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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
TDL TDL '3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)M' non-polymer 51 32 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_TDL
#
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
TDL OL3 O OC -0.500 0.000 0.000 0.000
TDL CLC C C 0.000 0.000 0.000 0.000
TDL OL2 O OC -0.500 0.000 0.000 0.000
TDL CLA C CT 0.000 0.000 0.000 0.000
TDL OL1 O OH1 0.000 0.000 0.000 0.000
TDL HL1 H H 0.000 0.000 0.000 0.000
TDL CLB C CH3 0.000 0.000 0.000 0.000
TDL HLB3 H H 0.000 0.000 0.000 0.000
TDL HLB2 H H 0.000 0.000 0.000 0.000
TDL HLB1 H H 0.000 0.000 0.000 0.000
TDL C2 C CR5 0.000 0.000 0.000 0.000
TDL S1 S S2 0.000 0.000 0.000 0.000
TDL N3 N NR5 1.000 0.000 0.000 0.000
TDL "C7'" C CH2 0.000 0.000 0.000 0.000
TDL "H7'1" H H 0.000 0.000 0.000 0.000
TDL "H7'2" H H 0.000 0.000 0.000 0.000
TDL "C5'" C CR6 0.000 0.000 0.000 0.000
TDL "C4'" C CR6 0.000 0.000 0.000 0.000
TDL "N4'" N NH2 0.000 0.000 0.000 0.000
TDL "H4'2" H H 0.000 0.000 0.000 0.000
TDL "H4'1" H H 0.000 0.000 0.000 0.000
TDL "N3'" N NRD6 0.000 0.000 0.000 0.000
TDL "C2'" C CR6 0.000 0.000 0.000 0.000
TDL CM2 C CH3 0.000 0.000 0.000 0.000
TDL HM23 H H 0.000 0.000 0.000 0.000
TDL HM22 H H 0.000 0.000 0.000 0.000
TDL HM21 H H 0.000 0.000 0.000 0.000
TDL "N1'" N NRD6 0.000 0.000 0.000 0.000
TDL "C6'" C CR16 0.000 0.000 0.000 0.000
TDL "H6'" H H 0.000 0.000 0.000 0.000
TDL C4 C CR5 0.000 0.000 0.000 0.000
TDL CM4 C CH3 0.000 0.000 0.000 0.000
TDL HM43 H H 0.000 0.000 0.000 0.000
TDL HM42 H H 0.000 0.000 0.000 0.000
TDL HM41 H H 0.000 0.000 0.000 0.000
TDL C5 C CR5 0.000 0.000 0.000 0.000
TDL C6 C CH2 0.000 0.000 0.000 0.000
TDL H61 H H 0.000 0.000 0.000 0.000
TDL H62 H H 0.000 0.000 0.000 0.000
TDL C7 C CH2 0.000 0.000 0.000 0.000
TDL H71 H H 0.000 0.000 0.000 0.000
TDL H72 H H 0.000 0.000 0.000 0.000
TDL O7 O O2 0.000 0.000 0.000 0.000
TDL PA P P 0.000 0.000 0.000 0.000
TDL O1A O OP -0.500 0.000 0.000 0.000
TDL O2A O OP -0.500 0.000 0.000 0.000
TDL O3A O O2 0.000 0.000 0.000 0.000
TDL PB P P 0.000 0.000 0.000 0.000
TDL O1B O OP -0.666 0.000 0.000 0.000
TDL O2B O OP -0.666 0.000 0.000 0.000
TDL O3B O OP -0.666 0.000 0.000 0.000
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
TDL OL3 n/a CLC START
TDL CLC OL3 CLA .
TDL OL2 CLC . .
TDL CLA CLC C2 .
TDL OL1 CLA HL1 .
TDL HL1 OL1 . .
TDL CLB CLA HLB1 .
TDL HLB3 CLB . .
TDL HLB2 CLB . .
TDL HLB1 CLB . .
TDL C2 CLA N3 .
TDL S1 C2 . .
TDL N3 C2 C4 .
TDL "C7'" N3 "C5'" .
TDL "H7'1" "C7'" . .
TDL "H7'2" "C7'" . .
TDL "C5'" "C7'" "C4'" .
TDL "C4'" "C5'" "N3'" .
TDL "N4'" "C4'" "H4'1" .
TDL "H4'2" "N4'" . .
TDL "H4'1" "N4'" . .
TDL "N3'" "C4'" "C2'" .
TDL "C2'" "N3'" "N1'" .
TDL CM2 "C2'" HM21 .
TDL HM23 CM2 . .
TDL HM22 CM2 . .
TDL HM21 CM2 . .
TDL "N1'" "C2'" "C6'" .
TDL "C6'" "N1'" "H6'" .
TDL "H6'" "C6'" . .
TDL C4 N3 C5 .
TDL CM4 C4 HM41 .
TDL HM43 CM4 . .
TDL HM42 CM4 . .
TDL HM41 CM4 . .
TDL C5 C4 C6 .
TDL C6 C5 C7 .
TDL H61 C6 . .
TDL H62 C6 . .
TDL C7 C6 O7 .
TDL H71 C7 . .
TDL H72 C7 . .
TDL O7 C7 PA .
TDL PA O7 O3A .
TDL O1A PA . .
TDL O2A PA . .
TDL O3A PA PB .
TDL PB O3A O3B .
TDL O1B PB . .
TDL O2B PB . .
TDL O3B PB . END
TDL C5 S1 . ADD
TDL "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
TDL O1B PB deloc 1.510 0.020
TDL O2B PB deloc 1.510 0.020
TDL O3B PB deloc 1.510 0.020
TDL PB O3A single 1.610 0.020
TDL O3A PA single 1.610 0.020
TDL O1A PA deloc 1.510 0.020
TDL O2A PA deloc 1.510 0.020
TDL PA O7 single 1.610 0.020
TDL O7 C7 single 1.426 0.020
TDL C7 C6 single 1.524 0.020
TDL H71 C7 single 1.092 0.020
TDL H72 C7 single 1.092 0.020
TDL C6 C5 single 1.510 0.020
TDL H61 C6 single 1.092 0.020
TDL H62 C6 single 1.092 0.020
TDL C5 S1 single 1.745 0.020
TDL C5 C4 double 1.490 0.020
TDL S1 C2 single 1.745 0.020
TDL CM4 C4 single 1.506 0.020
TDL C4 N3 single 1.337 0.020
TDL HM41 CM4 single 1.059 0.020
TDL HM42 CM4 single 1.059 0.020
TDL HM43 CM4 single 1.059 0.020
TDL N3 C2 double 1.337 0.020
TDL "C7'" N3 single 1.462 0.020
TDL C2 CLA single 1.500 0.020
TDL OL1 CLA single 1.432 0.020
TDL CLB CLA single 1.524 0.020
TDL CLA CLC single 1.507 0.020
TDL HL1 OL1 single 0.967 0.020
TDL HLB1 CLB single 1.059 0.020
TDL HLB2 CLB single 1.059 0.020
TDL HLB3 CLB single 1.059 0.020
TDL OL2 CLC deloc 1.250 0.020
TDL CLC OL3 deloc 1.250 0.020
TDL "C5'" "C7'" single 1.511 0.020
TDL "H7'1" "C7'" single 1.092 0.020
TDL "H7'2" "C7'" single 1.092 0.020
TDL "C5'" "C6'" single 1.390 0.020
TDL "C4'" "C5'" double 1.487 0.020
TDL "C6'" "N1'" double 1.337 0.020
TDL "H6'" "C6'" single 1.083 0.020
TDL "N1'" "C2'" single 1.350 0.020
TDL CM2 "C2'" single 1.506 0.020
TDL "C2'" "N3'" double 1.350 0.020
TDL HM21 CM2 single 1.059 0.020
TDL HM22 CM2 single 1.059 0.020
TDL HM23 CM2 single 1.059 0.020
TDL "N3'" "C4'" single 1.350 0.020
TDL "N4'" "C4'" single 1.355 0.020
TDL "H4'1" "N4'" single 1.010 0.020
TDL "H4'2" "N4'" single 1.010 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
TDL OL3 CLC OL2 123.000 3.000
TDL OL3 CLC CLA 118.500 3.000
TDL OL2 CLC CLA 118.500 3.000
TDL CLC CLA OL1 109.470 3.000
TDL CLC CLA CLB 109.470 3.000
TDL CLC CLA C2 109.500 3.000
TDL OL1 CLA CLB 109.470 3.000
TDL OL1 CLA C2 109.500 3.000
TDL CLB CLA C2 109.470 3.000
TDL CLA OL1 HL1 109.470 3.000
TDL CLA CLB HLB3 109.470 3.000
TDL CLA CLB HLB2 109.470 3.000
TDL CLA CLB HLB1 109.470 3.000
TDL HLB3 CLB HLB2 109.470 3.000
TDL HLB3 CLB HLB1 109.470 3.000
TDL HLB2 CLB HLB1 109.470 3.000
TDL CLA C2 S1 108.000 3.000
TDL CLA C2 N3 108.000 3.000
TDL S1 C2 N3 108.000 3.000
TDL C2 S1 C5 90.000 3.000
TDL C2 N3 "C7'" 126.000 3.000
TDL C2 N3 C4 108.000 3.000
TDL "C7'" N3 C4 126.000 3.000
TDL N3 "C7'" "H7'1" 109.500 3.000
TDL N3 "C7'" "H7'2" 109.500 3.000
TDL N3 "C7'" "C5'" 109.500 3.000
TDL "H7'1" "C7'" "H7'2" 107.900 3.000
TDL "H7'1" "C7'" "C5'" 109.470 3.000
TDL "H7'2" "C7'" "C5'" 109.470 3.000
TDL "C7'" "C5'" "C4'" 120.000 3.000
TDL "C7'" "C5'" "C6'" 120.000 3.000
TDL "C4'" "C5'" "C6'" 120.000 3.000
TDL "C5'" "C4'" "N4'" 120.000 3.000
TDL "C5'" "C4'" "N3'" 120.000 3.000
TDL "N4'" "C4'" "N3'" 120.000 3.000
TDL "C4'" "N4'" "H4'2" 120.000 3.000
TDL "C4'" "N4'" "H4'1" 120.000 3.000
TDL "H4'2" "N4'" "H4'1" 120.000 3.000
TDL "C4'" "N3'" "C2'" 120.000 3.000
TDL "N3'" "C2'" CM2 120.000 3.000
TDL "N3'" "C2'" "N1'" 120.000 3.000
TDL CM2 "C2'" "N1'" 120.000 3.000
TDL "C2'" CM2 HM23 109.470 3.000
TDL "C2'" CM2 HM22 109.470 3.000
TDL "C2'" CM2 HM21 109.470 3.000
TDL HM23 CM2 HM22 109.470 3.000
TDL HM23 CM2 HM21 109.470 3.000
TDL HM22 CM2 HM21 109.470 3.000
TDL "C2'" "N1'" "C6'" 120.000 3.000
TDL "N1'" "C6'" "H6'" 120.000 3.000
TDL "N1'" "C6'" "C5'" 120.000 3.000
TDL "H6'" "C6'" "C5'" 120.000 3.000
TDL N3 C4 CM4 126.000 3.000
TDL N3 C4 C5 108.000 3.000
TDL CM4 C4 C5 126.000 3.000
TDL C4 CM4 HM43 109.470 3.000
TDL C4 CM4 HM42 109.470 3.000
TDL C4 CM4 HM41 109.470 3.000
TDL HM43 CM4 HM42 109.470 3.000
TDL HM43 CM4 HM41 109.470 3.000
TDL HM42 CM4 HM41 109.470 3.000
TDL C4 C5 C6 126.000 3.000
TDL C4 C5 S1 108.000 3.000
TDL C6 C5 S1 108.000 3.000
TDL C5 C6 H61 109.470 3.000
TDL C5 C6 H62 109.470 3.000
TDL C5 C6 C7 109.470 3.000
TDL H61 C6 H62 107.900 3.000
TDL H61 C6 C7 109.470 3.000
TDL H62 C6 C7 109.470 3.000
TDL C6 C7 H71 109.470 3.000
TDL C6 C7 H72 109.470 3.000
TDL C6 C7 O7 109.470 3.000
TDL H71 C7 H72 107.900 3.000
TDL H71 C7 O7 109.470 3.000
TDL H72 C7 O7 109.470 3.000
TDL C7 O7 PA 120.500 3.000
TDL O7 PA O1A 108.200 3.000
TDL O7 PA O2A 108.200 3.000
TDL O7 PA O3A 102.600 3.000
TDL O1A PA O2A 119.900 3.000
TDL O1A PA O3A 108.200 3.000
TDL O2A PA O3A 108.200 3.000
TDL PA O3A PB 120.500 3.000
TDL O3A PB O1B 108.200 3.000
TDL O3A PB O2B 108.200 3.000
TDL O3A PB O3B 108.200 3.000
TDL O1B PB O2B 119.900 3.000
TDL O1B PB O3B 119.900 3.000
TDL O2B PB O3B 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
TDL var_1 OL3 CLC CLA C2 0.000 20.000 1
TDL var_2 CLC CLA OL1 HL1 0.000 20.000 1
TDL var_3 CLC CLA CLB HLB1 0.000 20.000 1
TDL var_4 CLC CLA C2 N3 0.000 20.000 1
TDL CONST_1 CLA C2 S1 C5 0.000 0.000 0
TDL CONST_2 CLA C2 N3 C4 0.000 0.000 0
TDL var_5 C2 N3 "C7'" "C5'" 0.000 20.000 1
TDL var_6 N3 "C7'" "C5'" "C4'" 0.000 20.000 2
TDL CONST_3 "C7'" "C5'" "C6'" "N1'" 0.000 0.000 0
TDL CONST_4 "C7'" "C5'" "C4'" "N3'" 0.000 0.000 0
TDL CONST_5 "C5'" "C4'" "N4'" "H4'1" 0.000 0.000 0
TDL CONST_6 "C5'" "C4'" "N3'" "C2'" 0.000 0.000 0
TDL CONST_7 "C4'" "N3'" "C2'" "N1'" 0.000 0.000 0
TDL var_7 "N3'" "C2'" CM2 HM21 0.000 20.000 1
TDL CONST_8 "N3'" "C2'" "N1'" "C6'" 0.000 0.000 0
TDL CONST_9 "C2'" "N1'" "C6'" "C5'" 0.000 0.000 0
TDL CONST_10 C2 N3 C4 C5 0.000 0.000 0
TDL var_8 N3 C4 CM4 HM41 0.000 20.000 1
TDL CONST_11 N3 C4 C5 C6 0.000 0.000 0
TDL CONST_12 C4 C5 S1 C2 0.000 0.000 0
TDL var_9 C4 C5 C6 C7 0.000 20.000 2
TDL var_10 C5 C6 C7 O7 0.000 20.000 3
TDL var_11 C6 C7 O7 PA 0.000 20.000 1
TDL var_12 C7 O7 PA O3A 0.000 20.000 1
TDL var_13 O7 PA O3A PB 0.000 20.000 1
TDL var_14 PA O3A PB O3B 0.000 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
TDL chir_01 CLA C2 OL1 CLB 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
TDL plan-1 C5 0.020
TDL plan-1 C6 0.020
TDL plan-1 S1 0.020
TDL plan-1 C4 0.020
TDL plan-1 N3 0.020
TDL plan-1 C2 0.020
TDL plan-1 CM4 0.020
TDL plan-1 "C7'" 0.020
TDL plan-1 CLA 0.020
TDL plan-2 CLC 0.020
TDL plan-2 CLA 0.020
TDL plan-2 OL2 0.020
TDL plan-2 OL3 0.020
TDL plan-3 "C5'" 0.020
TDL plan-3 "C7'" 0.020
TDL plan-3 "C6'" 0.020
TDL plan-3 "C4'" 0.020
TDL plan-3 "N1'" 0.020
TDL plan-3 "C2'" 0.020
TDL plan-3 "N3'" 0.020
TDL plan-3 "H6'" 0.020
TDL plan-3 CM2 0.020
TDL plan-3 "N4'" 0.020
TDL plan-3 "H4'2" 0.020
TDL plan-3 "H4'1" 0.020
TDL plan-4 "N4'" 0.020
TDL plan-4 "C4'" 0.020
TDL plan-4 "H4'1" 0.020
TDL plan-4 "H4'2" 0.020
# ------------------------------------------------------
|
