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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
MDV MDV '(7S,8S)-3-(2-deoxy-5-O-phosphono-bet' non-polymer 40 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MDV
#
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
MDV O8 O OP -0.666 0.000 0.000 0.000
MDV P P P 0.000 -1.131 0.946 0.339
MDV O1P O OP -0.666 -1.359 1.894 -0.818
MDV O2P O OP -0.666 -0.773 1.737 1.577
MDV "O5'" O O2 0.000 -2.473 0.100 0.612
MDV "C5'" C CH2 0.000 -3.128 -0.669 -0.398
MDV "H5'" H H 0.000 -2.443 -1.431 -0.775
MDV "H5'A" H H 0.000 -3.426 -0.012 -1.218
MDV "C4'" C CH1 0.000 -4.367 -1.342 0.195
MDV "H4'" H H 0.000 -4.107 -1.895 1.109
MDV "C3'" C CH1 0.000 -5.028 -2.283 -0.844
MDV "H3'" H H 0.000 -4.973 -1.852 -1.853
MDV "O3'" O OH1 0.000 -4.429 -3.580 -0.810
MDV "HO3'" H H 0.000 -4.915 -4.174 -1.398
MDV "C2'" C CH2 0.000 -6.493 -2.338 -0.347
MDV "H2'A" H H 0.000 -6.686 -3.225 0.260
MDV "H2'" H H 0.000 -7.207 -2.301 -1.172
MDV "O4'" O O2 0.000 -5.395 -0.365 0.466
MDV "C1'" C CH1 0.000 -6.644 -1.075 0.523
MDV "H1'" H H 0.000 -6.866 -1.360 1.561
MDV N9 N NR5 0.000 -7.721 -0.233 -0.005
MDV C4 C CR56 0.000 -9.056 -0.357 0.271
MDV N3 N NRD6 0.000 -9.780 -1.193 1.033
MDV C2 C CR16 0.000 -11.072 -1.097 1.128
MDV H2 H H 0.000 -11.598 -1.803 1.758
MDV C8 C CR15 0.000 -7.576 0.818 -0.860
MDV H8 H H 0.000 -6.634 1.168 -1.264
MDV N7 N NRD5 0.000 -8.743 1.338 -1.118
MDV C5 C CR56 0.000 -9.693 0.653 -0.447
MDV C6 C CR6 0.000 -11.159 0.764 -0.342
MDV N6 N N 0.000 -11.979 1.612 -0.907
MDV C23 C CH1 0.000 -13.362 1.332 -0.502
MDV H141 H H 0.000 -13.790 2.194 0.030
MDV O26 O OH1 0.000 -14.159 0.999 -1.640
MDV H15 H H 0.000 -14.176 1.747 -2.251
MDV C22 C CH1 0.000 -13.240 0.121 0.441
MDV H1 H H 0.000 -13.787 -0.742 0.036
MDV N1 N NR6 0.000 -11.793 -0.149 0.470
MDV O24 O OH1 0.000 -13.716 0.451 1.746
MDV H16 H H 0.000 -14.666 0.624 1.708
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
MDV O8 n/a P START
MDV P O8 "O5'" .
MDV O1P P . .
MDV O2P P . .
MDV "O5'" P "C5'" .
MDV "C5'" "O5'" "C4'" .
MDV "H5'" "C5'" . .
MDV "H5'A" "C5'" . .
MDV "C4'" "C5'" "O4'" .
MDV "H4'" "C4'" . .
MDV "C3'" "C4'" "C2'" .
MDV "H3'" "C3'" . .
MDV "O3'" "C3'" "HO3'" .
MDV "HO3'" "O3'" . .
MDV "C2'" "C3'" "H2'" .
MDV "H2'A" "C2'" . .
MDV "H2'" "C2'" . .
MDV "O4'" "C4'" "C1'" .
MDV "C1'" "O4'" N9 .
MDV "H1'" "C1'" . .
MDV N9 "C1'" C8 .
MDV C4 N9 N3 .
MDV N3 C4 C2 .
MDV C2 N3 H2 .
MDV H2 C2 . .
MDV C8 N9 N7 .
MDV H8 C8 . .
MDV N7 C8 C5 .
MDV C5 N7 C6 .
MDV C6 C5 N6 .
MDV N6 C6 C23 .
MDV C23 N6 C22 .
MDV H141 C23 . .
MDV O26 C23 H15 .
MDV H15 O26 . .
MDV C22 C23 O24 .
MDV H1 C22 . .
MDV N1 C22 . .
MDV O24 C22 H16 .
MDV H16 O24 . END
MDV N1 C2 . ADD
MDV N1 C6 . ADD
MDV C4 C5 . ADD
MDV "C1'" "C2'" . 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
MDV O1P P deloc 1.510 0.020
MDV O2P P deloc 1.510 0.020
MDV "O5'" P single 1.610 0.020
MDV N1 C2 single 1.337 0.020
MDV N1 C6 single 1.410 0.020
MDV N1 C22 single 1.465 0.020
MDV C2 N3 double 1.337 0.020
MDV H2 C2 single 1.083 0.020
MDV N3 C4 single 1.355 0.020
MDV C4 C5 double 1.490 0.020
MDV C4 N9 single 1.337 0.020
MDV C6 C5 single 1.490 0.020
MDV C5 N7 single 1.350 0.020
MDV N6 C6 double 1.355 0.020
MDV C23 N6 single 1.455 0.020
MDV N7 C8 double 1.350 0.020
MDV C8 N9 single 1.337 0.020
MDV H8 C8 single 1.083 0.020
MDV N9 "C1'" single 1.485 0.020
MDV "C1'" "C2'" single 1.524 0.020
MDV "C1'" "O4'" single 1.426 0.020
MDV "H1'" "C1'" single 1.099 0.020
MDV "C2'" "C3'" single 1.524 0.020
MDV "H2'" "C2'" single 1.092 0.020
MDV "H2'A" "C2'" single 1.092 0.020
MDV C22 C23 single 1.524 0.020
MDV H1 C22 single 1.099 0.020
MDV O26 C23 single 1.432 0.020
MDV "O3'" "C3'" single 1.432 0.020
MDV "C3'" "C4'" single 1.524 0.020
MDV "H3'" "C3'" single 1.099 0.020
MDV "HO3'" "O3'" single 0.967 0.020
MDV "O4'" "C4'" single 1.426 0.020
MDV "C4'" "C5'" single 1.524 0.020
MDV "H4'" "C4'" single 1.099 0.020
MDV "C5'" "O5'" single 1.426 0.020
MDV "H5'" "C5'" single 1.092 0.020
MDV "H5'A" "C5'" single 1.092 0.020
MDV P O8 deloc 1.510 0.020
MDV O24 C22 single 1.432 0.020
MDV H141 C23 single 1.099 0.020
MDV H15 O26 single 0.967 0.020
MDV H16 O24 single 0.967 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
MDV O8 P O1P 119.900 3.000
MDV O8 P O2P 119.900 3.000
MDV O8 P "O5'" 108.200 3.000
MDV O1P P O2P 119.900 3.000
MDV O1P P "O5'" 108.200 3.000
MDV O2P P "O5'" 108.200 3.000
MDV P "O5'" "C5'" 120.500 3.000
MDV "O5'" "C5'" "H5'" 109.470 3.000
MDV "O5'" "C5'" "H5'A" 109.470 3.000
MDV "O5'" "C5'" "C4'" 109.470 3.000
MDV "H5'" "C5'" "H5'A" 107.900 3.000
MDV "H5'" "C5'" "C4'" 109.470 3.000
MDV "H5'A" "C5'" "C4'" 109.470 3.000
MDV "C5'" "C4'" "H4'" 108.340 3.000
MDV "C5'" "C4'" "C3'" 111.000 3.000
MDV "C5'" "C4'" "O4'" 109.470 3.000
MDV "H4'" "C4'" "C3'" 108.340 3.000
MDV "H4'" "C4'" "O4'" 109.470 3.000
MDV "C3'" "C4'" "O4'" 109.470 3.000
MDV "C4'" "C3'" "H3'" 108.340 3.000
MDV "C4'" "C3'" "O3'" 109.470 3.000
MDV "C4'" "C3'" "C2'" 111.000 3.000
MDV "H3'" "C3'" "O3'" 109.470 3.000
MDV "H3'" "C3'" "C2'" 108.340 3.000
MDV "O3'" "C3'" "C2'" 109.470 3.000
MDV "C3'" "O3'" "HO3'" 109.470 3.000
MDV "C3'" "C2'" "H2'A" 109.470 3.000
MDV "C3'" "C2'" "H2'" 109.470 3.000
MDV "C3'" "C2'" "C1'" 111.000 3.000
MDV "H2'A" "C2'" "H2'" 107.900 3.000
MDV "H2'A" "C2'" "C1'" 109.470 3.000
MDV "H2'" "C2'" "C1'" 109.470 3.000
MDV "C4'" "O4'" "C1'" 111.800 3.000
MDV "O4'" "C1'" "H1'" 109.470 3.000
MDV "O4'" "C1'" N9 109.470 3.000
MDV "O4'" "C1'" "C2'" 109.470 3.000
MDV "H1'" "C1'" N9 109.470 3.000
MDV "H1'" "C1'" "C2'" 108.340 3.000
MDV N9 "C1'" "C2'" 109.470 3.000
MDV "C1'" N9 C4 126.000 3.000
MDV "C1'" N9 C8 126.000 3.000
MDV C4 N9 C8 108.000 3.000
MDV N9 C4 N3 132.000 3.000
MDV N9 C4 C5 108.000 3.000
MDV N3 C4 C5 120.000 3.000
MDV C4 N3 C2 120.000 3.000
MDV N3 C2 H2 120.000 3.000
MDV N3 C2 N1 120.000 3.000
MDV H2 C2 N1 120.000 3.000
MDV N9 C8 H8 126.000 3.000
MDV N9 C8 N7 108.000 3.000
MDV H8 C8 N7 126.000 3.000
MDV C8 N7 C5 108.000 3.000
MDV N7 C5 C6 132.000 3.000
MDV N7 C5 C4 108.000 3.000
MDV C6 C5 C4 120.000 3.000
MDV C5 C6 N6 120.000 3.000
MDV C5 C6 N1 120.000 3.000
MDV N6 C6 N1 120.000 3.000
MDV C6 N6 C23 120.000 3.000
MDV N6 C23 H141 109.470 3.000
MDV N6 C23 O26 109.500 3.000
MDV N6 C23 C22 105.000 3.000
MDV H141 C23 O26 109.470 3.000
MDV H141 C23 C22 108.340 3.000
MDV O26 C23 C22 109.470 3.000
MDV C23 O26 H15 109.470 3.000
MDV C23 C22 H1 108.340 3.000
MDV C23 C22 N1 109.470 3.000
MDV C23 C22 O24 109.470 3.000
MDV H1 C22 N1 109.470 3.000
MDV H1 C22 O24 109.470 3.000
MDV N1 C22 O24 109.500 3.000
MDV C22 N1 C2 120.000 3.000
MDV C22 N1 C6 120.000 3.000
MDV C2 N1 C6 120.000 3.000
MDV C22 O24 H16 109.470 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
MDV var_1 O8 P "O5'" "C5'" -65.034 20.000 1
MDV var_2 P "O5'" "C5'" "C4'" -179.967 20.000 1
MDV var_3 "O5'" "C5'" "C4'" "O4'" 70.968 20.000 3
MDV var_4 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
MDV var_5 "C4'" "C3'" "O3'" "HO3'" 174.196 20.000 1
MDV var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
MDV var_7 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
MDV var_8 "C4'" "O4'" "C1'" N9 -150.000 20.000 1
MDV var_9 "O4'" "C1'" "C2'" "C3'" 0.000 20.000 3
MDV var_10 "O4'" "C1'" N9 C8 22.760 20.000 1
MDV CONST_1 "C1'" N9 C4 N3 0.000 0.000 0
MDV CONST_2 N9 C4 C5 N7 0.000 0.000 0
MDV CONST_3 N9 C4 N3 C2 180.000 0.000 0
MDV CONST_4 C4 N3 C2 N1 0.000 0.000 0
MDV CONST_5 "C1'" N9 C8 N7 180.000 0.000 0
MDV CONST_6 N9 C8 N7 C5 0.000 0.000 0
MDV CONST_7 C8 N7 C5 C6 180.000 0.000 0
MDV CONST_8 N7 C5 C6 N6 0.000 0.000 0
MDV var_11 C5 C6 N6 C23 180.000 20.000 1
MDV var_12 C6 N6 C23 C22 0.000 20.000 3
MDV var_13 N6 C23 O26 H15 -61.452 20.000 1
MDV var_14 N6 C23 C22 O24 120.000 20.000 3
MDV var_15 C23 C22 N1 C2 180.000 20.000 1
MDV CONST_9 C22 N1 C2 N3 180.000 0.000 0
MDV CONST_10 C22 N1 C6 C5 180.000 0.000 0
MDV var_16 C23 C22 O24 H16 65.877 20.000 1
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
MDV chir_01 "C1'" N9 "C2'" "O4'" negativ
MDV chir_02 C22 N1 C23 O24 positiv
MDV chir_03 C23 N6 C22 O26 positiv
MDV chir_04 "C3'" "C2'" "O3'" "C4'" positiv
MDV chir_05 "C4'" "C3'" "O4'" "C5'" 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
MDV plan-1 N1 0.020
MDV plan-1 C2 0.020
MDV plan-1 C6 0.020
MDV plan-1 C22 0.020
MDV plan-1 N3 0.020
MDV plan-1 H2 0.020
MDV plan-1 C4 0.020
MDV plan-1 C5 0.020
MDV plan-1 N9 0.020
MDV plan-1 N7 0.020
MDV plan-1 C8 0.020
MDV plan-1 N6 0.020
MDV plan-1 H8 0.020
MDV plan-1 "C1'" 0.020
MDV plan-2 N6 0.020
MDV plan-2 C6 0.020
MDV plan-2 C23 0.020
# ------------------------------------------------------
|
