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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
VDO VDO '"[(1R,2R,3S,4S,5S)-2,3,4-TRIHYDROXY-' non-polymer 51 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VDO
#
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
VDO OAX O OP -0.666 0.000 0.000 0.000
VDO PBA P P 0.000 -0.403 1.293 -0.674
VDO OAY O OP -0.666 0.172 2.463 0.093
VDO OAZ O OP -0.666 0.127 1.309 -2.091
VDO OAW O O2 0.000 -2.009 1.407 -0.701
VDO CAG C CH2 0.000 -2.814 1.313 0.475
VDO HAG1 H H 0.000 -2.535 2.107 1.171
VDO HAG2 H H 0.000 -2.655 0.342 0.949
VDO CAF C CH1 0.000 -4.289 1.462 0.095
VDO HAF H H 0.000 -4.547 0.719 -0.672
VDO CAE C CH1 0.000 -4.535 2.870 -0.453
VDO HAE H H 0.000 -4.277 3.613 0.314
VDO OAU O OH1 0.000 -3.723 3.078 -1.610
VDO HAU H H 0.000 -3.878 3.968 -1.956
VDO CAC C CH1 0.000 -6.010 3.019 -0.832
VDO HAC H H 0.000 -6.268 2.276 -1.600
VDO OAP O OH1 0.000 -6.240 4.333 -1.345
VDO HAP H H 0.000 -7.171 4.426 -1.585
VDO CAB C CH1 0.000 -6.880 2.796 0.405
VDO HAB H H 0.000 -6.622 3.539 1.173
VDO OAO O OH1 0.000 -8.257 2.935 0.052
VDO HAO H H 0.000 -8.412 3.824 -0.296
VDO CAA C CH1 0.000 -6.635 1.388 0.954
VDO HAA H H 0.000 -7.260 1.228 1.844
VDO CAV C CH2 0.000 -5.160 1.239 1.334
VDO HAV2 H H 0.000 -4.985 0.236 1.727
VDO HAV1 H H 0.000 -4.904 1.977 2.097
VDO NAN N NH1 0.000 -6.979 0.395 -0.071
VDO HAN H H 0.000 -6.962 0.571 -1.066
VDO CAM C CH1 0.000 -7.353 -0.886 0.541
VDO HAM H H 0.000 -6.772 -1.032 1.463
VDO CAJ C CH1 0.000 -7.046 -2.024 -0.435
VDO HAJ H H 0.000 -5.958 -2.151 -0.524
VDO OAT O OH1 0.000 -7.601 -1.720 -1.716
VDO HAT H H 0.000 -7.405 -2.441 -2.330
VDO CAI C CH1 0.000 -7.675 -3.313 0.107
VDO HAI H H 0.000 -7.359 -4.167 -0.509
VDO OAS O OH1 0.000 -7.263 -3.516 1.460
VDO HAS H H 0.000 -7.662 -4.329 1.800
VDO CAH C CH1 0.000 -9.198 -3.170 0.050
VDO HAH H H 0.000 -9.662 -3.998 0.603
VDO OAR O OH1 0.000 -9.626 -3.212 -1.313
VDO HAR H H 0.000 -10.588 -3.120 -1.351
VDO CAK C C 0.000 -9.617 -1.866 0.664
VDO CAL C C1 0.000 -8.816 -0.872 0.874
VDO HAL H H 0.000 -9.225 0.022 1.314
VDO CAD C CH2 0.000 -11.062 -1.706 1.061
VDO HAD1 H H 0.000 -11.322 -2.466 1.800
VDO HAD2 H H 0.000 -11.696 -1.824 0.180
VDO OAQ O OH1 0.000 -11.260 -0.406 1.622
VDO HAQ H H 0.000 -12.187 -0.304 1.877
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
VDO OAX n/a PBA START
VDO PBA OAX OAW .
VDO OAY PBA . .
VDO OAZ PBA . .
VDO OAW PBA CAG .
VDO CAG OAW CAF .
VDO HAG1 CAG . .
VDO HAG2 CAG . .
VDO CAF CAG CAE .
VDO HAF CAF . .
VDO CAE CAF CAC .
VDO HAE CAE . .
VDO OAU CAE HAU .
VDO HAU OAU . .
VDO CAC CAE CAB .
VDO HAC CAC . .
VDO OAP CAC HAP .
VDO HAP OAP . .
VDO CAB CAC CAA .
VDO HAB CAB . .
VDO OAO CAB HAO .
VDO HAO OAO . .
VDO CAA CAB NAN .
VDO HAA CAA . .
VDO CAV CAA HAV1 .
VDO HAV2 CAV . .
VDO HAV1 CAV . .
VDO NAN CAA CAM .
VDO HAN NAN . .
VDO CAM NAN CAJ .
VDO HAM CAM . .
VDO CAJ CAM CAI .
VDO HAJ CAJ . .
VDO OAT CAJ HAT .
VDO HAT OAT . .
VDO CAI CAJ CAH .
VDO HAI CAI . .
VDO OAS CAI HAS .
VDO HAS OAS . .
VDO CAH CAI CAK .
VDO HAH CAH . .
VDO OAR CAH HAR .
VDO HAR OAR . .
VDO CAK CAH CAD .
VDO CAL CAK HAL .
VDO HAL CAL . .
VDO CAD CAK OAQ .
VDO HAD1 CAD . .
VDO HAD2 CAD . .
VDO OAQ CAD HAQ .
VDO HAQ OAQ . END
VDO CAF CAV . ADD
VDO CAM CAL . 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
VDO OAY PBA deloc 1.510 0.020
VDO OAZ PBA deloc 1.510 0.020
VDO PBA OAX deloc 1.510 0.020
VDO OAW PBA single 1.610 0.020
VDO CAG OAW single 1.426 0.020
VDO CAF CAG single 1.524 0.020
VDO CAF CAV single 1.524 0.020
VDO CAE CAF single 1.524 0.020
VDO CAV CAA single 1.524 0.020
VDO OAU CAE single 1.432 0.020
VDO CAC CAE single 1.524 0.020
VDO OAP CAC single 1.432 0.020
VDO CAB CAC single 1.524 0.020
VDO OAO CAB single 1.432 0.020
VDO CAA CAB single 1.524 0.020
VDO NAN CAA single 1.450 0.020
VDO CAM NAN single 1.450 0.020
VDO CAM CAL single 1.510 0.020
VDO CAJ CAM single 1.524 0.020
VDO CAL CAK double 1.340 0.020
VDO OAT CAJ single 1.432 0.020
VDO CAI CAJ single 1.524 0.020
VDO OAS CAI single 1.432 0.020
VDO CAH CAI single 1.524 0.020
VDO OAR CAH single 1.432 0.020
VDO CAK CAH single 1.500 0.020
VDO CAD CAK single 1.510 0.020
VDO OAQ CAD single 1.432 0.020
VDO HAG1 CAG single 1.092 0.020
VDO HAG2 CAG single 1.092 0.020
VDO HAF CAF single 1.099 0.020
VDO HAV1 CAV single 1.092 0.020
VDO HAV2 CAV single 1.092 0.020
VDO HAE CAE single 1.099 0.020
VDO HAA CAA single 1.099 0.020
VDO HAU OAU single 0.967 0.020
VDO HAC CAC single 1.099 0.020
VDO HAP OAP single 0.967 0.020
VDO HAB CAB single 1.099 0.020
VDO HAO OAO single 0.967 0.020
VDO HAN NAN single 1.010 0.020
VDO HAM CAM single 1.099 0.020
VDO HAL CAL single 1.077 0.020
VDO HAJ CAJ single 1.099 0.020
VDO HAT OAT single 0.967 0.020
VDO HAI CAI single 1.099 0.020
VDO HAS OAS single 0.967 0.020
VDO HAH CAH single 1.099 0.020
VDO HAR OAR single 0.967 0.020
VDO HAD1 CAD single 1.092 0.020
VDO HAD2 CAD single 1.092 0.020
VDO HAQ OAQ single 0.967 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
VDO OAX PBA OAY 119.900 3.000
VDO OAX PBA OAZ 119.900 3.000
VDO OAX PBA OAW 108.200 3.000
VDO OAY PBA OAZ 119.900 3.000
VDO OAY PBA OAW 108.200 3.000
VDO OAZ PBA OAW 108.200 3.000
VDO PBA OAW CAG 120.500 3.000
VDO OAW CAG HAG1 109.470 3.000
VDO OAW CAG HAG2 109.470 3.000
VDO OAW CAG CAF 109.470 3.000
VDO HAG1 CAG HAG2 107.900 3.000
VDO HAG1 CAG CAF 109.470 3.000
VDO HAG2 CAG CAF 109.470 3.000
VDO CAG CAF HAF 108.340 3.000
VDO CAG CAF CAE 111.000 3.000
VDO CAG CAF CAV 109.470 3.000
VDO HAF CAF CAE 108.340 3.000
VDO HAF CAF CAV 108.340 3.000
VDO CAE CAF CAV 111.000 3.000
VDO CAF CAE HAE 108.340 3.000
VDO CAF CAE OAU 109.470 3.000
VDO CAF CAE CAC 111.000 3.000
VDO HAE CAE OAU 109.470 3.000
VDO HAE CAE CAC 108.340 3.000
VDO OAU CAE CAC 109.470 3.000
VDO CAE OAU HAU 109.470 3.000
VDO CAE CAC HAC 108.340 3.000
VDO CAE CAC OAP 109.470 3.000
VDO CAE CAC CAB 111.000 3.000
VDO HAC CAC OAP 109.470 3.000
VDO HAC CAC CAB 108.340 3.000
VDO OAP CAC CAB 109.470 3.000
VDO CAC OAP HAP 109.470 3.000
VDO CAC CAB HAB 108.340 3.000
VDO CAC CAB OAO 109.470 3.000
VDO CAC CAB CAA 111.000 3.000
VDO HAB CAB OAO 109.470 3.000
VDO HAB CAB CAA 108.340 3.000
VDO OAO CAB CAA 109.470 3.000
VDO CAB OAO HAO 109.470 3.000
VDO CAB CAA HAA 108.340 3.000
VDO CAB CAA CAV 111.000 3.000
VDO CAB CAA NAN 110.000 3.000
VDO HAA CAA CAV 108.340 3.000
VDO HAA CAA NAN 108.550 3.000
VDO CAV CAA NAN 110.000 3.000
VDO CAA CAV HAV2 109.470 3.000
VDO CAA CAV HAV1 109.470 3.000
VDO CAA CAV CAF 111.000 3.000
VDO HAV2 CAV HAV1 107.900 3.000
VDO HAV2 CAV CAF 109.470 3.000
VDO HAV1 CAV CAF 109.470 3.000
VDO CAA NAN HAN 118.500 3.000
VDO CAA NAN CAM 120.000 3.000
VDO HAN NAN CAM 118.500 3.000
VDO NAN CAM HAM 108.550 3.000
VDO NAN CAM CAJ 110.000 3.000
VDO NAN CAM CAL 111.600 3.000
VDO HAM CAM CAJ 108.340 3.000
VDO HAM CAM CAL 108.810 3.000
VDO CAJ CAM CAL 109.470 3.000
VDO CAM CAJ HAJ 108.340 3.000
VDO CAM CAJ OAT 109.470 3.000
VDO CAM CAJ CAI 111.000 3.000
VDO HAJ CAJ OAT 109.470 3.000
VDO HAJ CAJ CAI 108.340 3.000
VDO OAT CAJ CAI 109.470 3.000
VDO CAJ OAT HAT 109.470 3.000
VDO CAJ CAI HAI 108.340 3.000
VDO CAJ CAI OAS 109.470 3.000
VDO CAJ CAI CAH 111.000 3.000
VDO HAI CAI OAS 109.470 3.000
VDO HAI CAI CAH 108.340 3.000
VDO OAS CAI CAH 109.470 3.000
VDO CAI OAS HAS 109.470 3.000
VDO CAI CAH HAH 108.340 3.000
VDO CAI CAH OAR 109.470 3.000
VDO CAI CAH CAK 109.470 3.000
VDO HAH CAH OAR 109.470 3.000
VDO HAH CAH CAK 108.810 3.000
VDO OAR CAH CAK 109.470 3.000
VDO CAH OAR HAR 109.470 3.000
VDO CAH CAK CAL 120.000 3.000
VDO CAH CAK CAD 120.000 3.000
VDO CAL CAK CAD 120.000 3.000
VDO CAK CAL HAL 120.000 3.000
VDO CAK CAL CAM 120.500 3.000
VDO HAL CAL CAM 120.000 3.000
VDO CAK CAD HAD1 109.470 3.000
VDO CAK CAD HAD2 109.470 3.000
VDO CAK CAD OAQ 109.500 3.000
VDO HAD1 CAD HAD2 107.900 3.000
VDO HAD1 CAD OAQ 109.470 3.000
VDO HAD2 CAD OAQ 109.470 3.000
VDO CAD OAQ HAQ 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
VDO var_1 OAX PBA OAW CAG 54.973 20.000 1
VDO var_2 PBA OAW CAG CAF -179.990 20.000 1
VDO var_3 OAW CAG CAF CAE -65.007 20.000 3
VDO var_4 CAG CAF CAV CAA 180.000 20.000 3
VDO var_5 CAG CAF CAE CAC 180.000 20.000 3
VDO var_6 CAF CAE OAU HAU 179.993 20.000 1
VDO var_7 CAF CAE CAC CAB 60.000 20.000 3
VDO var_8 CAE CAC OAP HAP 179.967 20.000 1
VDO var_9 CAE CAC CAB CAA -60.000 20.000 3
VDO var_10 CAC CAB OAO HAO -59.961 20.000 1
VDO var_11 CAC CAB CAA NAN -60.000 20.000 3
VDO var_12 CAB CAA CAV CAF -60.000 20.000 3
VDO var_13 CAB CAA NAN CAM -154.087 20.000 3
VDO var_14 CAA NAN CAM CAJ -152.649 20.000 3
VDO var_15 NAN CAM CAL CAK 150.000 20.000 1
VDO var_16 NAN CAM CAJ CAI 180.000 20.000 3
VDO var_17 CAM CAJ OAT HAT -179.979 20.000 1
VDO var_18 CAM CAJ CAI CAH 60.000 20.000 3
VDO var_19 CAJ CAI OAS HAS 179.921 20.000 1
VDO var_20 CAJ CAI CAH CAK -60.000 20.000 3
VDO var_21 CAI CAH OAR HAR -179.946 20.000 1
VDO var_22 CAI CAH CAK CAD -150.000 20.000 3
VDO var_23 CAH CAK CAL CAM 0.000 20.000 1
VDO var_24 CAH CAK CAD OAQ -179.993 20.000 3
VDO var_25 CAK CAD OAQ HAQ -179.983 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
VDO chir_01 CAF CAG CAV CAE negativ
VDO chir_02 CAE CAF OAU CAC negativ
VDO chir_03 CAC CAE OAP CAB positiv
VDO chir_04 CAB CAC OAO CAA negativ
VDO chir_05 CAA CAV CAB NAN negativ
VDO chir_06 CAM NAN CAL CAJ negativ
VDO chir_07 CAJ CAM OAT CAI positiv
VDO chir_08 CAI CAJ OAS CAH negativ
VDO chir_09 CAH CAI OAR CAK 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
VDO plan-1 NAN 0.020
VDO plan-1 CAA 0.020
VDO plan-1 CAM 0.020
VDO plan-1 HAN 0.020
VDO plan-2 CAL 0.020
VDO plan-2 CAM 0.020
VDO plan-2 CAK 0.020
VDO plan-2 HAL 0.020
VDO plan-3 CAK 0.020
VDO plan-3 CAL 0.020
VDO plan-3 CAH 0.020
VDO plan-3 CAD 0.020
VDO plan-3 HAL 0.020
# ------------------------------------------------------
|
