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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
AVC AVC 'ADENOSINE-5'-MONOPHOSPHATE-2',3'-VAN' RNA 37 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AVC
#
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
AVC OP3 O OP -0.666 -4.538 2.933 0.955
AVC P P P 0.000 -4.802 1.911 -0.129
AVC OP1 O OP -0.666 -5.825 0.910 0.361
AVC OP2 O OP -0.666 -5.330 2.609 -1.363
AVC "O5'" O O2 0.000 -3.432 1.145 -0.490
AVC "C5'" C CH2 0.000 -2.742 0.306 0.438
AVC "H5'" H H 0.000 -3.396 -0.514 0.743
AVC "H5''" H H 0.000 -2.460 0.890 1.316
AVC "C4'" C CH1 0.000 -1.485 -0.261 -0.225
AVC "H4'" H H 0.000 -1.742 -0.805 -1.145
AVC "C3'" C CH1 0.000 -0.717 -1.177 0.755
AVC "H3'" H H 0.000 -0.728 -0.719 1.754
AVC "C2'" C CH1 0.000 0.718 -1.135 0.203
AVC "H2'" H H 0.000 1.456 -1.116 1.017
AVC "C1'" C CH1 0.000 0.759 0.175 -0.618
AVC "H1'" H H 0.000 0.973 -0.050 -1.672
AVC "O4'" O O2 0.000 -0.534 0.792 -0.502
AVC N9 N NR5 0.000 1.787 1.069 -0.079
AVC C4 C CR56 0.000 3.122 1.055 -0.398
AVC C5 C CR56 0.000 3.710 2.085 0.356
AVC N7 N NRD5 0.000 2.724 2.657 1.088
AVC C8 C CR15 0.000 1.595 2.062 0.834
AVC H8 H H 0.000 0.643 2.318 1.282
AVC N3 N NRD6 0.000 3.885 0.336 -1.214
AVC C2 C CR16 0.000 5.175 0.573 -1.310
AVC H2 H H 0.000 5.768 -0.036 -1.981
AVC N1 N NRD6 0.000 5.774 1.526 -0.618
AVC C6 C CR6 0.000 5.092 2.301 0.219
AVC N6 N NH2 0.000 5.727 3.297 0.940
AVC H62 H H 0.000 6.726 3.451 0.838
AVC H61 H H 0.000 5.202 3.886 1.579
AVC "O2'" O O2 0.000 0.993 -2.221 -0.732
AVC V V V 0.000 -0.029 -3.565 0.082
AVC O1V O O 0.000 -0.635 -4.567 -0.984
AVC O2V O OH1 0.000 0.927 -4.456 1.378
AVC HV H H 0.000 1.608 -5.030 1.082
AVC "O3'" O O2 0.000 -1.346 -2.465 0.827
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
AVC OP3 n/a P START
AVC P OP3 "O5'" .
AVC OP1 P . .
AVC OP2 P . .
AVC "O5'" P "C5'" .
AVC "C5'" "O5'" "C4'" .
AVC "H5'" "C5'" . .
AVC "H5''" "C5'" . .
AVC "C4'" "C5'" "C3'" .
AVC "H4'" "C4'" . .
AVC "C3'" "C4'" "C2'" .
AVC "H3'" "C3'" . .
AVC "C2'" "C3'" "O2'" .
AVC "H2'" "C2'" . .
AVC "C1'" "C2'" N9 .
AVC "H1'" "C1'" . .
AVC "O4'" "C1'" . .
AVC N9 "C1'" C4 .
AVC C4 N9 N3 .
AVC C5 C4 N7 .
AVC N7 C5 C8 .
AVC C8 N7 H8 .
AVC H8 C8 . .
AVC N3 C4 C2 .
AVC C2 N3 N1 .
AVC H2 C2 . .
AVC N1 C2 C6 .
AVC C6 N1 N6 .
AVC N6 C6 H61 .
AVC H62 N6 . .
AVC H61 N6 . .
AVC "O2'" "C2'" V .
AVC V "O2'" "O3'" .
AVC O1V V . .
AVC O2V V HV .
AVC HV O2V . .
AVC "O3'" V . END
AVC "C4'" "O4'" . ADD
AVC "C3'" "O3'" . ADD
AVC N9 C8 . ADD
AVC 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
AVC P OP3 deloc 1.510 0.020
AVC OP1 P deloc 1.510 0.020
AVC OP2 P deloc 1.510 0.020
AVC "O5'" P single 1.610 0.020
AVC "C5'" "O5'" single 1.426 0.020
AVC "C4'" "C5'" single 1.524 0.020
AVC "H5'" "C5'" single 1.092 0.020
AVC "H5''" "C5'" single 1.092 0.020
AVC "C4'" "O4'" single 1.426 0.020
AVC "C3'" "C4'" single 1.524 0.020
AVC "H4'" "C4'" single 1.099 0.020
AVC "O4'" "C1'" single 1.426 0.020
AVC "C3'" "O3'" single 1.426 0.020
AVC "C2'" "C3'" single 1.524 0.020
AVC "H3'" "C3'" single 1.099 0.020
AVC "O3'" V single 2.004 0.020
AVC "O2'" "C2'" single 1.426 0.020
AVC "C1'" "C2'" single 1.524 0.020
AVC "H2'" "C2'" single 1.099 0.020
AVC V "O2'" single 2.004 0.020
AVC N9 "C1'" single 1.485 0.020
AVC "H1'" "C1'" single 1.099 0.020
AVC O1V V double 1.910 0.020
AVC O2V V single 2.105 0.020
AVC HV O2V single 0.967 0.020
AVC N9 C8 single 1.337 0.020
AVC C4 N9 single 1.337 0.020
AVC C8 N7 double 1.350 0.020
AVC H8 C8 single 1.083 0.020
AVC N7 C5 single 1.350 0.020
AVC C5 C6 single 1.490 0.020
AVC C5 C4 double 1.490 0.020
AVC N6 C6 single 1.355 0.020
AVC C6 N1 double 1.350 0.020
AVC H61 N6 single 1.010 0.020
AVC H62 N6 single 1.010 0.020
AVC N1 C2 single 1.337 0.020
AVC C2 N3 double 1.337 0.020
AVC H2 C2 single 1.083 0.020
AVC N3 C4 single 1.355 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
AVC OP3 P OP1 119.900 3.000
AVC OP3 P OP2 119.900 3.000
AVC OP3 P "O5'" 108.200 3.000
AVC OP1 P OP2 119.900 3.000
AVC OP1 P "O5'" 108.200 3.000
AVC OP2 P "O5'" 108.200 3.000
AVC P "O5'" "C5'" 120.500 3.000
AVC "O5'" "C5'" "H5'" 109.470 3.000
AVC "O5'" "C5'" "H5''" 109.470 3.000
AVC "O5'" "C5'" "C4'" 109.470 3.000
AVC "H5'" "C5'" "H5''" 107.900 3.000
AVC "H5'" "C5'" "C4'" 109.470 3.000
AVC "H5''" "C5'" "C4'" 109.470 3.000
AVC "C5'" "C4'" "H4'" 108.340 3.000
AVC "C5'" "C4'" "C3'" 111.000 3.000
AVC "C5'" "C4'" "O4'" 109.470 3.000
AVC "H4'" "C4'" "C3'" 108.340 3.000
AVC "H4'" "C4'" "O4'" 109.470 3.000
AVC "C3'" "C4'" "O4'" 109.470 3.000
AVC "C4'" "C3'" "H3'" 108.340 3.000
AVC "C4'" "C3'" "C2'" 111.000 3.000
AVC "C4'" "C3'" "O3'" 109.470 3.000
AVC "H3'" "C3'" "C2'" 108.340 3.000
AVC "H3'" "C3'" "O3'" 109.470 3.000
AVC "C2'" "C3'" "O3'" 109.470 3.000
AVC "C3'" "C2'" "H2'" 108.340 3.000
AVC "C3'" "C2'" "C1'" 111.000 3.000
AVC "C3'" "C2'" "O2'" 109.470 3.000
AVC "H2'" "C2'" "C1'" 108.340 3.000
AVC "H2'" "C2'" "O2'" 109.470 3.000
AVC "C1'" "C2'" "O2'" 109.470 3.000
AVC "C2'" "C1'" "H1'" 108.340 3.000
AVC "C2'" "C1'" "O4'" 109.470 3.000
AVC "C2'" "C1'" N9 109.470 3.000
AVC "H1'" "C1'" "O4'" 109.470 3.000
AVC "H1'" "C1'" N9 109.470 3.000
AVC "O4'" "C1'" N9 109.470 3.000
AVC "C1'" "O4'" "C4'" 111.800 3.000
AVC "C1'" N9 C4 126.000 3.000
AVC "C1'" N9 C8 126.000 3.000
AVC C4 N9 C8 108.000 3.000
AVC N9 C4 C5 108.000 3.000
AVC N9 C4 N3 132.000 3.000
AVC C5 C4 N3 120.000 3.000
AVC C4 C5 N7 108.000 3.000
AVC C4 C5 C6 120.000 3.000
AVC N7 C5 C6 132.000 3.000
AVC C5 N7 C8 108.000 3.000
AVC N7 C8 H8 126.000 3.000
AVC N7 C8 N9 108.000 3.000
AVC H8 C8 N9 126.000 3.000
AVC C4 N3 C2 120.000 3.000
AVC N3 C2 H2 120.000 3.000
AVC N3 C2 N1 120.000 3.000
AVC H2 C2 N1 120.000 3.000
AVC C2 N1 C6 120.000 3.000
AVC N1 C6 N6 120.000 3.000
AVC N1 C6 C5 120.000 3.000
AVC N6 C6 C5 120.000 3.000
AVC C6 N6 H62 120.000 3.000
AVC C6 N6 H61 120.000 3.000
AVC H62 N6 H61 120.000 3.000
AVC "C2'" "O2'" V 120.000 3.000
AVC "O2'" V O2V 111.697 3.000
AVC "O2'" V O1V 111.717 3.000
AVC "O2'" V "O3'" 97.769 3.000
AVC O2V V O1V 111.498 3.000
AVC O2V V "O3'" 111.711 3.000
AVC O1V V "O3'" 111.762 3.000
AVC V O2V HV 120.000 3.000
AVC V "O3'" "C3'" 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
AVC var_1 OP3 P "O5'" "C5'" 65.000 20.000 1
AVC var_2 P "O5'" "C5'" "C4'" -179.990 20.000 1
AVC var_3 "O5'" "C5'" "C4'" "C3'" -179.882 20.000 3
AVC var_4 "C5'" "C4'" "O4'" "C1'" 158.017 20.000 1
AVC var_5 "C5'" "C4'" "C3'" "C2'" -156.069 20.000 3
AVC var_6 "C4'" "C3'" "O3'" V 114.197 20.000 1
AVC var_7 "C4'" "C3'" "C2'" "O2'" -92.782 20.000 3
AVC var_8 "C3'" "C2'" "C1'" N9 120.112 20.000 3
AVC var_9 "C2'" "C1'" "O4'" "C4'" -25.508 20.000 1
AVC var_10 "C2'" "C1'" N9 C4 85.433 20.000 1
AVC CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
AVC CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
AVC CONST_3 N9 C4 C5 N7 0.000 0.000 0
AVC CONST_4 C4 C5 C6 N1 0.000 0.000 0
AVC CONST_5 C4 C5 N7 C8 0.000 0.000 0
AVC CONST_6 C5 N7 C8 N9 0.000 0.000 0
AVC CONST_7 N9 C4 N3 C2 180.000 0.000 0
AVC CONST_8 C4 N3 C2 N1 0.000 0.000 0
AVC CONST_9 N3 C2 N1 C6 0.000 0.000 0
AVC CONST_10 C2 N1 C6 N6 180.000 0.000 0
AVC CONST_11 N1 C6 N6 H61 -179.930 0.000 0
AVC var_11 "C3'" "C2'" "O2'" V -35.439 20.000 1
AVC var_12 "C2'" "O2'" V "O3'" 30.222 20.000 1
AVC var_13 "O2'" V O2V HV -71.677 20.000 1
AVC var_14 "O2'" V "O3'" "C3'" -16.463 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
AVC chir_01 "C4'" "C5'" "O4'" "C3'" negativ
AVC chir_02 "C3'" "C4'" "O3'" "C2'" negativ
AVC chir_03 "C2'" "C3'" "O2'" "C1'" negativ
AVC 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
AVC plan-1 N9 0.020
AVC plan-1 "C1'" 0.020
AVC plan-1 C8 0.020
AVC plan-1 C4 0.020
AVC plan-1 N7 0.020
AVC plan-1 H8 0.020
AVC plan-1 C5 0.020
AVC plan-1 C6 0.020
AVC plan-1 N1 0.020
AVC plan-1 C2 0.020
AVC plan-1 N3 0.020
AVC plan-1 N6 0.020
AVC plan-1 H2 0.020
AVC plan-1 H62 0.020
AVC plan-1 H61 0.020
AVC plan-2 N6 0.020
AVC plan-2 C6 0.020
AVC plan-2 H61 0.020
AVC plan-2 H62 0.020
# ------------------------------------------------------
|
