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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
LAD LAD 'ADENOSINE-5'-[LYSYL-PHOSPHATE] ' non-polymer 57 32 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_LAD
#
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
LAD O2A O OP -0.500 0.000 0.000 0.000
LAD PA P P 0.000 -0.683 1.243 0.432
LAD O1A O OP -0.500 -0.198 1.632 1.778
LAD O3A O O2 -0.500 -0.276 2.449 -0.629
LAD C C C 0.000 0.907 2.807 -0.826
LAD O O O -0.500 1.840 2.247 -0.209
LAD CA C CH1 0.000 1.208 3.911 -1.807
LAD HA H H 0.000 0.363 4.612 -1.839
LAD CB C CH2 0.000 1.427 3.314 -3.197
LAD HB2 H H 0.000 0.525 2.783 -3.510
LAD HB1 H H 0.000 2.266 2.615 -3.165
LAD CG C CH2 0.000 1.732 4.433 -4.192
LAD HG2 H H 0.000 2.633 4.964 -3.876
LAD HG1 H H 0.000 0.892 5.131 -4.222
LAD CD C CH2 0.000 1.951 3.836 -5.582
LAD HD2 H H 0.000 1.050 3.304 -5.895
LAD HD1 H H 0.000 2.791 3.138 -5.549
LAD CE C CH2 0.000 2.256 4.957 -6.578
LAD HE2 H H 0.000 3.157 5.488 -6.262
LAD HE1 H H 0.000 1.416 5.654 -6.608
LAD NZ N NH2 0.000 2.467 4.383 -7.913
LAD HZ1 H H 0.000 2.399 3.382 -8.056
LAD HZ2 H H 0.000 2.681 4.984 -8.700
LAD N N NH2 0.000 2.420 4.624 -1.384
LAD H1 H H 0.000 2.859 4.406 -0.497
LAD H2A H H 0.000 2.825 5.339 -1.976
LAD "O5'" O O2 0.000 -2.272 0.991 0.486
LAD "C5'" C CH2 0.000 -2.491 -0.060 1.428
LAD "H5'2" H H 0.000 -2.112 0.243 2.406
LAD "H5'1" H H 0.000 -1.966 -0.959 1.098
LAD "C4'" C CH1 0.000 -3.990 -0.351 1.528
LAD "H4'" H H 0.000 -4.525 0.554 1.848
LAD "C3'" C CH1 0.000 -4.237 -1.489 2.535
LAD "H3'" H H 0.000 -3.283 -1.875 2.920
LAD "O3'" O OH1 0.000 -5.066 -1.045 3.611
LAD H3O1 H H 0.000 -5.256 -1.789 4.198
LAD "C2'" C CH1 0.000 -4.966 -2.577 1.703
LAD "H2'" H H 0.000 -4.258 -3.340 1.350
LAD "O2'" O OH1 0.000 -6.022 -3.173 2.457
LAD H2O1 H H 0.000 -5.647 -3.680 3.190
LAD "C1'" C CH1 0.000 -5.528 -1.755 0.517
LAD "H1'" H H 0.000 -6.461 -1.251 0.804
LAD "O4'" O O2 0.000 -4.489 -0.789 0.253
LAD N9 N NR5 0.000 -5.745 -2.611 -0.652
LAD C8 C CR15 0.000 -4.817 -2.941 -1.592
LAD H8 H H 0.000 -3.786 -2.607 -1.592
LAD N7 N NRD5 0.000 -5.350 -3.717 -2.490
LAD C5 C CR56 0.000 -6.651 -3.935 -2.183
LAD C4 C CR56 0.000 -6.919 -3.231 -0.997
LAD C6 C CR6 0.000 -7.696 -4.668 -2.770
LAD N6 N NH2 0.000 -7.490 -5.386 -3.935
LAD H61 H H 0.000 -6.579 -5.392 -4.383
LAD H62 H H 0.000 -8.248 -5.915 -4.356
LAD N1 N NRD6 0.000 -8.887 -4.658 -2.179
LAD C2 C CR16 0.000 -9.092 -3.977 -1.067
LAD H2 H H 0.000 -10.078 -3.995 -0.619
LAD N3 N NRD6 0.000 -8.143 -3.276 -0.482
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
LAD O2A n/a PA START
LAD PA O2A "O5'" .
LAD O1A PA . .
LAD O3A PA C .
LAD C O3A CA .
LAD O C . .
LAD CA C N .
LAD HA CA . .
LAD CB CA CG .
LAD HB2 CB . .
LAD HB1 CB . .
LAD CG CB CD .
LAD HG2 CG . .
LAD HG1 CG . .
LAD CD CG CE .
LAD HD2 CD . .
LAD HD1 CD . .
LAD CE CD NZ .
LAD HE2 CE . .
LAD HE1 CE . .
LAD NZ CE HZ2 .
LAD HZ1 NZ . .
LAD HZ2 NZ . .
LAD N CA H2A .
LAD H1 N . .
LAD H2A N . .
LAD "O5'" PA "C5'" .
LAD "C5'" "O5'" "C4'" .
LAD "H5'2" "C5'" . .
LAD "H5'1" "C5'" . .
LAD "C4'" "C5'" "C3'" .
LAD "H4'" "C4'" . .
LAD "C3'" "C4'" "C2'" .
LAD "H3'" "C3'" . .
LAD "O3'" "C3'" H3O1 .
LAD H3O1 "O3'" . .
LAD "C2'" "C3'" "C1'" .
LAD "H2'" "C2'" . .
LAD "O2'" "C2'" H2O1 .
LAD H2O1 "O2'" . .
LAD "C1'" "C2'" N9 .
LAD "H1'" "C1'" . .
LAD "O4'" "C1'" . .
LAD N9 "C1'" C8 .
LAD C8 N9 N7 .
LAD H8 C8 . .
LAD N7 C8 C5 .
LAD C5 N7 C6 .
LAD C4 C5 . .
LAD C6 C5 N1 .
LAD N6 C6 H62 .
LAD H61 N6 . .
LAD H62 N6 . .
LAD N1 C6 C2 .
LAD C2 N1 N3 .
LAD H2 C2 . .
LAD N3 C2 . END
LAD "C4'" "O4'" . ADD
LAD N9 C4 . ADD
LAD C4 N3 . 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
LAD N CA single 1.450 0.020
LAD H2A N single 1.010 0.020
LAD H1 N single 1.010 0.020
LAD CB CA single 1.524 0.020
LAD CA C single 1.500 0.020
LAD HA CA single 1.099 0.020
LAD CG CB single 1.524 0.020
LAD HB2 CB single 1.092 0.020
LAD HB1 CB single 1.092 0.020
LAD CD CG single 1.524 0.020
LAD HG2 CG single 1.092 0.020
LAD HG1 CG single 1.092 0.020
LAD CE CD single 1.524 0.020
LAD HD2 CD single 1.092 0.020
LAD HD1 CD single 1.092 0.020
LAD NZ CE single 1.450 0.020
LAD HE2 CE single 1.092 0.020
LAD HE1 CE single 1.092 0.020
LAD HZ2 NZ single 1.010 0.020
LAD HZ1 NZ single 1.010 0.020
LAD O C deloc 1.220 0.020
LAD C O3A deloc 1.454 0.020
LAD "O5'" PA single 1.610 0.020
LAD O1A PA deloc 1.510 0.020
LAD PA O2A deloc 1.510 0.020
LAD O3A PA single 1.610 0.020
LAD "C5'" "O5'" single 1.426 0.020
LAD "C4'" "C5'" single 1.524 0.020
LAD "H5'2" "C5'" single 1.092 0.020
LAD "H5'1" "C5'" single 1.092 0.020
LAD "C4'" "O4'" single 1.426 0.020
LAD "C3'" "C4'" single 1.524 0.020
LAD "H4'" "C4'" single 1.099 0.020
LAD "O4'" "C1'" single 1.426 0.020
LAD N9 "C1'" single 1.485 0.020
LAD "C1'" "C2'" single 1.524 0.020
LAD "H1'" "C1'" single 1.099 0.020
LAD N9 C4 single 1.337 0.020
LAD C8 N9 single 1.337 0.020
LAD C4 N3 double 1.355 0.020
LAD C4 C5 single 1.490 0.020
LAD N3 C2 single 1.337 0.020
LAD C2 N1 double 1.337 0.020
LAD H2 C2 single 1.083 0.020
LAD N1 C6 single 1.350 0.020
LAD N6 C6 single 1.355 0.020
LAD C6 C5 double 1.490 0.020
LAD H62 N6 single 1.010 0.020
LAD H61 N6 single 1.010 0.020
LAD C5 N7 single 1.350 0.020
LAD N7 C8 double 1.350 0.020
LAD H8 C8 single 1.083 0.020
LAD "O2'" "C2'" single 1.432 0.020
LAD "C2'" "C3'" single 1.524 0.020
LAD "H2'" "C2'" single 1.099 0.020
LAD H2O1 "O2'" single 0.967 0.020
LAD "O3'" "C3'" single 1.432 0.020
LAD "H3'" "C3'" single 1.099 0.020
LAD H3O1 "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
LAD O2A PA O1A 119.900 3.000
LAD O2A PA O3A 108.200 3.000
LAD O2A PA "O5'" 108.200 3.000
LAD O1A PA O3A 108.200 3.000
LAD O1A PA "O5'" 108.200 3.000
LAD O3A PA "O5'" 102.600 3.000
LAD PA O3A C 120.000 3.000
LAD O3A C O 119.000 3.000
LAD O3A C CA 120.000 3.000
LAD O C CA 120.500 3.000
LAD C CA HA 108.810 3.000
LAD C CA CB 109.470 3.000
LAD C CA N 109.470 3.000
LAD HA CA CB 108.340 3.000
LAD HA CA N 109.470 3.000
LAD CB CA N 109.470 3.000
LAD CA CB HB2 109.470 3.000
LAD CA CB HB1 109.470 3.000
LAD CA CB CG 111.000 3.000
LAD HB2 CB HB1 107.900 3.000
LAD HB2 CB CG 109.470 3.000
LAD HB1 CB CG 109.470 3.000
LAD CB CG HG2 109.470 3.000
LAD CB CG HG1 109.470 3.000
LAD CB CG CD 111.000 3.000
LAD HG2 CG HG1 107.900 3.000
LAD HG2 CG CD 109.470 3.000
LAD HG1 CG CD 109.470 3.000
LAD CG CD HD2 109.470 3.000
LAD CG CD HD1 109.470 3.000
LAD CG CD CE 111.000 3.000
LAD HD2 CD HD1 107.900 3.000
LAD HD2 CD CE 109.470 3.000
LAD HD1 CD CE 109.470 3.000
LAD CD CE HE2 109.470 3.000
LAD CD CE HE1 109.470 3.000
LAD CD CE NZ 109.470 3.000
LAD HE2 CE HE1 107.900 3.000
LAD HE2 CE NZ 109.470 3.000
LAD HE1 CE NZ 109.470 3.000
LAD CE NZ HZ1 120.000 3.000
LAD CE NZ HZ2 120.000 3.000
LAD HZ1 NZ HZ2 120.000 3.000
LAD CA N H1 120.000 3.000
LAD CA N H2A 120.000 3.000
LAD H1 N H2A 120.000 3.000
LAD PA "O5'" "C5'" 120.500 3.000
LAD "O5'" "C5'" "H5'2" 109.470 3.000
LAD "O5'" "C5'" "H5'1" 109.470 3.000
LAD "O5'" "C5'" "C4'" 109.470 3.000
LAD "H5'2" "C5'" "H5'1" 107.900 3.000
LAD "H5'2" "C5'" "C4'" 109.470 3.000
LAD "H5'1" "C5'" "C4'" 109.470 3.000
LAD "C5'" "C4'" "H4'" 108.340 3.000
LAD "C5'" "C4'" "C3'" 111.000 3.000
LAD "C5'" "C4'" "O4'" 109.470 3.000
LAD "H4'" "C4'" "C3'" 108.340 3.000
LAD "H4'" "C4'" "O4'" 109.470 3.000
LAD "C3'" "C4'" "O4'" 109.470 3.000
LAD "C4'" "C3'" "H3'" 108.340 3.000
LAD "C4'" "C3'" "O3'" 109.470 3.000
LAD "C4'" "C3'" "C2'" 111.000 3.000
LAD "H3'" "C3'" "O3'" 109.470 3.000
LAD "H3'" "C3'" "C2'" 108.340 3.000
LAD "O3'" "C3'" "C2'" 109.470 3.000
LAD "C3'" "O3'" H3O1 109.470 3.000
LAD "C3'" "C2'" "H2'" 108.340 3.000
LAD "C3'" "C2'" "O2'" 109.470 3.000
LAD "C3'" "C2'" "C1'" 111.000 3.000
LAD "H2'" "C2'" "O2'" 109.470 3.000
LAD "H2'" "C2'" "C1'" 108.340 3.000
LAD "O2'" "C2'" "C1'" 109.470 3.000
LAD "C2'" "O2'" H2O1 109.470 3.000
LAD "C2'" "C1'" "H1'" 108.340 3.000
LAD "C2'" "C1'" "O4'" 109.470 3.000
LAD "C2'" "C1'" N9 109.470 3.000
LAD "H1'" "C1'" "O4'" 109.470 3.000
LAD "H1'" "C1'" N9 109.470 3.000
LAD "O4'" "C1'" N9 109.470 3.000
LAD "C1'" "O4'" "C4'" 111.800 3.000
LAD "C1'" N9 C8 126.000 3.000
LAD "C1'" N9 C4 126.000 3.000
LAD C8 N9 C4 108.000 3.000
LAD N9 C8 H8 126.000 3.000
LAD N9 C8 N7 108.000 3.000
LAD H8 C8 N7 126.000 3.000
LAD C8 N7 C5 108.000 3.000
LAD N7 C5 C4 108.000 3.000
LAD N7 C5 C6 132.000 3.000
LAD C4 C5 C6 120.000 3.000
LAD C5 C4 N9 108.000 3.000
LAD C5 C4 N3 120.000 3.000
LAD N9 C4 N3 132.000 3.000
LAD C5 C6 N6 120.000 3.000
LAD C5 C6 N1 120.000 3.000
LAD N6 C6 N1 120.000 3.000
LAD C6 N6 H61 120.000 3.000
LAD C6 N6 H62 120.000 3.000
LAD H61 N6 H62 120.000 3.000
LAD C6 N1 C2 120.000 3.000
LAD N1 C2 H2 120.000 3.000
LAD N1 C2 N3 120.000 3.000
LAD H2 C2 N3 120.000 3.000
LAD C2 N3 C4 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
LAD var_1 O2A PA O3A C -59.162 20.000 1
LAD var_2 PA O3A C CA 179.977 20.000 1
LAD var_3 O3A C CA N 149.974 20.000 3
LAD var_4 C CA CB CG 179.967 20.000 3
LAD var_5 CA CB CG CD 179.972 20.000 3
LAD var_6 CB CG CD CE 179.983 20.000 3
LAD var_7 CG CD CE NZ 179.993 20.000 3
LAD var_8 CD CE NZ HZ2 -179.978 20.000 1
LAD var_9 C CA N H2A 173.811 20.000 1
LAD var_10 O2A PA "O5'" "C5'" 60.025 20.000 1
LAD var_11 PA "O5'" "C5'" "C4'" 179.992 20.000 1
LAD var_12 "O5'" "C5'" "C4'" "C3'" 179.692 20.000 3
LAD var_13 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
LAD var_14 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
LAD var_15 "C4'" "C3'" "O3'" H3O1 176.234 20.000 1
LAD var_16 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
LAD var_17 "C3'" "C2'" "O2'" H2O1 -67.304 20.000 1
LAD var_18 "C3'" "C2'" "C1'" N9 150.000 20.000 3
LAD var_19 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
LAD var_20 "C2'" "C1'" N9 C8 -85.603 20.000 1
LAD CONST_1 "C1'" N9 C4 C5 180.000 0.000 0
LAD CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
LAD CONST_3 N9 C8 N7 C5 0.000 0.000 0
LAD CONST_4 C8 N7 C5 C6 180.000 0.000 0
LAD CONST_5 N7 C5 C4 N9 0.000 0.000 0
LAD CONST_6 C5 C4 N3 C2 0.000 0.000 0
LAD CONST_7 N7 C5 C6 N1 180.000 0.000 0
LAD CONST_8 C5 C6 N6 H62 -179.978 0.000 0
LAD CONST_9 C5 C6 N1 C2 0.000 0.000 0
LAD CONST_10 C6 N1 C2 N3 0.000 0.000 0
LAD CONST_11 N1 C2 N3 C4 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
LAD chir_01 CA N CB C negativ
LAD chir_02 "C4'" "C5'" "O4'" "C3'" negativ
LAD chir_03 "C1'" "O4'" N9 "C2'" negativ
LAD chir_04 "C2'" "C1'" "O2'" "C3'" positiv
LAD chir_05 "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
LAD plan-1 N 0.020
LAD plan-1 CA 0.020
LAD plan-1 H2A 0.020
LAD plan-1 H1 0.020
LAD plan-2 NZ 0.020
LAD plan-2 CE 0.020
LAD plan-2 HZ2 0.020
LAD plan-2 HZ1 0.020
LAD plan-3 C 0.020
LAD plan-3 CA 0.020
LAD plan-3 O 0.020
LAD plan-3 O3A 0.020
LAD plan-4 N9 0.020
LAD plan-4 "C1'" 0.020
LAD plan-4 C4 0.020
LAD plan-4 C8 0.020
LAD plan-4 N7 0.020
LAD plan-4 N3 0.020
LAD plan-4 C5 0.020
LAD plan-4 C2 0.020
LAD plan-4 N1 0.020
LAD plan-4 C6 0.020
LAD plan-4 H2 0.020
LAD plan-4 N6 0.020
LAD plan-4 H8 0.020
LAD plan-4 H61 0.020
LAD plan-4 H62 0.020
LAD plan-5 N6 0.020
LAD plan-5 C6 0.020
LAD plan-5 H62 0.020
LAD plan-5 H61 0.020
# ------------------------------------------------------
|
