!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) 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 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 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 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 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 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 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 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 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 HAA NAD 0.310 6 HAB NAD 0.310 6 HAC NAD 0.310 6 HAD NAD 0.310 6 HAE NAD 0.310 6 HAF NAD 0.310 6 HAG NAD 0.310 6 HAH NAD 0.310 6 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 C3 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 C7 NDP 0.353 4 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 OP4 NDP -0.500 12 OP1 NDP -0.500 11 OP2 NDP -0.500 11 OP5 NDP -0.500 12 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 Niu, for GPB C6 LLP 0.210 4 C5 LLP 0.210 1 C5A LLP 0.210 3 O4P LLP -0.500 12 P LLP 1.390 13 O3P LLP -0.500 11 O2P LLP -0.500 11 O1P LLP -0.500 12 C4 LLP 0.210 1 C4A LLP 0.210 3 NZ LLP -0.520 10 CE LLP 0.210 3 CD LLP 0.210 3 CG LLP 0.210 3 CB LLP 0.210 3 CA LLP 0.210 4 C LLP 0.210 4 O LLP -0.500 11 N LLP -0.520 10 C3 LLP 0.210 1 O3 LLP -0.500 12 C2 LLP 0.210 1 C2A LLP 0.210 2 N SAM -0.520 10 Niu, for COMT CA SAM 0.210 4 CB SAM 0.210 3 CG SAM 0.210 3 SD SAM -0.025 14 C5' SAM 0.210 3 C4' SAM 0.210 4 C3' SAM 0.210 4 C2' SAM 0.210 4 C1' SAM 0.210 4 N9 SAM -0.520 10 C4 SAM 0.210 1 N3 SAM -0.520 8 C2 SAM 0.210 4 N1 SAM -0.520 8 C6 SAM 0.210 1 N6 SAM -0.520 10 C5 SAM 0.210 1 N7 SAM -0.520 8 C8 SAM 0.210 4 O4' SAM -0.500 12 O2' SAM -0.500 12 O3' SAM -0.500 12 CE SAM 0.210 3 C SAM 0.210 1 OXT SAM -0.500 11 O SAM -0.500 11 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 0.065 1 CHB HEM 0.084 1 CHC HEM -0.290 1 CHD HEM -0.220 1 NA HEM -0.368 8 C1A HEM -0.029 1 C2A HEM -0.182 1 C3A HEM -0.223 1 C4A HEM -0.047 1 CMA HEM -0.051 5 CAA HEM -0.004 5 CBA HEM -0.160 5 CGA HEM 0.488 1 O1A HEM -0.708 11 O2A HEM -0.719 11 NB HEM -0.364 8 C1B HEM -0.058 1 C2B HEM -0.101 1 C3B HEM -0.169 1 C4B HEM 0.152 1 CMB HEM -0.086 5 CAB HEM -0.012 1 CBB HEM -0.245 1 NC HEM -0.539 8 C1C HEM 0.181 1 C2C HEM -0.130 1 C3C HEM -0.123 1 C4C HEM 0.130 1 CMC HEM -0.077 5 CAC HEM -0.027 1 CBC HEM -0.242 1 ND HEM -0.377 8 C1D HEM 0.146 1 C2D HEM -0.149 1 C3D HEM -0.101 1 C4D HEM -0.028 1 CMD HEM -0.053 5 CAD HEM -0.035 5 CBD HEM -0.168 5 CGD HEM 0.498 1 O1D HEM -0.695 11 O2D HEM -0.718 11 H1 HEM 0.091 7 H2 HEM 0.084 7 H3 HEM 0.084 7 H4 HEM 0.082 7 H6 HEM 0.049 7 H7 HEM 0.026 7 H8 HEM 0.022 7 H9 HEM 0.031 7 H10 HEM 0.038 7 H11 HEM 0.042 7 H12 HEM 0.050 7 H13 HEM 0.051 7 H14 HEM 0.044 7 H15 HEM 0.051 7 H16 HEM 0.097 7 H17 HEM 0.083 7 H18 HEM 0.086 7 H20 HEM 0.047 7 H21 HEM 0.036 7 H22 HEM 0.052 7 H23 HEM 0.111 7 H24 HEM 0.085 7 H25 HEM 0.084 7 H26 HEM 0.054 7 H27 HEM 0.053 7 H28 HEM 0.037 7 H29 HEM 0.039 7 H30 HEM 0.054 7 H31 HEM 0.052 7 H32 HEM 0.038 7