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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
MBZ MBZ '1-[2-DEOXYRIBOFURANOSYL]-4-METHYL-BE' DNA 37 22 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MBZ
#
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
MBZ OP3 O OP -0.666 0.000 0.000 0.000
MBZ P P P 0.000 -0.815 -0.429 1.200
MBZ OP1 O OP -0.666 -1.002 0.749 2.131
MBZ OP2 O OP -0.666 -0.090 -1.539 1.930
MBZ "O5'" O O2 0.000 -2.254 -0.959 0.710
MBZ "C5'" C CH2 0.000 -2.886 0.127 0.033
MBZ "H5'" H H 0.000 -2.273 0.430 -0.819
MBZ "H5''" H H 0.000 -2.995 0.969 0.719
MBZ "C4'" C CH1 0.000 -4.266 -0.312 -0.461
MBZ "H4'" H H 0.000 -4.179 -1.192 -1.114
MBZ "O4'" O O2 0.000 -5.144 -0.591 0.652
MBZ "C1'" C CH1 0.000 -6.489 -0.492 0.156
MBZ "H1'" H H 0.000 -6.844 -1.482 -0.161
MBZ N1 N NR5 0.000 -7.366 0.042 1.202
MBZ C8 C CR15 0.000 -7.001 0.873 2.213
MBZ H8 H H 0.000 -5.999 1.251 2.375
MBZ N7 N NRD5 0.000 -8.031 1.148 2.959
MBZ C9 C CR56 0.000 -8.716 -0.208 1.342
MBZ C7 C CR56 0.000 -9.129 0.516 2.474
MBZ C10 C CR16 0.000 -9.639 -0.964 0.633
MBZ H10 H H 0.000 -9.328 -1.520 -0.243
MBZ C11 C CR16 0.000 -10.953 -1.004 1.048
MBZ H11 H H 0.000 -11.674 -1.594 0.496
MBZ C12 C CR16 0.000 -11.359 -0.293 2.168
MBZ H12 H H 0.000 -12.395 -0.332 2.482
MBZ C6 C CR6 0.000 -10.465 0.456 2.879
MBZ C5M C CH3 0.000 -10.919 1.222 4.094
MBZ H73 H H 0.000 -10.323 2.090 4.208
MBZ H72 H H 0.000 -11.933 1.503 3.975
MBZ H71 H H 0.000 -10.821 0.611 4.954
MBZ "C3'" C CH1 0.000 -4.975 0.848 -1.203
MBZ "H3'" H H 0.000 -4.765 1.811 -0.717
MBZ "C2'" C CH2 0.000 -6.467 0.467 -1.048
MBZ "H2''" H H 0.000 -6.852 -0.047 -1.932
MBZ "H2'" H H 0.000 -7.091 1.337 -0.834
MBZ "O3'" O OH1 0.000 -4.598 0.881 -2.582
MBZ "HO'3" H H 0.000 -5.141 1.561 -3.003
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
MBZ OP3 n/a P START
MBZ P OP3 "O5'" .
MBZ OP1 P . .
MBZ OP2 P . .
MBZ "O5'" P "C5'" .
MBZ "C5'" "O5'" "C4'" .
MBZ "H5'" "C5'" . .
MBZ "H5''" "C5'" . .
MBZ "C4'" "C5'" "C3'" .
MBZ "H4'" "C4'" . .
MBZ "O4'" "C4'" "C1'" .
MBZ "C1'" "O4'" N1 .
MBZ "H1'" "C1'" . .
MBZ N1 "C1'" C9 .
MBZ C8 N1 N7 .
MBZ H8 C8 . .
MBZ N7 C8 . .
MBZ C9 N1 C10 .
MBZ C7 C9 . .
MBZ C10 C9 C11 .
MBZ H10 C10 . .
MBZ C11 C10 C12 .
MBZ H11 C11 . .
MBZ C12 C11 C6 .
MBZ H12 C12 . .
MBZ C6 C12 C5M .
MBZ C5M C6 H71 .
MBZ H73 C5M . .
MBZ H72 C5M . .
MBZ H71 C5M . .
MBZ "C3'" "C4'" "O3'" .
MBZ "H3'" "C3'" . .
MBZ "C2'" "C3'" "H2'" .
MBZ "H2''" "C2'" . .
MBZ "H2'" "C2'" . .
MBZ "O3'" "C3'" . END
MBZ "HO'3" "O3'" . .
MBZ "C1'" "C2'" . ADD
MBZ C6 C7 . ADD
MBZ C7 N7 . 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
MBZ OP1 P deloc 1.510 0.020
MBZ OP2 P deloc 1.510 0.020
MBZ P OP3 deloc 1.510 0.020
MBZ "O5'" P single 1.610 0.020
MBZ "C5'" "O5'" single 1.426 0.020
MBZ "O3'" "C3'" single 1.432 0.020
MBZ "HO'3" "O3'" single 0.967 0.020
MBZ "C1'" "C2'" single 1.524 0.020
MBZ "C1'" "O4'" single 1.426 0.020
MBZ N1 "C1'" single 1.485 0.020
MBZ "H1'" "C1'" single 1.099 0.020
MBZ "C2'" "C3'" single 1.524 0.020
MBZ "H2'" "C2'" single 1.092 0.020
MBZ "H2''" "C2'" single 1.092 0.020
MBZ "C3'" "C4'" single 1.524 0.020
MBZ "H3'" "C3'" single 1.099 0.020
MBZ "C4'" "C5'" single 1.524 0.020
MBZ "O4'" "C4'" single 1.426 0.020
MBZ "H4'" "C4'" single 1.099 0.020
MBZ "H5'" "C5'" single 1.092 0.020
MBZ "H5''" "C5'" single 1.092 0.020
MBZ C5M C6 single 1.506 0.020
MBZ H71 C5M single 1.059 0.020
MBZ H72 C5M single 1.059 0.020
MBZ H73 C5M single 1.059 0.020
MBZ C6 C7 single 1.490 0.020
MBZ C6 C12 double 1.390 0.020
MBZ C7 N7 single 1.350 0.020
MBZ C7 C9 double 1.490 0.020
MBZ N7 C8 double 1.350 0.020
MBZ C8 N1 single 1.337 0.020
MBZ H8 C8 single 1.083 0.020
MBZ C9 N1 single 1.337 0.020
MBZ C10 C9 single 1.390 0.020
MBZ C11 C10 double 1.390 0.020
MBZ H10 C10 single 1.083 0.020
MBZ C12 C11 single 1.390 0.020
MBZ H11 C11 single 1.083 0.020
MBZ H12 C12 single 1.083 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
MBZ OP3 P OP1 119.900 3.000
MBZ OP3 P OP2 119.900 3.000
MBZ OP3 P "O5'" 108.200 3.000
MBZ OP1 P OP2 119.900 3.000
MBZ OP1 P "O5'" 108.200 3.000
MBZ OP2 P "O5'" 108.200 3.000
MBZ P "O5'" "C5'" 120.500 3.000
MBZ "O5'" "C5'" "H5'" 109.470 3.000
MBZ "O5'" "C5'" "H5''" 109.470 3.000
MBZ "O5'" "C5'" "C4'" 109.470 3.000
MBZ "H5'" "C5'" "H5''" 107.900 3.000
MBZ "H5'" "C5'" "C4'" 109.470 3.000
MBZ "H5''" "C5'" "C4'" 109.470 3.000
MBZ "C5'" "C4'" "H4'" 108.340 3.000
MBZ "C5'" "C4'" "O4'" 109.470 3.000
MBZ "C5'" "C4'" "C3'" 111.000 3.000
MBZ "H4'" "C4'" "O4'" 109.470 3.000
MBZ "H4'" "C4'" "C3'" 108.340 3.000
MBZ "O4'" "C4'" "C3'" 109.470 3.000
MBZ "C4'" "O4'" "C1'" 111.800 3.000
MBZ "O4'" "C1'" "H1'" 109.470 3.000
MBZ "O4'" "C1'" N1 109.470 3.000
MBZ "O4'" "C1'" "C2'" 109.470 3.000
MBZ "H1'" "C1'" N1 109.470 3.000
MBZ "H1'" "C1'" "C2'" 108.340 3.000
MBZ N1 "C1'" "C2'" 109.470 3.000
MBZ "C1'" N1 C8 126.000 3.000
MBZ "C1'" N1 C9 126.000 3.000
MBZ C8 N1 C9 108.000 3.000
MBZ N1 C8 H8 126.000 3.000
MBZ N1 C8 N7 108.000 3.000
MBZ H8 C8 N7 126.000 3.000
MBZ C8 N7 C7 108.000 3.000
MBZ N1 C9 C7 108.000 3.000
MBZ N1 C9 C10 132.000 3.000
MBZ C7 C9 C10 120.000 3.000
MBZ C9 C7 C6 120.000 3.000
MBZ C9 C7 N7 108.000 3.000
MBZ C6 C7 N7 132.000 3.000
MBZ C9 C10 H10 120.000 3.000
MBZ C9 C10 C11 120.000 3.000
MBZ H10 C10 C11 120.000 3.000
MBZ C10 C11 H11 120.000 3.000
MBZ C10 C11 C12 120.000 3.000
MBZ H11 C11 C12 120.000 3.000
MBZ C11 C12 H12 120.000 3.000
MBZ C11 C12 C6 120.000 3.000
MBZ H12 C12 C6 120.000 3.000
MBZ C12 C6 C5M 120.000 3.000
MBZ C12 C6 C7 120.000 3.000
MBZ C5M C6 C7 120.000 3.000
MBZ C6 C5M H73 109.470 3.000
MBZ C6 C5M H72 109.470 3.000
MBZ C6 C5M H71 109.470 3.000
MBZ H73 C5M H72 109.470 3.000
MBZ H73 C5M H71 109.470 3.000
MBZ H72 C5M H71 109.470 3.000
MBZ "C4'" "C3'" "H3'" 108.340 3.000
MBZ "C4'" "C3'" "C2'" 111.000 3.000
MBZ "C4'" "C3'" "O3'" 109.470 3.000
MBZ "H3'" "C3'" "C2'" 108.340 3.000
MBZ "H3'" "C3'" "O3'" 109.470 3.000
MBZ "C2'" "C3'" "O3'" 109.470 3.000
MBZ "C3'" "C2'" "H2''" 109.470 3.000
MBZ "C3'" "C2'" "H2'" 109.470 3.000
MBZ "C3'" "C2'" "C1'" 111.000 3.000
MBZ "H2''" "C2'" "H2'" 107.900 3.000
MBZ "H2''" "C2'" "C1'" 109.470 3.000
MBZ "H2'" "C2'" "C1'" 109.470 3.000
MBZ "C3'" "O3'" "HO'3" 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
MBZ var_1 OP3 P "O5'" "C5'" -60.039 20.000 1
MBZ var_2 P "O5'" "C5'" "C4'" -179.998 20.000 1
MBZ var_3 "O5'" "C5'" "C4'" "C3'" -179.951 20.000 3
MBZ var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
MBZ var_5 "C4'" "O4'" "C1'" N1 -150.000 20.000 1
MBZ var_6 "O4'" "C1'" "C2'" "C3'" 0.000 20.000 3
MBZ var_7 "O4'" "C1'" N1 C9 -151.667 20.000 1
MBZ CONST_1 "C1'" N1 C8 N7 180.000 0.000 0
MBZ CONST_2 N1 C8 N7 C7 0.000 0.000 0
MBZ CONST_3 "C1'" N1 C9 C10 0.000 0.000 0
MBZ CONST_4 N1 C9 C7 C6 180.000 0.000 0
MBZ CONST_5 C9 C7 N7 C8 0.000 0.000 0
MBZ CONST_6 N1 C9 C10 C11 180.000 0.000 0
MBZ CONST_7 C9 C10 C11 C12 0.000 0.000 0
MBZ CONST_8 C10 C11 C12 C6 0.000 0.000 0
MBZ CONST_9 C11 C12 C6 C5M 180.000 0.000 0
MBZ CONST_10 C12 C6 C7 C9 0.000 0.000 0
MBZ var_8 C12 C6 C5M H71 90.014 20.000 1
MBZ var_9 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
MBZ var_10 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
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
MBZ chir_01 "C1'" "C2'" "O4'" N1 negativ
MBZ chir_02 "C3'" "O3'" "C2'" "C4'" negativ
MBZ chir_03 "C4'" "C3'" "C5'" "O4'" 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
MBZ plan-1 C6 0.020
MBZ plan-1 C5M 0.020
MBZ plan-1 C7 0.020
MBZ plan-1 C12 0.020
MBZ plan-1 C10 0.020
MBZ plan-1 C11 0.020
MBZ plan-1 N7 0.020
MBZ plan-1 C9 0.020
MBZ plan-1 C8 0.020
MBZ plan-1 N1 0.020
MBZ plan-1 H8 0.020
MBZ plan-1 "C1'" 0.020
MBZ plan-1 H10 0.020
MBZ plan-1 H11 0.020
MBZ plan-1 H12 0.020
# ------------------------------------------------------
|
