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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
MAD MAD '6-HYDRO-1-METHYLADENOSINE-5'-MONOPHO' non-polymer 38 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MAD
#
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
MAD OXT O OP -0.666 0.000 0.000 0.000
MAD P P P 0.000 -1.179 0.114 -0.942
MAD OP1 O OP -0.666 -0.823 1.040 -2.084
MAD OP2 O OP -0.666 -1.521 -1.254 -1.490
MAD "O5'" O O2 0.000 -2.447 0.707 -0.145
MAD "C5'" C CH2 0.000 -2.732 -0.207 0.915
MAD "H5'" H H 0.000 -1.863 -0.285 1.571
MAD "H5''" H H 0.000 -2.960 -1.189 0.496
MAD "C4'" C CH1 0.000 -3.933 0.299 1.715
MAD "H4'" H H 0.000 -3.713 1.282 2.154
MAD "C3'" C CH1 0.000 -4.310 -0.711 2.822
MAD "H3'" H H 0.000 -3.965 -1.720 2.556
MAD "O3'" O OH1 0.000 -3.759 -0.307 4.077
MAD HA H H 0.000 -4.004 -0.950 4.757
MAD "C2'" C CH1 0.000 -5.855 -0.661 2.866
MAD "H2'" H H 0.000 -6.279 -1.645 2.622
MAD "O2'" O OH1 0.000 -6.305 -0.228 4.151
MAD HB H H 0.000 -6.010 -0.856 4.824
MAD "C1'" C CH1 0.000 -6.226 0.371 1.778
MAD "H1'" H H 0.000 -6.360 1.366 2.225
MAD "O4'" O O2 0.000 -5.103 0.376 0.872
MAD N9 N NR5 0.000 -7.444 -0.041 1.079
MAD C4 C CR56 0.000 -8.714 0.304 1.406
MAD C5 C CR56 0.000 -9.540 -0.311 0.447
MAD N7 N NRD5 0.000 -8.758 -0.997 -0.387
MAD C8 C CR15 0.000 -7.510 -0.846 -0.024
MAD H8 H H 0.000 -6.658 -1.291 -0.523
MAD N3 N NRD6 0.000 -9.242 1.066 2.379
MAD C2 C CR16 0.000 -10.543 1.106 2.526
MAD H2 H H 0.000 -10.954 1.771 3.276
MAD N1 N NR6 0.000 -11.406 0.355 1.786
MAD CM1 C CH3 0.000 -12.741 0.032 2.296
MAD HM13 H H 0.000 -13.474 0.419 1.637
MAD HM12 H H 0.000 -12.848 -1.019 2.365
MAD HM11 H H 0.000 -12.866 0.463 3.255
MAD C6 C CR6 0.000 -10.995 -0.107 0.533
MAD N6 N N 0.000 -11.820 -0.332 -0.462
MAD H6 H H 0.000 -12.746 -0.179 -0.339
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
MAD OXT n/a P START
MAD P OXT "O5'" .
MAD OP1 P . .
MAD OP2 P . .
MAD "O5'" P "C5'" .
MAD "C5'" "O5'" "C4'" .
MAD "H5'" "C5'" . .
MAD "H5''" "C5'" . .
MAD "C4'" "C5'" "C3'" .
MAD "H4'" "C4'" . .
MAD "C3'" "C4'" "C2'" .
MAD "H3'" "C3'" . .
MAD "O3'" "C3'" HA .
MAD HA "O3'" . .
MAD "C2'" "C3'" "C1'" .
MAD "H2'" "C2'" . .
MAD "O2'" "C2'" HB .
MAD HB "O2'" . .
MAD "C1'" "C2'" N9 .
MAD "H1'" "C1'" . .
MAD "O4'" "C1'" . .
MAD N9 "C1'" C4 .
MAD C4 N9 N3 .
MAD C5 C4 N7 .
MAD N7 C5 C8 .
MAD C8 N7 H8 .
MAD H8 C8 . .
MAD N3 C4 C2 .
MAD C2 N3 N1 .
MAD H2 C2 . .
MAD N1 C2 C6 .
MAD CM1 N1 HM11 .
MAD HM13 CM1 . .
MAD HM12 CM1 . .
MAD HM11 CM1 . .
MAD C6 N1 N6 .
MAD N6 C6 H6 .
MAD H6 N6 . END
MAD "C4'" "O4'" . ADD
MAD N9 C8 . ADD
MAD 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
MAD OP1 P deloc 1.510 0.020
MAD OP2 P deloc 1.510 0.020
MAD "O5'" P single 1.610 0.020
MAD P OXT deloc 1.510 0.020
MAD "C5'" "O5'" single 1.426 0.020
MAD "C4'" "C5'" single 1.524 0.020
MAD "H5'" "C5'" single 1.092 0.020
MAD "H5''" "C5'" single 1.092 0.020
MAD "C4'" "O4'" single 1.426 0.020
MAD "C3'" "C4'" single 1.524 0.020
MAD "H4'" "C4'" single 1.099 0.020
MAD "O4'" "C1'" single 1.426 0.020
MAD "O3'" "C3'" single 1.432 0.020
MAD "C2'" "C3'" single 1.524 0.020
MAD "H3'" "C3'" single 1.099 0.020
MAD HA "O3'" single 0.967 0.020
MAD "O2'" "C2'" single 1.432 0.020
MAD "C1'" "C2'" single 1.524 0.020
MAD "H2'" "C2'" single 1.099 0.020
MAD HB "O2'" single 0.967 0.020
MAD N9 "C1'" single 1.485 0.020
MAD "H1'" "C1'" single 1.099 0.020
MAD N9 C8 single 1.337 0.020
MAD C4 N9 single 1.337 0.020
MAD C8 N7 double 1.350 0.020
MAD H8 C8 single 1.083 0.020
MAD N7 C5 single 1.350 0.020
MAD C5 C6 single 1.490 0.020
MAD C5 C4 double 1.490 0.020
MAD N6 C6 double 1.355 0.020
MAD C6 N1 single 1.410 0.020
MAD H6 N6 single 0.954 0.020
MAD CM1 N1 single 1.465 0.020
MAD N1 C2 single 1.337 0.020
MAD HM11 CM1 single 1.059 0.020
MAD HM12 CM1 single 1.059 0.020
MAD HM13 CM1 single 1.059 0.020
MAD C2 N3 double 1.337 0.020
MAD H2 C2 single 1.083 0.020
MAD N3 C4 single 1.355 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
MAD OXT P OP1 119.900 3.000
MAD OXT P OP2 119.900 3.000
MAD OXT P "O5'" 108.200 3.000
MAD OP1 P OP2 119.900 3.000
MAD OP1 P "O5'" 108.200 3.000
MAD OP2 P "O5'" 108.200 3.000
MAD P "O5'" "C5'" 120.500 3.000
MAD "O5'" "C5'" "H5'" 109.470 3.000
MAD "O5'" "C5'" "H5''" 109.470 3.000
MAD "O5'" "C5'" "C4'" 109.470 3.000
MAD "H5'" "C5'" "H5''" 107.900 3.000
MAD "H5'" "C5'" "C4'" 109.470 3.000
MAD "H5''" "C5'" "C4'" 109.470 3.000
MAD "C5'" "C4'" "H4'" 108.340 3.000
MAD "C5'" "C4'" "C3'" 111.000 3.000
MAD "C5'" "C4'" "O4'" 109.470 3.000
MAD "H4'" "C4'" "C3'" 108.340 3.000
MAD "H4'" "C4'" "O4'" 109.470 3.000
MAD "C3'" "C4'" "O4'" 109.470 3.000
MAD "C4'" "C3'" "H3'" 108.340 3.000
MAD "C4'" "C3'" "O3'" 109.470 3.000
MAD "C4'" "C3'" "C2'" 111.000 3.000
MAD "H3'" "C3'" "O3'" 109.470 3.000
MAD "H3'" "C3'" "C2'" 108.340 3.000
MAD "O3'" "C3'" "C2'" 109.470 3.000
MAD "C3'" "O3'" HA 109.470 3.000
MAD "C3'" "C2'" "H2'" 108.340 3.000
MAD "C3'" "C2'" "O2'" 109.470 3.000
MAD "C3'" "C2'" "C1'" 111.000 3.000
MAD "H2'" "C2'" "O2'" 109.470 3.000
MAD "H2'" "C2'" "C1'" 108.340 3.000
MAD "O2'" "C2'" "C1'" 109.470 3.000
MAD "C2'" "O2'" HB 109.470 3.000
MAD "C2'" "C1'" "H1'" 108.340 3.000
MAD "C2'" "C1'" "O4'" 109.470 3.000
MAD "C2'" "C1'" N9 109.470 3.000
MAD "H1'" "C1'" "O4'" 109.470 3.000
MAD "H1'" "C1'" N9 109.470 3.000
MAD "O4'" "C1'" N9 109.470 3.000
MAD "C1'" "O4'" "C4'" 111.800 3.000
MAD "C1'" N9 C4 126.000 3.000
MAD "C1'" N9 C8 126.000 3.000
MAD C4 N9 C8 108.000 3.000
MAD N9 C4 C5 108.000 3.000
MAD N9 C4 N3 132.000 3.000
MAD C5 C4 N3 120.000 3.000
MAD C4 C5 N7 108.000 3.000
MAD C4 C5 C6 120.000 3.000
MAD N7 C5 C6 132.000 3.000
MAD C5 N7 C8 108.000 3.000
MAD N7 C8 H8 126.000 3.000
MAD N7 C8 N9 108.000 3.000
MAD H8 C8 N9 126.000 3.000
MAD C4 N3 C2 120.000 3.000
MAD N3 C2 H2 120.000 3.000
MAD N3 C2 N1 120.000 3.000
MAD H2 C2 N1 120.000 3.000
MAD C2 N1 CM1 120.000 3.000
MAD C2 N1 C6 120.000 3.000
MAD CM1 N1 C6 120.000 3.000
MAD N1 CM1 HM13 109.470 3.000
MAD N1 CM1 HM12 109.470 3.000
MAD N1 CM1 HM11 109.470 3.000
MAD HM13 CM1 HM12 109.470 3.000
MAD HM13 CM1 HM11 109.470 3.000
MAD HM12 CM1 HM11 109.470 3.000
MAD N1 C6 N6 120.000 3.000
MAD N1 C6 C5 120.000 3.000
MAD N6 C6 C5 120.000 3.000
MAD C6 N6 H6 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
MAD var_1 OXT P "O5'" "C5'" -60.061 20.000 1
MAD var_2 P "O5'" "C5'" "C4'" -179.981 20.000 1
MAD var_3 "O5'" "C5'" "C4'" "C3'" 176.932 20.000 3
MAD var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
MAD var_5 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
MAD var_6 "C4'" "C3'" "O3'" HA -179.929 20.000 1
MAD var_7 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
MAD var_8 "C3'" "C2'" "O2'" HB -61.404 20.000 1
MAD var_9 "C3'" "C2'" "C1'" N9 150.000 20.000 3
MAD var_10 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
MAD var_11 "C2'" "C1'" N9 C4 91.444 20.000 1
MAD CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
MAD CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
MAD CONST_3 N9 C4 C5 N7 0.000 0.000 0
MAD CONST_4 C4 C5 C6 N1 -30.000 0.000 0
MAD CONST_5 C4 C5 N7 C8 0.000 0.000 0
MAD CONST_6 C5 N7 C8 N9 0.000 0.000 0
MAD CONST_7 N9 C4 N3 C2 180.000 0.000 0
MAD CONST_8 C4 N3 C2 N1 0.000 0.000 0
MAD CONST_9 N3 C2 N1 C6 -30.000 0.000 0
MAD var_12 C2 N1 CM1 HM11 -0.019 20.000 1
MAD CONST_10 C2 N1 C6 N6 -150.000 0.000 0
MAD CONST_11 N1 C6 N6 H6 -0.114 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
MAD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
MAD chir_02 "C3'" "C4'" "O3'" "C2'" negativ
MAD chir_03 "C2'" "C3'" "O2'" "C1'" negativ
MAD chir_04 "C1'" "O4'" "C2'" N9 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
MAD plan-1 N9 0.020
MAD plan-1 "C1'" 0.020
MAD plan-1 C8 0.020
MAD plan-1 C4 0.020
MAD plan-1 N7 0.020
MAD plan-1 H8 0.020
MAD plan-1 C5 0.020
MAD plan-1 C6 0.020
MAD plan-1 N1 0.020
MAD plan-1 C2 0.020
MAD plan-1 N3 0.020
MAD plan-1 N6 0.020
MAD plan-1 H6 0.020
MAD plan-1 CM1 0.020
MAD plan-1 H2 0.020
# ------------------------------------------------------
|
