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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
2NT 2NT '. ' DNA 48 28 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2NT
#
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
2NT OP3 O OP -0.666 0.000 0.000 0.000
2NT P P P 0.000 0.523 -0.307 1.386
2NT OP2 O OP -0.666 0.612 -1.818 1.396
2NT OP1 O OP -0.666 1.799 0.410 1.770
2NT "O5'" O O2 0.000 -0.743 -0.012 2.350
2NT "C5'" C CH2 0.000 -1.976 -0.647 2.059
2NT "H5'" H H 0.000 -1.852 -1.731 2.097
2NT "H5''" H H 0.000 -2.317 -0.355 1.064
2NT "C4'" C CH1 0.000 -3.003 -0.214 3.098
2NT "H4'" H H 0.000 -2.642 -0.465 4.105
2NT "C3'" C CH1 0.000 -4.379 -0.830 2.876
2NT "H3'" H H 0.000 -4.314 -1.841 2.449
2NT "C2'" C CH1 0.000 -5.014 0.152 1.915
2NT "H2'" H H 0.000 -4.647 -0.033 0.895
2NT "O2'" O O2 0.000 -6.425 0.088 1.937
2NT "CB'" C CH2 0.000 -6.903 -1.205 1.579
2NT "HB'1" H H 0.000 -6.504 -1.949 2.271
2NT "HB'2" H H 0.000 -6.583 -1.446 0.563
2NT "CC'" C CH2 0.000 -8.418 -1.209 1.647
2NT "HC'1" H H 0.000 -8.795 -2.193 1.360
2NT "HC'2" H H 0.000 -8.818 -0.454 0.967
2NT "OD'" O O2 0.000 -8.823 -0.913 2.978
2NT "NE'" N NH1 0.000 -10.278 -0.926 3.006
2NT "HE'" H H 0.000 -10.904 -1.190 2.258
2NT "CF'" C CH2 0.000 -10.640 -0.474 4.344
2NT "HF'1" H H 0.000 -11.707 -0.243 4.338
2NT "HF'2" H H 0.000 -10.073 0.435 4.551
2NT "OG'" O OH1 0.000 -10.369 -1.443 5.349
2NT "HG'" H H 0.000 -9.455 -1.743 5.265
2NT "C1'" C CH1 0.000 -4.481 1.481 2.422
2NT "H1'" H H 0.000 -5.148 1.872 3.203
2NT "O4'" O O2 0.000 -3.185 1.214 2.984
2NT N1 N NR6 0.000 -4.344 2.453 1.375
2NT C2 C CR6 0.000 -5.369 3.385 1.101
2NT O2 O O 0.000 -6.431 3.437 1.723
2NT N3 N NR16 0.000 -5.100 4.272 0.053
2NT HN3 H H 0.000 -5.841 4.968 -0.168
2NT C4 C CR6 0.000 -3.952 4.324 -0.723
2NT O4 O O 0.000 -3.781 5.134 -1.630
2NT C5 C CR6 0.000 -2.919 3.312 -0.377
2NT C5M C CH3 0.000 -1.651 3.303 -1.169
2NT H73 H H 0.000 -1.658 4.112 -1.851
2NT H72 H H 0.000 -0.827 3.399 -0.513
2NT H71 H H 0.000 -1.577 2.391 -1.701
2NT C6 C CR16 0.000 -3.173 2.461 0.626
2NT H6 H H 0.000 -2.413 1.729 0.869
2NT "O3'" O OH1 0.000 -5.071 -0.820 4.124
2NT "HO3'" H H 0.000 -4.778 -1.606 4.607
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
2NT OP3 n/a P START
2NT P OP3 "O5'" .
2NT OP2 P . .
2NT OP1 P . .
2NT "O5'" P "C5'" .
2NT "C5'" "O5'" "C4'" .
2NT "H5'" "C5'" . .
2NT "H5''" "C5'" . .
2NT "C4'" "C5'" "C3'" .
2NT "H4'" "C4'" . .
2NT "C3'" "C4'" "O3'" .
2NT "H3'" "C3'" . .
2NT "C2'" "C3'" "C1'" .
2NT "H2'" "C2'" . .
2NT "O2'" "C2'" "CB'" .
2NT "CB'" "O2'" "CC'" .
2NT "HB'1" "CB'" . .
2NT "HB'2" "CB'" . .
2NT "CC'" "CB'" "OD'" .
2NT "HC'1" "CC'" . .
2NT "HC'2" "CC'" . .
2NT "OD'" "CC'" "NE'" .
2NT "NE'" "OD'" "CF'" .
2NT "HE'" "NE'" . .
2NT "CF'" "NE'" "OG'" .
2NT "HF'1" "CF'" . .
2NT "HF'2" "CF'" . .
2NT "OG'" "CF'" "HG'" .
2NT "HG'" "OG'" . .
2NT "C1'" "C2'" N1 .
2NT "H1'" "C1'" . .
2NT "O4'" "C1'" . .
2NT N1 "C1'" C2 .
2NT C2 N1 N3 .
2NT O2 C2 . .
2NT N3 C2 C4 .
2NT HN3 N3 . .
2NT C4 N3 C5 .
2NT O4 C4 . .
2NT C5 C4 C6 .
2NT C5M C5 H71 .
2NT H73 C5M . .
2NT H72 C5M . .
2NT H71 C5M . .
2NT C6 C5 H6 .
2NT H6 C6 . .
2NT "O3'" "C3'" . END
2NT "HO3'" "O3'" . .
2NT "C4'" "O4'" . ADD
2NT N1 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
2NT P OP3 deloc 1.510 0.020
2NT OP2 P deloc 1.510 0.020
2NT "O5'" P single 1.610 0.020
2NT OP1 P deloc 1.510 0.020
2NT "C5'" "O5'" single 1.426 0.020
2NT "C4'" "C5'" single 1.524 0.020
2NT "H5'" "C5'" single 1.092 0.020
2NT "H5''" "C5'" single 1.092 0.020
2NT "C4'" "O4'" single 1.426 0.020
2NT "C3'" "C4'" single 1.524 0.020
2NT "H4'" "C4'" single 1.099 0.020
2NT "O4'" "C1'" single 1.426 0.020
2NT N1 "C1'" single 1.465 0.020
2NT "C1'" "C2'" single 1.524 0.020
2NT "H1'" "C1'" single 1.099 0.020
2NT N1 C6 single 1.337 0.020
2NT C2 N1 single 1.410 0.020
2NT C6 C5 double 1.390 0.020
2NT H6 C6 single 1.083 0.020
2NT O2 C2 double 1.250 0.020
2NT N3 C2 single 1.337 0.020
2NT C4 N3 single 1.337 0.020
2NT HN3 N3 single 1.040 0.020
2NT O4 C4 double 1.250 0.020
2NT C5 C4 single 1.487 0.020
2NT C5M C5 single 1.506 0.020
2NT H71 C5M single 1.059 0.020
2NT H72 C5M single 1.059 0.020
2NT H73 C5M single 1.059 0.020
2NT "O2'" "C2'" single 1.426 0.020
2NT "C2'" "C3'" single 1.524 0.020
2NT "H2'" "C2'" single 1.099 0.020
2NT "CB'" "O2'" single 1.426 0.020
2NT "CC'" "CB'" single 1.524 0.020
2NT "HB'1" "CB'" single 1.092 0.020
2NT "HB'2" "CB'" single 1.092 0.020
2NT "OD'" "CC'" single 1.426 0.020
2NT "HC'1" "CC'" single 1.092 0.020
2NT "HC'2" "CC'" single 1.092 0.020
2NT "NE'" "OD'" single 1.335 0.020
2NT "CF'" "NE'" single 1.450 0.020
2NT "HE'" "NE'" single 1.010 0.020
2NT "OG'" "CF'" single 1.432 0.020
2NT "HF'1" "CF'" single 1.092 0.020
2NT "HF'2" "CF'" single 1.092 0.020
2NT "HG'" "OG'" single 0.967 0.020
2NT "O3'" "C3'" single 1.432 0.020
2NT "H3'" "C3'" single 1.099 0.020
2NT "HO3'" "O3'" 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
2NT OP3 P OP2 119.900 3.000
2NT OP3 P OP1 119.900 3.000
2NT OP3 P "O5'" 108.200 3.000
2NT OP2 P OP1 119.900 3.000
2NT OP2 P "O5'" 108.200 3.000
2NT OP1 P "O5'" 108.200 3.000
2NT P "O5'" "C5'" 120.500 3.000
2NT "O5'" "C5'" "H5'" 109.470 3.000
2NT "O5'" "C5'" "H5''" 109.470 3.000
2NT "O5'" "C5'" "C4'" 109.470 3.000
2NT "H5'" "C5'" "H5''" 107.900 3.000
2NT "H5'" "C5'" "C4'" 109.470 3.000
2NT "H5''" "C5'" "C4'" 109.470 3.000
2NT "C5'" "C4'" "H4'" 108.340 3.000
2NT "C5'" "C4'" "C3'" 111.000 3.000
2NT "C5'" "C4'" "O4'" 109.470 3.000
2NT "H4'" "C4'" "C3'" 108.340 3.000
2NT "H4'" "C4'" "O4'" 109.470 3.000
2NT "C3'" "C4'" "O4'" 109.470 3.000
2NT "C4'" "C3'" "H3'" 108.340 3.000
2NT "C4'" "C3'" "C2'" 111.000 3.000
2NT "C4'" "C3'" "O3'" 109.470 3.000
2NT "H3'" "C3'" "C2'" 108.340 3.000
2NT "H3'" "C3'" "O3'" 109.470 3.000
2NT "C2'" "C3'" "O3'" 109.470 3.000
2NT "C3'" "C2'" "H2'" 108.340 3.000
2NT "C3'" "C2'" "O2'" 109.470 3.000
2NT "C3'" "C2'" "C1'" 111.000 3.000
2NT "H2'" "C2'" "O2'" 109.470 3.000
2NT "H2'" "C2'" "C1'" 108.340 3.000
2NT "O2'" "C2'" "C1'" 109.470 3.000
2NT "C2'" "O2'" "CB'" 111.800 3.000
2NT "O2'" "CB'" "HB'1" 109.470 3.000
2NT "O2'" "CB'" "HB'2" 109.470 3.000
2NT "O2'" "CB'" "CC'" 109.470 3.000
2NT "HB'1" "CB'" "HB'2" 107.900 3.000
2NT "HB'1" "CB'" "CC'" 109.470 3.000
2NT "HB'2" "CB'" "CC'" 109.470 3.000
2NT "CB'" "CC'" "HC'1" 109.470 3.000
2NT "CB'" "CC'" "HC'2" 109.470 3.000
2NT "CB'" "CC'" "OD'" 109.470 3.000
2NT "HC'1" "CC'" "HC'2" 107.900 3.000
2NT "HC'1" "CC'" "OD'" 109.470 3.000
2NT "HC'2" "CC'" "OD'" 109.470 3.000
2NT "CC'" "OD'" "NE'" 120.000 3.000
2NT "OD'" "NE'" "HE'" 120.000 3.000
2NT "OD'" "NE'" "CF'" 120.000 3.000
2NT "HE'" "NE'" "CF'" 118.500 3.000
2NT "NE'" "CF'" "HF'1" 109.470 3.000
2NT "NE'" "CF'" "HF'2" 109.470 3.000
2NT "NE'" "CF'" "OG'" 109.500 3.000
2NT "HF'1" "CF'" "HF'2" 107.900 3.000
2NT "HF'1" "CF'" "OG'" 109.470 3.000
2NT "HF'2" "CF'" "OG'" 109.470 3.000
2NT "CF'" "OG'" "HG'" 109.470 3.000
2NT "C2'" "C1'" "H1'" 108.340 3.000
2NT "C2'" "C1'" "O4'" 109.470 3.000
2NT "C2'" "C1'" N1 109.470 3.000
2NT "H1'" "C1'" "O4'" 109.470 3.000
2NT "H1'" "C1'" N1 109.470 3.000
2NT "O4'" "C1'" N1 109.470 3.000
2NT "C1'" "O4'" "C4'" 111.800 3.000
2NT "C1'" N1 C2 120.000 3.000
2NT "C1'" N1 C6 120.000 3.000
2NT C2 N1 C6 120.000 3.000
2NT N1 C2 O2 120.000 3.000
2NT N1 C2 N3 120.000 3.000
2NT O2 C2 N3 120.000 3.000
2NT C2 N3 HN3 120.000 3.000
2NT C2 N3 C4 120.000 3.000
2NT HN3 N3 C4 120.000 3.000
2NT N3 C4 O4 120.000 3.000
2NT N3 C4 C5 120.000 3.000
2NT O4 C4 C5 120.000 3.000
2NT C4 C5 C5M 120.000 3.000
2NT C4 C5 C6 120.000 3.000
2NT C5M C5 C6 120.000 3.000
2NT C5 C5M H73 109.470 3.000
2NT C5 C5M H72 109.470 3.000
2NT C5 C5M H71 109.470 3.000
2NT H73 C5M H72 109.470 3.000
2NT H73 C5M H71 109.470 3.000
2NT H72 C5M H71 109.470 3.000
2NT C5 C6 H6 120.000 3.000
2NT C5 C6 N1 120.000 3.000
2NT H6 C6 N1 120.000 3.000
2NT "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
2NT var_1 OP3 P "O5'" "C5'" 53.194 20.000 1
2NT var_2 P "O5'" "C5'" "C4'" -179.986 20.000 1
2NT var_3 "O5'" "C5'" "C4'" "C3'" 179.497 20.000 3
2NT var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
2NT var_5 "C5'" "C4'" "C3'" "O3'" 150.000 20.000 3
2NT var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
2NT var_7 "C3'" "C2'" "O2'" "CB'" -59.966 20.000 1
2NT var_8 "C2'" "O2'" "CB'" "CC'" 179.001 20.000 1
2NT var_9 "O2'" "CB'" "CC'" "OD'" -60.850 20.000 3
2NT var_10 "CB'" "CC'" "OD'" "NE'" -179.989 20.000 1
2NT var_11 "CC'" "OD'" "NE'" "CF'" -173.909 20.000 1
2NT var_12 "OD'" "NE'" "CF'" "OG'" -72.056 20.000 3
2NT var_13 "NE'" "CF'" "OG'" "HG'" 51.587 20.000 1
2NT var_14 "C3'" "C2'" "C1'" N1 150.000 20.000 3
2NT var_15 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
2NT var_16 "C2'" "C1'" N1 C2 94.305 20.000 1
2NT CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
2NT CONST_2 "C1'" N1 C2 N3 180.000 0.000 0
2NT CONST_3 N1 C2 N3 C4 0.000 0.000 0
2NT CONST_4 C2 N3 C4 C5 0.000 0.000 0
2NT CONST_5 N3 C4 C5 C6 0.000 0.000 0
2NT var_17 C4 C5 C5M H71 -115.793 20.000 1
2NT CONST_6 C4 C5 C6 N1 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
2NT chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2NT chir_02 "C1'" "O4'" N1 "C2'" negativ
2NT chir_03 "C2'" "C1'" "O2'" "C3'" positiv
2NT 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
2NT plan-1 N1 0.020
2NT plan-1 "C1'" 0.020
2NT plan-1 C6 0.020
2NT plan-1 C2 0.020
2NT plan-1 N3 0.020
2NT plan-1 C4 0.020
2NT plan-1 C5 0.020
2NT plan-1 H6 0.020
2NT plan-1 O2 0.020
2NT plan-1 HN3 0.020
2NT plan-1 O4 0.020
2NT plan-1 C5M 0.020
2NT plan-2 "NE'" 0.020
2NT plan-2 "OD'" 0.020
2NT plan-2 "CF'" 0.020
2NT plan-2 "HE'" 0.020
# ------------------------------------------------------
|
