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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
TMP TMP 'THYMIDINE-5'-PHOSPHATE ' non-polymer 34 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_TMP
#
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
TMP O4 O O 0.000 0.000 0.000 0.000
TMP C4 C CR6 0.000 -1.127 -0.370 -0.275
TMP N3 N NR16 0.000 -2.118 -0.263 0.632
TMP HN3 H H 0.000 -1.920 0.136 1.571
TMP C2 C CR6 0.000 -3.364 -0.672 0.327
TMP O2 O O 0.000 -4.248 -0.573 1.157
TMP C5 C CR6 0.000 -1.410 -0.908 -1.554
TMP C5M C CH3 0.000 -0.320 -1.034 -2.587
TMP H53 H H 0.000 0.611 -1.178 -2.103
TMP H52 H H 0.000 -0.523 -1.862 -3.215
TMP H51 H H 0.000 -0.282 -0.150 -3.170
TMP C6 C CR16 0.000 -2.668 -1.311 -1.833
TMP H6 H H 0.000 -2.902 -1.728 -2.805
TMP N1 N NR6 0.000 -3.645 -1.189 -0.884
TMP "C1'" C CH1 0.000 -5.010 -1.627 -1.185
TMP "H1'" H H 0.000 -5.081 -1.925 -2.241
TMP "O4'" O O2 0.000 -5.936 -0.561 -0.915
TMP "C2'" C CH2 0.000 -5.393 -2.813 -0.280
TMP "H2'1" H H 0.000 -4.604 -3.053 0.435
TMP "H2'2" H H 0.000 -5.643 -3.705 -0.858
TMP "C3'" C CH1 0.000 -6.649 -2.320 0.480
TMP "H3'" H H 0.000 -6.379 -1.936 1.474
TMP "O3'" O OH1 0.000 -7.624 -3.359 0.583
TMP "HO3'" H H 0.000 -7.254 -4.100 1.082
TMP "C4'" C CH1 0.000 -7.154 -1.176 -0.436
TMP "H4'" H H 0.000 -7.737 -1.582 -1.274
TMP "C5'" C CH2 0.000 -7.989 -0.174 0.364
TMP "H5'1" H H 0.000 -7.354 0.319 1.103
TMP "H5'2" H H 0.000 -8.798 -0.701 0.874
TMP "O5'" O O2 0.000 -8.538 0.804 -0.522
TMP P P P 0.000 -9.399 1.821 0.382
TMP O1P O OP -0.666 -8.527 2.378 1.486
TMP O2P O OP -0.666 -9.909 2.954 -0.481
TMP O3P O OP -0.666 -10.572 1.083 0.991
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
TMP O4 n/a C4 START
TMP C4 O4 C5 .
TMP N3 C4 C2 .
TMP HN3 N3 . .
TMP C2 N3 O2 .
TMP O2 C2 . .
TMP C5 C4 C6 .
TMP C5M C5 H51 .
TMP H53 C5M . .
TMP H52 C5M . .
TMP H51 C5M . .
TMP C6 C5 N1 .
TMP H6 C6 . .
TMP N1 C6 "C1'" .
TMP "C1'" N1 "C2'" .
TMP "H1'" "C1'" . .
TMP "O4'" "C1'" . .
TMP "C2'" "C1'" "C3'" .
TMP "H2'1" "C2'" . .
TMP "H2'2" "C2'" . .
TMP "C3'" "C2'" "C4'" .
TMP "H3'" "C3'" . .
TMP "O3'" "C3'" "HO3'" .
TMP "HO3'" "O3'" . .
TMP "C4'" "C3'" "C5'" .
TMP "H4'" "C4'" . .
TMP "C5'" "C4'" "O5'" .
TMP "H5'1" "C5'" . .
TMP "H5'2" "C5'" . .
TMP "O5'" "C5'" P .
TMP P "O5'" O3P .
TMP O1P P . .
TMP O2P P . .
TMP O3P P . END
TMP "C4'" "O4'" . ADD
TMP N1 C2 . 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
TMP O1P P deloc 1.510 0.020
TMP O2P P deloc 1.510 0.020
TMP O3P P deloc 1.510 0.020
TMP P "O5'" single 1.610 0.020
TMP "O5'" "C5'" single 1.426 0.020
TMP "C5'" "C4'" single 1.524 0.020
TMP "H5'1" "C5'" single 1.092 0.020
TMP "H5'2" "C5'" single 1.092 0.020
TMP "C4'" "O4'" single 1.426 0.020
TMP "C4'" "C3'" single 1.524 0.020
TMP "H4'" "C4'" single 1.099 0.020
TMP "O4'" "C1'" single 1.426 0.020
TMP "O3'" "C3'" single 1.432 0.020
TMP "C3'" "C2'" single 1.524 0.020
TMP "H3'" "C3'" single 1.099 0.020
TMP "HO3'" "O3'" single 0.967 0.020
TMP "C2'" "C1'" single 1.524 0.020
TMP "H2'1" "C2'" single 1.092 0.020
TMP "H2'2" "C2'" single 1.092 0.020
TMP "C1'" N1 single 1.465 0.020
TMP "H1'" "C1'" single 1.099 0.020
TMP N1 C2 single 1.410 0.020
TMP N1 C6 single 1.337 0.020
TMP O2 C2 double 1.250 0.020
TMP C2 N3 single 1.337 0.020
TMP N3 C4 single 1.337 0.020
TMP HN3 N3 single 1.040 0.020
TMP C4 O4 double 1.250 0.020
TMP C5 C4 single 1.487 0.020
TMP C5M C5 single 1.506 0.020
TMP C6 C5 double 1.390 0.020
TMP H51 C5M single 1.059 0.020
TMP H52 C5M single 1.059 0.020
TMP H53 C5M single 1.059 0.020
TMP H6 C6 single 1.083 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
TMP O4 C4 N3 120.000 3.000
TMP O4 C4 C5 120.000 3.000
TMP N3 C4 C5 120.000 3.000
TMP C4 N3 HN3 120.000 3.000
TMP C4 N3 C2 120.000 3.000
TMP HN3 N3 C2 120.000 3.000
TMP N3 C2 O2 120.000 3.000
TMP N3 C2 N1 120.000 3.000
TMP O2 C2 N1 120.000 3.000
TMP C4 C5 C5M 120.000 3.000
TMP C4 C5 C6 120.000 3.000
TMP C5M C5 C6 120.000 3.000
TMP C5 C5M H53 109.470 3.000
TMP C5 C5M H52 109.470 3.000
TMP C5 C5M H51 109.470 3.000
TMP H53 C5M H52 109.470 3.000
TMP H53 C5M H51 109.470 3.000
TMP H52 C5M H51 109.470 3.000
TMP C5 C6 H6 120.000 3.000
TMP C5 C6 N1 120.000 3.000
TMP H6 C6 N1 120.000 3.000
TMP C6 N1 "C1'" 120.000 3.000
TMP C6 N1 C2 120.000 3.000
TMP "C1'" N1 C2 120.000 3.000
TMP N1 "C1'" "H1'" 109.470 3.000
TMP N1 "C1'" "O4'" 109.470 3.000
TMP N1 "C1'" "C2'" 109.470 3.000
TMP "H1'" "C1'" "O4'" 109.470 3.000
TMP "H1'" "C1'" "C2'" 108.340 3.000
TMP "O4'" "C1'" "C2'" 109.470 3.000
TMP "C1'" "O4'" "C4'" 111.800 3.000
TMP "C1'" "C2'" "H2'1" 109.470 3.000
TMP "C1'" "C2'" "H2'2" 109.470 3.000
TMP "C1'" "C2'" "C3'" 111.000 3.000
TMP "H2'1" "C2'" "H2'2" 107.900 3.000
TMP "H2'1" "C2'" "C3'" 109.470 3.000
TMP "H2'2" "C2'" "C3'" 109.470 3.000
TMP "C2'" "C3'" "H3'" 108.340 3.000
TMP "C2'" "C3'" "O3'" 109.470 3.000
TMP "C2'" "C3'" "C4'" 111.000 3.000
TMP "H3'" "C3'" "O3'" 109.470 3.000
TMP "H3'" "C3'" "C4'" 108.340 3.000
TMP "O3'" "C3'" "C4'" 109.470 3.000
TMP "C3'" "O3'" "HO3'" 109.470 3.000
TMP "C3'" "C4'" "H4'" 108.340 3.000
TMP "C3'" "C4'" "C5'" 111.000 3.000
TMP "C3'" "C4'" "O4'" 109.470 3.000
TMP "H4'" "C4'" "C5'" 108.340 3.000
TMP "H4'" "C4'" "O4'" 109.470 3.000
TMP "C5'" "C4'" "O4'" 109.470 3.000
TMP "C4'" "C5'" "H5'1" 109.470 3.000
TMP "C4'" "C5'" "H5'2" 109.470 3.000
TMP "C4'" "C5'" "O5'" 109.470 3.000
TMP "H5'1" "C5'" "H5'2" 107.900 3.000
TMP "H5'1" "C5'" "O5'" 109.470 3.000
TMP "H5'2" "C5'" "O5'" 109.470 3.000
TMP "C5'" "O5'" P 120.500 3.000
TMP "O5'" P O1P 108.200 3.000
TMP "O5'" P O2P 108.200 3.000
TMP "O5'" P O3P 108.200 3.000
TMP O1P P O2P 119.900 3.000
TMP O1P P O3P 119.900 3.000
TMP O2P P O3P 119.900 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
TMP CONST_1 O4 C4 N3 C2 180.000 0.000 0
TMP CONST_2 C4 N3 C2 O2 180.000 0.000 0
TMP CONST_3 O4 C4 C5 C6 180.000 0.000 0
TMP var_1 C4 C5 C5M H51 -90.303 20.000 1
TMP CONST_4 C4 C5 C6 N1 0.000 0.000 0
TMP CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
TMP CONST_6 C6 N1 C2 N3 0.000 0.000 0
TMP var_2 C6 N1 "C1'" "C2'" 115.273 20.000 1
TMP var_3 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
TMP var_4 N1 "C1'" "C2'" "C3'" 120.000 20.000 3
TMP var_5 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
TMP var_6 "C2'" "C3'" "O3'" "HO3'" 61.506 20.000 1
TMP var_7 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
TMP var_8 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
TMP var_9 "C3'" "C4'" "C5'" "O5'" -174.975 20.000 3
TMP var_10 "C4'" "C5'" "O5'" P -179.986 20.000 1
TMP var_11 "C5'" "O5'" P O3P -65.018 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
TMP chir_01 "C4'" "C5'" "O4'" "C3'" negativ
TMP chir_02 "C3'" "C4'" "O3'" "C2'" negativ
TMP chir_03 "C1'" "O4'" "C2'" N1 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
TMP plan-1 N1 0.020
TMP plan-1 "C1'" 0.020
TMP plan-1 C2 0.020
TMP plan-1 C6 0.020
TMP plan-1 N3 0.020
TMP plan-1 C4 0.020
TMP plan-1 C5 0.020
TMP plan-1 O2 0.020
TMP plan-1 HN3 0.020
TMP plan-1 O4 0.020
TMP plan-1 C5M 0.020
TMP plan-1 H6 0.020
# ------------------------------------------------------
|
