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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
AMD AMD 'ASPARTYL-2'-DEOXY-ADENOSINE-5'-MONOP' non-polymer 47 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AMD
#
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
AMD O O O -0.500 0.000 0.000 0.000
AMD C C C 0.000 -0.540 -0.531 -0.996
AMD CA C CH1 0.000 0.217 -1.544 -1.813
AMD HA H H 0.000 0.011 -1.383 -2.880
AMD CB C CH2 0.000 -0.225 -2.954 -1.415
AMD HB1 H H 0.000 -1.309 -3.035 -1.514
AMD HB2 H H 0.000 0.060 -3.144 -0.378
AMD CG C C 0.000 0.440 -3.963 -2.315
AMD OD2 O OC -0.500 0.214 -5.184 -2.161
AMD OD1 O OC -0.500 1.218 -3.580 -3.217
AMD N N NH2 0.000 1.658 -1.395 -1.565
AMD HN2 H H 0.000 2.289 -1.175 -2.328
AMD H H H 0.000 2.031 -1.512 -0.630
AMD O3P O O2 -0.500 -1.710 -0.219 -1.313
AMD P P P 0.000 -2.604 0.888 -0.462
AMD O1P O OP -0.500 -2.624 0.462 0.958
AMD O2P O OP -0.500 -1.939 2.209 -0.574
AMD "O5'" O O2 0.000 -4.114 0.999 -1.011
AMD "C5'" C CH2 0.000 -4.810 1.881 -0.128
AMD "H5'1" H H 0.000 -4.322 2.858 -0.131
AMD "H5'2" H H 0.000 -4.793 1.470 0.884
AMD "C4'" C CH1 0.000 -6.259 2.032 -0.596
AMD "H4'" H H 0.000 -6.295 2.348 -1.647
AMD "C3'" C CH1 0.000 -7.020 3.039 0.303
AMD "H3'" H H 0.000 -6.707 2.941 1.351
AMD "O3'" O OH1 0.000 -6.839 4.380 -0.158
AMD "HO'3" H H 0.000 -7.396 4.976 0.362
AMD "C2'" C CH2 0.000 -8.491 2.586 0.123
AMD "H2'1" H H 0.000 -9.016 3.188 -0.622
AMD "H2'2" H H 0.000 -9.044 2.609 1.064
AMD "C1'" C CH1 0.000 -8.380 1.131 -0.375
AMD "H1'" H H 0.000 -8.811 1.047 -1.383
AMD "O4'" O O2 0.000 -6.984 0.797 -0.411
AMD N9 N NR5 0.000 -9.084 0.233 0.544
AMD C8 C CR15 0.000 -8.531 -0.455 1.582
AMD H8 H H 0.000 -7.485 -0.423 1.861
AMD N7 N NRD5 0.000 -9.443 -1.157 2.189
AMD C5 C CR56 0.000 -10.638 -0.964 1.580
AMD C4 C CR56 0.000 -10.423 -0.065 0.521
AMD C6 C CR6 0.000 -11.942 -1.444 1.789
AMD N6 N NH2 0.000 -12.215 -2.326 2.820
AMD H62 H H 0.000 -13.159 -2.671 2.967
AMD H61 H H 0.000 -11.475 -2.638 3.441
AMD N1 N NRD6 0.000 -12.906 -1.032 0.973
AMD C2 C CR16 0.000 -12.656 -0.190 -0.013
AMD H2 H H 0.000 -13.472 0.120 -0.654
AMD N3 N NRD6 0.000 -11.450 0.285 -0.246
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
AMD O n/a C START
AMD C O O3P .
AMD CA C N .
AMD HA CA . .
AMD CB CA CG .
AMD HB1 CB . .
AMD HB2 CB . .
AMD CG CB OD1 .
AMD OD2 CG . .
AMD OD1 CG . .
AMD N CA H .
AMD HN2 N . .
AMD H N . .
AMD O3P C P .
AMD P O3P "O5'" .
AMD O1P P . .
AMD O2P P . .
AMD "O5'" P "C5'" .
AMD "C5'" "O5'" "C4'" .
AMD "H5'1" "C5'" . .
AMD "H5'2" "C5'" . .
AMD "C4'" "C5'" "C3'" .
AMD "H4'" "C4'" . .
AMD "C3'" "C4'" "C2'" .
AMD "H3'" "C3'" . .
AMD "O3'" "C3'" "HO'3" .
AMD "HO'3" "O3'" . .
AMD "C2'" "C3'" "C1'" .
AMD "H2'1" "C2'" . .
AMD "H2'2" "C2'" . .
AMD "C1'" "C2'" N9 .
AMD "H1'" "C1'" . .
AMD "O4'" "C1'" . .
AMD N9 "C1'" C8 .
AMD C8 N9 N7 .
AMD H8 C8 . .
AMD N7 C8 C5 .
AMD C5 N7 C6 .
AMD C4 C5 . .
AMD C6 C5 N1 .
AMD N6 C6 H61 .
AMD H62 N6 . .
AMD H61 N6 . .
AMD N1 C6 C2 .
AMD C2 N1 N3 .
AMD H2 C2 . .
AMD N3 C2 . END
AMD "C4'" "O4'" . ADD
AMD N9 C4 . ADD
AMD 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
AMD O1P P deloc 1.510 0.020
AMD O2P P deloc 1.510 0.020
AMD P O3P single 1.610 0.020
AMD "O5'" P single 1.610 0.020
AMD O3P C deloc 1.454 0.020
AMD "C5'" "O5'" single 1.426 0.020
AMD "C4'" "C5'" single 1.524 0.020
AMD "H5'1" "C5'" single 1.092 0.020
AMD "H5'2" "C5'" single 1.092 0.020
AMD "C4'" "O4'" single 1.426 0.020
AMD "C3'" "C4'" single 1.524 0.020
AMD "H4'" "C4'" single 1.099 0.020
AMD "O4'" "C1'" single 1.426 0.020
AMD N9 "C1'" single 1.485 0.020
AMD "C1'" "C2'" single 1.524 0.020
AMD "H1'" "C1'" single 1.099 0.020
AMD N9 C4 single 1.337 0.020
AMD C8 N9 single 1.337 0.020
AMD C4 N3 single 1.355 0.020
AMD C4 C5 double 1.490 0.020
AMD N3 C2 double 1.337 0.020
AMD C2 N1 single 1.337 0.020
AMD H2 C2 single 1.083 0.020
AMD N1 C6 double 1.350 0.020
AMD N6 C6 single 1.355 0.020
AMD C6 C5 single 1.490 0.020
AMD H61 N6 single 1.010 0.020
AMD H62 N6 single 1.010 0.020
AMD C5 N7 single 1.350 0.020
AMD N7 C8 double 1.350 0.020
AMD H8 C8 single 1.083 0.020
AMD "C2'" "C3'" single 1.524 0.020
AMD "H2'1" "C2'" single 1.092 0.020
AMD "H2'2" "C2'" single 1.092 0.020
AMD "O3'" "C3'" single 1.432 0.020
AMD "H3'" "C3'" single 1.099 0.020
AMD "HO'3" "O3'" single 0.967 0.020
AMD N CA single 1.450 0.020
AMD H N single 1.010 0.020
AMD HN2 N single 1.010 0.020
AMD CB CA single 1.524 0.020
AMD CA C single 1.500 0.020
AMD HA CA single 1.099 0.020
AMD CG CB single 1.510 0.020
AMD HB1 CB single 1.092 0.020
AMD HB2 CB single 1.092 0.020
AMD OD1 CG deloc 1.250 0.020
AMD OD2 CG deloc 1.250 0.020
AMD C O deloc 1.220 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
AMD O C CA 120.500 3.000
AMD O C O3P 119.000 3.000
AMD CA C O3P 120.000 3.000
AMD C CA HA 108.810 3.000
AMD C CA CB 109.470 3.000
AMD C CA N 109.470 3.000
AMD HA CA CB 108.340 3.000
AMD HA CA N 109.470 3.000
AMD CB CA N 109.470 3.000
AMD CA CB HB1 109.470 3.000
AMD CA CB HB2 109.470 3.000
AMD CA CB CG 109.470 3.000
AMD HB1 CB HB2 107.900 3.000
AMD HB1 CB CG 109.470 3.000
AMD HB2 CB CG 109.470 3.000
AMD CB CG OD2 118.500 3.000
AMD CB CG OD1 118.500 3.000
AMD OD2 CG OD1 123.000 3.000
AMD CA N HN2 120.000 3.000
AMD CA N H 120.000 3.000
AMD HN2 N H 120.000 3.000
AMD C O3P P 120.000 3.000
AMD O3P P O1P 108.200 3.000
AMD O3P P O2P 108.200 3.000
AMD O3P P "O5'" 102.600 3.000
AMD O1P P O2P 119.900 3.000
AMD O1P P "O5'" 108.200 3.000
AMD O2P P "O5'" 108.200 3.000
AMD P "O5'" "C5'" 120.500 3.000
AMD "O5'" "C5'" "H5'1" 109.470 3.000
AMD "O5'" "C5'" "H5'2" 109.470 3.000
AMD "O5'" "C5'" "C4'" 109.470 3.000
AMD "H5'1" "C5'" "H5'2" 107.900 3.000
AMD "H5'1" "C5'" "C4'" 109.470 3.000
AMD "H5'2" "C5'" "C4'" 109.470 3.000
AMD "C5'" "C4'" "H4'" 108.340 3.000
AMD "C5'" "C4'" "C3'" 111.000 3.000
AMD "C5'" "C4'" "O4'" 109.470 3.000
AMD "H4'" "C4'" "C3'" 108.340 3.000
AMD "H4'" "C4'" "O4'" 109.470 3.000
AMD "C3'" "C4'" "O4'" 109.470 3.000
AMD "C4'" "C3'" "H3'" 108.340 3.000
AMD "C4'" "C3'" "O3'" 109.470 3.000
AMD "C4'" "C3'" "C2'" 111.000 3.000
AMD "H3'" "C3'" "O3'" 109.470 3.000
AMD "H3'" "C3'" "C2'" 108.340 3.000
AMD "O3'" "C3'" "C2'" 109.470 3.000
AMD "C3'" "O3'" "HO'3" 109.470 3.000
AMD "C3'" "C2'" "H2'1" 109.470 3.000
AMD "C3'" "C2'" "H2'2" 109.470 3.000
AMD "C3'" "C2'" "C1'" 111.000 3.000
AMD "H2'1" "C2'" "H2'2" 107.900 3.000
AMD "H2'1" "C2'" "C1'" 109.470 3.000
AMD "H2'2" "C2'" "C1'" 109.470 3.000
AMD "C2'" "C1'" "H1'" 108.340 3.000
AMD "C2'" "C1'" "O4'" 109.470 3.000
AMD "C2'" "C1'" N9 109.470 3.000
AMD "H1'" "C1'" "O4'" 109.470 3.000
AMD "H1'" "C1'" N9 109.470 3.000
AMD "O4'" "C1'" N9 109.470 3.000
AMD "C1'" "O4'" "C4'" 111.800 3.000
AMD "C1'" N9 C8 126.000 3.000
AMD "C1'" N9 C4 126.000 3.000
AMD C8 N9 C4 108.000 3.000
AMD N9 C8 H8 126.000 3.000
AMD N9 C8 N7 108.000 3.000
AMD H8 C8 N7 126.000 3.000
AMD C8 N7 C5 108.000 3.000
AMD N7 C5 C4 108.000 3.000
AMD N7 C5 C6 132.000 3.000
AMD C4 C5 C6 120.000 3.000
AMD C5 C4 N9 108.000 3.000
AMD C5 C4 N3 120.000 3.000
AMD N9 C4 N3 132.000 3.000
AMD C5 C6 N6 120.000 3.000
AMD C5 C6 N1 120.000 3.000
AMD N6 C6 N1 120.000 3.000
AMD C6 N6 H62 120.000 3.000
AMD C6 N6 H61 120.000 3.000
AMD H62 N6 H61 120.000 3.000
AMD C6 N1 C2 120.000 3.000
AMD N1 C2 H2 120.000 3.000
AMD N1 C2 N3 120.000 3.000
AMD H2 C2 N3 120.000 3.000
AMD 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
AMD var_1 O C CA N -19.974 20.000 3
AMD var_2 C CA CB CG 175.003 20.000 3
AMD var_3 CA CB CG OD1 -0.019 20.000 3
AMD var_4 C CA N H 60.038 20.000 1
AMD var_5 O C O3P P 0.037 20.000 1
AMD var_6 C O3P P "O5'" -174.923 20.000 1
AMD var_7 O3P P "O5'" "C5'" 174.710 20.000 1
AMD var_8 P "O5'" "C5'" "C4'" 179.975 20.000 1
AMD var_9 "O5'" "C5'" "C4'" "C3'" -177.167 20.000 3
AMD var_10 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
AMD var_11 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
AMD var_12 "C4'" "C3'" "O3'" "HO'3" 174.170 20.000 1
AMD var_13 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
AMD var_14 "C3'" "C2'" "C1'" N9 120.000 20.000 3
AMD var_15 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
AMD var_16 "C2'" "C1'" N9 C8 -94.312 20.000 1
AMD CONST_1 "C1'" N9 C4 C5 180.000 0.000 0
AMD CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
AMD CONST_3 N9 C8 N7 C5 0.000 0.000 0
AMD CONST_4 C8 N7 C5 C6 180.000 0.000 0
AMD CONST_5 N7 C5 C4 N9 0.000 0.000 0
AMD CONST_6 C5 C4 N3 C2 0.000 0.000 0
AMD CONST_7 N7 C5 C6 N1 180.000 0.000 0
AMD CONST_8 C5 C6 N6 H61 0.044 0.000 0
AMD CONST_9 C5 C6 N1 C2 0.000 0.000 0
AMD CONST_10 C6 N1 C2 N3 0.000 0.000 0
AMD 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
AMD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
AMD chir_02 "C1'" "O4'" N9 "C2'" negativ
AMD chir_03 "C3'" "C4'" "C2'" "O3'" positiv
AMD chir_04 CA N CB C 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
AMD plan-1 N9 0.020
AMD plan-1 "C1'" 0.020
AMD plan-1 C4 0.020
AMD plan-1 C8 0.020
AMD plan-1 N7 0.020
AMD plan-1 N3 0.020
AMD plan-1 C5 0.020
AMD plan-1 C2 0.020
AMD plan-1 N1 0.020
AMD plan-1 C6 0.020
AMD plan-1 H2 0.020
AMD plan-1 N6 0.020
AMD plan-1 H8 0.020
AMD plan-1 H62 0.020
AMD plan-1 H61 0.020
AMD plan-2 N6 0.020
AMD plan-2 C6 0.020
AMD plan-2 H61 0.020
AMD plan-2 H62 0.020
AMD plan-3 N 0.020
AMD plan-3 CA 0.020
AMD plan-3 H 0.020
AMD plan-3 HN2 0.020
AMD plan-4 CG 0.020
AMD plan-4 CB 0.020
AMD plan-4 OD1 0.020
AMD plan-4 OD2 0.020
AMD plan-5 C 0.020
AMD plan-5 O3P 0.020
AMD plan-5 CA 0.020
AMD plan-5 O 0.020
# ------------------------------------------------------
|
