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|
global_
_lib_name ?
_lib_version ?
_lib_update ?
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
SMM SMM 'S-ADENOSYLMETHIONINE METHYL ESTER ' non-polymer 54 28 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SMM
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
SMM O O O -0.500 0.000 0.000 0.000
SMM C C C 0.000 -1.044 -0.629 0.282
SMM OXT O O2 -0.500 -1.224 -1.849 0.072
SMM CXT C CH3 0.000 -0.149 -2.654 -0.557
SMM HXT3 H H 0.000 -0.225 -3.670 -0.253
SMM HXT2 H H 0.000 -0.227 -2.607 -1.617
SMM HXT1 H H 0.000 0.805 -2.281 -0.269
SMM CA C CH1 0.000 -2.253 0.033 0.929
SMM HA1 H H 0.000 -2.472 -0.497 1.866
SMM N N NH2 0.000 -1.982 1.413 1.248
SMM HN2 H H 0.000 -2.029 1.726 2.205
SMM HN1 H H 0.000 -1.747 2.062 0.512
SMM CB C CH2 0.000 -3.475 -0.094 0.013
SMM HB1 H H 0.000 -4.316 0.398 0.506
SMM HB2 H H 0.000 -3.695 -1.157 -0.105
SMM CG C CH2 0.000 -3.247 0.535 -1.356
SMM HG1 H H 0.000 -2.386 0.050 -1.822
SMM HG2 H H 0.000 -3.035 1.597 -1.219
SMM SD S ST 0.000 -4.663 0.343 -2.392
SMM HD1 H H 0.000 -4.974 -0.839 -2.557
SMM CE C CH3 0.000 -4.285 1.165 -3.909
SMM HE3 H H 0.000 -3.229 1.232 -4.047
SMM HE2 H H 0.000 -4.698 0.634 -4.737
SMM HE1 H H 0.000 -4.686 2.153 -3.911
SMM "C5'" C CH2 0.000 -5.947 1.284 -1.625
SMM "H5'1" H H 0.000 -5.595 2.310 -1.500
SMM "H5'2" H H 0.000 -6.153 0.849 -0.644
SMM "C4'" C CH1 0.000 -7.219 1.280 -2.461
SMM "H4'" H H 0.000 -7.005 1.684 -3.460
SMM "C3'" C CH1 0.000 -8.354 2.070 -1.819
SMM "H3'" H H 0.000 -7.979 2.898 -1.201
SMM "O3'" O OH1 0.000 -9.234 2.528 -2.847
SMM "HO3'" H H 0.000 -9.922 3.084 -2.457
SMM "C2'" C CH1 0.000 -9.054 1.015 -0.987
SMM "H2'" H H 0.000 -8.499 0.841 -0.054
SMM "O2'" O OH1 0.000 -10.398 1.338 -0.698
SMM "HO2'" H H 0.000 -10.831 0.572 -0.301
SMM "C1'" C CH1 0.000 -8.946 -0.204 -1.892
SMM "H1'" H H 0.000 -9.757 -0.171 -2.632
SMM "O4'" O O2 0.000 -7.684 -0.084 -2.576
SMM N9 N NR5 0.000 -9.003 -1.480 -1.182
SMM C8 C CR15 0.000 -7.942 -2.135 -0.610
SMM H8 H H 0.000 -6.925 -1.765 -0.625
SMM N7 N NRD5 0.000 -8.305 -3.265 -0.041
SMM C5 C CR56 0.000 -9.658 -3.349 -0.253
SMM C4 C CR56 0.000 -10.112 -2.247 -0.960
SMM C6 C CR6 0.000 -10.606 -4.302 0.105
SMM N6 N NH2 0.000 -10.234 -5.451 0.824
SMM HN62 H H 0.000 -9.771 -6.232 0.360
SMM HN61 H H 0.000 -10.418 -5.525 1.824
SMM N1 N NRD6 0.000 -11.899 -4.109 -0.250
SMM C2 C CR16 0.000 -12.197 -2.984 -0.943
SMM H2 H H 0.000 -13.239 -2.862 -1.211
SMM N3 N NRD6 0.000 -11.371 -1.993 -1.344
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
SMM O n/a C START
SMM C O CA .
SMM OXT C CXT .
SMM CXT OXT HXT1 .
SMM HXT3 CXT . .
SMM HXT2 CXT . .
SMM HXT1 CXT . .
SMM CA C CB .
SMM HA1 CA . .
SMM N CA HN1 .
SMM HN2 N . .
SMM HN1 N . .
SMM CB CA CG .
SMM HB1 CB . .
SMM HB2 CB . .
SMM CG CB SD .
SMM HG1 CG . .
SMM HG2 CG . .
SMM SD CG "C5'" .
SMM HD1 SD . .
SMM CE SD HE1 .
SMM HE3 CE . .
SMM HE2 CE . .
SMM HE1 CE . .
SMM "C5'" SD "C4'" .
SMM "H5'1" "C5'" . .
SMM "H5'2" "C5'" . .
SMM "C4'" "C5'" "C3'" .
SMM "H4'" "C4'" . .
SMM "C3'" "C4'" "C2'" .
SMM "H3'" "C3'" . .
SMM "O3'" "C3'" "HO3'" .
SMM "HO3'" "O3'" . .
SMM "C2'" "C3'" "C1'" .
SMM "H2'" "C2'" . .
SMM "O2'" "C2'" "HO2'" .
SMM "HO2'" "O2'" . .
SMM "C1'" "C2'" N9 .
SMM "H1'" "C1'" . .
SMM "O4'" "C1'" . .
SMM N9 "C1'" C8 .
SMM C8 N9 N7 .
SMM H8 C8 . .
SMM N7 C8 C5 .
SMM C5 N7 C6 .
SMM C4 C5 . .
SMM C6 C5 N1 .
SMM N6 C6 HN61 .
SMM HN62 N6 . .
SMM HN61 N6 . .
SMM N1 C6 C2 .
SMM C2 N1 N3 .
SMM H2 C2 . .
SMM N3 C2 . END
SMM "C4'" "O4'" . ADD
SMM N9 C4 . ADD
SMM C4 N3 . ADD
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
SMM N CA single 1.450 0.020
SMM HN1 N single 1.010 0.020
SMM HN2 N single 1.010 0.020
SMM CB CA single 1.524 0.020
SMM CA C single 1.500 0.020
SMM HA1 CA single 1.099 0.020
SMM CG CB single 1.524 0.020
SMM HB1 CB single 1.092 0.020
SMM HB2 CB single 1.092 0.020
SMM SD CG single 1.662 0.020
SMM HG1 CG single 1.092 0.020
SMM HG2 CG single 1.092 0.020
SMM CE SD single 1.662 0.020
SMM "C5'" SD single 1.662 0.020
SMM HD1 SD single 1.234 0.020
SMM HE1 CE single 1.059 0.020
SMM HE2 CE single 1.059 0.020
SMM HE3 CE single 1.059 0.020
SMM "C4'" "C5'" single 1.524 0.020
SMM "H5'1" "C5'" single 1.092 0.020
SMM "H5'2" "C5'" single 1.092 0.020
SMM "C4'" "O4'" single 1.426 0.020
SMM "C3'" "C4'" single 1.524 0.020
SMM "H4'" "C4'" single 1.099 0.020
SMM "O4'" "C1'" single 1.426 0.020
SMM N9 "C1'" single 1.485 0.020
SMM "C1'" "C2'" single 1.524 0.020
SMM "H1'" "C1'" single 1.099 0.020
SMM N9 C4 single 1.337 0.020
SMM C8 N9 single 1.337 0.020
SMM C4 N3 double 1.355 0.020
SMM C4 C5 single 1.490 0.020
SMM N3 C2 single 1.337 0.020
SMM C2 N1 double 1.337 0.020
SMM H2 C2 single 1.083 0.020
SMM N1 C6 single 1.350 0.020
SMM N6 C6 single 1.355 0.020
SMM C6 C5 double 1.490 0.020
SMM HN61 N6 single 1.010 0.020
SMM HN62 N6 single 1.010 0.020
SMM C5 N7 single 1.350 0.020
SMM N7 C8 double 1.350 0.020
SMM H8 C8 single 1.083 0.020
SMM "O2'" "C2'" single 1.432 0.020
SMM "C2'" "C3'" single 1.524 0.020
SMM "H2'" "C2'" single 1.099 0.020
SMM "HO2'" "O2'" single 0.967 0.020
SMM "O3'" "C3'" single 1.432 0.020
SMM "H3'" "C3'" single 1.099 0.020
SMM "HO3'" "O3'" single 0.967 0.020
SMM C O deloc 1.220 0.020
SMM OXT C deloc 1.454 0.020
SMM CXT OXT single 1.426 0.020
SMM HXT1 CXT single 1.059 0.020
SMM HXT2 CXT single 1.059 0.020
SMM HXT3 CXT single 1.059 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
SMM O C OXT 119.000 3.000
SMM O C CA 120.500 3.000
SMM OXT C CA 120.000 3.000
SMM C OXT CXT 120.000 3.000
SMM OXT CXT HXT3 109.470 3.000
SMM OXT CXT HXT2 109.470 3.000
SMM OXT CXT HXT1 109.470 3.000
SMM HXT3 CXT HXT2 109.470 3.000
SMM HXT3 CXT HXT1 109.470 3.000
SMM HXT2 CXT HXT1 109.470 3.000
SMM C CA HA1 108.810 3.000
SMM C CA N 109.470 3.000
SMM C CA CB 109.470 3.000
SMM HA1 CA N 109.470 3.000
SMM HA1 CA CB 108.340 3.000
SMM N CA CB 109.470 3.000
SMM CA N HN2 120.000 3.000
SMM CA N HN1 120.000 3.000
SMM HN2 N HN1 120.000 3.000
SMM CA CB HB1 109.470 3.000
SMM CA CB HB2 109.470 3.000
SMM CA CB CG 111.000 3.000
SMM HB1 CB HB2 107.900 3.000
SMM HB1 CB CG 109.470 3.000
SMM HB2 CB CG 109.470 3.000
SMM CB CG HG1 109.470 3.000
SMM CB CG HG2 109.470 3.000
SMM CB CG SD 109.500 3.000
SMM HG1 CG HG2 107.900 3.000
SMM HG1 CG SD 109.500 3.000
SMM HG2 CG SD 109.500 3.000
SMM CG SD HD1 109.500 3.000
SMM CG SD CE 109.500 3.000
SMM CG SD "C5'" 109.500 3.000
SMM HD1 SD CE 109.500 3.000
SMM HD1 SD "C5'" 109.500 3.000
SMM CE SD "C5'" 109.500 3.000
SMM SD CE HE3 109.500 3.000
SMM SD CE HE2 109.500 3.000
SMM SD CE HE1 109.500 3.000
SMM HE3 CE HE2 109.470 3.000
SMM HE3 CE HE1 109.470 3.000
SMM HE2 CE HE1 109.470 3.000
SMM SD "C5'" "H5'1" 109.500 3.000
SMM SD "C5'" "H5'2" 109.500 3.000
SMM SD "C5'" "C4'" 109.500 3.000
SMM "H5'1" "C5'" "H5'2" 107.900 3.000
SMM "H5'1" "C5'" "C4'" 109.470 3.000
SMM "H5'2" "C5'" "C4'" 109.470 3.000
SMM "C5'" "C4'" "H4'" 108.340 3.000
SMM "C5'" "C4'" "C3'" 111.000 3.000
SMM "C5'" "C4'" "O4'" 109.470 3.000
SMM "H4'" "C4'" "C3'" 108.340 3.000
SMM "H4'" "C4'" "O4'" 109.470 3.000
SMM "C3'" "C4'" "O4'" 109.470 3.000
SMM "C4'" "C3'" "H3'" 108.340 3.000
SMM "C4'" "C3'" "O3'" 109.470 3.000
SMM "C4'" "C3'" "C2'" 111.000 3.000
SMM "H3'" "C3'" "O3'" 109.470 3.000
SMM "H3'" "C3'" "C2'" 108.340 3.000
SMM "O3'" "C3'" "C2'" 109.470 3.000
SMM "C3'" "O3'" "HO3'" 109.470 3.000
SMM "C3'" "C2'" "H2'" 108.340 3.000
SMM "C3'" "C2'" "O2'" 109.470 3.000
SMM "C3'" "C2'" "C1'" 111.000 3.000
SMM "H2'" "C2'" "O2'" 109.470 3.000
SMM "H2'" "C2'" "C1'" 108.340 3.000
SMM "O2'" "C2'" "C1'" 109.470 3.000
SMM "C2'" "O2'" "HO2'" 109.470 3.000
SMM "C2'" "C1'" "H1'" 108.340 3.000
SMM "C2'" "C1'" "O4'" 109.470 3.000
SMM "C2'" "C1'" N9 109.470 3.000
SMM "H1'" "C1'" "O4'" 109.470 3.000
SMM "H1'" "C1'" N9 109.470 3.000
SMM "O4'" "C1'" N9 109.470 3.000
SMM "C1'" "O4'" "C4'" 111.800 3.000
SMM "C1'" N9 C8 126.000 3.000
SMM "C1'" N9 C4 126.000 3.000
SMM C8 N9 C4 108.000 3.000
SMM N9 C8 H8 126.000 3.000
SMM N9 C8 N7 108.000 3.000
SMM H8 C8 N7 126.000 3.000
SMM C8 N7 C5 108.000 3.000
SMM N7 C5 C4 108.000 3.000
SMM N7 C5 C6 132.000 3.000
SMM C4 C5 C6 120.000 3.000
SMM C5 C4 N9 108.000 3.000
SMM C5 C4 N3 120.000 3.000
SMM N9 C4 N3 132.000 3.000
SMM C5 C6 N6 120.000 3.000
SMM C5 C6 N1 120.000 3.000
SMM N6 C6 N1 120.000 3.000
SMM C6 N6 HN62 120.000 3.000
SMM C6 N6 HN61 120.000 3.000
SMM HN62 N6 HN61 120.000 3.000
SMM C6 N1 C2 120.000 3.000
SMM N1 C2 H2 120.000 3.000
SMM N1 C2 N3 120.000 3.000
SMM H2 C2 N3 120.000 3.000
SMM C2 N3 C4 120.000 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
SMM var_1 O C OXT CXT -0.008 20.000 1
SMM var_2 C OXT CXT HXT1 32.499 20.000 1
SMM var_3 O C CA CB 119.335 20.000 3
SMM var_4 C CA N HN1 60.759 20.000 1
SMM var_5 C CA CB CG -58.567 20.000 3
SMM var_6 CA CB CG SD 178.997 20.000 3
SMM var_7 CB CG SD "C5'" 65.116 20.000 1
SMM var_8 CG SD CE HE1 -96.619 20.000 1
SMM var_9 CG SD "C5'" "C4'" 176.513 20.000 1
SMM var_10 SD "C5'" "C4'" "C3'" 179.345 20.000 3
SMM var_11 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
SMM var_12 "C5'" "C4'" "C3'" "C2'" -90.000 20.000 3
SMM var_13 "C4'" "C3'" "O3'" "HO3'" -175.922 20.000 1
SMM var_14 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
SMM var_15 "C3'" "C2'" "O2'" "HO2'" 170.430 20.000 1
SMM var_16 "C3'" "C2'" "C1'" N9 150.000 20.000 3
SMM var_17 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
SMM var_18 "C2'" "C1'" N9 C8 -86.047 20.000 1
SMM CONST_1 "C1'" N9 C4 C5 180.000 0.000 0
SMM CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
SMM CONST_3 N9 C8 N7 C5 0.000 0.000 0
SMM CONST_4 C8 N7 C5 C6 180.000 0.000 0
SMM CONST_5 N7 C5 C4 N9 0.000 0.000 0
SMM CONST_6 C5 C4 N3 C2 0.000 0.000 0
SMM CONST_7 N7 C5 C6 N1 180.000 0.000 0
SMM CONST_8 C5 C6 N6 HN61 102.794 0.000 0
SMM CONST_9 C5 C6 N1 C2 0.000 0.000 0
SMM CONST_10 C6 N1 C2 N3 0.000 0.000 0
SMM CONST_11 N1 C2 N3 C4 0.000 0.000 0
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
SMM chir_01 CA N CB C negativ
SMM chir_02 SD CG CE "C5'" positiv
SMM chir_03 "C4'" "C5'" "O4'" "C3'" negativ
SMM chir_04 "C1'" "O4'" N9 "C2'" negativ
SMM chir_05 "C2'" "C1'" "O2'" "C3'" positiv
SMM chir_06 "C3'" "C4'" "C2'" "O3'" positiv
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
SMM plan-1 N 0.020
SMM plan-1 CA 0.020
SMM plan-1 HN1 0.020
SMM plan-1 HN2 0.020
SMM plan-2 N9 0.020
SMM plan-2 "C1'" 0.020
SMM plan-2 C4 0.020
SMM plan-2 C8 0.020
SMM plan-2 N7 0.020
SMM plan-2 N3 0.020
SMM plan-2 C5 0.020
SMM plan-2 C2 0.020
SMM plan-2 N1 0.020
SMM plan-2 C6 0.020
SMM plan-2 H2 0.020
SMM plan-2 N6 0.020
SMM plan-2 H8 0.020
SMM plan-2 HN62 0.020
SMM plan-2 HN61 0.020
SMM plan-3 N6 0.020
SMM plan-3 C6 0.020
SMM plan-3 HN61 0.020
SMM plan-3 HN62 0.020
SMM plan-4 C 0.020
SMM plan-4 CA 0.020
SMM plan-4 O 0.020
SMM plan-4 OXT 0.020
# ------------------------------------------------------
|
