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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
APX APX '2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHO' non-polymer 65 40 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_APX
#
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
APX OP3 O OP -0.666 0.000 0.000 0.000
APX P2 P P 0.000 -1.367 0.143 0.633
APX OP1 O OP -0.666 -1.549 1.564 1.121
APX OP2 O OP -0.666 -1.482 -0.810 1.802
APX O2B O O2 0.000 -2.501 -0.201 -0.455
APX C2B C CH1 0.000 -3.762 0.065 0.163
APX H2B H H 0.000 -3.616 0.443 1.185
APX C1B C CH1 0.000 -4.581 1.072 -0.674
APX H1B H H 0.000 -4.254 1.053 -1.723
APX N9A N NR5 0.000 -4.447 2.422 -0.122
APX C8A C CR15 0.000 -5.275 3.013 0.770
APX H8A H H 0.000 -6.159 2.563 1.203
APX N7A N NRD5 0.000 -4.833 4.219 1.022
APX C5A C CR5 0.000 -3.727 4.434 0.312
APX C6A C CH1 0.000 -2.859 5.667 0.251
APX HC6A H H 0.000 -2.227 5.723 1.148
APX N6A N NH2 0.000 -3.704 6.866 0.161
APX H6A1 H H 0.000 -3.714 7.542 0.916
APX H6A2 H H 0.000 -4.282 7.024 -0.656
APX N1A N NH1 0.000 -2.013 5.559 -0.951
APX H1A H H 0.000 -1.887 6.266 -1.662
APX C2A C CH2 0.000 -1.387 4.232 -0.922
APX HC2A H H 0.000 -0.995 4.046 0.080
APX H2A H H 0.000 -0.566 4.211 -1.642
APX N3A N NT2 1.000 -2.370 3.193 -1.267
APX HN3A H H 0.000 -1.948 2.257 -1.153
APX H3A H H 0.000 -2.681 3.313 -2.245
APX C4A C CR5 0.000 -3.466 3.319 -0.410
APX O4B O O2 0.000 -5.948 0.618 -0.565
APX C3B C CH1 0.000 -4.637 -1.210 0.179
APX H3B H H 0.000 -4.928 -1.465 1.208
APX O3B O OH1 0.000 -3.947 -2.301 -0.433
APX H3O2 H H 0.000 -4.530 -3.071 -0.470
APX C4B C CH1 0.000 -5.879 -0.822 -0.654
APX H4B H H 0.000 -5.752 -1.135 -1.700
APX C5B C CH2 0.000 -7.140 -1.452 -0.059
APX H5B2 H H 0.000 -7.293 -1.074 0.954
APX H5B1 H H 0.000 -7.024 -2.538 -0.027
APX O5B O O2 0.000 -8.268 -1.117 -0.869
APX PA P P 0.000 -9.553 -1.810 -0.189
APX O6B O OP -0.500 -9.652 -1.383 1.228
APX O7B O OP -0.500 -9.411 -3.284 -0.253
APX O3N O O2 0.000 -10.884 -1.364 -0.977
APX PM P P 0.000 -12.123 -1.623 0.017
APX O6M O OP -0.500 -11.785 -1.121 1.370
APX O7M O OP -0.500 -12.405 -3.078 0.086
APX O5M O O2 0.000 -13.424 -0.851 -0.533
APX C5M C CH2 0.000 -14.451 -1.021 0.446
APX H5M2 H H 0.000 -14.120 -0.597 1.397
APX H5M1 H H 0.000 -14.657 -2.086 0.576
APX C4M C CH1 0.000 -15.721 -0.307 -0.017
APX H4M H H 0.000 -15.497 0.744 -0.247
APX C3M C CH1 0.000 -16.797 -0.384 1.083
APX H3M H H 0.000 -16.433 -0.976 1.934
APX O3M O OH1 0.000 -17.178 0.925 1.511
APX H3O1 H H 0.000 -17.894 0.857 2.157
APX C2M C CH1 0.000 -17.989 -1.098 0.394
APX H2M H H 0.000 -17.990 -2.172 0.626
APX O2M O OH1 0.000 -19.229 -0.495 0.770
APX H2O1 H H 0.000 -19.948 -0.894 0.261
APX C1M C CH1 0.000 -17.690 -0.857 -1.107
APX H1M H H 0.000 -18.023 0.145 -1.412
APX O4M O O2 0.000 -16.251 -0.959 -1.183
APX O1N O OH1 0.000 -18.308 -1.859 -1.915
APX H1N H H 0.000 -18.053 -1.731 -2.839
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
APX OP3 n/a P2 START
APX P2 OP3 O2B .
APX OP1 P2 . .
APX OP2 P2 . .
APX O2B P2 C2B .
APX C2B O2B C3B .
APX H2B C2B . .
APX C1B C2B O4B .
APX H1B C1B . .
APX N9A C1B C8A .
APX C8A N9A N7A .
APX H8A C8A . .
APX N7A C8A C5A .
APX C5A N7A C4A .
APX C6A C5A N1A .
APX HC6A C6A . .
APX N6A C6A H6A2 .
APX H6A1 N6A . .
APX H6A2 N6A . .
APX N1A C6A C2A .
APX H1A N1A . .
APX C2A N1A N3A .
APX HC2A C2A . .
APX H2A C2A . .
APX N3A C2A H3A .
APX HN3A N3A . .
APX H3A N3A . .
APX C4A C5A . .
APX O4B C1B . .
APX C3B C2B C4B .
APX H3B C3B . .
APX O3B C3B H3O2 .
APX H3O2 O3B . .
APX C4B C3B C5B .
APX H4B C4B . .
APX C5B C4B O5B .
APX H5B2 C5B . .
APX H5B1 C5B . .
APX O5B C5B PA .
APX PA O5B O3N .
APX O6B PA . .
APX O7B PA . .
APX O3N PA PM .
APX PM O3N O5M .
APX O6M PM . .
APX O7M PM . .
APX O5M PM C5M .
APX C5M O5M C4M .
APX H5M2 C5M . .
APX H5M1 C5M . .
APX C4M C5M C3M .
APX H4M C4M . .
APX C3M C4M C2M .
APX H3M C3M . .
APX O3M C3M H3O1 .
APX H3O1 O3M . .
APX C2M C3M C1M .
APX H2M C2M . .
APX O2M C2M H2O1 .
APX H2O1 O2M . .
APX C1M C2M O1N .
APX H1M C1M . .
APX O4M C1M . .
APX O1N C1M H1N .
APX H1N O1N . END
APX C4M O4M . ADD
APX C4B O4B . ADD
APX N9A C4A . ADD
APX C4A N3A . 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
APX O6M PM deloc 1.510 0.020
APX O7M PM deloc 1.510 0.020
APX PM O3N single 1.610 0.020
APX O5M PM single 1.610 0.020
APX O3N PA single 1.610 0.020
APX C5M O5M single 1.426 0.020
APX C4M C5M single 1.524 0.020
APX H5M2 C5M single 1.092 0.020
APX H5M1 C5M single 1.092 0.020
APX C4M O4M single 1.426 0.020
APX C3M C4M single 1.524 0.020
APX H4M C4M single 1.099 0.020
APX O4M C1M single 1.426 0.020
APX O3M C3M single 1.432 0.020
APX C2M C3M single 1.524 0.020
APX H3M C3M single 1.099 0.020
APX H3O1 O3M single 0.967 0.020
APX O2M C2M single 1.432 0.020
APX C1M C2M single 1.524 0.020
APX H2M C2M single 1.099 0.020
APX H2O1 O2M single 0.967 0.020
APX O1N C1M single 1.432 0.020
APX H1M C1M single 1.099 0.020
APX H1N O1N single 0.967 0.020
APX O6B PA deloc 1.510 0.020
APX O7B PA deloc 1.510 0.020
APX PA O5B single 1.610 0.020
APX O5B C5B single 1.426 0.020
APX C5B C4B single 1.524 0.020
APX H5B2 C5B single 1.092 0.020
APX H5B1 C5B single 1.092 0.020
APX C4B O4B single 1.426 0.020
APX C4B C3B single 1.524 0.020
APX H4B C4B single 1.099 0.020
APX O4B C1B single 1.426 0.020
APX O3B C3B single 1.432 0.020
APX C3B C2B single 1.524 0.020
APX H3B C3B single 1.099 0.020
APX H3O2 O3B single 0.967 0.020
APX C2B O2B single 1.426 0.020
APX C1B C2B single 1.524 0.020
APX H2B C2B single 1.099 0.020
APX O2B P2 single 1.610 0.020
APX N9A C1B single 1.485 0.020
APX H1B C1B single 1.099 0.020
APX N9A C4A single 1.337 0.020
APX C8A N9A single 1.337 0.020
APX C4A N3A single 1.455 0.020
APX C4A C5A double 1.490 0.020
APX N3A C2A single 1.472 0.020
APX H3A N3A single 1.033 0.020
APX HN3A N3A single 1.033 0.020
APX C2A N1A single 1.450 0.020
APX HC2A C2A single 1.092 0.020
APX H2A C2A single 1.092 0.020
APX N1A C6A single 1.450 0.020
APX H1A N1A single 1.010 0.020
APX C6A C5A single 1.480 0.020
APX N6A C6A single 1.450 0.020
APX HC6A C6A single 1.099 0.020
APX C5A N7A single 1.350 0.020
APX N7A C8A double 1.350 0.020
APX H8A C8A single 1.083 0.020
APX H6A2 N6A single 1.010 0.020
APX H6A1 N6A single 1.010 0.020
APX OP1 P2 deloc 1.510 0.020
APX OP2 P2 deloc 1.510 0.020
APX P2 OP3 deloc 1.510 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
APX OP3 P2 OP1 119.900 3.000
APX OP3 P2 OP2 119.900 3.000
APX OP3 P2 O2B 108.200 3.000
APX OP1 P2 OP2 119.900 3.000
APX OP1 P2 O2B 108.200 3.000
APX OP2 P2 O2B 108.200 3.000
APX P2 O2B C2B 120.500 3.000
APX O2B C2B H2B 109.470 3.000
APX O2B C2B C1B 109.470 3.000
APX O2B C2B C3B 109.470 3.000
APX H2B C2B C1B 108.340 3.000
APX H2B C2B C3B 108.340 3.000
APX C1B C2B C3B 111.000 3.000
APX C2B C1B H1B 108.340 3.000
APX C2B C1B N9A 109.470 3.000
APX C2B C1B O4B 109.470 3.000
APX H1B C1B N9A 109.470 3.000
APX H1B C1B O4B 109.470 3.000
APX N9A C1B O4B 109.470 3.000
APX C1B N9A C8A 126.000 3.000
APX C1B N9A C4A 126.000 3.000
APX C8A N9A C4A 108.000 3.000
APX N9A C8A H8A 126.000 3.000
APX N9A C8A N7A 108.000 3.000
APX H8A C8A N7A 126.000 3.000
APX C8A N7A C5A 108.000 3.000
APX N7A C5A C6A 126.000 3.000
APX N7A C5A C4A 108.000 3.000
APX C6A C5A C4A 126.000 3.000
APX C5A C6A HC6A 109.470 3.000
APX C5A C6A N6A 109.470 3.000
APX C5A C6A N1A 109.470 3.000
APX HC6A C6A N6A 109.470 3.000
APX HC6A C6A N1A 108.550 3.000
APX N6A C6A N1A 109.500 3.000
APX C6A N6A H6A1 120.000 3.000
APX C6A N6A H6A2 120.000 3.000
APX H6A1 N6A H6A2 120.000 3.000
APX C6A N1A H1A 118.500 3.000
APX C6A N1A C2A 120.000 3.000
APX H1A N1A C2A 118.500 3.000
APX N1A C2A HC2A 109.470 3.000
APX N1A C2A H2A 109.470 3.000
APX N1A C2A N3A 109.500 3.000
APX HC2A C2A H2A 107.900 3.000
APX HC2A C2A N3A 109.500 3.000
APX H2A C2A N3A 109.500 3.000
APX C2A N3A HN3A 109.500 3.000
APX C2A N3A H3A 109.500 3.000
APX C2A N3A C4A 109.500 3.000
APX HN3A N3A H3A 109.500 3.000
APX HN3A N3A C4A 109.500 3.000
APX H3A N3A C4A 109.500 3.000
APX C5A C4A N9A 108.000 3.000
APX C5A C4A N3A 108.000 3.000
APX N9A C4A N3A 108.000 3.000
APX C1B O4B C4B 111.800 3.000
APX C2B C3B H3B 108.340 3.000
APX C2B C3B O3B 109.470 3.000
APX C2B C3B C4B 111.000 3.000
APX H3B C3B O3B 109.470 3.000
APX H3B C3B C4B 108.340 3.000
APX O3B C3B C4B 109.470 3.000
APX C3B O3B H3O2 109.470 3.000
APX C3B C4B H4B 108.340 3.000
APX C3B C4B C5B 111.000 3.000
APX C3B C4B O4B 109.470 3.000
APX H4B C4B C5B 108.340 3.000
APX H4B C4B O4B 109.470 3.000
APX C5B C4B O4B 109.470 3.000
APX C4B C5B H5B2 109.470 3.000
APX C4B C5B H5B1 109.470 3.000
APX C4B C5B O5B 109.470 3.000
APX H5B2 C5B H5B1 107.900 3.000
APX H5B2 C5B O5B 109.470 3.000
APX H5B1 C5B O5B 109.470 3.000
APX C5B O5B PA 120.500 3.000
APX O5B PA O6B 108.200 3.000
APX O5B PA O7B 108.200 3.000
APX O5B PA O3N 102.600 3.000
APX O6B PA O7B 119.900 3.000
APX O6B PA O3N 108.200 3.000
APX O7B PA O3N 108.200 3.000
APX PA O3N PM 120.500 3.000
APX O3N PM O6M 108.200 3.000
APX O3N PM O7M 108.200 3.000
APX O3N PM O5M 102.600 3.000
APX O6M PM O7M 119.900 3.000
APX O6M PM O5M 108.200 3.000
APX O7M PM O5M 108.200 3.000
APX PM O5M C5M 120.500 3.000
APX O5M C5M H5M2 109.470 3.000
APX O5M C5M H5M1 109.470 3.000
APX O5M C5M C4M 109.470 3.000
APX H5M2 C5M H5M1 107.900 3.000
APX H5M2 C5M C4M 109.470 3.000
APX H5M1 C5M C4M 109.470 3.000
APX C5M C4M H4M 108.340 3.000
APX C5M C4M C3M 111.000 3.000
APX C5M C4M O4M 109.470 3.000
APX H4M C4M C3M 108.340 3.000
APX H4M C4M O4M 109.470 3.000
APX C3M C4M O4M 109.470 3.000
APX C4M C3M H3M 108.340 3.000
APX C4M C3M O3M 109.470 3.000
APX C4M C3M C2M 111.000 3.000
APX H3M C3M O3M 109.470 3.000
APX H3M C3M C2M 108.340 3.000
APX O3M C3M C2M 109.470 3.000
APX C3M O3M H3O1 109.470 3.000
APX C3M C2M H2M 108.340 3.000
APX C3M C2M O2M 109.470 3.000
APX C3M C2M C1M 111.000 3.000
APX H2M C2M O2M 109.470 3.000
APX H2M C2M C1M 108.340 3.000
APX O2M C2M C1M 109.470 3.000
APX C2M O2M H2O1 109.470 3.000
APX C2M C1M H1M 108.340 3.000
APX C2M C1M O4M 109.470 3.000
APX C2M C1M O1N 109.470 3.000
APX H1M C1M O4M 109.470 3.000
APX H1M C1M O1N 109.470 3.000
APX O4M C1M O1N 109.470 3.000
APX C1M O4M C4M 111.800 3.000
APX C1M O1N H1N 109.470 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
APX var_1 OP3 P2 O2B C2B -175.001 20.000 1
APX var_2 P2 O2B C2B C3B -121.432 20.000 1
APX var_3 O2B C2B C1B O4B 150.000 20.000 3
APX var_4 C2B C1B N9A C8A -93.457 20.000 1
APX CONST_1 C1B N9A C4A C5A 180.000 0.000 0
APX CONST_2 C1B N9A C8A N7A 180.000 0.000 0
APX CONST_3 N9A C8A N7A C5A 0.000 0.000 0
APX CONST_4 C8A N7A C5A C4A 0.000 0.000 0
APX var_5 N7A C5A C6A N1A -150.000 20.000 1
APX var_6 C5A C6A N6A H6A2 -65.363 20.000 1
APX var_7 C5A C6A N1A C2A -60.000 20.000 3
APX var_8 C6A N1A C2A N3A 60.000 20.000 3
APX var_9 N1A C2A N3A C4A -60.000 20.000 1
APX CONST_5 N7A C5A C4A N9A 0.000 0.000 0
APX var_10 C5A C4A N3A C2A 30.000 20.000 1
APX var_11 C2B C1B O4B C4B -30.000 20.000 1
APX var_12 O2B C2B C3B C4B -120.000 20.000 3
APX var_13 C2B C3B O3B H3O2 -176.096 20.000 1
APX var_14 C2B C3B C4B C5B -150.000 20.000 3
APX var_15 C3B C4B O4B C1B 30.000 20.000 1
APX var_16 C3B C4B C5B O5B -178.120 20.000 3
APX var_17 C4B C5B O5B PA 179.990 20.000 1
APX var_18 C5B O5B PA O3N 174.971 20.000 1
APX var_19 O5B PA O3N PM -159.996 20.000 1
APX var_20 PA O3N PM O5M 165.027 20.000 1
APX var_21 O3N PM O5M C5M -175.012 20.000 1
APX var_22 PM O5M C5M C4M 179.997 20.000 1
APX var_23 O5M C5M C4M C3M -175.293 20.000 3
APX var_24 C5M C4M O4M C1M 150.000 20.000 1
APX var_25 C5M C4M C3M C2M -120.000 20.000 3
APX var_26 C4M C3M O3M H3O1 176.195 20.000 1
APX var_27 C4M C3M C2M C1M -30.000 20.000 3
APX var_28 C3M C2M O2M H2O1 174.165 20.000 1
APX var_29 C3M C2M C1M O1N 150.000 20.000 3
APX var_30 C2M C1M O4M C4M -30.000 20.000 1
APX var_31 C2M C1M O1N H1N -175.579 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
APX chir_01 C4M C5M O4M C3M negativ
APX chir_02 C3M C4M O3M C2M negativ
APX chir_03 C2M C3M O2M C1M negativ
APX chir_04 C1M O4M C2M O1N positiv
APX chir_05 C4B C5B O4B C3B negativ
APX chir_06 C3B C4B O3B C2B negativ
APX chir_07 C2B C3B O2B C1B negativ
APX chir_08 C1B O4B C2B N9A positiv
APX chir_09 C6A N1A C5A N6A 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
APX plan-1 N9A 0.020
APX plan-1 C1B 0.020
APX plan-1 C4A 0.020
APX plan-1 C8A 0.020
APX plan-1 C5A 0.020
APX plan-1 N7A 0.020
APX plan-1 N3A 0.020
APX plan-1 C6A 0.020
APX plan-1 H8A 0.020
APX plan-2 N1A 0.020
APX plan-2 C2A 0.020
APX plan-2 C6A 0.020
APX plan-2 H1A 0.020
APX plan-3 N6A 0.020
APX plan-3 C6A 0.020
APX plan-3 H6A2 0.020
APX plan-3 H6A1 0.020
# ------------------------------------------------------
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