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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
GKD GKD '. ' non-polymer 60 39 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GKD
#
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
GKD O4G O O 0.000 0.000 0.000 0.000
GKD C4G C C 0.000 -1.168 0.303 0.061
GKD C5G C CH1 0.000 -2.171 -0.583 0.766
GKD H5G H H 0.000 -2.537 -0.078 1.671
GKD C6G C CH2 0.000 -1.508 -1.908 1.151
GKD H6G1 H H 0.000 -0.619 -1.708 1.751
GKD H6G2 H H 0.000 -1.221 -2.447 0.245
GKD O6A O OH1 0.000 -2.428 -2.699 1.906
GKD H6A H H 0.000 -2.008 -3.535 2.149
GKD O5G O O2 0.000 -3.266 -0.835 -0.117
GKD C3G C CH1 0.000 -1.680 1.584 -0.567
GKD H3G H H 0.000 -0.927 1.987 -1.260
GKD O3G O OH1 0.000 -1.964 2.545 0.452
GKD HD H H 0.000 -1.157 2.733 0.950
GKD C2G C CH1 0.000 -2.963 1.237 -1.336
GKD H2G H H 0.000 -2.711 0.649 -2.230
GKD O2G O OH1 0.000 -3.630 2.440 -1.724
GKD HC H H 0.000 -3.046 2.962 -2.292
GKD C1G C CH1 0.000 -3.876 0.417 -0.421
GKD H1G H H 0.000 -4.050 0.972 0.511
GKD O1B O O2 0.000 -5.125 0.190 -1.077
GKD PB P P 0.000 -6.244 0.090 0.075
GKD O2B O OP -0.500 -6.195 1.309 0.919
GKD O3B O OP -0.500 -5.984 -1.104 0.916
GKD O3A O O2 0.000 -7.700 -0.037 -0.601
GKD PA P P 0.000 -8.773 0.398 0.519
GKD O1A O OP -0.500 -8.915 -0.692 1.515
GKD O2A O OP -0.500 -8.306 1.631 1.198
GKD "O5'" O O2 0.000 -10.196 0.676 -0.180
GKD "C5'" C CH2 0.000 -11.067 1.168 0.839
GKD "H5'1" H H 0.000 -10.654 2.088 1.257
GKD "H5'2" H H 0.000 -11.162 0.420 1.629
GKD "C4'" C CH1 0.000 -12.445 1.454 0.237
GKD "H4'" H H 0.000 -12.356 2.149 -0.609
GKD "C3'" C CH1 0.000 -13.394 2.032 1.311
GKD "H3'" H H 0.000 -13.069 1.729 2.316
GKD "O3'" O OH1 0.000 -13.452 3.458 1.212
GKD HB H H 0.000 -14.049 3.803 1.890
GKD "C2'" C CH1 0.000 -14.768 1.409 0.975
GKD "H2'" H H 0.000 -15.127 0.794 1.813
GKD "O2'" O OH1 0.000 -15.718 2.429 0.660
GKD HA H H 0.000 -15.835 3.006 1.427
GKD "O4'" O O2 0.000 -13.074 0.225 -0.186
GKD "C1'" C CH1 0.000 -14.485 0.525 -0.260
GKD "H1'" H H 0.000 -14.711 1.076 -1.184
GKD N9 N NR5 0.000 -15.272 -0.709 -0.196
GKD C4 C CR56 0.000 -16.554 -0.875 -0.647
GKD N3 N NRD6 0.000 -17.447 -0.071 -1.237
GKD C2 C CR6 0.000 -18.640 -0.511 -1.570
GKD N2 N NH2 0.000 -19.522 0.350 -2.173
GKD H2N2 H H 0.000 -20.447 0.031 -2.438
GKD H2N1 H H 0.000 -19.255 1.309 -2.357
GKD C8 C CR15 0.000 -14.862 -1.903 0.323
GKD H8 H H 0.000 -13.889 -2.091 0.759
GKD N7 N NRD5 0.000 -15.816 -2.781 0.214
GKD C5 C CR56 0.000 -16.891 -2.206 -0.378
GKD C6 C CR6 0.000 -18.177 -2.666 -0.742
GKD O6 O O 0.000 -18.513 -3.818 -0.527
GKD N1 N NR16 0.000 -19.028 -1.795 -1.330
GKD H1 H H 0.000 -19.983 -2.106 -1.600
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
GKD O4G n/a C4G START
GKD C4G O4G C3G .
GKD C5G C4G O5G .
GKD H5G C5G . .
GKD C6G C5G O6A .
GKD H6G1 C6G . .
GKD H6G2 C6G . .
GKD O6A C6G H6A .
GKD H6A O6A . .
GKD O5G C5G . .
GKD C3G C4G C2G .
GKD H3G C3G . .
GKD O3G C3G HD .
GKD HD O3G . .
GKD C2G C3G C1G .
GKD H2G C2G . .
GKD O2G C2G HC .
GKD HC O2G . .
GKD C1G C2G O1B .
GKD H1G C1G . .
GKD O1B C1G PB .
GKD PB O1B O3A .
GKD O2B PB . .
GKD O3B PB . .
GKD O3A PB PA .
GKD PA O3A "O5'" .
GKD O1A PA . .
GKD O2A PA . .
GKD "O5'" PA "C5'" .
GKD "C5'" "O5'" "C4'" .
GKD "H5'1" "C5'" . .
GKD "H5'2" "C5'" . .
GKD "C4'" "C5'" "O4'" .
GKD "H4'" "C4'" . .
GKD "C3'" "C4'" "C2'" .
GKD "H3'" "C3'" . .
GKD "O3'" "C3'" HB .
GKD HB "O3'" . .
GKD "C2'" "C3'" "O2'" .
GKD "H2'" "C2'" . .
GKD "O2'" "C2'" HA .
GKD HA "O2'" . .
GKD "O4'" "C4'" "C1'" .
GKD "C1'" "O4'" N9 .
GKD "H1'" "C1'" . .
GKD N9 "C1'" C8 .
GKD C4 N9 N3 .
GKD N3 C4 C2 .
GKD C2 N3 N2 .
GKD N2 C2 H2N1 .
GKD H2N2 N2 . .
GKD H2N1 N2 . .
GKD C8 N9 N7 .
GKD H8 C8 . .
GKD N7 C8 C5 .
GKD C5 N7 C6 .
GKD C6 C5 N1 .
GKD O6 C6 . .
GKD N1 C6 H1 .
GKD H1 N1 . END
GKD C2 N1 . ADD
GKD C4 C5 . ADD
GKD "C1'" "C2'" . ADD
GKD C1G O5G . 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
GKD N2 C2 single 1.355 0.020
GKD H2N1 N2 single 1.010 0.020
GKD H2N2 N2 single 1.010 0.020
GKD C2 N1 single 1.337 0.020
GKD C2 N3 double 1.350 0.020
GKD N1 C6 single 1.337 0.020
GKD H1 N1 single 1.040 0.020
GKD N3 C4 single 1.355 0.020
GKD C4 C5 double 1.490 0.020
GKD C4 N9 single 1.337 0.020
GKD C6 C5 single 1.490 0.020
GKD C5 N7 single 1.350 0.020
GKD O6 C6 double 1.250 0.020
GKD N7 C8 double 1.350 0.020
GKD C8 N9 single 1.337 0.020
GKD H8 C8 single 1.083 0.020
GKD N9 "C1'" single 1.485 0.020
GKD "C1'" "C2'" single 1.524 0.020
GKD "C1'" "O4'" single 1.426 0.020
GKD "H1'" "C1'" single 1.099 0.020
GKD "O2'" "C2'" single 1.432 0.020
GKD "C2'" "C3'" single 1.524 0.020
GKD "H2'" "C2'" single 1.099 0.020
GKD HA "O2'" single 0.967 0.020
GKD "O3'" "C3'" single 1.432 0.020
GKD "C3'" "C4'" single 1.524 0.020
GKD "H3'" "C3'" single 1.099 0.020
GKD HB "O3'" single 0.967 0.020
GKD "O4'" "C4'" single 1.426 0.020
GKD "C4'" "C5'" single 1.524 0.020
GKD "H4'" "C4'" single 1.099 0.020
GKD "C5'" "O5'" single 1.426 0.020
GKD "H5'1" "C5'" single 1.092 0.020
GKD "H5'2" "C5'" single 1.092 0.020
GKD "O5'" PA single 1.610 0.020
GKD O1A PA deloc 1.510 0.020
GKD O2A PA deloc 1.510 0.020
GKD PA O3A single 1.610 0.020
GKD O3A PB single 1.610 0.020
GKD O2B PB deloc 1.510 0.020
GKD O3B PB deloc 1.510 0.020
GKD PB O1B single 1.610 0.020
GKD O1B C1G single 1.426 0.020
GKD C1G O5G single 1.426 0.020
GKD C1G C2G single 1.524 0.020
GKD H1G C1G single 1.099 0.020
GKD O5G C5G single 1.426 0.020
GKD C6G C5G single 1.524 0.020
GKD C5G C4G single 1.500 0.020
GKD H5G C5G single 1.099 0.020
GKD O6A C6G single 1.432 0.020
GKD H6G1 C6G single 1.092 0.020
GKD H6G2 C6G single 1.092 0.020
GKD H6A O6A single 0.967 0.020
GKD O2G C2G single 1.432 0.020
GKD C2G C3G single 1.524 0.020
GKD H2G C2G single 1.099 0.020
GKD HC O2G single 0.967 0.020
GKD O3G C3G single 1.432 0.020
GKD C3G C4G single 1.500 0.020
GKD H3G C3G single 1.099 0.020
GKD HD O3G single 0.967 0.020
GKD C4G O4G double 1.220 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
GKD O4G C4G C5G 120.500 3.000
GKD O4G C4G C3G 120.500 3.000
GKD C5G C4G C3G 120.000 3.000
GKD C4G C5G H5G 108.810 3.000
GKD C4G C5G C6G 109.470 3.000
GKD C4G C5G O5G 109.470 3.000
GKD H5G C5G C6G 108.340 3.000
GKD H5G C5G O5G 109.470 3.000
GKD C6G C5G O5G 109.470 3.000
GKD C5G C6G H6G1 109.470 3.000
GKD C5G C6G H6G2 109.470 3.000
GKD C5G C6G O6A 109.470 3.000
GKD H6G1 C6G H6G2 107.900 3.000
GKD H6G1 C6G O6A 109.470 3.000
GKD H6G2 C6G O6A 109.470 3.000
GKD C6G O6A H6A 109.470 3.000
GKD C5G O5G C1G 111.800 3.000
GKD C4G C3G H3G 108.810 3.000
GKD C4G C3G O3G 109.470 3.000
GKD C4G C3G C2G 109.470 3.000
GKD H3G C3G O3G 109.470 3.000
GKD H3G C3G C2G 108.340 3.000
GKD O3G C3G C2G 109.470 3.000
GKD C3G O3G HD 109.470 3.000
GKD C3G C2G H2G 108.340 3.000
GKD C3G C2G O2G 109.470 3.000
GKD C3G C2G C1G 111.000 3.000
GKD H2G C2G O2G 109.470 3.000
GKD H2G C2G C1G 108.340 3.000
GKD O2G C2G C1G 109.470 3.000
GKD C2G O2G HC 109.470 3.000
GKD C2G C1G H1G 108.340 3.000
GKD C2G C1G O1B 109.470 3.000
GKD C2G C1G O5G 109.470 3.000
GKD H1G C1G O1B 109.470 3.000
GKD H1G C1G O5G 109.470 3.000
GKD O1B C1G O5G 109.470 3.000
GKD C1G O1B PB 120.500 3.000
GKD O1B PB O2B 108.200 3.000
GKD O1B PB O3B 108.200 3.000
GKD O1B PB O3A 102.600 3.000
GKD O2B PB O3B 119.900 3.000
GKD O2B PB O3A 108.200 3.000
GKD O3B PB O3A 108.200 3.000
GKD PB O3A PA 120.500 3.000
GKD O3A PA O1A 108.200 3.000
GKD O3A PA O2A 108.200 3.000
GKD O3A PA "O5'" 102.600 3.000
GKD O1A PA O2A 119.900 3.000
GKD O1A PA "O5'" 108.200 3.000
GKD O2A PA "O5'" 108.200 3.000
GKD PA "O5'" "C5'" 120.500 3.000
GKD "O5'" "C5'" "H5'1" 109.470 3.000
GKD "O5'" "C5'" "H5'2" 109.470 3.000
GKD "O5'" "C5'" "C4'" 109.470 3.000
GKD "H5'1" "C5'" "H5'2" 107.900 3.000
GKD "H5'1" "C5'" "C4'" 109.470 3.000
GKD "H5'2" "C5'" "C4'" 109.470 3.000
GKD "C5'" "C4'" "H4'" 108.340 3.000
GKD "C5'" "C4'" "C3'" 111.000 3.000
GKD "C5'" "C4'" "O4'" 109.470 3.000
GKD "H4'" "C4'" "C3'" 108.340 3.000
GKD "H4'" "C4'" "O4'" 109.470 3.000
GKD "C3'" "C4'" "O4'" 109.470 3.000
GKD "C4'" "C3'" "H3'" 108.340 3.000
GKD "C4'" "C3'" "O3'" 109.470 3.000
GKD "C4'" "C3'" "C2'" 111.000 3.000
GKD "H3'" "C3'" "O3'" 109.470 3.000
GKD "H3'" "C3'" "C2'" 108.340 3.000
GKD "O3'" "C3'" "C2'" 109.470 3.000
GKD "C3'" "O3'" HB 109.470 3.000
GKD "C3'" "C2'" "H2'" 108.340 3.000
GKD "C3'" "C2'" "O2'" 109.470 3.000
GKD "C3'" "C2'" "C1'" 111.000 3.000
GKD "H2'" "C2'" "O2'" 109.470 3.000
GKD "H2'" "C2'" "C1'" 108.340 3.000
GKD "O2'" "C2'" "C1'" 109.470 3.000
GKD "C2'" "O2'" HA 109.470 3.000
GKD "C4'" "O4'" "C1'" 111.800 3.000
GKD "O4'" "C1'" "H1'" 109.470 3.000
GKD "O4'" "C1'" N9 109.470 3.000
GKD "O4'" "C1'" "C2'" 109.470 3.000
GKD "H1'" "C1'" N9 109.470 3.000
GKD "H1'" "C1'" "C2'" 108.340 3.000
GKD N9 "C1'" "C2'" 109.470 3.000
GKD "C1'" N9 C4 126.000 3.000
GKD "C1'" N9 C8 126.000 3.000
GKD C4 N9 C8 108.000 3.000
GKD N9 C4 N3 132.000 3.000
GKD N9 C4 C5 108.000 3.000
GKD N3 C4 C5 120.000 3.000
GKD C4 N3 C2 120.000 3.000
GKD N3 C2 N2 120.000 3.000
GKD N3 C2 N1 120.000 3.000
GKD N2 C2 N1 120.000 3.000
GKD C2 N2 H2N2 120.000 3.000
GKD C2 N2 H2N1 120.000 3.000
GKD H2N2 N2 H2N1 120.000 3.000
GKD N9 C8 H8 126.000 3.000
GKD N9 C8 N7 108.000 3.000
GKD H8 C8 N7 126.000 3.000
GKD C8 N7 C5 108.000 3.000
GKD N7 C5 C6 132.000 3.000
GKD N7 C5 C4 108.000 3.000
GKD C6 C5 C4 120.000 3.000
GKD C5 C6 O6 120.000 3.000
GKD C5 C6 N1 120.000 3.000
GKD O6 C6 N1 120.000 3.000
GKD C6 N1 H1 120.000 3.000
GKD C6 N1 C2 120.000 3.000
GKD H1 N1 C2 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
GKD var_1 O4G C4G C5G O5G -120.000 20.000 3
GKD var_2 C4G C5G C6G O6A 175.540 20.000 3
GKD var_3 C5G C6G O6A H6A -179.979 20.000 1
GKD var_4 C4G C5G O5G C1G -60.000 20.000 1
GKD var_5 O4G C4G C3G C2G 120.000 20.000 3
GKD var_6 C4G C3G O3G HD 59.990 20.000 1
GKD var_7 C4G C3G C2G C1G 60.000 20.000 3
GKD var_8 C3G C2G O2G HC 60.039 20.000 1
GKD var_9 C3G C2G C1G O1B 180.000 20.000 3
GKD var_10 C2G C1G O5G C5G 60.000 20.000 1
GKD var_11 C2G C1G O1B PB -149.722 20.000 1
GKD var_12 C1G O1B PB O3A 175.047 20.000 1
GKD var_13 O1B PB O3A PA -159.982 20.000 1
GKD var_14 PB O3A PA "O5'" 164.986 20.000 1
GKD var_15 O3A PA "O5'" "C5'" -175.001 20.000 1
GKD var_16 PA "O5'" "C5'" "C4'" 179.998 20.000 1
GKD var_17 "O5'" "C5'" "C4'" "O4'" 66.461 20.000 3
GKD var_18 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
GKD var_19 "C4'" "C3'" "O3'" HB -179.945 20.000 1
GKD var_20 "C4'" "C3'" "C2'" "O2'" -120.000 20.000 3
GKD var_21 "C3'" "C2'" "O2'" HA -61.484 20.000 1
GKD var_22 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
GKD var_23 "C4'" "O4'" "C1'" N9 -150.000 20.000 1
GKD var_24 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
GKD var_25 "O4'" "C1'" N9 C8 22.028 20.000 1
GKD CONST_1 "C1'" N9 C4 N3 0.000 0.000 0
GKD CONST_2 N9 C4 C5 N7 0.000 0.000 0
GKD CONST_3 N9 C4 N3 C2 180.000 0.000 0
GKD CONST_4 C4 N3 C2 N2 180.000 0.000 0
GKD CONST_5 N3 C2 N1 C6 0.000 0.000 0
GKD CONST_6 N3 C2 N2 H2N1 -0.048 0.000 0
GKD CONST_7 "C1'" N9 C8 N7 180.000 0.000 0
GKD CONST_8 N9 C8 N7 C5 0.000 0.000 0
GKD CONST_9 C8 N7 C5 C6 180.000 0.000 0
GKD CONST_10 N7 C5 C6 N1 180.000 0.000 0
GKD CONST_11 C5 C6 N1 C2 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
GKD chir_01 "C1'" N9 "C2'" "O4'" negativ
GKD chir_02 "C2'" "C1'" "O2'" "C3'" positiv
GKD chir_03 "C3'" "C2'" "O3'" "C4'" positiv
GKD chir_04 "C4'" "C3'" "O4'" "C5'" positiv
GKD chir_05 C1G O1B O5G C2G negativ
GKD chir_06 C5G O5G C6G C4G negativ
GKD chir_07 C2G C1G O2G C3G negativ
GKD chir_08 C3G C2G O3G C4G 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
GKD plan-1 N2 0.020
GKD plan-1 C2 0.020
GKD plan-1 H2N1 0.020
GKD plan-1 H2N2 0.020
GKD plan-2 C2 0.020
GKD plan-2 N2 0.020
GKD plan-2 N1 0.020
GKD plan-2 N3 0.020
GKD plan-2 C6 0.020
GKD plan-2 H1 0.020
GKD plan-2 C4 0.020
GKD plan-2 C5 0.020
GKD plan-2 N9 0.020
GKD plan-2 N7 0.020
GKD plan-2 C8 0.020
GKD plan-2 O6 0.020
GKD plan-2 H8 0.020
GKD plan-2 "C1'" 0.020
GKD plan-2 H2N2 0.020
GKD plan-2 H2N1 0.020
GKD plan-3 C4G 0.020
GKD plan-3 C5G 0.020
GKD plan-3 C3G 0.020
GKD plan-3 O4G 0.020
# ------------------------------------------------------
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