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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
MOD MOD 'L-METHIONYL ADENYLATE ' non-polymer 56 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MOD
#
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
MOD O2S O OP -0.500 0.000 0.000 0.000
MOD P1 P P 0.000 -1.415 -0.411 -0.173
MOD O1S O OP -0.500 -1.860 -1.162 1.026
MOD O1 O O2 0.000 -1.545 -1.350 -1.474
MOD C9 C CH2 0.000 -0.622 -2.426 -1.301
MOD H91 H H 0.000 -0.875 -2.980 -0.394
MOD H92 H H 0.000 0.390 -2.026 -1.210
MOD CA C CH1 0.000 -0.696 -3.361 -2.509
MOD HA H H 0.000 -1.734 -3.693 -2.653
MOD CB C CH2 0.000 0.200 -4.578 -2.269
MOD HB1 H H 0.000 -0.082 -5.057 -1.329
MOD HB2 H H 0.000 1.242 -4.257 -2.214
MOD CG C CH2 0.000 0.030 -5.572 -3.421
MOD HG1 H H 0.000 0.312 -5.091 -4.360
MOD HG2 H H 0.000 -1.013 -5.891 -3.475
MOD SD S S2 0.000 1.092 -7.015 -3.135
MOD CE C CH3 0.000 0.696 -7.993 -4.611
MOD HE3 H H 0.000 1.248 -8.901 -4.604
MOD HE2 H H 0.000 -0.342 -8.221 -4.629
MOD HE1 H H 0.000 0.944 -7.446 -5.487
MOD N2 N NH2 0.000 -0.240 -2.647 -3.710
MOD HN22 H H 0.000 -0.860 -2.528 -4.502
MOD HN21 H H 0.000 0.700 -2.268 -3.754
MOD "O5'" O O2 0.000 -2.335 0.897 -0.359
MOD "C5'" C CH2 0.000 -2.086 1.741 0.767
MOD "H5'1" H H 0.000 -1.028 2.010 0.793
MOD "H5'2" H H 0.000 -2.348 1.210 1.684
MOD "C4'" C CH1 0.000 -2.934 3.009 0.650
MOD "H4'" H H 0.000 -2.749 3.494 -0.319
MOD "C3'" C CH1 0.000 -2.588 3.979 1.796
MOD "H3'" H H 0.000 -1.848 3.526 2.471
MOD "O3'" O OH1 0.000 -2.101 5.220 1.282
MOD H2 H H 0.000 -1.947 5.833 2.013
MOD "C2'" C CH1 0.000 -3.936 4.188 2.533
MOD H1 H H 0.000 -4.011 3.529 3.409
MOD "O2'" O OH1 0.000 -4.104 5.556 2.910
MOD "H2'" H H 0.000 -3.453 5.785 3.588
MOD "C1'" C CH1 0.000 -4.966 3.784 1.447
MOD "H1'" H H 0.000 -5.138 4.615 0.749
MOD "O4'" O O2 0.000 -4.328 2.678 0.773
MOD N9 N NR5 0.000 -6.227 3.357 2.059
MOD C4 C CH1 0.000 -7.549 3.963 1.881
MOD H4 H H 0.000 -7.988 3.693 0.910
MOD C5 C CR56 0.000 -8.331 3.348 3.040
MOD N7 N NRD5 0.000 -7.609 2.288 3.448
MOD C8 C CR15 0.000 -6.417 2.301 2.932
MOD H8 H H 0.000 -5.656 1.565 3.160
MOD N3 N NRD6 0.000 -7.563 5.409 2.091
MOD C2 C CR16 0.000 -8.680 5.938 2.518
MOD H3 H H 0.000 -8.754 7.006 2.684
MOD N1 N NR16 0.000 -9.767 5.114 2.756
MOD HN1 H H 0.000 -10.728 5.363 2.446
MOD C6 C CR6 0.000 -9.487 3.910 3.448
MOD N6 N NH2 0.000 -10.309 3.371 4.433
MOD HN62 H H 0.000 -11.171 3.838 4.702
MOD HN61 H H 0.000 -10.059 2.502 4.899
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
MOD O2S n/a P1 START
MOD P1 O2S "O5'" .
MOD O1S P1 . .
MOD O1 P1 C9 .
MOD C9 O1 CA .
MOD H91 C9 . .
MOD H92 C9 . .
MOD CA C9 N2 .
MOD HA CA . .
MOD CB CA CG .
MOD HB1 CB . .
MOD HB2 CB . .
MOD CG CB SD .
MOD HG1 CG . .
MOD HG2 CG . .
MOD SD CG CE .
MOD CE SD HE1 .
MOD HE3 CE . .
MOD HE2 CE . .
MOD HE1 CE . .
MOD N2 CA HN21 .
MOD HN22 N2 . .
MOD HN21 N2 . .
MOD "O5'" P1 "C5'" .
MOD "C5'" "O5'" "C4'" .
MOD "H5'1" "C5'" . .
MOD "H5'2" "C5'" . .
MOD "C4'" "C5'" "C3'" .
MOD "H4'" "C4'" . .
MOD "C3'" "C4'" "C2'" .
MOD "H3'" "C3'" . .
MOD "O3'" "C3'" H2 .
MOD H2 "O3'" . .
MOD "C2'" "C3'" "C1'" .
MOD H1 "C2'" . .
MOD "O2'" "C2'" "H2'" .
MOD "H2'" "O2'" . .
MOD "C1'" "C2'" N9 .
MOD "H1'" "C1'" . .
MOD "O4'" "C1'" . .
MOD N9 "C1'" C4 .
MOD C4 N9 N3 .
MOD H4 C4 . .
MOD C5 C4 N7 .
MOD N7 C5 C8 .
MOD C8 N7 H8 .
MOD H8 C8 . .
MOD N3 C4 C2 .
MOD C2 N3 N1 .
MOD H3 C2 . .
MOD N1 C2 C6 .
MOD HN1 N1 . .
MOD C6 N1 N6 .
MOD N6 C6 HN61 .
MOD HN62 N6 . .
MOD HN61 N6 . END
MOD "C4'" "O4'" . ADD
MOD N9 C8 . ADD
MOD C5 C6 . 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
MOD N2 CA single 1.450 0.020
MOD HN21 N2 single 1.010 0.020
MOD HN22 N2 single 1.010 0.020
MOD CB CA single 1.524 0.020
MOD CA C9 single 1.524 0.020
MOD HA CA single 1.099 0.020
MOD CG CB single 1.524 0.020
MOD HB1 CB single 1.092 0.020
MOD HB2 CB single 1.092 0.020
MOD SD CG single 1.762 0.020
MOD HG1 CG single 1.092 0.020
MOD HG2 CG single 1.092 0.020
MOD CE SD single 1.762 0.020
MOD HE1 CE single 1.059 0.020
MOD HE2 CE single 1.059 0.020
MOD HE3 CE single 1.059 0.020
MOD C9 O1 single 1.426 0.020
MOD H91 C9 single 1.092 0.020
MOD H92 C9 single 1.092 0.020
MOD O1 P1 single 1.610 0.020
MOD O1S P1 deloc 1.510 0.020
MOD P1 O2S deloc 1.510 0.020
MOD "O5'" P1 single 1.610 0.020
MOD "C5'" "O5'" single 1.426 0.020
MOD "C4'" "C5'" single 1.524 0.020
MOD "H5'1" "C5'" single 1.092 0.020
MOD "H5'2" "C5'" single 1.092 0.020
MOD "C4'" "O4'" single 1.426 0.020
MOD "C3'" "C4'" single 1.524 0.020
MOD "H4'" "C4'" single 1.099 0.020
MOD "O4'" "C1'" single 1.426 0.020
MOD "O3'" "C3'" single 1.432 0.020
MOD "C2'" "C3'" single 1.524 0.020
MOD "H3'" "C3'" single 1.099 0.020
MOD H2 "O3'" single 0.967 0.020
MOD "O2'" "C2'" single 1.432 0.020
MOD "C1'" "C2'" single 1.524 0.020
MOD H1 "C2'" single 1.099 0.020
MOD "H2'" "O2'" single 0.967 0.020
MOD N9 "C1'" single 1.485 0.020
MOD "H1'" "C1'" single 1.099 0.020
MOD N9 C8 single 1.337 0.020
MOD C4 N9 single 1.485 0.020
MOD C8 N7 double 1.350 0.020
MOD H8 C8 single 1.083 0.020
MOD N7 C5 single 1.350 0.020
MOD C5 C6 double 1.490 0.020
MOD C5 C4 single 1.460 0.020
MOD N6 C6 single 1.355 0.020
MOD C6 N1 single 1.337 0.020
MOD HN61 N6 single 1.010 0.020
MOD HN62 N6 single 1.010 0.020
MOD N1 C2 single 1.337 0.020
MOD HN1 N1 single 1.040 0.020
MOD C2 N3 double 1.337 0.020
MOD H3 C2 single 1.083 0.020
MOD N3 C4 single 1.465 0.020
MOD H4 C4 single 1.099 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
MOD O2S P1 O1S 119.900 3.000
MOD O2S P1 O1 108.200 3.000
MOD O2S P1 "O5'" 108.200 3.000
MOD O1S P1 O1 108.200 3.000
MOD O1S P1 "O5'" 108.200 3.000
MOD O1 P1 "O5'" 102.600 3.000
MOD P1 O1 C9 120.500 3.000
MOD O1 C9 H91 109.470 3.000
MOD O1 C9 H92 109.470 3.000
MOD O1 C9 CA 109.470 3.000
MOD H91 C9 H92 107.900 3.000
MOD H91 C9 CA 109.470 3.000
MOD H92 C9 CA 109.470 3.000
MOD C9 CA HA 108.340 3.000
MOD C9 CA CB 109.470 3.000
MOD C9 CA N2 109.470 3.000
MOD HA CA CB 108.340 3.000
MOD HA CA N2 109.470 3.000
MOD CB CA N2 109.470 3.000
MOD CA CB HB1 109.470 3.000
MOD CA CB HB2 109.470 3.000
MOD CA CB CG 111.000 3.000
MOD HB1 CB HB2 107.900 3.000
MOD HB1 CB CG 109.470 3.000
MOD HB2 CB CG 109.470 3.000
MOD CB CG HG1 109.470 3.000
MOD CB CG HG2 109.470 3.000
MOD CB CG SD 109.500 3.000
MOD HG1 CG HG2 107.900 3.000
MOD HG1 CG SD 109.500 3.000
MOD HG2 CG SD 109.500 3.000
MOD CG SD CE 99.953 3.000
MOD SD CE HE3 109.500 3.000
MOD SD CE HE2 109.500 3.000
MOD SD CE HE1 109.500 3.000
MOD HE3 CE HE2 109.470 3.000
MOD HE3 CE HE1 109.470 3.000
MOD HE2 CE HE1 109.470 3.000
MOD CA N2 HN22 120.000 3.000
MOD CA N2 HN21 120.000 3.000
MOD HN22 N2 HN21 120.000 3.000
MOD P1 "O5'" "C5'" 120.500 3.000
MOD "O5'" "C5'" "H5'1" 109.470 3.000
MOD "O5'" "C5'" "H5'2" 109.470 3.000
MOD "O5'" "C5'" "C4'" 109.470 3.000
MOD "H5'1" "C5'" "H5'2" 107.900 3.000
MOD "H5'1" "C5'" "C4'" 109.470 3.000
MOD "H5'2" "C5'" "C4'" 109.470 3.000
MOD "C5'" "C4'" "H4'" 108.340 3.000
MOD "C5'" "C4'" "C3'" 111.000 3.000
MOD "C5'" "C4'" "O4'" 109.470 3.000
MOD "H4'" "C4'" "C3'" 108.340 3.000
MOD "H4'" "C4'" "O4'" 109.470 3.000
MOD "C3'" "C4'" "O4'" 109.470 3.000
MOD "C4'" "C3'" "H3'" 108.340 3.000
MOD "C4'" "C3'" "O3'" 109.470 3.000
MOD "C4'" "C3'" "C2'" 111.000 3.000
MOD "H3'" "C3'" "O3'" 109.470 3.000
MOD "H3'" "C3'" "C2'" 108.340 3.000
MOD "O3'" "C3'" "C2'" 109.470 3.000
MOD "C3'" "O3'" H2 109.470 3.000
MOD "C3'" "C2'" H1 108.340 3.000
MOD "C3'" "C2'" "O2'" 109.470 3.000
MOD "C3'" "C2'" "C1'" 111.000 3.000
MOD H1 "C2'" "O2'" 109.470 3.000
MOD H1 "C2'" "C1'" 108.340 3.000
MOD "O2'" "C2'" "C1'" 109.470 3.000
MOD "C2'" "O2'" "H2'" 109.470 3.000
MOD "C2'" "C1'" "H1'" 108.340 3.000
MOD "C2'" "C1'" "O4'" 109.470 3.000
MOD "C2'" "C1'" N9 109.470 3.000
MOD "H1'" "C1'" "O4'" 109.470 3.000
MOD "H1'" "C1'" N9 109.470 3.000
MOD "O4'" "C1'" N9 109.470 3.000
MOD "C1'" "O4'" "C4'" 111.800 3.000
MOD "C1'" N9 C4 108.000 3.000
MOD "C1'" N9 C8 126.000 3.000
MOD C4 N9 C8 126.000 3.000
MOD N9 C4 H4 109.470 3.000
MOD N9 C4 C5 109.500 3.000
MOD N9 C4 N3 109.500 3.000
MOD H4 C4 C5 109.500 3.000
MOD H4 C4 N3 109.500 3.000
MOD C5 C4 N3 109.500 3.000
MOD C4 C5 N7 120.000 3.000
MOD C4 C5 C6 120.000 3.000
MOD N7 C5 C6 132.000 3.000
MOD C5 N7 C8 108.000 3.000
MOD N7 C8 H8 126.000 3.000
MOD N7 C8 N9 108.000 3.000
MOD H8 C8 N9 126.000 3.000
MOD C4 N3 C2 120.000 3.000
MOD N3 C2 H3 120.000 3.000
MOD N3 C2 N1 120.000 3.000
MOD H3 C2 N1 120.000 3.000
MOD C2 N1 HN1 120.000 3.000
MOD C2 N1 C6 120.000 3.000
MOD HN1 N1 C6 120.000 3.000
MOD N1 C6 N6 120.000 3.000
MOD N1 C6 C5 120.000 3.000
MOD N6 C6 C5 120.000 3.000
MOD C6 N6 HN62 120.000 3.000
MOD C6 N6 HN61 120.000 3.000
MOD HN62 N6 HN61 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
MOD var_1 O2S P1 O1 C9 54.974 20.000 1
MOD var_2 P1 O1 C9 CA 179.976 20.000 1
MOD var_3 O1 C9 CA N2 65.028 20.000 3
MOD var_4 C9 CA CB CG 175.022 20.000 3
MOD var_5 CA CB CG SD -179.967 20.000 3
MOD var_6 CB CG SD CE 179.990 20.000 1
MOD var_7 CG SD CE HE1 60.040 20.000 1
MOD var_8 C9 CA N2 HN21 59.966 20.000 1
MOD var_9 O2S P1 "O5'" "C5'" -55.003 20.000 1
MOD var_10 P1 "O5'" "C5'" "C4'" 179.956 20.000 1
MOD var_11 "O5'" "C5'" "C4'" "C3'" -175.311 20.000 3
MOD var_12 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
MOD var_13 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
MOD var_14 "C4'" "C3'" "O3'" H2 176.199 20.000 1
MOD var_15 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
MOD var_16 "C3'" "C2'" "O2'" "H2'" -67.381 20.000 1
MOD var_17 "C3'" "C2'" "C1'" N9 150.000 20.000 3
MOD var_18 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
MOD var_19 "C2'" "C1'" N9 C4 119.077 20.000 1
MOD CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
MOD CONST_2 "C1'" N9 C4 N3 -60.000 0.000 0
MOD CONST_3 N9 C4 C5 N7 -30.000 0.000 0
MOD CONST_4 C4 C5 C6 N1 0.000 0.000 0
MOD CONST_5 C4 C5 N7 C8 0.000 0.000 0
MOD CONST_6 C5 N7 C8 N9 0.000 0.000 0
MOD CONST_7 N9 C4 N3 C2 -150.000 0.000 0
MOD CONST_8 C4 N3 C2 N1 0.000 0.000 0
MOD CONST_9 N3 C2 N1 C6 30.000 0.000 0
MOD CONST_10 C2 N1 C6 N6 150.000 0.000 0
MOD CONST_11 N1 C6 N6 HN61 -179.973 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
MOD chir_01 CA N2 CB C9 negativ
MOD chir_02 "C4'" "C5'" "O4'" "C3'" negativ
MOD chir_03 "C3'" "C4'" "O3'" "C2'" negativ
MOD chir_04 "C2'" "C3'" "O2'" "C1'" negativ
MOD chir_05 "C1'" "O4'" "C2'" N9 positiv
MOD chir_06 C4 N9 C5 N3 negativ
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
MOD plan-1 N2 0.020
MOD plan-1 CA 0.020
MOD plan-1 HN21 0.020
MOD plan-1 HN22 0.020
MOD plan-2 N9 0.020
MOD plan-2 "C1'" 0.020
MOD plan-2 C8 0.020
MOD plan-2 C4 0.020
MOD plan-2 N7 0.020
MOD plan-2 H8 0.020
MOD plan-2 C5 0.020
MOD plan-2 C6 0.020
MOD plan-2 N1 0.020
MOD plan-2 C2 0.020
MOD plan-2 N3 0.020
MOD plan-2 N6 0.020
MOD plan-2 HN1 0.020
MOD plan-2 H3 0.020
MOD plan-2 HN62 0.020
MOD plan-2 HN61 0.020
MOD plan-3 N6 0.020
MOD plan-3 C6 0.020
MOD plan-3 HN61 0.020
MOD plan-3 HN62 0.020
# ------------------------------------------------------
|
