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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
RPD RPD '. ' non-polymer 49 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_RPD
#
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
RPD OKA O OC -0.500 0.000 0.000 0.000
RPD C9A C C 0.000 0.147 0.672 1.045
RPD OJA O OC -0.500 0.917 0.268 1.944
RPD C8A C CH1 0.000 -0.602 1.966 1.220
RPD H81 H H 0.000 -0.662 2.488 0.254
RPD NAA N NT 0.000 0.103 2.813 2.191
RPD CBA C CH2 0.000 -0.591 4.108 2.203
RPD H111 H H 0.000 -0.101 4.775 2.916
RPD H112 H H 0.000 -1.631 3.960 2.501
RPD OBA O OH1 0.000 -0.545 4.686 0.899
RPD H11 H H 0.000 -1.002 5.538 0.908
RPD OAA O OH1 0.000 -0.108 2.209 3.506
RPD H10 H H 0.000 0.323 1.344 3.537
RPD C7A C CH2 0.000 -2.014 1.673 1.728
RPD H71 H H 0.000 -2.524 2.613 1.947
RPD H72 H H 0.000 -1.955 1.072 2.638
RPD C6A C CH2 0.000 -2.793 0.906 0.659
RPD H61 H H 0.000 -2.317 -0.062 0.487
RPD H62 H H 0.000 -2.796 1.479 -0.270
RPD C5A C CH2 0.000 -4.233 0.691 1.132
RPD H51 H H 0.000 -4.706 1.659 1.306
RPD H52 H H 0.000 -4.228 0.118 2.062
RPD N3 N NR5 0.000 -4.979 -0.044 0.108
RPD C2 C CR5 0.000 -5.066 -1.379 0.054
RPD O2 O O 0.000 -4.533 -2.125 0.852
RPD N1 N NR15 0.000 -5.810 -1.803 -0.986
RPD HN1 H H 0.000 -6.023 -2.789 -1.239
RPD C4 C CR5 0.000 -5.668 0.539 -0.895
RPD O4 O O 0.000 -5.782 1.725 -1.115
RPD "C1'" C CT 0.000 -6.260 -0.599 -1.688
RPD "O4'" O O2 0.000 -7.681 -0.517 -1.726
RPD "C2'" C CH1 0.000 -5.736 -0.587 -3.133
RPD H2 H H 0.000 -4.913 -1.304 -3.257
RPD "O2'" O OH1 0.000 -5.329 0.727 -3.517
RPD "HO2'" H H 0.000 -5.091 0.729 -4.454
RPD "C3'" C CH1 0.000 -6.988 -1.036 -3.936
RPD H3 H H 0.000 -7.071 -2.132 -3.957
RPD "O3'" O OH1 0.000 -6.973 -0.497 -5.259
RPD "HO3'" H H 0.000 -7.810 -0.701 -5.699
RPD "C4'" C CH1 0.000 -8.124 -0.409 -3.090
RPD H4 H H 0.000 -8.262 0.647 -3.363
RPD "C5'" C CH2 0.000 -9.429 -1.182 -3.289
RPD "H5'2" H H 0.000 -9.273 -2.231 -3.027
RPD "H5'1" H H 0.000 -9.737 -1.111 -4.334
RPD "O5'" O O2 0.000 -10.445 -0.627 -2.453
RPD P P P 0.000 -11.782 -1.486 -2.712
RPD O1P O OP -0.666 -11.528 -2.935 -2.357
RPD O2P O OP -0.666 -12.903 -0.945 -1.851
RPD O3P O OP -0.666 -12.172 -1.384 -4.170
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
RPD OKA n/a C9A START
RPD C9A OKA C8A .
RPD OJA C9A . .
RPD C8A C9A C7A .
RPD H81 C8A . .
RPD NAA C8A OAA .
RPD CBA NAA OBA .
RPD H111 CBA . .
RPD H112 CBA . .
RPD OBA CBA H11 .
RPD H11 OBA . .
RPD OAA NAA H10 .
RPD H10 OAA . .
RPD C7A C8A C6A .
RPD H71 C7A . .
RPD H72 C7A . .
RPD C6A C7A C5A .
RPD H61 C6A . .
RPD H62 C6A . .
RPD C5A C6A N3 .
RPD H51 C5A . .
RPD H52 C5A . .
RPD N3 C5A C4 .
RPD C2 N3 N1 .
RPD O2 C2 . .
RPD N1 C2 HN1 .
RPD HN1 N1 . .
RPD C4 N3 "C1'" .
RPD O4 C4 . .
RPD "C1'" C4 "C2'" .
RPD "O4'" "C1'" . .
RPD "C2'" "C1'" "C3'" .
RPD H2 "C2'" . .
RPD "O2'" "C2'" "HO2'" .
RPD "HO2'" "O2'" . .
RPD "C3'" "C2'" "C4'" .
RPD H3 "C3'" . .
RPD "O3'" "C3'" "HO3'" .
RPD "HO3'" "O3'" . .
RPD "C4'" "C3'" "C5'" .
RPD H4 "C4'" . .
RPD "C5'" "C4'" "O5'" .
RPD "H5'2" "C5'" . .
RPD "H5'1" "C5'" . .
RPD "O5'" "C5'" P .
RPD P "O5'" O3P .
RPD O1P P . .
RPD O2P P . .
RPD O3P P . END
RPD "C4'" "O4'" . ADD
RPD "C1'" N1 . 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
RPD O1P P deloc 1.510 0.020
RPD O2P P deloc 1.510 0.020
RPD O3P P deloc 1.510 0.020
RPD P "O5'" single 1.610 0.020
RPD "O5'" "C5'" single 1.426 0.020
RPD "C5'" "C4'" single 1.524 0.020
RPD "H5'1" "C5'" single 1.092 0.020
RPD "H5'2" "C5'" single 1.092 0.020
RPD "C4'" "O4'" single 1.426 0.020
RPD "C4'" "C3'" single 1.524 0.020
RPD H4 "C4'" single 1.099 0.020
RPD "O4'" "C1'" single 1.426 0.020
RPD "O3'" "C3'" single 1.432 0.020
RPD "C3'" "C2'" single 1.524 0.020
RPD H3 "C3'" single 1.099 0.020
RPD "HO3'" "O3'" single 0.967 0.020
RPD "O2'" "C2'" single 1.432 0.020
RPD "C2'" "C1'" single 1.524 0.020
RPD H2 "C2'" single 1.099 0.020
RPD "HO2'" "O2'" single 0.967 0.020
RPD "C1'" N1 single 1.462 0.020
RPD "C1'" C4 single 1.500 0.020
RPD N1 C2 single 1.340 0.020
RPD HN1 N1 single 1.040 0.020
RPD O2 C2 double 1.285 0.020
RPD C2 N3 single 1.337 0.020
RPD C4 N3 single 1.337 0.020
RPD N3 C5A single 1.462 0.020
RPD O4 C4 double 1.285 0.020
RPD C5A C6A single 1.524 0.020
RPD H51 C5A single 1.092 0.020
RPD H52 C5A single 1.092 0.020
RPD C6A C7A single 1.524 0.020
RPD H61 C6A single 1.092 0.020
RPD H62 C6A single 1.092 0.020
RPD C7A C8A single 1.524 0.020
RPD H71 C7A single 1.092 0.020
RPD H72 C7A single 1.092 0.020
RPD C8A C9A single 1.500 0.020
RPD NAA C8A single 1.469 0.020
RPD H81 C8A single 1.099 0.020
RPD OJA C9A deloc 1.250 0.020
RPD C9A OKA deloc 1.250 0.020
RPD OAA NAA single 1.460 0.020
RPD CBA NAA single 1.469 0.020
RPD H10 OAA single 0.967 0.020
RPD OBA CBA single 1.432 0.020
RPD H111 CBA single 1.092 0.020
RPD H112 CBA single 1.092 0.020
RPD H11 OBA 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
RPD OKA C9A OJA 123.000 3.000
RPD OKA C9A C8A 118.500 3.000
RPD OJA C9A C8A 118.500 3.000
RPD C9A C8A H81 108.810 3.000
RPD C9A C8A NAA 109.500 3.000
RPD C9A C8A C7A 109.470 3.000
RPD H81 C8A NAA 109.500 3.000
RPD H81 C8A C7A 108.340 3.000
RPD NAA C8A C7A 109.500 3.000
RPD C8A NAA CBA 109.470 3.000
RPD C8A NAA OAA 109.500 3.000
RPD CBA NAA OAA 109.500 3.000
RPD NAA CBA H111 109.470 3.000
RPD NAA CBA H112 109.470 3.000
RPD NAA CBA OBA 109.500 3.000
RPD H111 CBA H112 107.900 3.000
RPD H111 CBA OBA 109.470 3.000
RPD H112 CBA OBA 109.470 3.000
RPD CBA OBA H11 109.470 3.000
RPD NAA OAA H10 109.470 3.000
RPD C8A C7A H71 109.470 3.000
RPD C8A C7A H72 109.470 3.000
RPD C8A C7A C6A 111.000 3.000
RPD H71 C7A H72 107.900 3.000
RPD H71 C7A C6A 109.470 3.000
RPD H72 C7A C6A 109.470 3.000
RPD C7A C6A H61 109.470 3.000
RPD C7A C6A H62 109.470 3.000
RPD C7A C6A C5A 111.000 3.000
RPD H61 C6A H62 107.900 3.000
RPD H61 C6A C5A 109.470 3.000
RPD H62 C6A C5A 109.470 3.000
RPD C6A C5A H51 109.470 3.000
RPD C6A C5A H52 109.470 3.000
RPD C6A C5A N3 109.500 3.000
RPD H51 C5A H52 107.900 3.000
RPD H51 C5A N3 109.500 3.000
RPD H52 C5A N3 109.500 3.000
RPD C5A N3 C2 126.000 3.000
RPD C5A N3 C4 126.000 3.000
RPD C2 N3 C4 108.000 3.000
RPD N3 C2 O2 108.000 3.000
RPD N3 C2 N1 108.000 3.000
RPD O2 C2 N1 108.000 3.000
RPD C2 N1 HN1 126.000 3.000
RPD C2 N1 "C1'" 108.000 3.000
RPD HN1 N1 "C1'" 108.000 3.000
RPD N3 C4 O4 108.000 3.000
RPD N3 C4 "C1'" 108.000 3.000
RPD O4 C4 "C1'" 108.000 3.000
RPD C4 "C1'" "O4'" 109.500 3.000
RPD C4 "C1'" "C2'" 109.470 3.000
RPD C4 "C1'" N1 109.500 3.000
RPD "O4'" "C1'" "C2'" 109.470 3.000
RPD "O4'" "C1'" N1 109.500 3.000
RPD "C2'" "C1'" N1 109.500 3.000
RPD "C1'" "O4'" "C4'" 111.800 3.000
RPD "C1'" "C2'" H2 108.340 3.000
RPD "C1'" "C2'" "O2'" 109.470 3.000
RPD "C1'" "C2'" "C3'" 111.000 3.000
RPD H2 "C2'" "O2'" 109.470 3.000
RPD H2 "C2'" "C3'" 108.340 3.000
RPD "O2'" "C2'" "C3'" 109.470 3.000
RPD "C2'" "O2'" "HO2'" 109.470 3.000
RPD "C2'" "C3'" H3 108.340 3.000
RPD "C2'" "C3'" "O3'" 109.470 3.000
RPD "C2'" "C3'" "C4'" 111.000 3.000
RPD H3 "C3'" "O3'" 109.470 3.000
RPD H3 "C3'" "C4'" 108.340 3.000
RPD "O3'" "C3'" "C4'" 109.470 3.000
RPD "C3'" "O3'" "HO3'" 109.470 3.000
RPD "C3'" "C4'" H4 108.340 3.000
RPD "C3'" "C4'" "C5'" 111.000 3.000
RPD "C3'" "C4'" "O4'" 109.470 3.000
RPD H4 "C4'" "C5'" 108.340 3.000
RPD H4 "C4'" "O4'" 109.470 3.000
RPD "C5'" "C4'" "O4'" 109.470 3.000
RPD "C4'" "C5'" "H5'2" 109.470 3.000
RPD "C4'" "C5'" "H5'1" 109.470 3.000
RPD "C4'" "C5'" "O5'" 109.470 3.000
RPD "H5'2" "C5'" "H5'1" 107.900 3.000
RPD "H5'2" "C5'" "O5'" 109.470 3.000
RPD "H5'1" "C5'" "O5'" 109.470 3.000
RPD "C5'" "O5'" P 120.500 3.000
RPD "O5'" P O1P 108.200 3.000
RPD "O5'" P O2P 108.200 3.000
RPD "O5'" P O3P 108.200 3.000
RPD O1P P O2P 119.900 3.000
RPD O1P P O3P 119.900 3.000
RPD O2P P O3P 119.900 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
RPD var_1 OKA C9A C8A C7A 82.915 20.000 3
RPD var_2 C9A C8A NAA OAA -72.305 20.000 1
RPD var_3 C8A NAA CBA OBA -60.023 20.000 1
RPD var_4 NAA CBA OBA H11 -179.991 20.000 1
RPD var_5 C8A NAA OAA H10 65.343 20.000 1
RPD var_6 C9A C8A C7A C6A -65.369 20.000 3
RPD var_7 C8A C7A C6A C5A -176.408 20.000 3
RPD var_8 C7A C6A C5A N3 179.979 20.000 3
RPD var_9 C6A C5A N3 C4 -90.153 20.000 1
RPD CONST_1 C5A N3 C2 N1 180.000 0.000 0
RPD CONST_2 N3 C2 N1 "C1'" 0.000 0.000 0
RPD CONST_3 C5A N3 C4 "C1'" 180.000 0.000 0
RPD CONST_4 N3 C4 "C1'" "C2'" -120.000 0.000 0
RPD CONST_5 C4 "C1'" N1 C2 0.000 0.000 0
RPD var_10 C4 "C1'" "O4'" "C4'" 120.000 20.000 1
RPD var_11 C4 "C1'" "C2'" "C3'" -150.000 20.000 1
RPD var_12 "C1'" "C2'" "O2'" "HO2'" -174.155 20.000 1
RPD var_13 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
RPD var_14 "C2'" "C3'" "O3'" "HO3'" -173.161 20.000 1
RPD var_15 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
RPD var_16 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
RPD var_17 "C3'" "C4'" "C5'" "O5'" 177.266 20.000 3
RPD var_18 "C4'" "C5'" "O5'" P -179.930 20.000 1
RPD var_19 "C5'" "O5'" P O3P -60.036 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
RPD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
RPD chir_02 "C3'" "C4'" "O3'" "C2'" negativ
RPD chir_03 "C2'" "C3'" "O2'" "C1'" negativ
RPD chir_04 "C1'" "O4'" "C2'" N1 positiv
RPD chir_05 C8A C7A C9A NAA positiv
RPD chir_06 NAA C8A OAA CBA 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
RPD plan-1 N1 0.020
RPD plan-1 "C1'" 0.020
RPD plan-1 C2 0.020
RPD plan-1 HN1 0.020
RPD plan-1 N3 0.020
RPD plan-1 C4 0.020
RPD plan-1 O2 0.020
RPD plan-1 C5A 0.020
RPD plan-1 O4 0.020
RPD plan-2 C9A 0.020
RPD plan-2 C8A 0.020
RPD plan-2 OJA 0.020
RPD plan-2 OKA 0.020
# ------------------------------------------------------
|
