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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
GNP GNP 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLAT' non-polymer 48 32 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GNP
#
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
GNP O6 O O 0.000 0.000 0.000 0.000
GNP C6 C CR6 0.000 -0.685 -0.496 0.878
GNP N1 N NR16 0.000 -0.156 -1.382 1.750
GNP HN1 H H 0.000 0.848 -1.643 1.678
GNP C2 C CR6 0.000 -0.933 -1.936 2.724
GNP N2 N NH2 0.000 -0.370 -2.838 3.592
GNP HN22 H H 0.000 0.608 -3.090 3.505
GNP HN21 H H 0.000 -0.928 -3.259 4.326
GNP N3 N NRD6 0.000 -2.203 -1.626 2.860
GNP C4 C CR56 0.000 -2.793 -0.752 2.037
GNP C5 C CR56 0.000 -2.051 -0.154 1.013
GNP N7 N NRD5 0.000 -2.887 0.676 0.343
GNP C8 C CR15 0.000 -4.070 0.624 0.881
GNP H8 H H 0.000 -4.932 1.186 0.546
GNP N9 N NR5 0.000 -4.061 -0.246 1.933
GNP "C1'" C CH1 0.000 -5.199 -0.577 2.792
GNP "H1'" H H 0.000 -5.114 -1.610 3.156
GNP "O4'" O O2 0.000 -6.440 -0.397 2.074
GNP "C2'" C CH1 0.000 -5.282 0.406 3.980
GNP "H2'" H H 0.000 -4.789 1.356 3.727
GNP "O2'" O OH1 0.000 -4.696 -0.164 5.152
GNP "HO2'" H H 0.000 -4.812 0.441 5.896
GNP "C3'" C CH1 0.000 -6.800 0.622 4.182
GNP "H3'" H H 0.000 -7.062 1.678 4.030
GNP "O3'" O OH1 0.000 -7.199 0.189 5.483
GNP "HO3'" H H 0.000 -6.782 0.751 6.151
GNP "C4'" C CH1 0.000 -7.453 -0.259 3.094
GNP "H4'" H H 0.000 -7.716 -1.243 3.507
GNP "C5'" C CH2 0.000 -8.693 0.428 2.523
GNP "H5'2" H H 0.000 -8.417 1.409 2.131
GNP "H5'1" H H 0.000 -9.438 0.549 3.312
GNP "O5'" O O2 0.000 -9.238 -0.371 1.470
GNP PA P P 0.000 -10.534 0.407 0.918
GNP O1A O OP -0.500 -10.130 1.741 0.411
GNP O2A O OP -0.500 -11.517 0.574 2.016
GNP O3A O O2 0.000 -11.202 -0.440 -0.275
GNP PB P P 0.000 -12.485 0.393 -0.777
GNP O1B O O 0.000 -12.052 1.723 -1.258
GNP O2B O OH1 0.000 -13.519 0.573 0.443
GNP HOB2 H H 0.000 -13.899 -0.205 0.873
GNP N3B N NH1 0.000 -13.238 -0.439 -2.032
GNP HNB3 H H 0.000 -12.951 -1.323 -2.427
GNP PG P P 0.000 -14.562 0.489 -2.501
GNP O1G O O 0.000 -14.097 1.817 -2.955
GNP O3G O OH1 0.000 -15.561 0.667 -1.253
GNP HOG3 H H 0.000 -15.956 -0.111 -0.836
GNP O2G O OH1 0.000 -15.334 -0.249 -3.706
GNP HOG2 H H 0.000 -16.123 0.154 -4.094
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
GNP O6 n/a C6 START
GNP C6 O6 N1 .
GNP N1 C6 C2 .
GNP HN1 N1 . .
GNP C2 N1 N3 .
GNP N2 C2 HN21 .
GNP HN22 N2 . .
GNP HN21 N2 . .
GNP N3 C2 C4 .
GNP C4 N3 N9 .
GNP C5 C4 N7 .
GNP N7 C5 C8 .
GNP C8 N7 H8 .
GNP H8 C8 . .
GNP N9 C4 "C1'" .
GNP "C1'" N9 "C2'" .
GNP "H1'" "C1'" . .
GNP "O4'" "C1'" . .
GNP "C2'" "C1'" "C3'" .
GNP "H2'" "C2'" . .
GNP "O2'" "C2'" "HO2'" .
GNP "HO2'" "O2'" . .
GNP "C3'" "C2'" "C4'" .
GNP "H3'" "C3'" . .
GNP "O3'" "C3'" "HO3'" .
GNP "HO3'" "O3'" . .
GNP "C4'" "C3'" "C5'" .
GNP "H4'" "C4'" . .
GNP "C5'" "C4'" "O5'" .
GNP "H5'2" "C5'" . .
GNP "H5'1" "C5'" . .
GNP "O5'" "C5'" PA .
GNP PA "O5'" O3A .
GNP O1A PA . .
GNP O2A PA . .
GNP O3A PA PB .
GNP PB O3A N3B .
GNP O1B PB . .
GNP O2B PB HOB2 .
GNP HOB2 O2B . .
GNP N3B PB PG .
GNP HNB3 N3B . .
GNP PG N3B O2G .
GNP O1G PG . .
GNP O3G PG HOG3 .
GNP HOG3 O3G . .
GNP O2G PG HOG2 .
GNP HOG2 O2G . END
GNP "C4'" "O4'" . ADD
GNP N9 C8 . ADD
GNP 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
GNP O1G PG double 1.480 0.020
GNP O2G PG single 1.610 0.020
GNP O3G PG single 1.610 0.020
GNP PG N3B single 1.750 0.020
GNP HOG2 O2G single 0.967 0.020
GNP HOG3 O3G single 0.967 0.020
GNP N3B PB single 1.750 0.020
GNP HNB3 N3B single 1.010 0.020
GNP O1B PB double 1.480 0.020
GNP O2B PB single 1.610 0.020
GNP PB O3A single 1.610 0.020
GNP HOB2 O2B single 0.967 0.020
GNP O3A PA single 1.610 0.020
GNP O1A PA deloc 1.510 0.020
GNP O2A PA deloc 1.510 0.020
GNP PA "O5'" single 1.610 0.020
GNP "O5'" "C5'" single 1.426 0.020
GNP "C5'" "C4'" single 1.524 0.020
GNP "H5'2" "C5'" single 1.092 0.020
GNP "H5'1" "C5'" single 1.092 0.020
GNP "C4'" "O4'" single 1.426 0.020
GNP "C4'" "C3'" single 1.524 0.020
GNP "H4'" "C4'" single 1.099 0.020
GNP "O4'" "C1'" single 1.426 0.020
GNP "O3'" "C3'" single 1.432 0.020
GNP "C3'" "C2'" single 1.524 0.020
GNP "H3'" "C3'" single 1.099 0.020
GNP "HO3'" "O3'" single 0.967 0.020
GNP "O2'" "C2'" single 1.432 0.020
GNP "C2'" "C1'" single 1.524 0.020
GNP "H2'" "C2'" single 1.099 0.020
GNP "HO2'" "O2'" single 0.967 0.020
GNP "C1'" N9 single 1.485 0.020
GNP "H1'" "C1'" single 1.099 0.020
GNP N9 C8 single 1.337 0.020
GNP N9 C4 single 1.337 0.020
GNP C8 N7 double 1.350 0.020
GNP H8 C8 single 1.083 0.020
GNP N7 C5 single 1.350 0.020
GNP C5 C6 single 1.490 0.020
GNP C5 C4 double 1.490 0.020
GNP C6 O6 double 1.250 0.020
GNP N1 C6 single 1.337 0.020
GNP C2 N1 single 1.337 0.020
GNP HN1 N1 single 1.040 0.020
GNP N2 C2 single 1.355 0.020
GNP N3 C2 double 1.350 0.020
GNP HN21 N2 single 1.010 0.020
GNP HN22 N2 single 1.010 0.020
GNP C4 N3 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
GNP O6 C6 N1 120.000 3.000
GNP O6 C6 C5 120.000 3.000
GNP N1 C6 C5 120.000 3.000
GNP C6 N1 HN1 120.000 3.000
GNP C6 N1 C2 120.000 3.000
GNP HN1 N1 C2 120.000 3.000
GNP N1 C2 N2 120.000 3.000
GNP N1 C2 N3 120.000 3.000
GNP N2 C2 N3 120.000 3.000
GNP C2 N2 HN22 120.000 3.000
GNP C2 N2 HN21 120.000 3.000
GNP HN22 N2 HN21 120.000 3.000
GNP C2 N3 C4 120.000 3.000
GNP N3 C4 C5 120.000 3.000
GNP N3 C4 N9 132.000 3.000
GNP C5 C4 N9 108.000 3.000
GNP C4 C5 N7 108.000 3.000
GNP C4 C5 C6 120.000 3.000
GNP N7 C5 C6 132.000 3.000
GNP C5 N7 C8 108.000 3.000
GNP N7 C8 H8 126.000 3.000
GNP N7 C8 N9 108.000 3.000
GNP H8 C8 N9 126.000 3.000
GNP C4 N9 "C1'" 126.000 3.000
GNP C4 N9 C8 108.000 3.000
GNP "C1'" N9 C8 126.000 3.000
GNP N9 "C1'" "H1'" 109.470 3.000
GNP N9 "C1'" "O4'" 109.470 3.000
GNP N9 "C1'" "C2'" 109.470 3.000
GNP "H1'" "C1'" "O4'" 109.470 3.000
GNP "H1'" "C1'" "C2'" 108.340 3.000
GNP "O4'" "C1'" "C2'" 109.470 3.000
GNP "C1'" "O4'" "C4'" 111.800 3.000
GNP "C1'" "C2'" "H2'" 108.340 3.000
GNP "C1'" "C2'" "O2'" 109.470 3.000
GNP "C1'" "C2'" "C3'" 111.000 3.000
GNP "H2'" "C2'" "O2'" 109.470 3.000
GNP "H2'" "C2'" "C3'" 108.340 3.000
GNP "O2'" "C2'" "C3'" 109.470 3.000
GNP "C2'" "O2'" "HO2'" 109.470 3.000
GNP "C2'" "C3'" "H3'" 108.340 3.000
GNP "C2'" "C3'" "O3'" 109.470 3.000
GNP "C2'" "C3'" "C4'" 111.000 3.000
GNP "H3'" "C3'" "O3'" 109.470 3.000
GNP "H3'" "C3'" "C4'" 108.340 3.000
GNP "O3'" "C3'" "C4'" 109.470 3.000
GNP "C3'" "O3'" "HO3'" 109.470 3.000
GNP "C3'" "C4'" "H4'" 108.340 3.000
GNP "C3'" "C4'" "C5'" 111.000 3.000
GNP "C3'" "C4'" "O4'" 109.470 3.000
GNP "H4'" "C4'" "C5'" 108.340 3.000
GNP "H4'" "C4'" "O4'" 109.470 3.000
GNP "C5'" "C4'" "O4'" 109.470 3.000
GNP "C4'" "C5'" "H5'2" 109.470 3.000
GNP "C4'" "C5'" "H5'1" 109.470 3.000
GNP "C4'" "C5'" "O5'" 109.470 3.000
GNP "H5'2" "C5'" "H5'1" 107.900 3.000
GNP "H5'2" "C5'" "O5'" 109.470 3.000
GNP "H5'1" "C5'" "O5'" 109.470 3.000
GNP "C5'" "O5'" PA 120.500 3.000
GNP "O5'" PA O1A 108.200 3.000
GNP "O5'" PA O2A 108.200 3.000
GNP "O5'" PA O3A 102.600 3.000
GNP O1A PA O2A 119.900 3.000
GNP O1A PA O3A 108.200 3.000
GNP O2A PA O3A 108.200 3.000
GNP PA O3A PB 120.500 3.000
GNP O3A PB O1B 109.500 3.000
GNP O3A PB O2B 109.500 3.000
GNP O3A PB N3B 109.500 3.000
GNP O1B PB O2B 109.500 3.000
GNP O1B PB N3B 109.500 3.000
GNP O2B PB N3B 109.500 3.000
GNP PB O2B HOB2 120.000 3.000
GNP PB N3B HNB3 120.000 3.000
GNP PB N3B PG 120.000 3.000
GNP HNB3 N3B PG 120.000 3.000
GNP N3B PG O1G 109.500 3.000
GNP N3B PG O3G 109.500 3.000
GNP N3B PG O2G 109.500 3.000
GNP O1G PG O3G 109.500 3.000
GNP O1G PG O2G 109.500 3.000
GNP O3G PG O2G 109.500 3.000
GNP PG O3G HOG3 120.000 3.000
GNP PG O2G HOG2 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
GNP CONST_1 O6 C6 N1 C2 180.000 0.000 0
GNP CONST_2 C6 N1 C2 N3 0.000 0.000 0
GNP CONST_3 N1 C2 N2 HN21 179.753 0.000 0
GNP CONST_4 N1 C2 N3 C4 0.000 0.000 0
GNP CONST_5 C2 N3 C4 N9 180.000 0.000 0
GNP CONST_6 N3 C4 C5 N7 180.000 0.000 0
GNP CONST_7 C4 C5 C6 O6 180.000 0.000 0
GNP CONST_8 C4 C5 N7 C8 0.000 0.000 0
GNP CONST_9 C5 N7 C8 N9 0.000 0.000 0
GNP CONST_10 N3 C4 N9 "C1'" 0.000 0.000 0
GNP CONST_11 C4 N9 C8 N7 0.000 0.000 0
GNP var_1 C4 N9 "C1'" "C2'" 91.493 20.000 1
GNP var_2 N9 "C1'" "O4'" "C4'" -150.000 20.000 1
GNP var_3 N9 "C1'" "C2'" "C3'" 150.000 20.000 3
GNP var_4 "C1'" "C2'" "O2'" "HO2'" -176.206 20.000 1
GNP var_5 "C1'" "C2'" "C3'" "C4'" 0.000 20.000 3
GNP var_6 "C2'" "C3'" "O3'" "HO3'" 65.338 20.000 1
GNP var_7 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
GNP var_8 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
GNP var_9 "C3'" "C4'" "C5'" "O5'" 176.901 20.000 3
GNP var_10 "C4'" "C5'" "O5'" PA 179.980 20.000 1
GNP var_11 "C5'" "O5'" PA O3A -179.980 20.000 1
GNP var_12 "O5'" PA O3A PB -179.962 20.000 1
GNP var_13 PA O3A PB N3B -179.994 20.000 1
GNP var_14 O3A PB O2B HOB2 -60.005 20.000 1
GNP var_15 O3A PB N3B PG -179.991 20.000 1
GNP var_16 PB N3B PG O2G 179.988 20.000 1
GNP var_17 N3B PG O3G HOG3 -59.985 20.000 1
GNP var_18 N3B PG O2G HOG2 179.977 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
GNP chir_01 "C4'" "C5'" "O4'" "C3'" negativ
GNP chir_02 "C3'" "C4'" "O3'" "C2'" negativ
GNP chir_03 "C2'" "C3'" "O2'" "C1'" negativ
GNP 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
GNP plan-1 N3B 0.020
GNP plan-1 PG 0.020
GNP plan-1 PB 0.020
GNP plan-1 HNB3 0.020
GNP plan-2 N9 0.020
GNP plan-2 "C1'" 0.020
GNP plan-2 C8 0.020
GNP plan-2 C4 0.020
GNP plan-2 N7 0.020
GNP plan-2 H8 0.020
GNP plan-2 C5 0.020
GNP plan-2 C6 0.020
GNP plan-2 N1 0.020
GNP plan-2 C2 0.020
GNP plan-2 N3 0.020
GNP plan-2 O6 0.020
GNP plan-2 HN1 0.020
GNP plan-2 N2 0.020
GNP plan-2 HN22 0.020
GNP plan-2 HN21 0.020
GNP plan-3 N2 0.020
GNP plan-3 C2 0.020
GNP plan-3 HN21 0.020
GNP plan-3 HN22 0.020
# ------------------------------------------------------
|
