!CORRESPONDENCE OF PDB TYPES WITH CHARGES & NUMERICAL TYPE INDICATORS ! ! --AMBER united-atom charges, based on Weiner et al., ! JACS 106, 765 (1984) ! --names as per AMBER convention ! ! --termini not from the reference above; 0.416=(0.248 + 1.0)/3 ! --0.248 is the amide H charge in the residues above ! --simplistic way of making the N-terminus have a net charge of +1 ! and the C-terminus have a net charge of -1 ! !aaaxxxrrrnnnncqqqqqqqqxtt format (A4, 3x, A3, A4, A1, F8.3, 1x, I2) ! N ALA -0.520 8 ALANINE CA ALA 0.215 4 C ALA 0.526 1 O ALA -0.500 11 HN ALA 0.248 6 CB ALA 0.031 2 N ALB -0.520 8 ALANINE more polar by 0.4 per polar atom CA ALB 0.215 4 C ALB 0.526 1 O ALB -0.900 11 HN ALB 0.648 6 CB ALB 0.031 2 N ARG -0.520 8 ARGININE (+) C ARG 0.526 1 O ARG -0.500 11 CA ARG 0.237 4 CB ARG 0.049 3 CG ARG 0.058 3 CD ARG 0.111 3 NE ARG -0.493 8 CZ ARG 0.813 1 NH1 ARG -0.635 8 NH2 ARG -0.634 8 HN ARG 0.248 6 HNE ARG 0.294 6 HN11 ARG 0.361 6 HN12 ARG 0.362 6 HN21 ARG 0.361 6 HN22 ARG 0.362 6 N ARH -0.520 8 ARGININE (+) more polar by 0.4 per polar atom C ARH 0.526 1 O ARH -0.900 11 CA ARH 0.237 4 CB ARH 0.049 3 CG ARH 0.058 3 CD ARH 0.111 3 NE ARH -0.493 8 CZ ARH 0.813 1 NH1 ARH -0.635 8 NH2 ARH -0.634 8 HN ARH 0.648 6 HNE ARH 0.294 6 HN11 ARH 0.361 6 HN12 ARH 0.362 6 HN21 ARH 0.361 6 HN22 ARH 0.362 6 N ASN -0.520 8 ASPARAGINE CA ASN 0.217 4 C ASN 0.526 1 O ASN -0.500 11 CB ASN 0.003 3 ND2 ASN -0.867 8 AD2 ASN -0.867 8 CG ASN 0.675 1 OD1 ASN -0.470 11 AD1 ASN -0.470 11 HN ASN 0.248 6 HND1 ASN 0.344 6 HND2 ASN 0.344 6 N ASO -0.520 8 ASPARAGINE more polar by 0.4 per polar atom CA ASO 0.217 4 C ASO 0.526 1 O ASO -0.900 11 CB ASO 0.003 3 ND2 ASO -0.867 8 AD2 ASO -0.867 8 CG ASO 0.675 1 OD1 ASO -0.870 11 AD1 ASO -0.870 11 HN ASO 0.648 6 HND1 ASO 0.544 6 HND2 ASO 0.544 6 OD1 ASP -0.706 11 ASPARTIC ACID (-) OD2 ASP -0.706 11 CA ASP 0.246 4 CB ASP -0.208 3 CG ASP 0.620 1 N ASP -0.520 8 C ASP 0.526 1 O ASP -0.500 11 HN ASP 0.248 6 OD1 ASQ -0.706 11 ASPARTIC ACID (-) more polar by 0.4 per polar atom OD2 ASQ -0.706 11 CA ASQ 0.246 4 CB ASQ -0.208 3 CG ASQ 0.620 1 N ASQ -0.520 8 C ASQ 0.526 1 O ASQ -0.900 11 HN ASQ 0.648 6 OD1 ASH -0.522 12 ASPARTIC ACID (neutral, fudged) HD2 ASH 0.319 6 OD2 ASH -0.405 11 CA ASH 0.200 4 CB ASH 0.003 3 CG ASH 0.651 1 N ASH -0.520 8 C ASH 0.526 1 O ASH -0.500 11 HN ASH 0.248 6 OD1 ASZ -0.522 12 ASPARTIC ACID (neutral, niu) HD2 ASZ 0.319 6 OD2 ASZ -0.405 11 CA ASZ 0.200 4 CB ASZ 0.003 3 CG ASZ 0.651 1 N ASZ -0.520 8 C ASZ 0.526 1 O ASZ -0.500 11 HN ASZ 0.248 6 N CYS -0.520 8 CYSTEINE C CYS 0.526 1 O CYS -0.500 11 CA CYS 0.146 4 CB CYS 0.100 3 SG CYS -0.135 14 HN CYS 0.248 6 HSG CYS 0.135 6 N CYT -0.520 8 CYSTEINE more polar by 0.4 per polar atom C CYT 0.526 1 O CYT -0.900 11 CA CYT 0.146 4 CB CYT 0.100 3 SG CYT -0.535 14 HN CYT 0.648 6 HSG CYT 0.535 6 N CYX -0.520 8 CYSTINE (disulfide bridge) C CYX 0.526 1 O CYX -0.500 11 CA CYX 0.088 4 CB CYX 0.143 3 SG CYX 0.015 14 HN CYX 0.248 6 N CYY -0.520 8 CYSTINE (disulfide bridge) more polar by 0.4 per polar atom C CYY 0.526 1 O CYY -0.900 11 CA CYY 0.088 4 CB CYY 0.143 3 SG CYY 0.015 14 HN CYY 0.648 6 N GLN -0.520 8 GLUTAMINE CA GLN 0.210 4 C GLN 0.526 1 O GLN -0.500 11 CB GLN 0.053 3 CG GLN -0.043 3 NE2 GLN -0.867 8 AE2 GLN -0.867 8 CD GLN 0.675 1 OE1 GLN -0.470 11 AE1 GLN -0.470 11 HN GLN 0.248 6 HNE1 GLN 0.344 6 HNE2 GLN 0.344 6 N GLO -0.520 8 GLUTAMINE more polar by 0.4 per polar atom CA GLO 0.210 4 C GLO 0.526 1 O GLO -0.900 11 CB GLO 0.053 3 CG GLO -0.043 3 NE2 GLO -0.867 8 AE2 GLO -0.867 8 CD GLO 0.675 1 OE1 GLO -0.870 11 AE1 GLO -0.870 11 HN GLO 0.648 6 HNE1 GLO 0.544 6 HNE2 GLO 0.544 6 OE1 GLU -0.706 11 GLUTAMIC ACID (-) OE2 GLU -0.706 11 CD GLU 0.620 1 N GLU -0.520 8 C GLU 0.526 1 O GLU -0.500 11 CA GLU 0.246 4 CB GLU 0.000 3 CG GLU -0.208 3 HN GLU 0.248 6 OE1 GLH -0.522 12 GLUTAMIC ACID (neutral, fudged) HE2 GLH 0.319 6 OE2 GLH -0.405 11 CD GLH 0.660 1 N GLH -0.520 8 C GLH 0.526 1 O GLH -0.500 11 CA GLH 0.246 4 CB GLH 0.000 3 CG GLH -0.052 3 HN GLH 0.248 6 OE1 GLV -0.706 11 GLUTAMIC ACID (-) more polar by 0.4 per polar atom OE2 GLV -0.706 11 CD GLV 0.620 1 N GLV -0.520 8 C GLV 0.526 1 O GLV -0.900 11 CA GLV 0.246 4 CB GLV 0.000 3 CG GLV -0.208 3 HN GLV 0.648 6 N GLY -0.520 8 GLYCINE CA GLY 0.246 4 C GLY 0.526 1 O GLY -0.500 11 HN GLY 0.248 6 N GLZ -0.520 8 GLYCINE more polar by 0.4 per polar atom CA GLZ 0.246 4 C GLZ 0.526 1 O GLZ -0.900 11 HN GLZ 0.648 6 N HID -0.520 8 HISTIDINE neutral delta proton C HID 0.526 1 O HID -0.500 11 CA HID 0.219 4 CB HID 0.060 3 CG HID 0.089 1 CD2 HID 0.145 1 AD2 HID 0.145 1 CE1 HID 0.384 1 AE1 HID 0.384 1 ND1 HID -0.444 8 AD1 HID -0.444 8 NE2 HID -0.527 8 AE2 HID -0.527 8 HN HID 0.248 6 HND HID 0.320 6 N HIC -0.520 8 HISTIDINE neutral delta proton more polar by 0.4 per polar atom C HIC 0.526 1 O HIC -0.900 11 CA HIC 0.219 4 CB HIC 0.060 3 CG HIC 0.089 1 CD2 HIC 0.145 1 AD2 HIC 0.145 1 CE1 HIC 0.384 1 AE1 HIC 0.384 1 ND1 HIC -0.444 8 AD1 HIC -0.444 8 NE2 HIC -0.527 8 AE2 HIC -0.527 8 HN HIC 0.648 6 HND HIC 0.320 6 N HIE -0.520 8 HISTIDINE neutral epsilon proton C HIE 0.526 1 O HIE -0.500 11 CA HIE 0.219 4 CB HIE 0.060 3 CG HIE 0.112 1 CD2 HIE 0.122 1 AD2 HIE 0.122 1 CE1 HIE 0.384 1 AE1 HIE 0.384 1 ND1 HIE -0.527 8 AD1 HIE -0.527 8 NE2 HIE -0.444 8 AE2 HIE -0.444 8 HN HIE 0.248 6 HNE HIE 0.320 6 N HIF -0.520 8 HISTIDINE neutral epsilon proton more polar by 0.4 per polar atom C HIF 0.526 1 O HIF -0.900 11 CA HIF 0.219 4 CB HIF 0.060 3 CG HIF 0.112 1 CD2 HIF 0.122 1 AD2 HIF 0.122 1 CE1 HIF 0.384 1 AE1 HIF 0.384 1 ND1 HIF -0.527 8 AD1 HIF -0.527 8 NE2 HIF -0.444 8 AE2 HIF -0.444 8 HN HIF 0.648 6 HNE HIF 0.320 6 N HIP -0.520 8 HISTIDINE (+) C HIP 0.526 1 O HIP -0.500 11 CA HIP 0.195 4 CB HIP 0.211 3 CG HIP 0.103 1 CD2 HIP 0.353 1 AD2 HIP 0.353 1 CE1 HIP 0.719 1 AE1 HIP 0.719 1 ND1 HIP -0.613 8 AD1 HIP -0.613 8 NE2 HIP -0.686 8 AE2 HIP -0.686 8 HN HIP 0.248 6 HND HIP 0.478 6 HNE HIP 0.486 6 N HIQ -0.520 8 HISTIDINE (+) more polar by 0.4 per polar atom C HIQ 0.526 1 O HIQ -0.900 11 CA HIQ 0.195 4 CB HIQ 0.211 3 CG HIQ 0.103 1 CD2 HIQ 0.353 1 AD2 HIQ 0.353 1 CE1 HIQ 0.719 1 AE1 HIQ 0.719 1 ND1 HIQ -0.613 8 AD1 HIQ -0.613 8 NE2 HIQ -0.686 8 AE2 HIQ -0.686 8 HN HIQ 0.648 6 HND HIQ 0.478 6 HNE HIQ 0.486 6 N HIS -0.520 8 HISTIDINE (+0.5) C HIS 0.526 1 O HIS -0.500 11 CA HIS 0.219 4 CB HIS 0.060 3 CG HIS 0.112 1 CD2 HIS 0.122 1 AD2 HIS 0.122 1 CE1 HIS 0.384 1 AE1 HIS 0.384 1 ND1 HIS -0.277 8 AD1 HIS -0.277 8 NE2 HIS -0.194 8 AE2 HIS -0.194 8 HN HIS 0.248 6 HND HIS 0.320 6 N HIT -0.520 8 HISTIDINE (+0.5) more polar by 0.4 per polar atom C HIT 0.526 1 O HIT -0.900 11 CA HIT 0.219 4 CB HIT 0.060 3 CG HIT 0.112 1 CD2 HIT 0.122 1 AD2 HIT 0.122 1 CE1 HIT 0.384 1 AE1 HIT 0.384 1 ND1 HIT -0.277 8 AD1 HIT -0.277 8 NE2 HIT -0.194 8 AE2 HIT -0.194 8 HN HIT 0.648 6 HND HIT 0.320 6 N ILE -0.520 8 ISOLEUCINE C ILE 0.526 1 O ILE -0.500 11 CA ILE 0.199 4 CB ILE 0.030 4 CG1 ILE 0.017 3 CG2 ILE 0.001 2 CD1 ILE -0.001 2 HN ILE 0.248 6 N ILF -0.520 8 ISOLEUCINE more polar by 0.4 per polar atom C ILF 0.526 1 O ILF -0.900 11 CA ILF 0.199 4 CB ILF 0.030 4 CG1 ILF 0.017 3 CG2 ILF 0.001 2 CD1 ILF -0.001 2 HN ILF 0.648 6 N LEU -0.520 8 LEUCINE C LEU 0.526 1 O LEU -0.500 11 CA LEU 0.204 4 CB LEU 0.016 3 CG LEU 0.054 4 CD1 LEU -0.014 2 CD2 LEU -0.014 2 HN LEU 0.248 6 N LEV -0.520 8 LEUCINE more polar by 0.4 per polar atom C LEV 0.526 1 O LEV -0.900 11 CA LEV 0.204 4 CB LEV 0.016 3 CG LEV 0.054 4 CD1 LEV -0.014 2 CD2 LEV -0.014 2 HN LEV 0.648 6 N LYS -0.520 8 LYSINE (+) C LYS 0.526 1 O LYS -0.500 11 CA LYS 0.227 4 CB LYS 0.039 3 CG LYS 0.053 3 CD LYS 0.048 3 CE LYS 0.218 3 NZ LYS -0.272 9 HN LYS 0.248 6 HNZ1 LYS 0.311 6 HNZ2 LYS 0.311 6 HNZ3 LYS 0.311 6 N LYT -0.520 8 LYSINE (+) more polar by 0.4 per polar atom C LYT 0.526 1 O LYT -0.900 11 CA LYT 0.227 4 CB LYT 0.039 3 CG LYT 0.053 3 CD LYT 0.048 3 CE LYT 0.218 3 NZ LYT -0.272 9 HN LYT 0.648 6 HNZ1 LYT 0.311 6 HNZ2 LYT 0.311 6 HNZ3 LYT 0.311 6 N LYZ -0.520 8 LYSINE neutralized by niu C LYZ 0.526 1 O LYZ -0.500 11 CA LYZ 0.227 4 CB LYZ 0.039 3 CG LYZ 0.053 3 CD LYZ 0.048 3 CE LYZ 0.041 3 niu NZ LYZ -0.872 9 niu HN LYZ 0.248 6 HNZ1 LYZ 0.355 6 niu HNZ2 LYZ 0.355 6 niu, using OPLS as reference N MET -0.520 8 METHIONINE C MET 0.526 1 O MET -0.500 11 CA MET 0.137 4 CB MET 0.037 3 CG MET 0.090 3 SD MET -0.025 14 CE MET 0.007 2 HN MET 0.248 6 N MEU -0.520 8 METHIONINE more polar by 0.4 per polar atom C MEU 0.526 1 O MEU -0.900 11 CA MEU 0.137 4 CB MEU 0.037 3 CG MEU 0.090 3 SD MEU -0.025 14 CE MEU 0.007 2 HN MEU 0.648 6 N PHE -0.520 8 PHENYLALANINE C PHE 0.526 1 O PHE -0.500 11 CA PHE 0.214 4 CB PHE 0.038 3 CG PHE 0.011 1 CD1 PHE -0.011 1 CD2 PHE -0.011 1 CE1 PHE 0.004 1 CE2 PHE 0.004 1 CZ PHE -0.003 1 HN PHE 0.248 6 N PHF -0.520 8 PHENYLALANINE more polar by 0.4 per polar atom C PHF 0.526 1 O PHF -0.900 11 CA PHF 0.214 4 CB PHF 0.038 3 CG PHF 0.011 1 CD1 PHF -0.011 1 CD2 PHF -0.011 1 CE1 PHF 0.004 1 CE2 PHF 0.004 1 CZ PHF -0.003 1 HN PHF 0.648 6 N PRO -0.257 8 PROLINE CA PRO 0.112 4 C PRO 0.526 1 O PRO -0.500 11 CB PRO -0.001 3 CG PRO 0.036 3 CD PRO 0.084 3 N PRP -0.257 8 PROLINE more polar by 0.4 per polar atom CA PRP 0.112 4 C PRP 0.526 1 O PRP -0.500 11 CB PRP -0.001 3 CG PRP 0.036 3 CD PRP 0.084 3 N SER -0.520 8 SERINE C SER 0.526 1 O SER -0.500 11 CA SER 0.292 4 CB SER 0.194 3 OG SER -0.550 12 HN SER 0.248 6 HOG SER 0.310 6 N SES -0.520 8 SERINE more polar by 0.4 per polar atom C SES 0.526 1 O SES -0.900 11 CA SES 0.292 4 CB SES 0.194 3 OG SES -0.950 12 HN SES 0.648 6 HOG SES 0.710 6 N THR -0.520 8 THREONINE C THR 0.526 1 O THR -0.500 11 OG1 THR -0.550 12 CA THR 0.268 4 CB THR 0.211 4 CG2 THR 0.007 2 HN THR 0.248 6 HOG THR 0.310 6 N THS -0.520 8 THREONINE more polar by 0.4 per polar atom C THS 0.526 1 O THS -0.900 11 OG1 THS -0.950 12 CA THS 0.268 4 CB THS 0.211 4 CG2 THS 0.007 2 HN THS 0.648 6 HOG THS 0.710 6 N TRP -0.520 8 TRYPTOPHAN C TRP 0.526 1 O TRP -0.500 11 CA TRP 0.248 4 CB TRP 0.020 3 CG TRP 0.046 1 CD1 TRP 0.117 1 CD2 TRP -0.275 1 NE1 TRP -0.330 8 CE2 TRP 0.000 1 CE3 TRP 0.145 1 CZ2 TRP 0.029 1 CZ3 TRP -0.082 1 CH2 TRP 0.034 1 HN TRP 0.248 6 HNE TRP 0.294 6 N TRQ -0.520 8 TRYPTOPHAN more polar by 0.4 per polar atom C TRQ 0.526 1 O TRQ -0.900 11 CA TRQ 0.248 4 CB TRQ 0.020 3 CG TRQ 0.046 1 CD1 TRQ 0.117 1 CD2 TRQ -0.275 1 NE1 TRQ -0.730 8 CE2 TRQ 0.000 1 CE3 TRQ 0.145 1 CZ2 TRQ 0.029 1 CZ3 TRQ -0.082 1 CH2 TRQ 0.034 1 HN TRQ 0.648 6 HNE TRQ 0.694 6 N TYR -0.520 8 TYROSINE C TYR 0.526 1 O TYR -0.500 11 OH TYR -0.368 12 CA TYR 0.245 4 CB TYR 0.022 3 CG TYR -0.001 1 CD1 TYR -0.035 1 CD2 TYR -0.035 1 CE1 TYR 0.100 1 CE2 TYR 0.100 1 CZ TYR -0.121 1 HN TYR 0.248 6 HOH TYR 0.339 6 N TYS -0.520 8 TYROSINE more polar by 0.4 per polar atom C TYS 0.526 1 O TYS -0.900 11 OH TYS -0.768 12 CA TYS 0.245 4 CB TYS 0.022 3 CG TYS -0.001 1 CD1 TYS -0.035 1 CD2 TYS -0.035 1 CE1 TYS 0.100 1 CE2 TYS 0.100 1 CZ TYS -0.121 1 HN TYS 0.648 6 HOH TYS 0.739 6 N VAL -0.520 8 VALINE C VAL 0.526 1 O VAL -0.500 11 CA VAL 0.201 4 CB VAL 0.033 4 CG1 VAL 0.006 2 CG2 VAL 0.006 2 HN VAL 0.248 6 N VAM -0.520 8 VALINE more polar by 0.4 per polar atom C VAM 0.526 1 O VAM -0.900 11 CA VAM 0.201 4 CB VAM 0.033 4 CG1 VAM 0.006 2 CG2 VAM 0.006 2 HN VAM 0.648 6 O ACE -0.500 11 ACETYL END GROUP C ACE 0.526 1 CH3 ACE -0.026 2 N NME -0.520 8 N-METHYL END GROUP HN NME 0.248 6 CM NME 0.272 2 N NMA -0.520 8 N-METHYL END GROUP (MAESTRO) HN NMA 0.248 6 CM NMA 0.272 2 OH2 TIP -0.834 12 TIP3P WATER CHARGES H1 TIP 0.417 6 H2 TIP 0.417 6 OW WAT -0.834 12 TIP3P WATER CHARGES HW1 WAT 0.417 6 HW2 WAT 0.417 6 OH2 SPC -0.82 12 SPC WATER CHARGES H1 SPC 0.41 6 H2 SPC 0.41 6 HN1 0.416 6 N-TERMINAL H HN2 0.416 6 N-TERMINAL H HN3 0.416 6 N-TERMINAL H HN1 PRO 0.500 6 N-TERMINAL H OF PRO HN2 PRO 0.500 6 N-TERMINAL H OF PRO HN3 PRO 0.500 6 N-TERMINAL H OF PRO OT -1.00 11 C-TERMINAL OXT OXT -1.00 11 C-TERMINAL OXT OT1 -0.75 11 C-TERMINAL OXYGENS, OT2 -0.75 11 CHARGE-EQUALIZED NA 1.00 19 CU 1.40 20 ZN 1.40 26 CO 2.00 20 FE 1.40 20 MG 1.40 20 MN 2.00 20 LI 1.00 20 AL 3.00 20 NI 1.40 20 CA 2.00 21 CL -1.00 22 NA 1.00 19 CU 1.40 20 ZN 1.40 26 CO 2.00 20 FE 1.40 20 MG 1.40 20 MN 2.00 20 LI 1.00 20 AL 3.00 20 NI 1.40 20 CA 2.00 21 CL -1.00 22 LJ 0.00 23 LENNARD-JONES WATER PARTICLE LP 0.00 6 LONE PAIR C CBX 0.000 1 created by S. McGovern, JJI O1 CBX -0.500 11 O2 CBX -0.500 11 C1 GAR 0.194 4 GAR for GART - susan O6 GAR -0.240 12 C2 GAR 0.194 4 O8 GAR -0.240 12 C3 GAR 0.292 4 O4 GAR -0.510 12 C5 GAR 0.211 4 C10 GAR 0.211 3 O12 GAR -0.510 12 N19 GAR -0.272 8 C21 GAR 0.526 1 O22 GAR -0.500 11 C23 GAR 0.246 3 N24 GAR 1.000 9 P15 GAR 1.390 13 O16 GAR -0.847 12 O17 GAR -0.847 12 O18 GAR -0.847 12 PA NAP 1.468 13 NAP AM1-BCC summed to heavies (MMM) O1A NAP -0.862 12 O2A NAP -0.886 12 O5B NAP -0.576 12 C5B NAP 0.282 3 C4B NAP 0.186 4 O4B NAP -0.401 12 C3B NAP 0.127 4 O3B NAP -0.157 12 C2B NAP 0.277 4 O2B NAP -0.569 12 C1B NAP 0.546 4 N9A NAP -0.630 8 C8A NAP 0.632 1 N7A NAP -0.572 8 C5A NAP -0.207 1 C6A NAP 0.671 1 N6A NAP -0.082 8 N1A NAP -0.814 8 C2A NAP 0.693 1 N3A NAP -0.713 8 C4A NAP 0.568 1 O3 NAP -0.680 12 PN NAP 1.450 13 O1N NAP -0.879 12 O2N NAP -0.814 12 O5D NAP -0.578 12 C5D NAP 0.332 3 C4D NAP 0.259 4 O4D NAP -0.384 12 C3D NAP 0.227 4 O3D NAP -0.178 12 C2D NAP 0.129 4 O2D NAP -0.188 12 C1D NAP 0.235 4 N1N NAP 0.001 8 C2N NAP 0.238 1 C3N NAP -0.153 1 C7N NAP 0.635 1 O7N NAP -0.582 11 N7N NAP -0.035 8 C4N NAP 0.230 1 C5N NAP 0.039 1 C6N NAP 0.350 1 P2B NAP 1.429 13 O1X NAP -0.688 12 O2X NAP -0.688 12 O3X NAP -0.688 12 C1 PVL -0.052 1 PYRUVOYL GROUP C2 PVL 0.526 1 C3 PVL 0.526 1 O3 PVL -0.500 11 O2 PVL -0.500 11 PA NDP 1.456 13 NDP AM1-BCC summed to heavies (MMM) O1A NDP -0.863 12 O2A NDP -0.863 12 O5B NDP -0.572 12 C5B NDP 0.281 3 C4B NDP 0.187 4 O4B NDP -0.395 12 C3B NDP 0.122 4 O3B NDP -0.156 12 C2B NDP 0.266 4 O2B NDP -0.567 12 C1B NDP 0.543 4 N9A NDP -0.628 8 C8A NDP 0.643 1 N7A NDP -0.575 8 C5A NDP -0.206 1 C6A NDP 0.680 1 N6A NDP -0.087 8 N1A NDP -0.821 8 C2A NDP 0.685 1 N3A NDP -0.715 8 C4A NDP 0.566 1 O3 NDP -0.679 12 PN NDP 1.447 13 O1N NDP -0.856 12 O2N NDP -0.856 12 O5D NDP -0.580 12 C5D NDP 0.317 3 C4D NDP 0.240 4 O4D NDP -0.391 12 C3D NDP 0.188 4 O3D NDP -0.199 12 C2D NDP 0.122 4 O2D NDP -0.204 12 C1D NDP 0.461 4 N1N NDP -0.526 8 C2N NDP 0.294 1 C3N NDP -0.303 1 C7N NDP 0.683 1 O7N NDP -0.666 11 N7N NDP -0.117 8 C4N NDP 0.137 3 C5N NDP -0.094 1 C6N NDP 0.240 1 P2B NDP 1.437 13 O1X NDP -0.692 12 O2X NDP -0.692 12 O3X NDP -0.692 12 PA NAD 1.461 13 NAD AM1-BCC summed to heavies (MMM) O1A NAD -0.857 12 O2A NAD -0.875 12 O5B NAD -0.575 12 C5B NAD 0.298 3 C4B NAD 0.186 4 O4B NAD -0.389 12 C3B NAD 0.125 4 O3B NAD -0.177 12 C2B NAD 0.172 4 O2B NAD -0.167 12 C1B NAD 0.562 4 N9A NAD -0.645 8 C8A NAD 0.628 1 N7A NAD -0.546 8 C5A NAD -0.209 1 C6A NAD 0.686 1 N6A NAD -0.056 8 N1A NAD -0.807 8 C2A NAD 0.709 1 N3A NAD -0.747 8 C4A NAD 0.568 1 O3 NAD -0.681 12 PN NAD 1.440 13 O1N NAD -0.878 12 O2N NAD -0.813 12 O5D NAD -0.575 12 C5D NAD 0.328 3 C4D NAD 0.265 4 O4D NAD -0.386 12 C3D NAD 0.222 4 O3D NAD -0.176 12 C2D NAD 0.134 4 O2D NAD -0.188 12 C1D NAD 0.259 4 N1N NAD 0.036 8 C2N NAD 0.188 1 C3N NAD -0.159 1 C7N NAD 0.652 1 O7N NAD -0.569 11 N7N NAD -0.015 8 C4N NAD 0.224 1 C5N NAD 0.055 1 C6N NAD 0.292 1 N1 UMP -0.235 8 C2 UMP 0.315 3 N3 UMP -0.077 8 C4 UMP 0.245 3 C5 UMP 0.083 3 C6 UMP 0.087 3 O2 UMP -0.252 11 O4 UMP -0.270 11 C1' UMP 0.216 2 C2' UMP 0.085 2 C3' UMP 0.149 2 C4' UMP 0.175 2 O3' UMP -0.179 12 O4' UMP -0.350 12 C5' UMP 0.199 2 O5' UMP -0.352 12 P UMP 0.061 13 OP1 UMP -0.633 12 OP2 UMP -0.633 12 OP3 UMP -0.633 12 P ACP 1.390 13 For AK, niu O2 ACP -0.500 11 O1 ACP -0.500 12 O3 ACP -0.500 11 C3 ACP 0.353 3 O2' ACP -0.500 12 C2' ACP 0.353 4 C1' ACP 0.353 4 N9 ACP -0.520 8 C4 ACP 0.353 1 N3 ACP -0.520 8 C2 ACP 0.353 4 N1 ACP -0.520 8 C6 ACP 0.353 1 N6 ACP -0.520 10 C5 ACP 0.353 1 N7 ACP -0.520 8 C8 ACP 0.353 4 O4' ACP -0.500 12 C4' ACP 0.353 4 C3' ACP 0.353 4 O3' ACP -0.500 12 C5' ACP 0.353 3 O5' ACP -0.500 12 N SAM 0.570 9 S-ADENOSYLMETHIONINE (AM1-BCC +1 net charge) CA SAM 0.087 5 C SAM 0.868 1 O SAM -0.777 11 OXT SAM -0.746 11 CB SAM 0.046 5 CG SAM 0.325 5 SD SAM -0.180 14 CE SAM 0.439 5 C5' SAM 0.282 5 C4' SAM 0.236 5 O4' SAM -0.428 12 C3' SAM 0.230 5 O3' SAM -0.157 12 C2' SAM 0.176 5 O2' SAM -0.155 12 C1' SAM 0.498 5 N9 SAM -0.687 8 C8 SAM 0.595 1 N7 SAM -0.527 8 C5 SAM -0.182 1 C6 SAM 0.774 1 N6 SAM -0.054 8 N1 SAM -0.843 8 C2 SAM 0.785 1 N3 SAM -0.754 8 C4 SAM 0.579 1 S SO4 1.400 14 Niu for TK O2 SO4 -0.600 12 O1 SO4 -0.600 12 O3 SO4 -0.600 11 O4 SO4 -0.600 12 CHA HEM 0.041 1 Heme group AM1-BCC summed to heavies (MMM) CHB HEM 0.053 1 CHC HEM 0.066 1 CHD HEM -0.078 1 C1A HEM 0.477 1 C2A HEM -0.163 1 C3A HEM -0.170 1 C4A HEM 0.146 1 CMA HEM 0.084 2 CAA HEM 0.099 3 CBA HEM -0.110 3 CGA HEM 0.895 1 O1A HEM -0.850 11 O2A HEM -0.850 11 C1B HEM -0.044 1 C2B HEM -0.116 1 C3B HEM -0.120 1 C4B HEM -0.060 1 CMB HEM 0.097 2 CAB HEM 0.050 1 CBB HEM -0.016 1 C1C HEM 0.100 1 C2C HEM -0.122 1 C3C HEM -0.209 1 C4C HEM 0.466 1 CMC HEM 0.069 2 CAC HEM 0.033 1 CBC HEM -0.024 1 C1D HEM 0.126 1 C2D HEM -0.152 1 C3D HEM -0.046 1 C4D HEM 0.105 1 CMD HEM 0.108 2 CAD HEM 0.110 3 CBD HEM -0.104 3 CGD HEM 0.895 1 O1D HEM -0.849 11 O2D HEM -0.849 11 NA HEM -0.622 8 NB HEM -0.622 8 NC HEM -0.622 8 ND HEM -0.622 8 N LLP 0.520 8 C LLP 0.526 1 O LLP -0.500 11 HN LLP 0.248 6 CA LLP 0.227 5 CB LLP 0.039 5 CG LLP 0.053 5 CD LLP 0.048 5 CE LLP 0.218 5 NZ LLP 0.099 9 N1 LLP -0.690 8 C2 LLP 0.188 1 C2' LLP 0.006 5 C3 LLP 0.002 1 O3 LLP -0.229 12 C4 LLP -0.136 1 C4' LLP 0.253 5 C5 LLP -0.075 1 C6 LLP 0.306 1 C5' LLP 0.173 5 OP4 LLP -0.672 12 P LLP 1.153 13 OP1 LLP -0.905 12 OP2 LLP -0.947 11 OP3 LLP -0.905 12