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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
A A 'ADENOSINE-5'-MONOPHOSPHATE ' RNA 35 23 .
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_A
#
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
A P P P 0.000 -0.003 -0.405 0.200
A OP3 O OP -0.660 0.429 -1.625 0.978
A OP1 O OP -0.660 0.213 0.886 0.959
A OP2 O OP -0.660 0.528 -0.386 -1.216
A "O5'" O O2 0.000 -1.607 -0.542 0.062
A "C5'" C CH2 0.000 -2.368 0.488 -0.595
A "H5' " H H 0.000 -1.931 0.694 -1.575
A "H5''" H H 0.000 -2.347 1.397 0.009
A "C4'" C CH1 0.000 -3.806 0.025 -0.767
A "H4'" H H 0.000 -3.772 -0.934 -1.301
A "C3'" C CH1 0.000 -4.830 0.914 -1.500
A "H3'" H H 0.000 -4.486 1.958 -1.511
A "O3'" O OH1 0.000 -5.049 0.450 -2.841
A "HO3'" H H 0.000 -5.750 0.973 -3.254
A "C2'" C CH1 0.000 -6.131 0.786 -0.657
A "H2'" H H 0.000 -6.410 1.774 -0.265
A "O2'" O OH1 0.000 -7.229 0.243 -1.404
A "HO2'" H H 0.000 -7.986 0.112 -0.816
A "C1'" C CH1 0.000 -5.796 -0.154 0.517
A "H1'" H H 0.000 -6.179 -1.151 0.257
A "O4'" O O2 0.000 -4.359 -0.239 0.540
A N9 N NR5 0.000 -6.368 0.208 1.842
A C4 C CR56 0.000 -7.478 -0.316 2.375
A C5 C CR56 0.000 -7.695 0.416 3.664
A N7 N NRD5 0.000 -6.556 1.058 3.891
A C8 C CR15 0.000 -5.716 0.765 2.869
A H8 H H 0.000 -4.650 0.957 2.883
A N3 N NRD6 0.000 -8.459 -1.089 1.874
A C2 C CR16 0.000 -9.586 -1.221 2.569
A H2 H H 0.000 -10.383 -1.815 2.140
A N1 N NRD6 0.000 -9.794 -0.659 3.773
A C6 C CR6 0.000 -8.924 0.147 4.423
A N6 N NH2 0.000 -9.258 0.673 5.620
A H62 H H 0.000 -10.157 0.465 6.028
A H61 H H 0.000 -8.609 1.275 6.104
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
A "O5'" n/a "C5'" START
A P "O5'" . .
A OP3 P . .
A OP1 P . .
A OP2 P . .
A "C5'" "O5'" "C4'" .
A "H5' " "C5'" . .
A "H5''" "C5'" . .
A "C4'" "C5'" "C3'" .
A "H4'" "C4'" . .
A "C3'" "C4'" "C2'" .
A "H3'" "C3'" . .
A "O3'" "C3'" "HO3'" .
A "HO3'" "O3'" . .
A "C2'" "C3'" "C1'" .
A "H2'" "C2'" . .
A "O2'" "C2'" "HO2'" .
A "HO2'" "O2'" . .
A "C1'" "C2'" N9 .
A "H1'" "C1'" . .
A "O4'" "C1'" . .
A N9 "C1'" C4 .
A C4 N9 N3 .
A C5 C4 N7 .
A N7 C5 C8 .
A C8 N7 H8 .
A H8 C8 . .
A N3 C4 C2 .
A C2 N3 N1 .
A H2 C2 . .
A N1 C2 C6 .
A C6 N1 N6 .
A N6 C6 H61 .
A H62 N6 . .
A H61 N6 . END
A "C4'" "O4'" . ADD
A N9 C8 . ADD
A 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
A OP3 P deloc 1.485 0.017
A OP1 P deloc 1.485 0.017
A OP2 P deloc 1.485 0.017
A "O5'" P single 1.593 0.010
A "C5'" "O5'" single 1.440 0.016
A "C4'" "C5'" single 1.510 0.013
A "C4'" "O4'" single 1.453 0.012
A "C3'" "C4'" single 1.528 0.010
A "O4'" "C1'" single 1.414 0.012
A "O3'" "C3'" single 1.423 0.014
A "C2'" "C3'" single 1.525 0.011
A "O2'" "C2'" single 1.413 0.013
A "C1'" "C2'" single 1.528 0.010
A N9 "C1'" single 1.462 0.010
A N9 C8 single 1.373 0.008
A C4 N9 single 1.374 0.006
A C8 N7 double 1.311 0.007
A N7 C5 single 1.388 0.006
A C5 C6 single 1.406 0.009
A C5 C4 double 1.383 0.007
A N6 C6 single 1.335 0.008
A C6 N1 double 1.351 0.007
A N1 C2 single 1.339 0.009
A C2 N3 double 1.331 0.009
A N3 C4 single 1.344 0.006
A "H5' " "C5'" single 1.092 0.020
A "H5''" "C5'" single 1.092 0.020
A "H4'" "C4'" single 1.099 0.020
A "H3'" "C3'" single 1.099 0.020
A "HO3'" "O3'" single 0.967 0.020
A "H2'" "C2'" single 1.099 0.020
A "HO2'" "O2'" single 0.967 0.020
A "H1'" "C1'" single 1.099 0.020
A H8 C8 single 1.083 0.020
A H61 N6 single 1.010 0.020
A H62 N6 single 1.010 0.020
A H2 C2 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
A OP3 P OP1 107.400 3.200
A OP3 P OP2 108.300 3.200
A OP1 P OP2 119.600 1.500
A OP3 P "O5'" 104.000 1.900
A OP1 P "O5'" 108.100 2.900
A OP2 P "O5'" 108.300 2.700
A P "O5'" "C5'" 120.900 1.600
A "O5'" "C5'" "H5' " 109.470 3.000
A "O5'" "C5'" "H5''" 109.470 3.000
A "O5'" "C5'" "C4'" 110.200 1.400
A "H5' " "C5'" "H5''" 107.900 3.000
A "H5' " "C5'" "C4'" 109.470 3.000
A "H5''" "C5'" "C4'" 109.470 3.000
A "C5'" "C4'" "H4'" 108.340 3.000
A "C5'" "C4'" "C3'" 115.500 1.500
A "C5'" "C4'" "O4'" 109.200 1.400
A "H4'" "C4'" "C3'" 108.340 3.000
A "H4'" "C4'" "O4'" 109.470 3.000
A "C3'" "C4'" "O4'" 105.500 1.400
A "C4'" "C3'" "H3'" 108.340 3.000
A "C4'" "C3'" "O3'" 110.600 2.600
A "C4'" "C3'" "C2'" 102.700 1.000
A "H3'" "C3'" "O3'" 109.470 3.000
A "H3'" "C3'" "C2'" 108.340 3.000
A "O3'" "C3'" "C2'" 111.000 2.800
A "C3'" "O3'" "HO3'" 109.470 3.000
A "C3'" "C2'" "H2'" 108.340 3.000
A "C3'" "C2'" "O2'" 113.300 2.900
A "C3'" "C2'" "C1'" 101.500 0.900
A "H2'" "C2'" "O2'" 109.470 3.000
A "H2'" "C2'" "C1'" 108.340 3.000
A "O2'" "C2'" "C1'" 110.600 3.000
A "C2'" "O2'" "HO2'" 109.470 3.000
A "C2'" "C1'" "H1'" 108.340 3.000
A "C2'" "C1'" "O4'" 106.400 1.400
A "C2'" "C1'" N9 113.400 1.600
A "H1'" "C1'" "O4'" 109.470 3.000
A "H1'" "C1'" N9 109.470 3.000
A "O4'" "C1'" N9 108.200 1.000
A "C1'" "O4'" "C4'" 109.600 0.900
A "C1'" N9 C4 126.300 1.800
A "C1'" N9 C8 127.700 1.800
A C4 N9 C8 105.800 0.400
A N9 C4 C5 105.800 0.400
A N9 C4 N3 127.400 0.800
A C5 C4 N3 126.800 0.700
A C4 C5 N7 110.700 0.500
A C4 C5 C6 117.000 0.500
A N7 C5 C6 132.300 0.700
A C5 N7 C8 103.900 0.500
A N7 C8 H8 126.000 3.000
A N7 C8 N9 113.800 0.500
A H8 C8 N9 126.000 3.000
A C4 N3 C2 110.600 0.500
A N3 C2 H2 120.000 3.000
A N3 C2 N1 129.300 0.500
A H2 C2 N1 120.000 3.000
A C2 N1 C6 118.600 0.600
A N1 C6 N6 118.600 0.600
A N1 C6 C5 117.700 0.500
A N6 C6 C5 123.700 0.800
A C6 N6 H62 120.000 3.000
A C6 N6 H61 120.000 3.000
A H62 N6 H61 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
A var_1 OP2 P "O5'" "C5'" -60.045 20.000 1
A var_2 P "O5'" "C5'" "C4'" -179.925 20.000 1
A var_3 "O5'" "C5'" "C4'" "C3'" 176.951 20.000 3
A var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
A var_5 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
A var_6 "C4'" "C3'" "O3'" "HO3'" 175.000 20.000 1
A var_7 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
A var_8 "C3'" "C2'" "O2'" "HO2'" 175.000 20.000 1
A var_9 "C3'" "C2'" "C1'" N9 150.000 20.000 3
A var_10 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
A var_11 "C2'" "C1'" N9 C4 91.469 20.000 1
A CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
A CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
A CONST_3 N9 C4 C5 N7 0.000 0.000 0
A CONST_4 C4 C5 C6 N1 0.000 0.000 0
A CONST_5 C4 C5 N7 C8 0.000 0.000 0
A CONST_6 C5 N7 C8 N9 0.000 0.000 0
A CONST_7 N9 C4 N3 C2 180.000 0.000 0
A CONST_8 C4 N3 C2 N1 0.000 0.000 0
A CONST_9 N3 C2 N1 C6 0.000 0.000 0
A CONST_10 C2 N1 C6 N6 180.000 0.000 0
A CONST_11 N1 C6 N6 H61 180.000 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
A chir_01 "C4'" "C5'" "O4'" "C3'" negativ
A chir_02 "C3'" "C4'" "O3'" "C2'" negativ
A chir_03 "C2'" "C3'" "O2'" "C1'" negativ
A 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
A plan-1 N9 0.020
A plan-1 "C1'" 0.020
A plan-1 C8 0.020
A plan-1 C4 0.020
A plan-1 N7 0.020
A plan-1 H8 0.020
A plan-1 C5 0.020
A plan-1 C6 0.020
A plan-1 N1 0.020
A plan-1 C2 0.020
A plan-1 N3 0.020
A plan-1 N6 0.020
A plan-1 H2 0.020
A plan-1 H62 0.020
A plan-1 H61 0.020
A plan-2 N6 0.020
A plan-2 C6 0.020
A plan-2 H61 0.020
A plan-2 H62 0.020
# ------------------------------------------------------
# ------------------------------------------------------
# ------------------------------------------------------
|
