# Version: August 13, 1993 # # LIBRARY OF ATOM RADII FOR DIFFERENT TOPOLOGY MODELS # # MODELLER 1.1, Copyright Andrej Sali # # # The library contains radii of each CHARMM atom type for each topology model. # # Search for ? to find radii that have to be checked and possibly corrected. # The rule: add 0.05 A for each H when dealing with extended atoms. # # The order of records is not important, but this file must list all of the # atom types defined in the CHARMM residue topology library. # # Number of topology models: 10 # ALLH POLH HEAV MCCB MNCH MCWO CA MNSS CA3 CACB H 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! polar H HC 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! N-ter H HA 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! nonpolar H HT 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! TIPS3P WATER HYDROGEN HP 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! aromatic H HB 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! backbone H HR1 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! his he1, (+) his HG,HD2 HR2 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! (+) his HE1 HR3 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! neutral his HG, HD2 HS 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! cys C 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! polar C CA 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! aromatic C CT1 1.80 1.80 1.80 1.80 1.80 1.80 2.65 1.80 1.80 1.80 ! aliphatic sp3 C for CH CT2 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! aliphatic sp3 C for CH2 CT3 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! aliphatic sp3 C for CH3 CPH1 1.80 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 ! his CG and CD2 carbons CPH2 1.80 1.90 1.90 1.90 1.90 1.90 1.95 1.90 1.90 1.90 ! his CE1 carbon CPT 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! trp C between rings CY 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! TRP C in pyrrole ring CP1 1.80 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 ! tetrahedral C (proline CA) CP2 1.80 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 ! tetrahedral C (proline CB/CG) ? CP3 1.80 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 ! tetrahedral C (proline CD) ? CC 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! carbonyl C for sidechains asn,asp,gln,glu CD 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! carbonyl C for none amides, asp,glu,cter CPA 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! heme alpha-C ? CPB 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! heme beta-C ? CPM 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! heme meso-C ? CM 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! heme CO carbon ? CS 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! thiolate carbon ? N 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! proline N NR1 1.60 1.60 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 ! neutral his protonated ring nitrogen ? NR2 1.60 1.60 1.65 1.65 1.65 1.65 1.65 1.65 1.65 1.65 ! neutral his unprotonated ring nitrogen ? NR3 1.60 1.60 1.65 1.65 1.65 1.65 1.65 1.65 1.65 1.65 ! charged his ring nitrogen ? NH1 1.60 1.60 1.65 1.65 1.65 1.65 1.65 1.65 1.65 1.65 ! peptide nitrogen NH2 1.60 1.60 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 ! amide nitrogen NH3 1.60 1.60 1.75 1.75 1.75 1.75 1.75 1.75 1.75 1.75 ! ammonium nitrogen NC2 1.60 1.60 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 ! guanidinium nitrogen ? NY 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! TRP N in pyrrole ring ? NP 1.60 1.60 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 ! Proline ring NH2+ (N-terminal) NPH 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! heme pyrrole N ? NP1 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! heme pyrrole N ? PA 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! PB ; correct PB 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! PB ; correct O 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! carbonyl oxygen OB 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! carbonyl oxygen in acetic acid OC 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! carboxylate oxygen OH1 1.55 1.55 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! hydroxyl oxygen OS 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! ester oxygen OT 1.55 1.55 1.65 1.65 1.65 1.65 1.65 1.65 1.65 1.65 ! TIPS3P WATER OXYGEN OM 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! heme CO/O2 oxygen CAH 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 ! Helical CA CAS 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 ! Strand CA CAT 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 ! Turn CA VCC 2.61 2.61 2.61 2.61 2.61 2.61 2.61 2.61 2.61 2.61 ! HH model VCCC 2.75 2.75 2.75 2.75 2.75 2.75 2.75 2.75 2.75 2.75 ! HH model CCCL 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 ! HH model CCCP 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 2.70 ! HH model V6RF 2.79 2.79 2.79 2.79 2.79 2.79 2.79 2.79 2.79 2.79 ! HH model V6RY 2.81 2.81 2.81 2.81 2.81 2.81 2.81 2.81 2.81 2.81 ! HH model VCCN 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 ! HH model VCCO 2.66 2.66 2.66 2.66 2.66 2.66 2.66 2.66 2.66 2.66 ! HH model VCO2 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 ! HH model VCON 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 ! HH model VCOH 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.37 ! HH model VCS 2.52 2.52 2.52 2.52 2.52 2.52 2.52 2.52 2.52 2.52 ! HH model VCSC 2.59 2.59 2.59 2.59 2.59 2.59 2.59 2.59 2.59 2.59 ! HH model VN3C 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 ! HH model V5RH 2.44 2.44 2.44 2.44 2.44 2.44 2.44 2.44 2.44 2.44 ! HH model VNH3 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 ! HH model CH3E 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.16 ! HH model CH2E 2.23 2.23 2.23 2.23 2.23 2.23 2.23 2.23 2.23 2.23 ! HH model S 1.90 1.90 1.95 1.95 1.95 1.95 1.95 1.95 1.95 1.90 ! sulphur SM 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 ! sulfur C-S-S-C type SS 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 1.90 ! thiolate sulfur CAL 0.94 0.94 0.94 0.94 0.94 0.94 0.94 0.94 0.94 0.94 ! calcium 2+ ZN 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 ! zinc (II) cation FE 0.65 0.65 0.65 0.65 0.65 0.65 0.65 0.65 0.65 0.65 ! heme iron 56 UNDF 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 ! undefined OE 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! ether oxygen MMG 0.72 0.72 0.72 0.72 0.72 0.72 0.72 0.72 0.72 0.72 ! magnesium (II), coordination no 6 MK 1.38 1.38 1.38 1.38 1.38 1.38 1.38 1.38 1.38 1.38 ! potassium, coordination no 6 CE1 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! for alkene; RHC=CR CE2 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! for alkene; H2C=CR CN1 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid carbonyl carbon CN1A 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! NAD+/NADH amide carbonyl carbon CN2 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid aromatic carbon to amide CN3 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid aromatic carbon CN3A 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! NAD+ aromatic carbon CN3B 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! NAD+ aromatic carbon CN3C 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! NADH aromatic carbon CN3D 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid aromatic carbon for 5MC CN4 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid purine C8 and ADE C2 CN5 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid purine C4 and C5 CN6 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid sp3 ribose ring carbon CN6B 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid sp3 ribose ring carbon, C1' CN6C 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid sp3 deoxyribose ring carbon, C2' CN7 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid carbon (equivalent to protein CT1) CN8 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid carbon (equivalent to protein CT2) CN9 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! Nucleic acid carbon (equivalent to protein CT3) DUM 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ! dummy atom HA1 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! for alkene; RHC=CR HA2 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! for alkene; H2C=CR HE 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! helium HN1 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! Nucleic acid amine proton HN2 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! Nucleic acid ring nitrogen proton HN3 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! Nucleic acid aromatic carbon proton HN3B 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! NAD+ aromatic hydrogen HN4 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! Nucleic acid phosphate hydroxyl proton HN5 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! Nucleic acid ribose hydroxyl proton HN6 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! Nucleic acid ribose aliphatic proton HN7 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.80 ! Nucleic acid proton (equivalent to protein HA) MG 0.72 0.72 0.72 0.72 0.72 0.72 0.72 0.72 0.72 0.72 ! Magnesium Ion NE 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! neon NN1 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! Nucleic acid amide nitrogen NN2 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! Nucleic acid protonated ring nitrogen NN2G 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! Nucleic acid protonated ring nitrogen, gua N1 NN2U 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! Nucleic acid protonated ring nitrogen, ura N3 NN3 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! Nucleic acid unprotonated ring nitrogen NN3A 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 NN3I 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! Nucleic acid unprotonated ring nitrogen, inosine N3 NN4 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! Nucleic acid purine N7 NN5 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 1.60 ! Nucleic acid sp2 amine nitrogen ON1 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! Nucleic acid carbonyl oxygen ON1C 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! Nucleic acid carbonyl oxygen, cyt O2 ON2 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! Nucleic acid phosphate ester oxygen ON2B 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! Nucleic acid phosphate ester oxygen, tyr-phosphate ON3 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! Nucleic acid =O in phosphate ON4 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! Nucleic acid phosphate hydroxyl oxygen ON5 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! Nucleic acid ribose hydroxyl oxygen ON6 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 1.55 ! Nucleic acid ribose ring oxygen P 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! phosphorus P2 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 ! pyrophosphate phosphorus SOD 1.90 1.90 1.95 1.95 1.95 1.95 1.95 1.95 1.95 1.90 ! Sodium Ion