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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
R R '. ' DNA 51 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_R
#
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
R OP3 O OP -0.666 0.000 0.000 0.000
R P P P 0.000 -0.991 -0.803 0.814
R OP1 O OP -0.666 -1.380 -0.023 2.051
R OP2 O OP -0.666 -0.361 -2.116 1.224
R "O5'" O O2 0.000 -2.304 -1.091 -0.073
R "C5'" C CH2 0.000 -2.851 0.179 -0.426
R "H5'" H H 0.000 -2.113 0.747 -0.997
R "H5''" H H 0.000 -3.108 0.729 0.482
R "C4'" C CH1 0.000 -4.108 -0.025 -1.274
R "H4'" H H 0.000 -3.878 -0.621 -2.168
R "C3'" C CH1 0.000 -4.725 1.340 -1.673
R "H3'" H H 0.000 -4.637 2.064 -0.851
R "C2'" C CH2 0.000 -6.207 0.966 -1.923
R "H2'" H H 0.000 -6.415 0.804 -2.982
R "H2''" H H 0.000 -6.891 1.721 -1.529
R "C1'" C CH1 0.000 -6.397 -0.354 -1.152
R "H1'" H H 0.000 -6.656 -1.161 -1.852
R "O4'" O O2 0.000 -5.153 -0.654 -0.499
R N9 N NR5 0.000 -7.459 -0.201 -0.155
R C4 C CR56 0.000 -8.795 -0.448 -0.348
R C5 C CR56 0.000 -9.423 -0.158 0.875
R N7 N NRD5 0.000 -8.454 0.235 1.736
R C8 C CR15 0.000 -7.303 0.214 1.132
R H8 H H 0.000 -6.359 0.486 1.587
R N3 N NRD6 0.000 -9.534 -0.865 -1.370
R C2 C CR16 0.000 -10.836 -1.010 -1.242
R H2 H H 0.000 -11.409 -1.351 -2.095
R N1 N NRD6 0.000 -11.470 -0.755 -0.112
R C6 C CR6 0.000 -10.814 -0.334 0.964
R N6 N NH1 0.000 -11.487 -0.070 2.144
R H6 H H 0.000 -10.977 0.250 2.955
R CA C CH1 0.000 -12.938 -0.254 2.218
R HA H H 0.000 -13.381 -0.071 1.229
R CB C CH2 0.000 -13.249 -1.685 2.660
R HB1 H H 0.000 -12.830 -2.387 1.936
R HB2 H H 0.000 -14.332 -1.821 2.713
R OB O OH1 0.000 -12.674 -1.923 3.945
R HB H H 0.000 -12.871 -2.827 4.223
R CJ C CR6 0.000 -13.517 0.716 3.214
R "CO'" C CR16 0.000 -12.764 1.127 4.297
R "HO'" H H 0.000 -11.758 0.749 4.432
R "CM'" C CR16 0.000 -13.294 2.022 5.208
R "HM'" H H 0.000 -12.700 2.349 6.053
R CP C CR16 0.000 -14.581 2.497 5.042
R HP H H 0.000 -14.997 3.195 5.758
R CM C CR16 0.000 -15.337 2.081 3.962
R HM H H 0.000 -16.346 2.453 3.832
R CO C CR16 0.000 -14.805 1.191 3.047
R HO H H 0.000 -15.397 0.865 2.201
R "O3'" O OH1 0.000 -4.119 1.845 -2.865
R "HO3'" H H 0.000 -4.607 2.643 -3.110
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
R OP3 n/a P START
R P OP3 "O5'" .
R OP1 P . .
R OP2 P . .
R "O5'" P "C5'" .
R "C5'" "O5'" "C4'" .
R "H5'" "C5'" . .
R "H5''" "C5'" . .
R "C4'" "C5'" "C3'" .
R "H4'" "C4'" . .
R "C3'" "C4'" "O3'" .
R "H3'" "C3'" . .
R "C2'" "C3'" "C1'" .
R "H2'" "C2'" . .
R "H2''" "C2'" . .
R "C1'" "C2'" N9 .
R "H1'" "C1'" . .
R "O4'" "C1'" . .
R N9 "C1'" C4 .
R C4 N9 N3 .
R C5 C4 N7 .
R N7 C5 C8 .
R C8 N7 H8 .
R H8 C8 . .
R N3 C4 C2 .
R C2 N3 N1 .
R H2 C2 . .
R N1 C2 C6 .
R C6 N1 N6 .
R N6 C6 CA .
R H6 N6 . .
R CA N6 CJ .
R HA CA . .
R CB CA OB .
R HB1 CB . .
R HB2 CB . .
R OB CB HB .
R HB OB . .
R CJ CA "CO'" .
R "CO'" CJ "CM'" .
R "HO'" "CO'" . .
R "CM'" "CO'" CP .
R "HM'" "CM'" . .
R CP "CM'" CM .
R HP CP . .
R CM CP CO .
R HM CM . .
R CO CM HO .
R HO CO . .
R "O3'" "C3'" . END
R "HO3'" "O3'" . .
R "C4'" "O4'" . ADD
R N9 C8 . ADD
R C5 C6 . ADD
R CJ CO . 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
R OP1 P deloc 1.510 0.020
R OP2 P deloc 1.510 0.020
R P OP3 deloc 1.510 0.020
R "O5'" P single 1.610 0.020
R "C5'" "O5'" single 1.426 0.020
R "C4'" "C5'" single 1.524 0.020
R "H5'" "C5'" single 1.092 0.020
R "H5''" "C5'" single 1.092 0.020
R "C4'" "O4'" single 1.426 0.020
R "C3'" "C4'" single 1.524 0.020
R "H4'" "C4'" single 1.099 0.020
R "O4'" "C1'" single 1.426 0.020
R "O3'" "C3'" single 1.432 0.020
R "C2'" "C3'" single 1.524 0.020
R "H3'" "C3'" single 1.099 0.020
R "HO3'" "O3'" single 0.967 0.020
R "C1'" "C2'" single 1.524 0.020
R "H2'" "C2'" single 1.092 0.020
R "H2''" "C2'" single 1.092 0.020
R N9 "C1'" single 1.485 0.020
R "H1'" "C1'" single 1.099 0.020
R N9 C8 single 1.337 0.020
R C4 N9 single 1.337 0.020
R C8 N7 double 1.350 0.020
R H8 C8 single 1.083 0.020
R N7 C5 single 1.350 0.020
R C5 C6 single 1.490 0.020
R C5 C4 double 1.490 0.020
R N6 C6 single 1.350 0.020
R C6 N1 double 1.350 0.020
R CA N6 single 1.450 0.020
R H6 N6 single 1.010 0.020
R N1 C2 single 1.337 0.020
R C2 N3 double 1.337 0.020
R H2 C2 single 1.083 0.020
R N3 C4 single 1.355 0.020
R CB CA single 1.524 0.020
R CJ CA single 1.480 0.020
R HA CA single 1.099 0.020
R OB CB single 1.432 0.020
R HB1 CB single 1.092 0.020
R HB2 CB single 1.092 0.020
R HB OB single 0.967 0.020
R CJ CO double 1.390 0.020
R "CO'" CJ single 1.390 0.020
R CO CM single 1.390 0.020
R HO CO single 1.083 0.020
R "CM'" "CO'" double 1.390 0.020
R "HO'" "CO'" single 1.083 0.020
R CM CP double 1.390 0.020
R HM CM single 1.083 0.020
R CP "CM'" single 1.390 0.020
R "HM'" "CM'" single 1.083 0.020
R HP CP 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
R OP3 P OP1 119.900 3.000
R OP3 P OP2 119.900 3.000
R OP3 P "O5'" 108.200 3.000
R OP1 P OP2 119.900 3.000
R OP1 P "O5'" 108.200 3.000
R OP2 P "O5'" 108.200 3.000
R P "O5'" "C5'" 120.500 3.000
R "O5'" "C5'" "H5'" 109.470 3.000
R "O5'" "C5'" "H5''" 109.470 3.000
R "O5'" "C5'" "C4'" 109.470 3.000
R "H5'" "C5'" "H5''" 107.900 3.000
R "H5'" "C5'" "C4'" 109.470 3.000
R "H5''" "C5'" "C4'" 109.470 3.000
R "C5'" "C4'" "H4'" 108.340 3.000
R "C5'" "C4'" "C3'" 111.000 3.000
R "C5'" "C4'" "O4'" 109.470 3.000
R "H4'" "C4'" "C3'" 108.340 3.000
R "H4'" "C4'" "O4'" 109.470 3.000
R "C3'" "C4'" "O4'" 109.470 3.000
R "C4'" "C3'" "H3'" 108.340 3.000
R "C4'" "C3'" "C2'" 111.000 3.000
R "C4'" "C3'" "O3'" 109.470 3.000
R "H3'" "C3'" "C2'" 108.340 3.000
R "H3'" "C3'" "O3'" 109.470 3.000
R "C2'" "C3'" "O3'" 109.470 3.000
R "C3'" "C2'" "H2'" 109.470 3.000
R "C3'" "C2'" "H2''" 109.470 3.000
R "C3'" "C2'" "C1'" 111.000 3.000
R "H2'" "C2'" "H2''" 107.900 3.000
R "H2'" "C2'" "C1'" 109.470 3.000
R "H2''" "C2'" "C1'" 109.470 3.000
R "C2'" "C1'" "H1'" 108.340 3.000
R "C2'" "C1'" "O4'" 109.470 3.000
R "C2'" "C1'" N9 109.470 3.000
R "H1'" "C1'" "O4'" 109.470 3.000
R "H1'" "C1'" N9 109.470 3.000
R "O4'" "C1'" N9 109.470 3.000
R "C1'" "O4'" "C4'" 111.800 3.000
R "C1'" N9 C4 126.000 3.000
R "C1'" N9 C8 126.000 3.000
R C4 N9 C8 108.000 3.000
R N9 C4 C5 108.000 3.000
R N9 C4 N3 132.000 3.000
R C5 C4 N3 120.000 3.000
R C4 C5 N7 108.000 3.000
R C4 C5 C6 120.000 3.000
R N7 C5 C6 132.000 3.000
R C5 N7 C8 108.000 3.000
R N7 C8 H8 126.000 3.000
R N7 C8 N9 108.000 3.000
R H8 C8 N9 126.000 3.000
R C4 N3 C2 120.000 3.000
R N3 C2 H2 120.000 3.000
R N3 C2 N1 120.000 3.000
R H2 C2 N1 120.000 3.000
R C2 N1 C6 120.000 3.000
R N1 C6 N6 120.000 3.000
R N1 C6 C5 120.000 3.000
R N6 C6 C5 120.000 3.000
R C6 N6 H6 120.000 3.000
R C6 N6 CA 120.000 3.000
R H6 N6 CA 118.500 3.000
R N6 CA HA 108.550 3.000
R N6 CA CB 110.000 3.000
R N6 CA CJ 109.470 3.000
R HA CA CB 108.340 3.000
R HA CA CJ 109.470 3.000
R CB CA CJ 109.470 3.000
R CA CB HB1 109.470 3.000
R CA CB HB2 109.470 3.000
R CA CB OB 109.470 3.000
R HB1 CB HB2 107.900 3.000
R HB1 CB OB 109.470 3.000
R HB2 CB OB 109.470 3.000
R CB OB HB 109.470 3.000
R CA CJ "CO'" 120.000 3.000
R CA CJ CO 120.000 3.000
R "CO'" CJ CO 120.000 3.000
R CJ "CO'" "HO'" 120.000 3.000
R CJ "CO'" "CM'" 120.000 3.000
R "HO'" "CO'" "CM'" 120.000 3.000
R "CO'" "CM'" "HM'" 120.000 3.000
R "CO'" "CM'" CP 120.000 3.000
R "HM'" "CM'" CP 120.000 3.000
R "CM'" CP HP 120.000 3.000
R "CM'" CP CM 120.000 3.000
R HP CP CM 120.000 3.000
R CP CM HM 120.000 3.000
R CP CM CO 120.000 3.000
R HM CM CO 120.000 3.000
R CM CO HO 120.000 3.000
R CM CO CJ 120.000 3.000
R HO CO CJ 120.000 3.000
R "C3'" "O3'" "HO3'" 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
R var_1 OP3 P "O5'" "C5'" -60.077 20.000 1
R var_2 P "O5'" "C5'" "C4'" 179.991 20.000 1
R var_3 "O5'" "C5'" "C4'" "C3'" -179.991 20.000 3
R var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
R var_5 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
R var_6 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
R var_7 "C3'" "C2'" "C1'" N9 120.000 20.000 3
R var_8 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
R var_9 "C2'" "C1'" N9 C4 90.241 20.000 1
R CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
R CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
R CONST_3 N9 C4 C5 N7 0.000 0.000 0
R CONST_4 C4 C5 C6 N1 0.000 0.000 0
R CONST_5 C4 C5 N7 C8 0.000 0.000 0
R CONST_6 C5 N7 C8 N9 0.000 0.000 0
R CONST_7 N9 C4 N3 C2 180.000 0.000 0
R CONST_8 C4 N3 C2 N1 0.000 0.000 0
R CONST_9 N3 C2 N1 C6 0.000 0.000 0
R CONST_10 C2 N1 C6 N6 180.000 0.000 0
R var_10 N1 C6 N6 CA 0.035 20.000 1
R var_11 C6 N6 CA CJ -150.005 20.000 3
R var_12 N6 CA CB OB 60.021 20.000 3
R var_13 CA CB OB HB -179.974 20.000 1
R var_14 N6 CA CJ "CO'" -30.322 20.000 1
R CONST_11 CA CJ CO CM 180.000 0.000 0
R CONST_12 CA CJ "CO'" "CM'" 180.000 0.000 0
R CONST_13 CJ "CO'" "CM'" CP 0.000 0.000 0
R CONST_14 "CO'" "CM'" CP CM 0.000 0.000 0
R CONST_15 "CM'" CP CM CO 0.000 0.000 0
R CONST_16 CP CM CO CJ 0.000 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
R chir_01 "C4'" "C5'" "O4'" "C3'" negativ
R chir_02 "C3'" "C4'" "O3'" "C2'" negativ
R chir_03 "C1'" "O4'" "C2'" N9 positiv
R chir_04 CA N6 CB CJ 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
R plan-1 N9 0.020
R plan-1 "C1'" 0.020
R plan-1 C8 0.020
R plan-1 C4 0.020
R plan-1 N7 0.020
R plan-1 H8 0.020
R plan-1 C5 0.020
R plan-1 C6 0.020
R plan-1 N1 0.020
R plan-1 C2 0.020
R plan-1 N3 0.020
R plan-1 N6 0.020
R plan-1 H2 0.020
R plan-1 H6 0.020
R plan-2 N6 0.020
R plan-2 C6 0.020
R plan-2 CA 0.020
R plan-2 H6 0.020
R plan-3 CJ 0.020
R plan-3 CA 0.020
R plan-3 CO 0.020
R plan-3 "CO'" 0.020
R plan-3 CM 0.020
R plan-3 "CM'" 0.020
R plan-3 CP 0.020
R plan-3 HO 0.020
R plan-3 "HO'" 0.020
R plan-3 HM 0.020
R plan-3 "HM'" 0.020
R plan-3 HP 0.020
# ------------------------------------------------------
|
