*>>>>>> CHARMM topology for peptidoglycan <<<<<< * Contains topology entries for NAG, NAM, d-gamma-glutamate (DGG), * and L-meso-diaminopimelic acid (DAP) and its amidated form (DAPA) 36 1 MASS 174 CC3161 12.01100 C ! C2, C3, C4 CH bound to OH MASS 175 CC3162 12.01100 C ! C1 (anomeric) CH bound to OH MASS 176 CC3163 12.01100 C ! C5 CH bound to exocylic CH2OH MASS 177 CC321 12.01100 C ! generic acyclic CH2 carbon (hexopyranose C6) MASS 180 CC331 12.01100 C ! generic acyclic CH3 carbon (xyl C6, glcna/galna CT) MASS 185 HCA1 1.00800 H ! aliphatic proton, CH MASS 186 HCA2 1.00800 H ! aliphatic proton, CH2 MASS 187 HCA3 1.00800 H ! aliphatic proton, CH3 MASS 188 HCP1 1.00800 H ! polar H MASS 191 OC311 15.99940 O ! hydroxyl oxygen MASS 192 OC3C61 15.99940 O ! ether in six membered ring MASS 193 OC301 15.99940 O ! generic linear ether AUTOGENERATE angles dihedrals ! DEFAults for patching FIRSt and LAST residues DEFA FIRS NONE LAST NONE RESI NAG 0.000 ! N-Acetyl glucosamine GROU ! ATOM C1 CC3162 0.340 ! O6-HO6 ATOM H1 HCA1 0.090 ! | ATOM O1 OC311 -0.650 ! H61-C6-H62 ATOM HO1 HCP1 0.420 ! | ATOM C5 CC3163 0.110 ! H5-C5---O5 ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 ATOM O5 OC3C61 -0.400 ! \ / HO3 \ / GROU ! C4 | C1 ATOM C2 CC3161 0.134 ! / \ O3 H2 / \ ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 GROU ! C3---C2 ATOM C3 CC3161 0.140 ! | | ATOM H3 HCA1 0.090 ! H3 |...(acetamide) ATOM O3 OC311 -0.650 ! | ATOM HO3 HCP1 0.420 ! HC1 | GROU ! \ | ATOM C4 CC3161 0.140 ! HC2--CC--CM--NC ATOM H4 HCA1 0.090 ! / || \ ATOM O4 OC311 -0.650 ! HC3 OM HN ATOM HO4 HCP1 0.420 ! GROU ATOM C6 CC321 0.050 ATOM H61 HCA2 0.090 ATOM H62 HCA2 0.090 ATOM O6 OC311 -0.650 ATOM HO6 HCP1 0.420 GROU ATOM CC CT3 -0.27 ATOM CM CC 0.55 ATOM NC NH1 -0.587 ATOM HN H 0.363 ATOM OM O -0.55 ATOM HC1 HA 0.09 ATOM HC2 HA 0.09 ATOM HC3 HA 0.09 ! BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 BOND C2 H2 C2 C3 C3 H3 BOND C3 O3 O3 HO3 C3 C4 C4 H4 C4 O4 BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 BOND C6 H62 C6 O6 O6 HO6 C5 O5 ! BOND CM NC NC HN NC C2 DOUBLE CM OM BOND CM CC CC HC1 CC HC2 CC HC3 IMPR CM CC NC OM IMPR NC CM HN C2 ! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) IC O1 C2 *C1 H1 1.3899 110.90 120.10 104.58 1.0836 IC O1 O5 *C1 C2 1.3899 108.62 122.10 110.88 1.5316 IC O2 C3 *C2 H2 1.4594 108.12 -118.78 111.06 1.1375 IC O2 C1 *C2 C3 1.4594 115.65 -125.60 113.28 1.4983 IC O3 C4 *C3 H3 1.4071 113.48 122.06 103.39 1.0895 IC O3 C2 *C3 C4 1.4071 108.48 124.18 109.26 1.5497 IC O4 C5 *C4 H4 1.3940 111.12 -110.35 108.66 1.0857 IC O4 C3 *C4 C5 1.3940 112.77 -129.39 115.62 1.5530 IC C6 O5 *C5 H5 1.5597 111.17 120.85 110.98 1.1092 IC C6 C4 *C5 O5 1.5597 109.90 122.92 110.30 1.4512 IC O6 H62 *C6 H61 1.4589 116.11 -112.93 103.57 1.1467 IC O6 C5 *C6 H62 1.4589 109.41 -135.95 118.22 1.0853 IC O5 C1 C2 C3 1.4620 110.88 57.82 113.28 1.4983 IC C1 C2 C3 C4 1.5316 113.28 -48.40 109.26 1.5497 IC C2 C3 C4 C5 1.4983 109.26 45.07 115.62 1.5530 IC C3 C4 C5 O5 1.5497 115.62 -49.19 110.30 1.4512 IC C4 C5 O5 C1 1.5530 110.30 56.36 112.12 1.4620 IC C5 O5 C1 C2 1.4512 112.12 -61.39 110.88 1.5316 IC C4 C5 C6 O6 1.5530 109.90 -177.46 109.41 1.4589 IC O5 C1 O1 HO1 1.4620 108.62 72.25 106.48 0.9328 IC C1 C2 O2 HO2 1.5316 115.65 135.41 116.81 0.9527 IC C2 C3 O3 HO3 1.4983 108.48 -71.46 120.86 0.9441 IC C3 C4 O4 HO4 1.5497 112.77 47.45 109.31 0.9911 IC C5 C6 O6 HO6 1.5597 109.41 -54.60 118.82 0.95210 PATC FIRS NONE LAST NONE RESI NAM 0.000 ! N-Acetylmuramic acid, NAG + lactic acid GROU ! ATOM C1 CC3162 0.340 ! O6-HO6 ATOM H1 HCA1 0.090 ! | ATOM O1 OC311 -0.650 ! H61-C6-H62 ATOM HO1 HCP1 0.420 ! | ATOM C5 CC3163 0.110 ! H5-C5---O5 ATOM H5 HCA1 0.090 ! H4 / \ O1-HO1 ATOM O5 OC3C61 -0.400 ! \ / \ / GROU ! C4 C1 ATOM C2 CC3161 0.134 ! / \ H3 H2 / \ ATOM H2 HCA1 0.090 ! HO4-O4 \| | / H1 GROU ! C3---C2 ATOM C3 CC3161 -0.024 ! (lactic acid) | | ATOM H3 HCA1 0.090 ! HB1 O3 |...(acetamide) ATOM O3 OC311 -0.406 ! \ / | GROU ! HB2--CB-CA-HA | HC1 ATOM C4 CC3161 0.140 ! / | | / ATOM H4 HCA1 0.090 ! HB3 C NC---CM--CC--HC2 ATOM O4 OC311 -0.650 ! / \\ / || \ ATOM HO4 HCP1 0.420 ! OE1 O HN OM HC3 GROU ! | ATOM C6 CC321 0.050 ! HE1 ATOM H61 HCA2 0.090 ATOM H62 HCA2 0.090 ATOM O6 OC311 -0.650 ATOM HO6 HCP1 0.420 GROU ATOM CC CT3 -0.27 ATOM CM CC 0.55 ATOM NC NH1 -0.587 ATOM HN H 0.363 ATOM OM O -0.55 ATOM HC1 HA 0.09 ATOM HC2 HA 0.09 ATOM HC3 HA 0.09 GROUP ATOM CA CT1 0.250 ATOM HA HB 0.09 GROUP ATOM CB CT3 -0.27 ATOM HB1 HA 0.09 ATOM HB2 HA 0.09 ATOM HB3 HA 0.09 GROUP ATOM C CD 0.72 ATOM O OB -0.55 ATOM OE1 OH1 -0.61 ATOM HE1 H 0.44 ! BOND C1 O1 C1 H1 O1 HO1 C1 O5 C1 C2 BOND C2 H2 C2 C3 C3 H3 BOND C3 O3 C3 C4 C4 H4 C4 O4 BOND O4 HO4 C4 C5 C5 H5 C5 C6 C6 H61 BOND C6 H62 C6 O6 O6 HO6 C5 O5 ! BOND CM NC NC HN NC C2 DOUBLE CM OM BOND CM CC CC HC1 CC HC2 CC HC3 ! BOND O3 CA CA HA CA C BOND CA CB CB HB1 CB HB2 CB HB3 BOND C OE1 OE1 HE1 DOUBLE C O IMPR CM CC NC OM IMPR NC CM HN C2 ! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) IC O1 C2 *C1 H1 1.3899 110.90 120.10 104.58 1.0836 IC O1 O5 *C1 C2 1.3899 108.62 122.10 110.88 1.5316 IC O2 C3 *C2 H2 1.4594 108.12 -118.78 111.06 1.1375 IC O2 C1 *C2 C3 1.4594 115.65 -125.60 113.28 1.4983 IC O3 C4 *C3 H3 1.4071 113.48 122.06 103.39 1.0895 IC O3 C2 *C3 C4 1.4071 108.48 124.18 109.26 1.5497 IC O4 C5 *C4 H4 1.3940 111.12 -110.35 108.66 1.0857 IC O4 C3 *C4 C5 1.3940 112.77 -129.39 115.62 1.5530 IC C6 O5 *C5 H5 1.5597 111.17 120.85 110.98 1.1092 IC C6 C4 *C5 O5 1.5597 109.90 122.92 110.30 1.4512 IC O6 H62 *C6 H61 1.4589 116.11 -112.93 103.57 1.1467 IC O6 C5 *C6 H62 1.4589 109.41 -135.95 118.22 1.0853 IC O5 C1 C2 C3 1.4620 110.88 57.82 113.28 1.4983 IC C1 C2 C3 C4 1.5316 113.28 -48.40 109.26 1.5497 IC C2 C3 C4 C5 1.4983 109.26 45.07 115.62 1.5530 IC C3 C4 C5 O5 1.5497 115.62 -49.19 110.30 1.4512 IC C4 C5 O5 C1 1.5530 110.30 56.36 112.12 1.4620 IC C5 O5 C1 C2 1.4512 112.12 -61.39 110.88 1.5316 IC C4 C5 C6 O6 1.5530 109.90 -177.46 109.41 1.4589 IC O5 C1 O1 HO1 1.4620 108.62 72.25 106.48 0.9328 IC C1 C2 O2 HO2 1.5316 115.65 135.41 116.81 0.9527 IC C2 C3 O3 HO3 1.4983 108.48 -71.46 120.86 0.9441 IC C3 C4 O4 HO4 1.5497 112.77 47.45 109.31 0.9911 IC C5 C6 O6 HO6 1.5597 109.41 -54.60 118.82 0.95210 PATC FIRS NONE LAST NONE RESI DGG -1.00 ! D-gamma-glutamate GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 -0.03 ! | OE1 ATOM HA HB 0.09 ! | // GROUP ! HA-CA--CD ATOM CB CT2 -0.18 ! | \ ATOM HB1 HA 0.09 ! | OE2(-) ATOM HB2 HA 0.09 ! HB1-CB-HB2 GROUP ! | ATOM CG CT2 -0.18 ! | ATOM HG1 HA 0.09 ! HG1-CG-HG2 ATOM HG2 HA 0.09 ! | ATOM CD CC 0.62 ! | ATOM OE1 OC -0.76 ! C==0 ATOM OE2 OC -0.76 ! | GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CA OE2 CD BOND N HN N CA C CG BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 DOUBLE O C CD OE1 IMPR N -C CA HN C CG +N O IMPR CD CA OE2 OE1 !!CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR OE1 CD ACCEPTOR OE2 CD ACCEPTOR O C RESI DAP 0.00 GROUP ATOM N NH1 -0.47 ! | OZ1 ATOM HN H 0.31 ! HN-N || ATOM CA CT1 0.07 ! | HB1 HG1 HD1 CZ--OZ2(-) ATOM HA HB 0.09 ! | | | | / GROUP ! HA-CA--CB--CG--CD----CE HZ1 ATOM CB CT2 -0.18 ! | | | | | \ / ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE NZ--HZ2 ATOM HB2 HA 0.09 ! O=C \ GROUP ! | HZ3+ ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 -0.18 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 GROUP !!taken from NTER ATOM NZ NH3 -0.30 ATOM HZ1 HC 0.33 ATOM HZ2 HC 0.33 ATOM HZ3 HC 0.33 ATOM CE CT1 0.21 ATOM HE HB 0.10 GROUP !!taken from CTER ATOM CZ CC 0.34 ATOM OZ1 OC -0.67 ATOM OZ2 OC -0.67 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG CE CD NZ CE BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 CD HD1 CD HD2 CE HE BOND CE CZ CZ OZ2 DOUBLE O C CZ OZ1 BOND NZ HZ1 NZ HZ2 NZ HZ3 IMPR N -C CA HN C CA +N O IMPR CZ CE OZ2 OZ1 CMAP -C N CA C N CA C +N DONOR HN N DONOR HZ1 NZ DONOR HZ2 NZ DONOR HZ3 NZ ACCEPTOR O C IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 IC NZ CD *CE HE 1.4604 110.4600 119.9100 110.5100 1.1128 IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 IC NZ CE CZ OZ2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OZ2 CE *CZ OZ1 0.0000 0.0000 180.0000 0.0000 0.0000 RESI DAPA 1.00 GROUP ATOM N NH1 -0.47 ! | OZ HT1 ATOM HN H 0.31 ! HN-N || / ATOM CA CT1 0.07 ! | HB1 HG1 HD1 CZ--NT--HT2 ATOM HA HB 0.09 ! | | | | / GROUP ! HA-CA--CB--CG--CD----CE HZ1 ATOM CB CT2 -0.18 ! | | | | | \ / ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE NZ--HZ2 ATOM HB2 HA 0.09 ! O=C \ GROUP ! | HZ3+ ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 -0.18 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 GROUP !!taken from NTER ATOM NZ NH3 -0.30 ATOM HZ1 HC 0.33 ATOM HZ2 HC 0.33 ATOM HZ3 HC 0.33 ATOM CE CT1 0.21 ATOM HE HB 0.10 GROUP !!taken from CT2 ATOM CZ CC 0.55 ATOM OZ O -0.55 ATOM NT NH2 -0.62 ATOM HT1 H 0.32 ATOM HT2 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG CE CD NZ CE BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 CD HD1 CD HD2 CE HE BOND CE CZ CZ OZ CZ NT NT HT1 NT HT2 DOUBLE O C BOND NZ HZ1 NZ HZ2 NZ HZ3 IMPR N -C CA HN C CA +N O IMPR CZ NT CE OZ CZ CE NT OZ IMPR NT CZ HT1 HT2 NT CZ HT2 HT1 CMAP -C N CA C N CA C +N DONOR HN N DONOR HZ1 NZ DONOR HZ2 NZ DONOR HZ3 NZ DONOR HT1 NT DONOR HT2 NT ACCEPTOR O C IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 IC NZ CD *CE HE 1.4604 110.4600 119.9100 110.5100 1.1128 IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 IC NZ CE CZ OZ 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CE *CZ OZ 0.0000 0.0000 180.0000 0.0000 0.0000 IC CE CZ NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT1 CZ *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 ! link NAM <-> NAG PRES 14bb 0.02 ! (i)1->4(i-1) equatorial at C1 and equatorial at C4 dele atom 1HO4 dele atom 2HO1 dele atom 2O1 ATOM 1C4 CC3161 0.09 ! ATOM 1O4 OC301 -0.36 ! ATOM 2C1 CC3162 0.29 ! BOND 1O4 2C1 ! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL) IC 1C3 1C4 1O4 2C1 1.5009 110.76 81.86 121.00 1.3902 ! psi IC 1C4 1O4 2C1 2O5 1.4560 121.00 -130.97 108.63 1.4470 ! phi IC 2O5 1O4 *2C1 2C2 1.4470 108.63 -122.09 110.89 1.5316 IC 2O5 1O4 *2C1 2H1 1.4470 108.63 121.92 111.32 1.0837 PRES CNAM 0.00 ! DELETE ATOM HO1 ! 0.42 GROUP ATOM C1 CC3162 0.29 ! 0.340 ATOM O1 OC301 -0.35 ! -0.65 ATOM CT1 CC331 -0.10 ! ATOM HT1 HCA3 0.09 ! ATOM HT2 HCA3 0.09 ! ATOM HT3 HCA3 0.09 ! BOND O1 CT1 BOND CT1 HT1 CT1 HT2 CT1 HT3 ! bond NAM -> ALA PRES LPG 0.00 DELETE ATOM 1OE1 ! +0.61 DELETE ATOM 1HE1 ! -0.44 ATOM 1C C 0.51 ! 0.72 -.21 ATOM 1O O -0.51 ! -0.55 +.04 BOND 1C 2N CMAP 1C 2N 2CA 2C 1N 1CA 1C 2N IMPR 1C 1CA 2N 1O ! bond DAP -> ALA PRES LNK3 -1.00 ATOM 1CE CT1 0.07 ATOM 1HE HB 0.09 ATOM 1NZ NH1 -0.47 ATOM 1HZ1 H 0.31 BOND 1NZ 2C DELETE ATOM 1HZ2 DELETE ATOM 1HZ3 IMPR 1NZ 2C 1CE 1HZ1 2C 2CA 1NZ 2O CMAP 2C 1NZ 1CE 1CZ 2N 2CA 2C 1NZ