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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
UPR UPR '2'-DEOXYURIDINE-5'-ALPHA,BETA-AMINOP' non-polymer 45 29 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_UPR
#
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
UPR O4 O O 0.000 0.000 0.000 0.000
UPR C4 C CR6 0.000 -1.074 -0.470 -0.330
UPR N3 N NR16 0.000 -1.981 -0.816 0.606
UPR HN3 H H 0.000 -1.762 -0.685 1.614
UPR C2 C CR6 0.000 -3.171 -1.330 0.240
UPR O2 O O 0.000 -3.979 -1.637 1.095
UPR C5 C CR16 0.000 -1.382 -0.658 -1.699
UPR H5 H H 0.000 -0.667 -0.385 -2.465
UPR C6 C CR16 0.000 -2.580 -1.181 -2.037
UPR H6 H H 0.000 -2.833 -1.332 -3.079
UPR N1 N NR6 0.000 -3.473 -1.518 -1.057
UPR "C1'" C CH1 0.000 -4.773 -2.085 -1.423
UPR "H1'" H H 0.000 -4.912 -2.048 -2.513
UPR "O4'" O O2 0.000 -5.840 -1.376 -0.757
UPR "C2'" C CH2 0.000 -4.889 -3.540 -0.916
UPR "H2'1" H H 0.000 -4.238 -3.729 -0.060
UPR "H2'2" H H 0.000 -4.675 -4.267 -1.702
UPR "C3'" C CH1 0.000 -6.365 -3.669 -0.480
UPR H1 H H 0.000 -6.431 -3.899 0.592
UPR "O3'" O OH1 0.000 -7.028 -4.675 -1.249
UPR "H3'" H H 0.000 -6.619 -5.534 -1.077
UPR "C4'" C CH1 0.000 -6.970 -2.278 -0.774
UPR "H4'" H H 0.000 -7.449 -2.271 -1.763
UPR "C5'" C CH2 0.000 -7.978 -1.889 0.309
UPR "H5'1" H H 0.000 -7.470 -1.828 1.274
UPR "H5'2" H H 0.000 -8.765 -2.644 0.360
UPR "O5'" O O2 0.000 -8.553 -0.620 -0.009
UPR PA P P1 0.000 -9.807 -0.341 1.134
UPR O1A O OH1 0.000 -8.639 -0.262 2.394
UPR H1A H H 0.000 -8.942 -0.106 3.284
UPR O2A O OH1 0.000 -10.523 -1.849 0.717
UPR H2A H H 0.000 -10.343 -2.214 -0.144
UPR O3A O OH1 0.000 -11.061 -0.062 2.278
UPR H3A H H 0.000 -10.947 0.638 2.914
UPR N3A N NH1 0.000 -10.283 1.162 0.246
UPR H2 H H 0.000 -9.661 1.821 -0.200
UPR PB P P 0.000 -11.963 1.250 0.308
UPR O1B O O 0.000 -12.534 -0.105 0.147
UPR O2B O OH1 0.000 -12.416 1.857 1.729
UPR H2B H H 0.000 -12.127 2.742 1.992
UPR O3B O O2 0.000 -12.495 2.202 -0.877
UPR PG P P 0.000 -14.100 2.240 -0.757
UPR O2G O OP -0.666 -14.493 2.435 0.691
UPR O1G O OP -0.666 -14.640 3.385 -1.585
UPR O3G O OP -0.666 -14.674 0.935 -1.265
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
UPR O4 n/a C4 START
UPR C4 O4 C5 .
UPR N3 C4 C2 .
UPR HN3 N3 . .
UPR C2 N3 O2 .
UPR O2 C2 . .
UPR C5 C4 C6 .
UPR H5 C5 . .
UPR C6 C5 N1 .
UPR H6 C6 . .
UPR N1 C6 "C1'" .
UPR "C1'" N1 "C2'" .
UPR "H1'" "C1'" . .
UPR "O4'" "C1'" . .
UPR "C2'" "C1'" "C3'" .
UPR "H2'1" "C2'" . .
UPR "H2'2" "C2'" . .
UPR "C3'" "C2'" "C4'" .
UPR H1 "C3'" . .
UPR "O3'" "C3'" "H3'" .
UPR "H3'" "O3'" . .
UPR "C4'" "C3'" "C5'" .
UPR "H4'" "C4'" . .
UPR "C5'" "C4'" "O5'" .
UPR "H5'1" "C5'" . .
UPR "H5'2" "C5'" . .
UPR "O5'" "C5'" PA .
UPR PA "O5'" N3A .
UPR O1A PA H1A .
UPR H1A O1A . .
UPR O2A PA H2A .
UPR H2A O2A . .
UPR O3A PA H3A .
UPR H3A O3A . .
UPR N3A PA PB .
UPR H2 N3A . .
UPR PB N3A O3B .
UPR O1B PB . .
UPR O2B PB H2B .
UPR H2B O2B . .
UPR O3B PB PG .
UPR PG O3B O3G .
UPR O2G PG . .
UPR O1G PG . .
UPR O3G PG . END
UPR "C4'" "O4'" . ADD
UPR 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
UPR O1A PA single 1.835 0.020
UPR O2A PA single 1.835 0.020
UPR O3A PA single 1.835 0.020
UPR N3A PA single 1.800 0.020
UPR PA "O5'" single 1.735 0.020
UPR H1A O1A single 0.967 0.020
UPR H2A O2A single 0.967 0.020
UPR H3A O3A single 0.967 0.020
UPR PB N3A single 1.750 0.020
UPR H2 N3A single 1.010 0.020
UPR O1B PB double 1.480 0.020
UPR O2B PB single 1.610 0.020
UPR O3B PB single 1.610 0.020
UPR H2B O2B single 0.967 0.020
UPR PG O3B single 1.610 0.020
UPR O2G PG deloc 1.510 0.020
UPR O1G PG deloc 1.510 0.020
UPR O3G PG deloc 1.510 0.020
UPR "O5'" "C5'" single 1.426 0.020
UPR "C5'" "C4'" single 1.524 0.020
UPR "H5'1" "C5'" single 1.092 0.020
UPR "H5'2" "C5'" single 1.092 0.020
UPR "C4'" "O4'" single 1.426 0.020
UPR "C4'" "C3'" single 1.524 0.020
UPR "H4'" "C4'" single 1.099 0.020
UPR "O4'" "C1'" single 1.426 0.020
UPR "O3'" "C3'" single 1.432 0.020
UPR "C3'" "C2'" single 1.524 0.020
UPR H1 "C3'" single 1.099 0.020
UPR "H3'" "O3'" single 0.967 0.020
UPR "C2'" "C1'" single 1.524 0.020
UPR "H2'1" "C2'" single 1.092 0.020
UPR "H2'2" "C2'" single 1.092 0.020
UPR "C1'" N1 single 1.465 0.020
UPR "H1'" "C1'" single 1.099 0.020
UPR N1 C2 single 1.410 0.020
UPR N1 C6 single 1.337 0.020
UPR O2 C2 double 1.250 0.020
UPR C2 N3 single 1.337 0.020
UPR N3 C4 single 1.337 0.020
UPR HN3 N3 single 1.040 0.020
UPR C4 O4 double 1.250 0.020
UPR C5 C4 single 1.390 0.020
UPR C6 C5 double 1.390 0.020
UPR H5 C5 single 1.083 0.020
UPR 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
UPR O4 C4 N3 120.000 3.000
UPR O4 C4 C5 120.000 3.000
UPR N3 C4 C5 120.000 3.000
UPR C4 N3 HN3 120.000 3.000
UPR C4 N3 C2 120.000 3.000
UPR HN3 N3 C2 120.000 3.000
UPR N3 C2 O2 120.000 3.000
UPR N3 C2 N1 120.000 3.000
UPR O2 C2 N1 120.000 3.000
UPR C4 C5 H5 120.000 3.000
UPR C4 C5 C6 120.000 3.000
UPR H5 C5 C6 120.000 3.000
UPR C5 C6 H6 120.000 3.000
UPR C5 C6 N1 120.000 3.000
UPR H6 C6 N1 120.000 3.000
UPR C6 N1 "C1'" 120.000 3.000
UPR C6 N1 C2 120.000 3.000
UPR "C1'" N1 C2 120.000 3.000
UPR N1 "C1'" "H1'" 109.470 3.000
UPR N1 "C1'" "O4'" 109.470 3.000
UPR N1 "C1'" "C2'" 109.470 3.000
UPR "H1'" "C1'" "O4'" 109.470 3.000
UPR "H1'" "C1'" "C2'" 108.340 3.000
UPR "O4'" "C1'" "C2'" 109.470 3.000
UPR "C1'" "O4'" "C4'" 111.800 3.000
UPR "C1'" "C2'" "H2'1" 109.470 3.000
UPR "C1'" "C2'" "H2'2" 109.470 3.000
UPR "C1'" "C2'" "C3'" 111.000 3.000
UPR "H2'1" "C2'" "H2'2" 107.900 3.000
UPR "H2'1" "C2'" "C3'" 109.470 3.000
UPR "H2'2" "C2'" "C3'" 109.470 3.000
UPR "C2'" "C3'" H1 108.340 3.000
UPR "C2'" "C3'" "O3'" 109.470 3.000
UPR "C2'" "C3'" "C4'" 111.000 3.000
UPR H1 "C3'" "O3'" 109.470 3.000
UPR H1 "C3'" "C4'" 108.340 3.000
UPR "O3'" "C3'" "C4'" 109.470 3.000
UPR "C3'" "O3'" "H3'" 109.470 3.000
UPR "C3'" "C4'" "H4'" 108.340 3.000
UPR "C3'" "C4'" "C5'" 111.000 3.000
UPR "C3'" "C4'" "O4'" 109.470 3.000
UPR "H4'" "C4'" "C5'" 108.340 3.000
UPR "H4'" "C4'" "O4'" 109.470 3.000
UPR "C5'" "C4'" "O4'" 109.470 3.000
UPR "C4'" "C5'" "H5'1" 109.470 3.000
UPR "C4'" "C5'" "H5'2" 109.470 3.000
UPR "C4'" "C5'" "O5'" 109.470 3.000
UPR "H5'1" "C5'" "H5'2" 107.900 3.000
UPR "H5'1" "C5'" "O5'" 109.470 3.000
UPR "H5'2" "C5'" "O5'" 109.470 3.000
UPR "C5'" "O5'" PA 120.000 3.000
UPR "O5'" PA O1A 120.000 3.000
UPR "O5'" PA O2A 120.000 3.000
UPR "O5'" PA O3A 120.000 3.000
UPR "O5'" PA N3A 120.000 3.000
UPR O1A PA O2A 120.000 3.000
UPR O1A PA O3A 120.000 3.000
UPR O2A PA O3A 120.000 3.000
UPR O1A PA N3A 120.000 3.000
UPR O2A PA N3A 120.000 3.000
UPR O3A PA N3A 120.000 3.000
UPR PA O1A H1A 120.000 3.000
UPR PA O2A H2A 120.000 3.000
UPR PA O3A H3A 120.000 3.000
UPR PA N3A H2 120.000 3.000
UPR PA N3A PB 120.000 3.000
UPR H2 N3A PB 120.000 3.000
UPR N3A PB O1B 109.500 3.000
UPR N3A PB O2B 109.500 3.000
UPR N3A PB O3B 109.500 3.000
UPR O1B PB O2B 109.500 3.000
UPR O1B PB O3B 109.500 3.000
UPR O2B PB O3B 109.500 3.000
UPR PB O2B H2B 120.000 3.000
UPR PB O3B PG 120.500 3.000
UPR O3B PG O2G 108.200 3.000
UPR O3B PG O1G 108.200 3.000
UPR O3B PG O3G 108.200 3.000
UPR O2G PG O1G 119.900 3.000
UPR O2G PG O3G 119.900 3.000
UPR O1G PG O3G 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
UPR CONST_1 O4 C4 N3 C2 180.000 0.000 0
UPR CONST_2 C4 N3 C2 O2 180.000 0.000 0
UPR CONST_3 O4 C4 C5 C6 180.000 0.000 0
UPR CONST_4 C4 C5 C6 N1 0.000 0.000 0
UPR CONST_5 C5 C6 N1 "C1'" 180.000 0.000 0
UPR CONST_6 C6 N1 C2 N3 0.000 0.000 0
UPR var_1 C6 N1 "C1'" "C2'" 114.985 20.000 1
UPR var_2 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
UPR var_3 N1 "C1'" "C2'" "C3'" 150.000 20.000 3
UPR var_4 "C1'" "C2'" "C3'" "C4'" 0.000 20.000 3
UPR var_5 "C2'" "C3'" "O3'" "H3'" 63.309 20.000 1
UPR var_6 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
UPR var_7 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
UPR var_8 "C3'" "C4'" "C5'" "O5'" -178.130 20.000 3
UPR var_9 "C4'" "C5'" "O5'" PA 173.117 20.000 1
UPR var_10 "C5'" "O5'" PA N3A -174.413 20.000 1
UPR var_11 "O5'" PA O1A H1A -179.951 20.000 1
UPR var_12 "O5'" PA O2A H2A -24.390 20.000 1
UPR var_13 "O5'" PA O3A H3A 58.001 20.000 1
UPR var_14 "O5'" PA N3A PB 142.566 20.000 1
UPR var_15 PA N3A PB O3B -159.005 20.000 1
UPR var_16 N3A PB O2B H2B 60.076 20.000 1
UPR var_17 N3A PB O3B PG 179.994 20.000 1
UPR var_18 PB O3B PG O3G -75.019 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
UPR chir_01 "C4'" "C5'" "O4'" "C3'" negativ
UPR chir_02 "C3'" "C4'" "O3'" "C2'" negativ
UPR 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
UPR plan-1 N3A 0.020
UPR plan-1 PA 0.020
UPR plan-1 PB 0.020
UPR plan-1 H2 0.020
UPR plan-2 N1 0.020
UPR plan-2 "C1'" 0.020
UPR plan-2 C2 0.020
UPR plan-2 C6 0.020
UPR plan-2 N3 0.020
UPR plan-2 C4 0.020
UPR plan-2 C5 0.020
UPR plan-2 O2 0.020
UPR plan-2 HN3 0.020
UPR plan-2 O4 0.020
UPR plan-2 H5 0.020
UPR plan-2 H6 0.020
# ------------------------------------------------------
|
