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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
MMT MMT '5'-O-(DIMETHYLAMINO)-THYMIDINE ' non-polymer 39 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_MMT
#
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
MMT O4 O O 0.000 0.000 0.000 0.000
MMT C4 C CR6 0.000 -1.196 0.224 -0.051
MMT N3 N NR16 0.000 -2.084 -0.758 0.200
MMT H3 H H 0.000 -1.747 -1.713 0.434
MMT C2 C CR6 0.000 -3.406 -0.508 0.149
MMT O2 O O 0.000 -4.195 -1.404 0.379
MMT C5 C CR6 0.000 -1.666 1.519 -0.375
MMT C5M C CH3 0.000 -0.694 2.635 -0.660
MMT H73 H H 0.000 -0.852 2.999 -1.642
MMT H72 H H 0.000 -0.844 3.420 0.035
MMT H71 H H 0.000 0.297 2.272 -0.573
MMT C6 C CR16 0.000 -2.997 1.741 -0.423
MMT H6 H H 0.000 -3.376 2.726 -0.668
MMT N1 N NR6 0.000 -3.865 0.717 -0.161
MMT "C1'" C CH1 0.000 -5.308 0.958 -0.214
MMT "H1'" H H 0.000 -5.502 2.010 -0.468
MMT "O4'" O O2 0.000 -5.903 0.645 1.056
MMT "C2'" C CH2 0.000 -5.960 0.036 -1.264
MMT "H2'" H H 0.000 -5.236 -0.647 -1.713
MMT "H2''" H H 0.000 -6.461 0.603 -2.051
MMT "C3'" C CH1 0.000 -7.007 -0.773 -0.461
MMT "H3'" H H 0.000 -6.606 -1.756 -0.176
MMT "O3'" O OH1 0.000 -8.219 -0.917 -1.205
MMT "HO3'" H H 0.000 -8.039 -1.399 -2.024
MMT "C4'" C CH1 0.000 -7.220 0.119 0.787
MMT "H4'" H H 0.000 -7.924 0.933 0.565
MMT "C5'" C CH2 0.000 -7.718 -0.715 1.969
MMT "H5'" H H 0.000 -7.001 -1.511 2.180
MMT "H5''" H H 0.000 -8.686 -1.156 1.719
MMT "O5'" O O2 0.000 -7.857 0.120 3.117
MMT NP N NT 0.000 -8.334 -0.731 4.206
MMT CP C CH3 0.000 -9.547 -0.099 4.740
MMT HNP3 H H 0.000 -9.869 -0.624 5.601
MMT HNP2 H H 0.000 -9.336 0.907 4.997
MMT HNP1 H H 0.000 -10.309 -0.123 4.005
MMT C3X C CH3 0.000 -7.322 -0.665 5.269
MMT HC33 H H 0.000 -7.217 0.338 5.595
MMT HC32 H H 0.000 -7.625 -1.270 6.084
MMT HC31 H H 0.000 -6.394 -1.014 4.896
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
MMT O4 n/a C4 START
MMT C4 O4 C5 .
MMT N3 C4 C2 .
MMT H3 N3 . .
MMT C2 N3 O2 .
MMT O2 C2 . .
MMT C5 C4 C6 .
MMT C5M C5 H71 .
MMT H73 C5M . .
MMT H72 C5M . .
MMT H71 C5M . .
MMT C6 C5 N1 .
MMT H6 C6 . .
MMT N1 C6 "C1'" .
MMT "C1'" N1 "C2'" .
MMT "H1'" "C1'" . .
MMT "O4'" "C1'" . .
MMT "C2'" "C1'" "C3'" .
MMT "H2'" "C2'" . .
MMT "H2''" "C2'" . .
MMT "C3'" "C2'" "C4'" .
MMT "H3'" "C3'" . .
MMT "O3'" "C3'" "HO3'" .
MMT "HO3'" "O3'" . .
MMT "C4'" "C3'" "C5'" .
MMT "H4'" "C4'" . .
MMT "C5'" "C4'" "O5'" .
MMT "H5'" "C5'" . .
MMT "H5''" "C5'" . .
MMT "O5'" "C5'" NP .
MMT NP "O5'" C3X .
MMT CP NP HNP1 .
MMT HNP3 CP . .
MMT HNP2 CP . .
MMT HNP1 CP . .
MMT C3X NP HC31 .
MMT HC33 C3X . .
MMT HC32 C3X . .
MMT HC31 C3X . END
MMT "C4'" "O4'" . ADD
MMT N1 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
MMT C3X NP single 1.469 0.020
MMT HC31 C3X single 1.059 0.020
MMT HC32 C3X single 1.059 0.020
MMT HC33 C3X single 1.059 0.020
MMT CP NP single 1.469 0.020
MMT NP "O5'" single 1.345 0.020
MMT HNP1 CP single 1.059 0.020
MMT HNP2 CP single 1.059 0.020
MMT HNP3 CP single 1.059 0.020
MMT "O5'" "C5'" single 1.426 0.020
MMT "C5'" "C4'" single 1.524 0.020
MMT "H5'" "C5'" single 1.092 0.020
MMT "H5''" "C5'" single 1.092 0.020
MMT "C4'" "O4'" single 1.426 0.020
MMT "C4'" "C3'" single 1.524 0.020
MMT "H4'" "C4'" single 1.099 0.020
MMT "O4'" "C1'" single 1.426 0.020
MMT "C2'" "C1'" single 1.524 0.020
MMT "C1'" N1 single 1.465 0.020
MMT "H1'" "C1'" single 1.099 0.020
MMT "C3'" "C2'" single 1.524 0.020
MMT "H2'" "C2'" single 1.092 0.020
MMT "H2''" "C2'" single 1.092 0.020
MMT "O3'" "C3'" single 1.432 0.020
MMT "H3'" "C3'" single 1.099 0.020
MMT "HO3'" "O3'" single 0.967 0.020
MMT N1 C2 single 1.410 0.020
MMT N1 C6 single 1.337 0.020
MMT C2 N3 single 1.337 0.020
MMT O2 C2 double 1.250 0.020
MMT N3 C4 single 1.337 0.020
MMT H3 N3 single 1.040 0.020
MMT C5 C4 single 1.487 0.020
MMT C4 O4 double 1.250 0.020
MMT C6 C5 double 1.390 0.020
MMT C5M C5 single 1.506 0.020
MMT H6 C6 single 1.083 0.020
MMT H71 C5M single 1.059 0.020
MMT H72 C5M single 1.059 0.020
MMT H73 C5M single 1.059 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
MMT O4 C4 N3 120.000 3.000
MMT O4 C4 C5 120.000 3.000
MMT N3 C4 C5 120.000 3.000
MMT C4 N3 H3 120.000 3.000
MMT C4 N3 C2 120.000 3.000
MMT H3 N3 C2 120.000 3.000
MMT N3 C2 O2 120.000 3.000
MMT N3 C2 N1 120.000 3.000
MMT O2 C2 N1 120.000 3.000
MMT C4 C5 C5M 120.000 3.000
MMT C4 C5 C6 120.000 3.000
MMT C5M C5 C6 120.000 3.000
MMT C5 C5M H73 109.470 3.000
MMT C5 C5M H72 109.470 3.000
MMT C5 C5M H71 109.470 3.000
MMT H73 C5M H72 109.470 3.000
MMT H73 C5M H71 109.470 3.000
MMT H72 C5M H71 109.470 3.000
MMT C5 C6 H6 120.000 3.000
MMT C5 C6 N1 120.000 3.000
MMT H6 C6 N1 120.000 3.000
MMT C6 N1 "C1'" 120.000 3.000
MMT C6 N1 C2 120.000 3.000
MMT "C1'" N1 C2 120.000 3.000
MMT N1 "C1'" "H1'" 109.470 3.000
MMT N1 "C1'" "O4'" 109.470 3.000
MMT N1 "C1'" "C2'" 109.470 3.000
MMT "H1'" "C1'" "O4'" 109.470 3.000
MMT "H1'" "C1'" "C2'" 108.340 3.000
MMT "O4'" "C1'" "C2'" 109.470 3.000
MMT "C1'" "O4'" "C4'" 111.800 3.000
MMT "C1'" "C2'" "H2'" 109.470 3.000
MMT "C1'" "C2'" "H2''" 109.470 3.000
MMT "C1'" "C2'" "C3'" 111.000 3.000
MMT "H2'" "C2'" "H2''" 107.900 3.000
MMT "H2'" "C2'" "C3'" 109.470 3.000
MMT "H2''" "C2'" "C3'" 109.470 3.000
MMT "C2'" "C3'" "H3'" 108.340 3.000
MMT "C2'" "C3'" "O3'" 109.470 3.000
MMT "C2'" "C3'" "C4'" 111.000 3.000
MMT "H3'" "C3'" "O3'" 109.470 3.000
MMT "H3'" "C3'" "C4'" 108.340 3.000
MMT "O3'" "C3'" "C4'" 109.470 3.000
MMT "C3'" "O3'" "HO3'" 109.470 3.000
MMT "C3'" "C4'" "H4'" 108.340 3.000
MMT "C3'" "C4'" "C5'" 111.000 3.000
MMT "C3'" "C4'" "O4'" 109.470 3.000
MMT "H4'" "C4'" "C5'" 108.340 3.000
MMT "H4'" "C4'" "O4'" 109.470 3.000
MMT "C5'" "C4'" "O4'" 109.470 3.000
MMT "C4'" "C5'" "H5'" 109.470 3.000
MMT "C4'" "C5'" "H5''" 109.470 3.000
MMT "C4'" "C5'" "O5'" 109.470 3.000
MMT "H5'" "C5'" "H5''" 107.900 3.000
MMT "H5'" "C5'" "O5'" 109.470 3.000
MMT "H5''" "C5'" "O5'" 109.470 3.000
MMT "C5'" "O5'" NP 120.000 3.000
MMT "O5'" NP CP 109.500 3.000
MMT "O5'" NP C3X 109.500 3.000
MMT CP NP C3X 109.470 3.000
MMT NP CP HNP3 109.470 3.000
MMT NP CP HNP2 109.470 3.000
MMT NP CP HNP1 109.470 3.000
MMT HNP3 CP HNP2 109.470 3.000
MMT HNP3 CP HNP1 109.470 3.000
MMT HNP2 CP HNP1 109.470 3.000
MMT NP C3X HC33 109.470 3.000
MMT NP C3X HC32 109.470 3.000
MMT NP C3X HC31 109.470 3.000
MMT HC33 C3X HC32 109.470 3.000
MMT HC33 C3X HC31 109.470 3.000
MMT HC32 C3X HC31 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
MMT CONST_1 O4 C4 N3 C2 180.000 0.000 0
MMT CONST_2 C4 N3 C2 O2 180.000 0.000 0
MMT CONST_3 O4 C4 C5 C6 180.000 0.000 0
MMT var_1 C4 C5 C5M H71 0.032 20.000 1
MMT CONST_4 C4 C5 C6 N1 0.000 0.000 0
MMT CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
MMT CONST_6 C6 N1 C2 N3 0.000 0.000 0
MMT var_2 C6 N1 "C1'" "C2'" 120.611 20.000 1
MMT var_3 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
MMT var_4 N1 "C1'" "C2'" "C3'" 120.000 20.000 3
MMT var_5 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
MMT var_6 "C2'" "C3'" "O3'" "HO3'" 61.366 20.000 1
MMT var_7 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
MMT var_8 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
MMT var_9 "C3'" "C4'" "C5'" "O5'" 177.787 20.000 3
MMT var_10 "C4'" "C5'" "O5'" NP 179.989 20.000 1
MMT var_11 "C5'" "O5'" NP C3X 120.036 20.000 1
MMT var_12 "O5'" NP CP HNP1 66.174 20.000 1
MMT var_13 "O5'" NP C3X HC31 -59.942 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
MMT chir_01 NP C3X CP "O5'" negativ
MMT chir_02 "C4'" "C5'" "O4'" "C3'" negativ
MMT chir_03 "C1'" "O4'" "C2'" N1 positiv
MMT chir_04 "C3'" "C4'" "C2'" "O3'" 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
MMT plan-1 N1 0.020
MMT plan-1 "C1'" 0.020
MMT plan-1 C2 0.020
MMT plan-1 C6 0.020
MMT plan-1 N3 0.020
MMT plan-1 C4 0.020
MMT plan-1 C5 0.020
MMT plan-1 O2 0.020
MMT plan-1 H3 0.020
MMT plan-1 O4 0.020
MMT plan-1 C5M 0.020
MMT plan-1 H6 0.020
# ------------------------------------------------------
|
