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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
CDF CDF '4-AMINO-1-{5-O-[(R)-HYDROXY(PHOSPHON' non-polymer 37 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CDF
#
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
CDF O2 O O 0.000 0.000 0.000 0.000
CDF C2 C CR6 0.000 -0.619 -0.949 0.453
CDF N3 N NRD6 0.000 0.046 -2.019 0.884
CDF C4 C CR6 0.000 -0.603 -3.065 1.381
CDF N4 N NH2 0.000 0.094 -4.165 1.824
CDF H42N H H 0.000 -0.398 -4.965 2.204
CDF H41N H H 0.000 1.107 -4.184 1.774
CDF C5 C CR16 0.000 -2.011 -3.041 1.452
CDF H5 H H 0.000 -2.556 -3.888 1.850
CDF C6 C CR16 0.000 -2.672 -1.943 1.015
CDF H6 H H 0.000 -3.753 -1.898 1.067
CDF N1 N NR6 0.000 -1.963 -0.896 0.509
CDF "C1'" C CH1 0.000 -2.666 0.295 0.027
CDF "H1'" H H 0.000 -2.435 0.472 -1.033
CDF "O4'" O O2 0.000 -4.083 0.147 0.212
CDF "C2'" C CH1 0.000 -2.274 1.531 0.877
CDF "H2'" H H 0.000 -2.153 1.261 1.935
CDF "O2'" O OH1 0.000 -1.094 2.153 0.366
CDF HB H H 0.000 -0.933 2.979 0.842
CDF "C3'" C CH1 0.000 -3.519 2.437 0.670
CDF "H3'" H H 0.000 -3.433 3.013 -0.262
CDF "O3'" O OH1 0.000 -3.707 3.304 1.790
CDF HA H H 0.000 -2.981 3.941 1.830
CDF "C4'" C CH1 0.000 -4.663 1.406 0.576
CDF "H4'" H H 0.000 -5.167 1.317 1.548
CDF "C5'" C CH2 0.000 -5.667 1.841 -0.493
CDF "H5'1" H H 0.000 -5.183 1.832 -1.472
CDF "H5'2" H H 0.000 -6.019 2.851 -0.271
CDF "O5'" O O2 0.000 -6.776 0.940 -0.500
CDF PA P P 0.000 -8.027 1.095 -1.502
CDF O1A O OP -0.500 -7.568 0.902 -2.899
CDF O2A O OP -0.500 -8.610 2.451 -1.357
CDF O3A O O2 0.000 -9.142 -0.010 -1.146
CDF PB P P 0.000 -10.693 -0.199 -1.533
CDF O3B O OP -0.666 -10.878 0.056 -3.012
CDF O1B O OP -0.666 -11.534 0.781 -0.743
CDF O2B O OP -0.666 -11.125 -1.612 -1.207
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
CDF O2 n/a C2 START
CDF C2 O2 N3 .
CDF N3 C2 C4 .
CDF C4 N3 C5 .
CDF N4 C4 H41N .
CDF H42N N4 . .
CDF H41N N4 . .
CDF C5 C4 C6 .
CDF H5 C5 . .
CDF C6 C5 N1 .
CDF H6 C6 . .
CDF N1 C6 "C1'" .
CDF "C1'" N1 "C2'" .
CDF "H1'" "C1'" . .
CDF "O4'" "C1'" . .
CDF "C2'" "C1'" "C3'" .
CDF "H2'" "C2'" . .
CDF "O2'" "C2'" HB .
CDF HB "O2'" . .
CDF "C3'" "C2'" "C4'" .
CDF "H3'" "C3'" . .
CDF "O3'" "C3'" HA .
CDF HA "O3'" . .
CDF "C4'" "C3'" "C5'" .
CDF "H4'" "C4'" . .
CDF "C5'" "C4'" "O5'" .
CDF "H5'1" "C5'" . .
CDF "H5'2" "C5'" . .
CDF "O5'" "C5'" PA .
CDF PA "O5'" O3A .
CDF O1A PA . .
CDF O2A PA . .
CDF O3A PA PB .
CDF PB O3A O2B .
CDF O3B PB . .
CDF O1B PB . .
CDF O2B PB . END
CDF "C4'" "O4'" . ADD
CDF 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
CDF O3B PB deloc 1.510 0.020
CDF O1B PB deloc 1.510 0.020
CDF O2B PB deloc 1.510 0.020
CDF PB O3A single 1.610 0.020
CDF O3A PA single 1.610 0.020
CDF O1A PA deloc 1.510 0.020
CDF O2A PA deloc 1.510 0.020
CDF PA "O5'" single 1.610 0.020
CDF "O5'" "C5'" single 1.426 0.020
CDF "C5'" "C4'" single 1.524 0.020
CDF "C4'" "O4'" single 1.426 0.020
CDF "C4'" "C3'" single 1.524 0.020
CDF "O4'" "C1'" single 1.426 0.020
CDF "O3'" "C3'" single 1.432 0.020
CDF "C3'" "C2'" single 1.524 0.020
CDF "O2'" "C2'" single 1.432 0.020
CDF "C2'" "C1'" single 1.524 0.020
CDF "C1'" N1 single 1.465 0.020
CDF N1 C2 single 1.410 0.020
CDF N1 C6 single 1.337 0.020
CDF C2 O2 double 1.250 0.020
CDF N3 C2 single 1.350 0.020
CDF C4 N3 double 1.350 0.020
CDF N4 C4 single 1.355 0.020
CDF C5 C4 single 1.390 0.020
CDF "H5'1" "C5'" single 1.092 0.020
CDF "H5'2" "C5'" single 1.092 0.020
CDF "H4'" "C4'" single 1.099 0.020
CDF "H3'" "C3'" single 1.099 0.020
CDF "H1'" "C1'" single 1.099 0.020
CDF HA "O3'" single 0.967 0.020
CDF "H2'" "C2'" single 1.099 0.020
CDF HB "O2'" single 0.967 0.020
CDF H41N N4 single 1.010 0.020
CDF H42N N4 single 1.010 0.020
CDF C6 C5 double 1.390 0.020
CDF H5 C5 single 1.083 0.020
CDF H6 C6 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
CDF O2 C2 N3 120.000 3.000
CDF O2 C2 N1 120.000 3.000
CDF N3 C2 N1 120.000 3.000
CDF C2 N3 C4 120.000 3.000
CDF N3 C4 N4 120.000 3.000
CDF N3 C4 C5 120.000 3.000
CDF N4 C4 C5 120.000 3.000
CDF C4 N4 H42N 120.000 3.000
CDF C4 N4 H41N 120.000 3.000
CDF H42N N4 H41N 120.000 3.000
CDF C4 C5 H5 120.000 3.000
CDF C4 C5 C6 120.000 3.000
CDF H5 C5 C6 120.000 3.000
CDF C5 C6 H6 120.000 3.000
CDF C5 C6 N1 120.000 3.000
CDF H6 C6 N1 120.000 3.000
CDF C6 N1 "C1'" 120.000 3.000
CDF C6 N1 C2 120.000 3.000
CDF "C1'" N1 C2 120.000 3.000
CDF N1 "C1'" "H1'" 109.470 3.000
CDF N1 "C1'" "O4'" 109.470 3.000
CDF N1 "C1'" "C2'" 109.470 3.000
CDF "H1'" "C1'" "O4'" 109.470 3.000
CDF "H1'" "C1'" "C2'" 108.340 3.000
CDF "O4'" "C1'" "C2'" 109.470 3.000
CDF "C1'" "O4'" "C4'" 111.800 3.000
CDF "C1'" "C2'" "H2'" 108.340 3.000
CDF "C1'" "C2'" "O2'" 109.470 3.000
CDF "C1'" "C2'" "C3'" 111.000 3.000
CDF "H2'" "C2'" "O2'" 109.470 3.000
CDF "H2'" "C2'" "C3'" 108.340 3.000
CDF "O2'" "C2'" "C3'" 109.470 3.000
CDF "C2'" "O2'" HB 109.470 3.000
CDF "C2'" "C3'" "H3'" 108.340 3.000
CDF "C2'" "C3'" "O3'" 109.470 3.000
CDF "C2'" "C3'" "C4'" 111.000 3.000
CDF "H3'" "C3'" "O3'" 109.470 3.000
CDF "H3'" "C3'" "C4'" 108.340 3.000
CDF "O3'" "C3'" "C4'" 109.470 3.000
CDF "C3'" "O3'" HA 109.470 3.000
CDF "C3'" "C4'" "H4'" 108.340 3.000
CDF "C3'" "C4'" "C5'" 111.000 3.000
CDF "C3'" "C4'" "O4'" 109.470 3.000
CDF "H4'" "C4'" "C5'" 108.340 3.000
CDF "H4'" "C4'" "O4'" 109.470 3.000
CDF "C5'" "C4'" "O4'" 109.470 3.000
CDF "C4'" "C5'" "H5'1" 109.470 3.000
CDF "C4'" "C5'" "H5'2" 109.470 3.000
CDF "C4'" "C5'" "O5'" 109.470 3.000
CDF "H5'1" "C5'" "H5'2" 107.900 3.000
CDF "H5'1" "C5'" "O5'" 109.470 3.000
CDF "H5'2" "C5'" "O5'" 109.470 3.000
CDF "C5'" "O5'" PA 120.500 3.000
CDF "O5'" PA O1A 108.200 3.000
CDF "O5'" PA O2A 108.200 3.000
CDF "O5'" PA O3A 102.600 3.000
CDF O1A PA O2A 119.900 3.000
CDF O1A PA O3A 108.200 3.000
CDF O2A PA O3A 108.200 3.000
CDF PA O3A PB 120.500 3.000
CDF O3A PB O3B 108.200 3.000
CDF O3A PB O1B 108.200 3.000
CDF O3A PB O2B 108.200 3.000
CDF O3B PB O1B 119.900 3.000
CDF O3B PB O2B 119.900 3.000
CDF O1B PB O2B 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
CDF CONST_1 O2 C2 N3 C4 180.000 0.000 0
CDF CONST_2 C2 N3 C4 C5 0.000 0.000 0
CDF CONST_3 N3 C4 N4 H41N 0.008 0.000 0
CDF CONST_4 N3 C4 C5 C6 0.000 0.000 0
CDF CONST_5 C4 C5 C6 N1 0.000 0.000 0
CDF CONST_6 C5 C6 N1 "C1'" 180.000 0.000 0
CDF CONST_7 C6 N1 C2 O2 180.000 0.000 0
CDF var_1 C6 N1 "C1'" "C2'" 116.892 20.000 1
CDF var_2 N1 "C1'" "O4'" "C4'" 150.000 20.000 1
CDF var_3 N1 "C1'" "C2'" "C3'" -150.000 20.000 3
CDF var_4 "C1'" "C2'" "O2'" HB 173.036 20.000 1
CDF var_5 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
CDF var_6 "C2'" "C3'" "O3'" HA 67.142 20.000 1
CDF var_7 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
CDF var_8 "C3'" "C4'" "O4'" "C1'" 0.000 20.000 1
CDF var_9 "C3'" "C4'" "C5'" "O5'" -175.396 20.000 3
CDF var_10 "C4'" "C5'" "O5'" PA 179.992 20.000 1
CDF var_11 "C5'" "O5'" PA O3A -175.042 20.000 1
CDF var_12 "O5'" PA O3A PB 164.940 20.000 1
CDF var_13 PA O3A PB O2B 165.010 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
CDF chir_01 "C4'" "C5'" "O4'" "C3'" negativ
CDF chir_02 "C3'" "C4'" "O3'" "C2'" negativ
CDF chir_03 "C2'" "C3'" "O2'" "C1'" positiv
CDF chir_04 "C1'" "O4'" "C2'" N1 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
CDF plan-1 N1 0.020
CDF plan-1 "C1'" 0.020
CDF plan-1 C2 0.020
CDF plan-1 C6 0.020
CDF plan-1 N3 0.020
CDF plan-1 C4 0.020
CDF plan-1 C5 0.020
CDF plan-1 O2 0.020
CDF plan-1 N4 0.020
CDF plan-1 H6 0.020
CDF plan-1 H5 0.020
CDF plan-1 H42N 0.020
CDF plan-1 H41N 0.020
CDF plan-2 N4 0.020
CDF plan-2 C4 0.020
CDF plan-2 H41N 0.020
CDF plan-2 H42N 0.020
# ------------------------------------------------------
|
