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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
GAP GAP 'GLYCYL-ADENOSINE-5'-PHOSPHATE ' non-polymer 44 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_GAP
#
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
GAP O2A O OP -0.500 0.000 0.000 0.000
GAP PA P P 0.000 -0.563 -0.480 1.285
GAP O1A O OP -0.500 -0.010 -1.820 1.598
GAP O3A O O2 -0.500 -0.088 0.571 2.475
GAP C C C 0.000 1.111 0.867 2.676
GAP O O O -0.500 2.008 0.363 1.965
GAP CA C CH2 0.000 1.475 1.830 3.777
GAP HA1 H H 0.000 1.135 1.432 4.735
GAP HA2 H H 0.000 0.992 2.793 3.592
GAP N N NT3 1.000 2.932 2.010 3.808
GAP H3 H H 0.000 3.383 1.099 3.983
GAP H2A H H 0.000 3.248 2.385 2.900
GAP H1 H H 0.000 3.178 2.670 4.561
GAP "O5'" O O2 0.000 -2.167 -0.578 1.165
GAP "C5'" C CH2 0.000 -2.446 -1.408 0.036
GAP "H5'1" H H 0.000 -2.008 -2.396 0.193
GAP "H5'2" H H 0.000 -2.016 -0.959 -0.862
GAP "C4'" C CH1 0.000 -3.961 -1.542 -0.136
GAP "H4'" H H 0.000 -4.419 -1.923 0.788
GAP "C3'" C CH1 0.000 -4.290 -2.475 -1.322
GAP "H3'" H H 0.000 -3.455 -2.498 -2.036
GAP "O3'" O OH1 0.000 -4.587 -3.792 -0.856
GAP "HO'3" H H 0.000 -4.790 -4.362 -1.611
GAP "C2'" C CH1 0.000 -5.540 -1.833 -1.970
GAP "H2'" H H 0.000 -5.326 -1.538 -3.007
GAP "O2'" O OH1 0.000 -6.645 -2.736 -1.926
GAP "HO'2" H H 0.000 -6.430 -3.534 -2.428
GAP "C1'" C CH1 0.000 -5.814 -0.587 -1.099
GAP "H1'" H H 0.000 -6.557 -0.820 -0.323
GAP "O4'" O O2 0.000 -4.541 -0.269 -0.495
GAP N9 N NR5 0.000 -6.277 0.525 -1.931
GAP C4 C CR56 0.000 -7.572 0.775 -2.305
GAP C5 C CR56 0.000 -7.530 1.935 -3.098
GAP N7 N NRD5 0.000 -6.236 2.331 -3.157
GAP C8 C CR15 0.000 -5.498 1.504 -2.475
GAP H8 H H 0.000 -4.424 1.581 -2.358
GAP N3 N NRD6 0.000 -8.743 0.185 -2.086
GAP C2 C CR16 0.000 -9.850 0.681 -2.598
GAP H2 H H 0.000 -10.787 0.175 -2.401
GAP N1 N NRD6 0.000 -9.861 1.770 -3.343
GAP C6 C CR6 0.000 -8.739 2.429 -3.616
GAP N6 N NH2 0.000 -8.761 3.571 -4.399
GAP H62 H H 0.000 -7.901 4.071 -4.605
GAP H61 H H 0.000 -9.636 3.922 -4.776
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
GAP O2A n/a PA START
GAP PA O2A "O5'" .
GAP O1A PA . .
GAP O3A PA C .
GAP C O3A CA .
GAP O C . .
GAP CA C N .
GAP HA1 CA . .
GAP HA2 CA . .
GAP N CA H1 .
GAP H3 N . .
GAP H2A N . .
GAP H1 N . .
GAP "O5'" PA "C5'" .
GAP "C5'" "O5'" "C4'" .
GAP "H5'1" "C5'" . .
GAP "H5'2" "C5'" . .
GAP "C4'" "C5'" "C3'" .
GAP "H4'" "C4'" . .
GAP "C3'" "C4'" "C2'" .
GAP "H3'" "C3'" . .
GAP "O3'" "C3'" "HO'3" .
GAP "HO'3" "O3'" . .
GAP "C2'" "C3'" "C1'" .
GAP "H2'" "C2'" . .
GAP "O2'" "C2'" "HO'2" .
GAP "HO'2" "O2'" . .
GAP "C1'" "C2'" N9 .
GAP "H1'" "C1'" . .
GAP "O4'" "C1'" . .
GAP N9 "C1'" C4 .
GAP C4 N9 N3 .
GAP C5 C4 N7 .
GAP N7 C5 C8 .
GAP C8 N7 H8 .
GAP H8 C8 . .
GAP N3 C4 C2 .
GAP C2 N3 N1 .
GAP H2 C2 . .
GAP N1 C2 C6 .
GAP C6 N1 N6 .
GAP N6 C6 H61 .
GAP H62 N6 . .
GAP H61 N6 . END
GAP "C4'" "O4'" . ADD
GAP N9 C8 . ADD
GAP 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
GAP N CA single 1.488 0.020
GAP H1 N single 1.033 0.020
GAP H2A N single 1.033 0.020
GAP H3 N single 1.033 0.020
GAP CA C single 1.510 0.020
GAP HA1 CA single 1.092 0.020
GAP HA2 CA single 1.092 0.020
GAP O C deloc 1.220 0.020
GAP C O3A deloc 1.454 0.020
GAP O1A PA deloc 1.510 0.020
GAP PA O2A deloc 1.510 0.020
GAP O3A PA single 1.610 0.020
GAP "O5'" PA single 1.610 0.020
GAP "C5'" "O5'" single 1.426 0.020
GAP "C4'" "C5'" single 1.524 0.020
GAP "H5'1" "C5'" single 1.092 0.020
GAP "H5'2" "C5'" single 1.092 0.020
GAP "C4'" "O4'" single 1.426 0.020
GAP "C3'" "C4'" single 1.524 0.020
GAP "H4'" "C4'" single 1.099 0.020
GAP "O4'" "C1'" single 1.426 0.020
GAP "O3'" "C3'" single 1.432 0.020
GAP "C2'" "C3'" single 1.524 0.020
GAP "H3'" "C3'" single 1.099 0.020
GAP "HO'3" "O3'" single 0.967 0.020
GAP "O2'" "C2'" single 1.432 0.020
GAP "C1'" "C2'" single 1.524 0.020
GAP "H2'" "C2'" single 1.099 0.020
GAP "HO'2" "O2'" single 0.967 0.020
GAP N9 "C1'" single 1.485 0.020
GAP "H1'" "C1'" single 1.099 0.020
GAP N9 C8 single 1.337 0.020
GAP C4 N9 single 1.337 0.020
GAP C8 N7 double 1.350 0.020
GAP H8 C8 single 1.083 0.020
GAP N7 C5 single 1.350 0.020
GAP C5 C6 single 1.490 0.020
GAP C5 C4 double 1.490 0.020
GAP N6 C6 single 1.355 0.020
GAP C6 N1 double 1.350 0.020
GAP H61 N6 single 1.010 0.020
GAP H62 N6 single 1.010 0.020
GAP N1 C2 single 1.337 0.020
GAP C2 N3 double 1.337 0.020
GAP H2 C2 single 1.083 0.020
GAP 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
GAP O2A PA O1A 119.900 3.000
GAP O2A PA O3A 108.200 3.000
GAP O2A PA "O5'" 108.200 3.000
GAP O1A PA O3A 108.200 3.000
GAP O1A PA "O5'" 108.200 3.000
GAP O3A PA "O5'" 102.600 3.000
GAP PA O3A C 120.000 3.000
GAP O3A C O 119.000 3.000
GAP O3A C CA 120.000 3.000
GAP O C CA 120.500 3.000
GAP C CA HA1 109.470 3.000
GAP C CA HA2 109.470 3.000
GAP C CA N 111.600 3.000
GAP HA1 CA HA2 107.900 3.000
GAP HA1 CA N 109.470 3.000
GAP HA2 CA N 109.470 3.000
GAP CA N H3 109.470 3.000
GAP CA N H2A 109.470 3.000
GAP CA N H1 109.470 3.000
GAP H3 N H2A 109.470 3.000
GAP H3 N H1 109.470 3.000
GAP H2A N H1 109.470 3.000
GAP PA "O5'" "C5'" 120.500 3.000
GAP "O5'" "C5'" "H5'1" 109.470 3.000
GAP "O5'" "C5'" "H5'2" 109.470 3.000
GAP "O5'" "C5'" "C4'" 109.470 3.000
GAP "H5'1" "C5'" "H5'2" 107.900 3.000
GAP "H5'1" "C5'" "C4'" 109.470 3.000
GAP "H5'2" "C5'" "C4'" 109.470 3.000
GAP "C5'" "C4'" "H4'" 108.340 3.000
GAP "C5'" "C4'" "C3'" 111.000 3.000
GAP "C5'" "C4'" "O4'" 109.470 3.000
GAP "H4'" "C4'" "C3'" 108.340 3.000
GAP "H4'" "C4'" "O4'" 109.470 3.000
GAP "C3'" "C4'" "O4'" 109.470 3.000
GAP "C4'" "C3'" "H3'" 108.340 3.000
GAP "C4'" "C3'" "O3'" 109.470 3.000
GAP "C4'" "C3'" "C2'" 111.000 3.000
GAP "H3'" "C3'" "O3'" 109.470 3.000
GAP "H3'" "C3'" "C2'" 108.340 3.000
GAP "O3'" "C3'" "C2'" 109.470 3.000
GAP "C3'" "O3'" "HO'3" 109.470 3.000
GAP "C3'" "C2'" "H2'" 108.340 3.000
GAP "C3'" "C2'" "O2'" 109.470 3.000
GAP "C3'" "C2'" "C1'" 111.000 3.000
GAP "H2'" "C2'" "O2'" 109.470 3.000
GAP "H2'" "C2'" "C1'" 108.340 3.000
GAP "O2'" "C2'" "C1'" 109.470 3.000
GAP "C2'" "O2'" "HO'2" 109.470 3.000
GAP "C2'" "C1'" "H1'" 108.340 3.000
GAP "C2'" "C1'" "O4'" 109.470 3.000
GAP "C2'" "C1'" N9 109.470 3.000
GAP "H1'" "C1'" "O4'" 109.470 3.000
GAP "H1'" "C1'" N9 109.470 3.000
GAP "O4'" "C1'" N9 109.470 3.000
GAP "C1'" "O4'" "C4'" 111.800 3.000
GAP "C1'" N9 C4 126.000 3.000
GAP "C1'" N9 C8 126.000 3.000
GAP C4 N9 C8 108.000 3.000
GAP N9 C4 C5 108.000 3.000
GAP N9 C4 N3 132.000 3.000
GAP C5 C4 N3 120.000 3.000
GAP C4 C5 N7 108.000 3.000
GAP C4 C5 C6 120.000 3.000
GAP N7 C5 C6 132.000 3.000
GAP C5 N7 C8 108.000 3.000
GAP N7 C8 H8 126.000 3.000
GAP N7 C8 N9 108.000 3.000
GAP H8 C8 N9 126.000 3.000
GAP C4 N3 C2 120.000 3.000
GAP N3 C2 H2 120.000 3.000
GAP N3 C2 N1 120.000 3.000
GAP H2 C2 N1 120.000 3.000
GAP C2 N1 C6 120.000 3.000
GAP N1 C6 N6 120.000 3.000
GAP N1 C6 C5 120.000 3.000
GAP N6 C6 C5 120.000 3.000
GAP C6 N6 H62 120.000 3.000
GAP C6 N6 H61 120.000 3.000
GAP H62 N6 H61 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
GAP var_1 O2A PA O3A C -54.267 20.000 1
GAP var_2 PA O3A C CA -179.965 20.000 1
GAP var_3 O3A C CA N 179.971 20.000 3
GAP var_4 C CA N H1 179.950 20.000 1
GAP var_5 O2A PA "O5'" "C5'" 54.970 20.000 1
GAP var_6 PA "O5'" "C5'" "C4'" -179.988 20.000 1
GAP var_7 "O5'" "C5'" "C4'" "C3'" -178.072 20.000 3
GAP var_8 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
GAP var_9 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
GAP var_10 "C4'" "C3'" "O3'" "HO'3" 179.946 20.000 1
GAP var_11 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
GAP var_12 "C3'" "C2'" "O2'" "HO'2" -61.518 20.000 1
GAP var_13 "C3'" "C2'" "C1'" N9 150.000 20.000 3
GAP var_14 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
GAP var_15 "C2'" "C1'" N9 C4 86.540 20.000 1
GAP CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
GAP CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
GAP CONST_3 N9 C4 C5 N7 0.000 0.000 0
GAP CONST_4 C4 C5 C6 N1 0.000 0.000 0
GAP CONST_5 C4 C5 N7 C8 0.000 0.000 0
GAP CONST_6 C5 N7 C8 N9 0.000 0.000 0
GAP CONST_7 N9 C4 N3 C2 180.000 0.000 0
GAP CONST_8 C4 N3 C2 N1 0.000 0.000 0
GAP CONST_9 N3 C2 N1 C6 0.000 0.000 0
GAP CONST_10 C2 N1 C6 N6 180.000 0.000 0
GAP CONST_11 N1 C6 N6 H61 -0.002 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
GAP chir_01 "C4'" "C5'" "O4'" "C3'" negativ
GAP chir_02 "C3'" "C4'" "O3'" "C2'" negativ
GAP chir_03 "C2'" "C3'" "O2'" "C1'" negativ
GAP 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
GAP plan-1 C 0.020
GAP plan-1 CA 0.020
GAP plan-1 O 0.020
GAP plan-1 O3A 0.020
GAP plan-2 N9 0.020
GAP plan-2 "C1'" 0.020
GAP plan-2 C8 0.020
GAP plan-2 C4 0.020
GAP plan-2 N7 0.020
GAP plan-2 H8 0.020
GAP plan-2 C5 0.020
GAP plan-2 C6 0.020
GAP plan-2 N1 0.020
GAP plan-2 C2 0.020
GAP plan-2 N3 0.020
GAP plan-2 N6 0.020
GAP plan-2 H2 0.020
GAP plan-2 H62 0.020
GAP plan-2 H61 0.020
GAP plan-3 N6 0.020
GAP plan-3 C6 0.020
GAP plan-3 H61 0.020
GAP plan-3 H62 0.020
# ------------------------------------------------------
|
