! pod/er By analogy with "OS CD CT1" (55.000 109.00 20.00 2.32600) and QM O C ON2 90.000 120.30 ! pod/er By analogy with "OS CD OB" (90.000 125.90 160.00 2.25760) and QM C ON2 P 40.000 129.90 ! pod/er By analogy with "CT3 OS CD" (40.000 109.60 30.00 2.26510) and QM CT2 ON2 P 20.0 120.0 35.00 2.33 !pod from "CN8B ON2 P" NF, 11/97, C5'O5'P ON2 CT2 HA 60.0 109.5 !pod from "HN8 CN8B ON2", From HN7 CN8 ON2 ON2 CT2 CT1 70.0 108.4 !pod from "CN7 CN8B ON2" NF, 11/97, C4'C5'O5' DIHEDRALS CSP CT1 CT2 ON2 0.2000 3 0.00 !Analogy with X CT1 CT2 X in Serine for SPA - AS 05/05 CSP CT1 CT2 HA 0.2000 3 0.00 !Analogy with X CT1 CT2 X in Serine for SPA - AS 05/05 OSP CSP CT1 CT2 1.4000 1 0.00 !Analogy with O C CT1 CT2 for SPA - AS 05/05 CT2 CT1 CSP OP -0.15 1 180.00 !Analogy with CTL2 CTL2 CL OSL in ester linkage CT2 CT1 CSP OP 0.53 2 180.00 !in lipids for SPA - AS 05/05 HC NH3 CT1 CSP 0.1000 3 0.00 !Analogy with X NH3 CT1 X as in Serine patch residue for SPA- AS 05/05 OSP CSP CT1 NH3 0.0000 1 0.00 !Analogy with O C CT1 NH3 as in Serine for SPA- AS 05/05 NH3 CT1 CSP OP 0.2000 3 0.00 !Analogy with "X CT1 CT2 X" as in Serine for SPA- AS 05/05 OSP CSP CT1 HB 0.0000 1 0.00 !Analogy with O C CT1 HB as in Serine for SPA- AS 05/05 OP CSP CT1 HB 0.00 6 180.00 !Analogy with OSL CL CTL2 HAL2 as in ester linkage in lipids for SPA- AS 05/05 CT1 CSP OP CN7 2.05 2 180.00 !Analogy with X CL OSL X as in ester linkage in lipids for SPA - AS 05/05 OSP CSP OP CN7 0.965 1 180.00 !Analogy with OBL CL OSL CTL1 as in ester linkage OSP CSP OP CN7 3.85 2 180.00 !in lipids for SPA - AS 05/05 HN7 CN7 OP CSP 0.00 3 0.00 !Analogy with X CTL1 OSL X as in ester linkage in lipids for SPA - AS 05/05 CN7B CN7 OP CSP 0.7 1 180.00 !Analogy with CTL2 CTL1 OSL CL as in ester linkage in lipids for SPA - AS 05/05 CN7 CN7 OP CSP 0.7 1 180.00 !Analogy with CTL2 CTL1 OSL CL as in ester linkage in lipids for SPA - AS 05/05 OP CN7 CN7B HN7 0.195 3 0.0 !Analogy with ON2 CN7 CN7B HN7 as in adenine in RNA for SPA - AS 05/05 ON5 CN7B CN7 OP 0.000 3 0.0 !Analogy with ON5 CN7B CN7 ON2 as in adenine in RNA for SPA - AS 05/05 OP CN7 CN7B CN7B 0.6 6 0.0 !Analogy with ON2 CN7 CN7B CN7B OP CN7 CN7B CN7B 0.0 5 0.0 !as in adenine ( RNA c2/c3 endo in RNA) OP CN7 CN7B CN7B 1.6 3 180.0 !AS 05/05 HN7 CN7 CN7 OP 0.195 3 0.0 !Analogy with HN7 CN7 CN7 ON2 as in adenine in RNA for SPA - AS 05/05 OP CN7 CN7 ON6B 0.4 6 0.0 !Analogy with ON2 CN7 CN7 ON6B OP CN7 CN7 ON6B 0.0 5 0.0 !as in adenine in RNA for SPA OP CN7 CN7 ON6B 0.0 4 180.0 ! OP CN7 CN7 ON6B 1.6 3 0.0 !AS 05/05 OP CN7 CN7 CN8B 0.2 4 0.0 !Analogy with ON2 CN7 CN7 CN8B OP CN7 CN7 CN8B 0.8 3 180.0 !as in adenine in RNA for SPA - AS 05/05 P ON2 CT2 HA 0.000 3 0.0 !pod from, "P ON2 CN8B HN8" dmp,beta, H-C5'-O5'-P P ON2 CT2 CT1 0.2 1 120.0 !pod "CN7 CN8B ON2 P" bet C4'-C5'-O5'-P, adm jr. ON3 P ON2 CT2 0.10 3 0.0 !pod from "ON3 P ON2 CN8B", dmp,bet, O1P-P-O5'-C5' C CT1 CT2 ON2 0.2000 3 0.00 !pod analogy from "X CT1 CT2 X", ALLOW ALI NH1 CT1 CT2 ON2 0.2000 3 0.00 !pod analogy from "X CT1 CT2 X", ALLOW ALI HB CT1 CT2 ON2 0.2000 3 0.00 !pod analogy from "X CT1 CT2 X", ALLOW ALI HB CT1 C ON2 0.0000 6 180.00 !pod from ER By analogy with X CT1 CD X NH1 CT1 C ON2 0.0000 6 180.00 !pod from ER By analogy with X CT1 CD X NH3 CT1 C ON2 0.0000 6 180.00 !pod from ER By analogy with X CT1 CD X CT2 CT1 C ON2 0.0000 6 180.00 !pod from ER By analogy with X CT1 CD X CT1 C ON2 P 2.0500 2 180.00 !pod from ER By analogy with X CD OS X O C ON2 P 0.9650 1 180.00 !pod from ER By analogy with OB CD OS CT3 O C ON2 P 3.8500 2 180.00 !pod from ER By analogy with OB CD OS CT3 C ON2 P ON3 -0.1000 3 0.00 !pod from ER By analogy with X CT3 OS X C ON2 P ON2 -0.1000 3 0.00 !pod from ER By analogy with X CT3 OS X IMPROPER OSP CT1 OP CSP 100.00 0 0.00 !Analogy with OBL X X CL from ester linkage in !lipid for SPA - AS 05/05. NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - CSP 0.0 -0.070 2.00 ! Analogy with ester linkage in lipids for SPA - AS 05/05 OP 0.0 -0.1521 1.77 ! Analogy with ester linkage in lipids for SPA - AS 05/05 OSP 0.0 -0.12 1.70 0.0 -0.12 1.4! Analogy with ester linkage in lipids for SPA - AS 05/05. END