!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 0.575 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) HD1 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 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 (hic) 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 (hif) 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 (hiq) 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 (+) (same except res name) C HIS 0.526 1 O HIS -0.500 11 CA HIS 0.195 4 CB HIS 0.211 3 CG HIS 0.103 1 CD2 HIS 0.353 1 AD2 HIS 0.353 1 CE1 HIS 0.719 1 AE1 HIS 0.719 1 ND1 HIS -0.613 8 AD1 HIS -0.613 8 NE2 HIS -0.686 8 AE2 HIS -0.686 8 HN HIS 0.248 6 HND HIS 0.478 6 HNE HIS 0.486 6 N HIT -0.520 8 HISTIDINE (+) (same except res name) more polar by 0.4 C HIT 0.526 1 O HIT -0.900 11 CA HIT 0.195 4 CB HIT 0.211 3 CG HIT 0.103 1 CD2 HIT 0.353 1 AD2 HIT 0.353 1 CE1 HIT 0.719 1 AE1 HIT 0.719 1 ND1 HIT -0.613 8 AD1 HIT -0.613 8 NE2 HIT -0.686 8 AE2 HIT -0.686 8 HN HIT 0.648 6 HND HIT 0.478 6 HNE HIT 0.486 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 LYN -0.520 8 LYSINE neutralized by niu C LYN 0.526 1 O LYN -0.500 11 CA LYN 0.227 4 CB LYN 0.039 3 CG LYN 0.053 3 CD LYN 0.048 3 CE LYN 0.041 3 niu NZ LYN -0.872 9 niu HN LYN 0.248 6 HNZ1 LYN 0.355 6 niu HNZ2 LYN 0.355 6 niu, using OPLS as reference 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 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 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 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 NA 1.00 19 CU 2.00 20 ZN 2.00 26 FE 2.00 20 MG 2.00 20 MN 2.00 20 LI 1.00 20 AL 3.00 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 0.00 1 created by S. McGovern for "AD" O1 CBX 0.00 11 O2 CBX 0.00 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 P1 NAP 1.390 13 NADP+ (slm, 9/02/02/) O2 NAP -0.500 12 O3 NAP -0.500 11 O4 NAP -0.500 12 C5 NAP 0.353 3 C6 NAP 0.353 4 O7 NAP -0.500 12 C8 NAP 0.353 4 O9 NAP -0.500 12 C10 NAP 0.353 4 O11 NAP -0.500 12 C12 NAP 0.353 4 N13 NAP -0.520 10 C14 NAP 0.353 1 N15 NAP -0.520 8 C16 NAP 0.353 1 C17 NAP 0.353 1 N18 NAP -0.520 10 N19 NAP -0.520 8 C20 NAP 0.353 1 N21 NAP -0.520 8 C22 NAP 0.353 1 O23 NAP -0.500 12 P24 NAP 1.390 13 O25 NAP -0.500 12 O26 NAP -0.500 11 O27 NAP -0.500 12 C28 NAP 0.353 3 C29 NAP 0.353 4 O30 NAP -0.500 12 C31 NAP 0.353 4 O32 NAP -0.500 12 C33 NAP 0.353 4 O34 NAP -0.500 12 C35 NAP 0.353 4 N36 NAP 0.213 8 C37 NAP 0.240 1 C38 NAP -0.133 1 C39 NAP 0.333 1 O40 NAP -0.299 11 N41 NAP 0.085 8 C42 NAP 0.258 1 C43 NAP 0.068 1 C44 NAP 0.371 1 P45 NAP 1.390 13 O46 NAP -0.500 12 O47 NAP -0.500 12 O48 NAP -0.500 11 OP3 NAP -0.500 12 the other nap (dhfr_apo) OP2 NAP -0.500 12 OP1 NAP -0.500 12 NP NAP 1.390 13 NO5 NAP -0.500 12 NC5 NAP 0.353 4 NC4 NAP 0.353 4 NC3 NAP 0.353 4 NO3 NAP -0.500 12 NO4 NAP -0.500 12 NO2 NAP -0.500 12 NO1 NAP -0.500 12 P1 NAH 1.390 13 NADP+ (slm, 9/02/02/) - copy of, for sahh - identical? rename? O2 NAH -0.500 12 O3 NAH -0.500 11 O4 NAH -0.500 12 C5 NAH 0.353 3 C6 NAH 0.353 4 O7 NAH -0.500 12 C8 NAH 0.353 4 O9 NAH -0.500 12 C10 NAH 0.353 4 O11 NAH -0.500 12 C12 NAH 0.353 4 N13 NAH -0.520 10 C14 NAH 0.353 1 N15 NAH -0.520 8 C16 NAH 0.353 1 C17 NAH 0.353 1 N18 NAH -0.520 10 N19 NAH -0.520 8 C20 NAH 0.353 1 N21 NAH -0.520 8 C22 NAH 0.353 1 O23 NAH -0.500 12 P24 NAH 1.390 13 O25 NAH -0.500 12 O26 NAH -0.500 11 O27 NAH -0.500 12 C28 NAH 0.353 3 C29 NAH 0.353 4 O30 NAH -0.500 12 C31 NAH 0.353 4 O32 NAH -0.500 12 C33 NAH 0.353 4 O34 NAH -0.500 12 C35 NAH 0.353 4 N36 NAH 0.213 8 C37 NAH 0.240 1 C38 NAH -0.133 1 C39 NAH 0.333 1 O40 NAH -0.299 11 N41 NAH 0.085 8 C42 NAH 0.258 1 C43 NAH 0.068 1 C44 NAH 0.371 1 P45 NAH 1.390 13 O46 NAH -0.500 12 O47 NAH -0.500 12 O48 NAH -0.500 11 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 HOP NDP 0.000 6 P1 NDP 1.390 13 P NDP 1.390 13 P2 NDP 1.390 13 O2 NDP -0.500 12 O1 NDP -0.500 12 O3 NDP -0.500 11 O4 NDP -0.500 12 C5 NDP 0.353 3 C6 NDP 0.353 4 O7 NDP -0.500 12 C8 NDP 0.353 4 O9 NDP -0.500 12 C10 NDP 0.353 4 O11 NDP -0.500 12 C12 NDP 0.353 4 N13 NDP -0.520 10 C14 NDP 0.353 1 N15 NDP -0.520 8 C16 NDP 0.353 1 C17 NDP 0.353 1 N18 NDP -0.520 10 N19 NDP -0.520 8 C20 NDP 0.353 1 N21 NDP -0.520 8 C22 NDP 0.353 1 O23 NDP -0.500 12 P24 NDP 1.390 13 O25 NDP -0.500 12 O26 NDP -0.500 11 O27 NDP -0.500 12 C28 NDP 0.353 3 C29 NDP 0.353 4 O30 NDP -0.500 12 C31 NDP 0.353 4 O32 NDP -0.500 12 C33 NDP 0.353 4 O34 NDP -0.500 12 C35 NDP 0.353 4 N36 NDP -0.520 8 C37 NDP 0.353 1 C38 NDP 0.353 1 C39 NDP 0.353 1 O40 NDP -0.500 11 N41 NDP -0.520 10 C42 NDP 0.353 1 C43 NDP 0.353 1 C44 NDP 0.353 1 P45 NDP 1.390 13 O46 NDP -0.847 12 O47 NDP -0.847 12 O48 NDP -0.847 11 P1 NDP 1.390 13 the other ndp OP3 NDP -0.500 12 OP2 NDP -0.500 11 OP1 NDP -0.500 11 O2' NDP -0.500 12 C2' NDP 0.353 3 C1' NDP 0.353 4 N9 NDP -0.520 10 C4 NDP 0.353 4 N3 NDP -0.520 10 C2 NDP 0.353 4 N1 NDP -0.520 10 C6 NDP 0.353 4 N6 NDP -0.520 10 C5 NDP 0.353 4 N7 NDP -0.520 10 C8 NDP 0.353 4 O4' NDP -0.500 12 C4' NDP 0.353 4 C3' NDP 0.353 4 O3' NDP -0.500 12 C5' NDP 0.353 1 O5' NDP -0.500 12 P3 NDP 1.390 13 NDP for kat O14 NDP -0.500 12 C21 NDP 0.353 3 C19 NDP 0.353 4 C18 NDP 0.353 4 C15 NDP 0.353 4 O13 NDP -0.500 12 C13 NDP 0.353 4 O12 NDP -0.500 12 C11 NDP 0.353 4 O10 NDP -0.500 12 O8 NDP -0.500 12 C1 NDP 0.353 4 C3 NDP 0.353 4 C9 NDP 0.353 4 C7 NDP 0.353 4 N5 NDP -0.520 10 N4 NDP -0.520 10 N2 NDP -0.520 10 O6 NDP -0.500 12 O5 NDP -0.500 12 OP4 NDP -0.500 12 OP1 NDP -0.500 11 OP2 NDP -0.500 11 OP5 NDP -0.500 12 P1 NAD 1.390 13 yet another nad (for sahh_model) O2 NAD -0.500 11 O3 NAD -0.500 12 O4 NAD -0.500 12 C5 NAD 0.353 3 C6 NAD 0.353 4 O7 NAD -0.500 12 C8 NAD 0.353 4 O9 NAD -0.500 12 C10 NAD 0.353 4 O11 NAD -0.500 12 C12 NAD 0.353 4 N13 NAD -0.520 10 C14 NAD 0.353 1 N15 NAD -0.520 8 C16 NAD 0.353 1 C17 NAD 0.353 1 N18 NAD -0.520 10 N19 NAD -0.520 8 C20 NAD 0.353 1 N21 NAD -0.520 8 C22 NAD 0.353 1 O23 NAD -0.500 12 P24 NAD 1.390 13 O25 NAD -0.500 12 O26 NAD -0.500 11 O27 NAD -0.500 12 C28 NAD 0.353 3 C29 NAD 0.353 4 O30 NAD -0.500 12 C31 NAD 0.353 4 O32 NAD -0.500 12 C33 NAD 0.353 4 O34 NAD -0.500 12 C35 NAD 0.353 4 N36 NAD 0.213 8 C37 NAD 0.240 1 C38 NAD -0.133 1 C39 NAD 0.333 1 O40 NAD -0.299 11 N41 NAD 0.085 10 C42 NAD 0.258 1 C43 NAD 0.068 1 C44 NAD 0.371 1 P45 NAD 1.390 13 O46 NAD -0.500 12 O47 NAD -0.500 12 O48 NAD -0.500 11 H51 NAD 0.418 6 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 O1P UMP -0.633 12 O2P UMP -0.633 12 O3P 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 N1 LLP -0.520 8 C6 LLP 0.353 4 C5 LLP 0.353 1 C5A LLP 0.353 3 O4P LLP -0.500 12 P LLP 1.390 13 niu, for GPB O3P LLP -0.500 11 O2P LLP -0.500 11 O1P LLP -0.500 12 C4 LLP 0.353 1 C4A LLP 0.353 3 NZ LLP -0.520 10 CE LLP 0.353 3 CD LLP 0.353 3 CG LLP 0.353 3 CB LLP 0.353 3 CA LLP 0.353 4 C LLP 0.353 4 O LLP -0.500 11 N LLP -0.520 10 C3 LLP 0.353 1 O3 LLP -0.500 12 C2 LLP 0.353 1 C2A LLP 0.353 2