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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
VDM VDM '(1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[' non-polymer 48 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VDM
#
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
VDM "O3'" O OH1 0.000 0.000 0.000 0.000
VDM HG H H 0.000 -0.176 -0.201 0.929
VDM "C3'" C CH1 0.000 -1.045 0.833 -0.514
VDM "H3'" H H 0.000 -0.635 1.508 -1.278
VDM "C2'" C CH1 0.000 -1.595 1.656 0.654
VDM "H2'" H H 0.000 -1.867 0.965 1.464
VDM "O2'" O OH1 0.000 -0.571 2.527 1.136
VDM HE H H 0.000 0.257 2.034 1.216
VDM "C4'" C CH1 0.000 -2.124 -0.058 -1.142
VDM "H4'" H H 0.000 -2.385 -0.857 -0.434
VDM "O4'" O OH1 0.000 -1.602 -0.646 -2.334
VDM HF H H 0.000 -1.252 0.048 -2.909
VDM "C5'" C CH1 0.000 -3.399 0.724 -1.506
VDM "H5'" H H 0.000 -3.150 1.426 -2.314
VDM "C7'" C CH2 0.000 -4.497 -0.216 -2.014
VDM "H7'1" H H 0.000 -5.369 0.363 -2.327
VDM "H7'2" H H 0.000 -4.788 -0.912 -1.225
VDM "O7'" O OH1 0.000 -3.988 -0.937 -3.118
VDM "H7'" H H 0.000 -3.375 -0.376 -3.610
VDM "C6'" C CH2 0.000 -3.914 1.540 -0.309
VDM "H6'1" H H 0.000 -4.245 0.836 0.458
VDM "H6'2" H H 0.000 -4.765 2.133 -0.650
VDM "C1'" C CH1 0.000 -2.843 2.468 0.275
VDM HD H H 0.000 -3.244 2.937 1.184
VDM "N1'" N NH1 0.000 -2.513 3.523 -0.690
VDM "H1'" H H 0.000 -1.596 3.674 -1.086
VDM C1 C CH1 0.000 -3.701 4.328 -0.999
VDM H1 H H 0.000 -4.480 3.653 -1.379
VDM C6 C C1 0.000 -4.211 4.966 0.263
VDM H6 H H 0.000 -4.724 4.339 0.973
VDM C2 C CH1 0.000 -3.409 5.381 -2.084
VDM H2 H H 0.000 -4.367 5.766 -2.462
VDM O2 O OH1 0.000 -2.698 4.791 -3.173
VDM HC H H 0.000 -2.912 5.262 -3.990
VDM C3 C CH1 0.000 -2.603 6.553 -1.527
VDM H3 H H 0.000 -1.618 6.197 -1.193
VDM O3 O OH1 0.000 -2.436 7.518 -2.570
VDM HB H H 0.000 -1.519 7.506 -2.876
VDM C4 C CH1 0.000 -3.334 7.227 -0.352
VDM H4 H H 0.000 -4.063 7.940 -0.761
VDM O4 O OH1 0.000 -2.350 7.959 0.381
VDM HA H H 0.000 -1.673 7.350 0.707
VDM C5 C C 0.000 -4.066 6.269 0.562
VDM C7 C CH2 0.000 -4.661 6.843 1.819
VDM H7C1 H H 0.000 -3.865 7.264 2.437
VDM H7C2 H H 0.000 -5.171 6.052 2.372
VDM O7 O OH1 0.000 -5.587 7.859 1.484
VDM H7 H H 0.000 -5.109 8.630 1.155
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
VDM "O3'" n/a "C3'" START
VDM HG "O3'" . .
VDM "C3'" "O3'" "C4'" .
VDM "H3'" "C3'" . .
VDM "C2'" "C3'" "O2'" .
VDM "H2'" "C2'" . .
VDM "O2'" "C2'" HE .
VDM HE "O2'" . .
VDM "C4'" "C3'" "C5'" .
VDM "H4'" "C4'" . .
VDM "O4'" "C4'" HF .
VDM HF "O4'" . .
VDM "C5'" "C4'" "C6'" .
VDM "H5'" "C5'" . .
VDM "C7'" "C5'" "O7'" .
VDM "H7'1" "C7'" . .
VDM "H7'2" "C7'" . .
VDM "O7'" "C7'" "H7'" .
VDM "H7'" "O7'" . .
VDM "C6'" "C5'" "C1'" .
VDM "H6'1" "C6'" . .
VDM "H6'2" "C6'" . .
VDM "C1'" "C6'" "N1'" .
VDM HD "C1'" . .
VDM "N1'" "C1'" C1 .
VDM "H1'" "N1'" . .
VDM C1 "N1'" C2 .
VDM H1 C1 . .
VDM C6 C1 H6 .
VDM H6 C6 . .
VDM C2 C1 C3 .
VDM H2 C2 . .
VDM O2 C2 HC .
VDM HC O2 . .
VDM C3 C2 C4 .
VDM H3 C3 . .
VDM O3 C3 HB .
VDM HB O3 . .
VDM C4 C3 C5 .
VDM H4 C4 . .
VDM O4 C4 HA .
VDM HA O4 . .
VDM C5 C4 C7 .
VDM C7 C5 O7 .
VDM H7C1 C7 . .
VDM H7C2 C7 . .
VDM O7 C7 H7 .
VDM H7 O7 . END
VDM C5 C6 . ADD
VDM "C1'" "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
VDM O7 C7 single 1.432 0.020
VDM H7 O7 single 0.967 0.020
VDM C7 C5 single 1.510 0.020
VDM H7C1 C7 single 1.092 0.020
VDM H7C2 C7 single 1.092 0.020
VDM C5 C6 double 1.340 0.020
VDM C5 C4 single 1.500 0.020
VDM C6 C1 single 1.510 0.020
VDM H6 C6 single 1.077 0.020
VDM O4 C4 single 1.432 0.020
VDM C4 C3 single 1.524 0.020
VDM H4 C4 single 1.099 0.020
VDM HA O4 single 0.967 0.020
VDM O3 C3 single 1.432 0.020
VDM C3 C2 single 1.524 0.020
VDM H3 C3 single 1.099 0.020
VDM HB O3 single 0.967 0.020
VDM O2 C2 single 1.432 0.020
VDM C2 C1 single 1.524 0.020
VDM H2 C2 single 1.099 0.020
VDM HC O2 single 0.967 0.020
VDM C1 "N1'" single 1.450 0.020
VDM H1 C1 single 1.099 0.020
VDM "N1'" "C1'" single 1.450 0.020
VDM "H1'" "N1'" single 1.010 0.020
VDM HD "C1'" single 1.099 0.020
VDM "C1'" "C2'" single 1.524 0.020
VDM "C1'" "C6'" single 1.524 0.020
VDM "H2'" "C2'" single 1.099 0.020
VDM "O2'" "C2'" single 1.432 0.020
VDM "C2'" "C3'" single 1.524 0.020
VDM HE "O2'" single 0.967 0.020
VDM "H6'1" "C6'" single 1.092 0.020
VDM "H6'2" "C6'" single 1.092 0.020
VDM "C6'" "C5'" single 1.524 0.020
VDM "H5'" "C5'" single 1.099 0.020
VDM "C7'" "C5'" single 1.524 0.020
VDM "C5'" "C4'" single 1.524 0.020
VDM "H7'1" "C7'" single 1.092 0.020
VDM "H7'2" "C7'" single 1.092 0.020
VDM "O7'" "C7'" single 1.432 0.020
VDM "H7'" "O7'" single 0.967 0.020
VDM "H4'" "C4'" single 1.099 0.020
VDM "O4'" "C4'" single 1.432 0.020
VDM "C4'" "C3'" single 1.524 0.020
VDM HF "O4'" single 0.967 0.020
VDM "H3'" "C3'" single 1.099 0.020
VDM "C3'" "O3'" single 1.432 0.020
VDM HG "O3'" 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
VDM HG "O3'" "C3'" 109.470 3.000
VDM "O3'" "C3'" "H3'" 109.470 3.000
VDM "O3'" "C3'" "C2'" 109.470 3.000
VDM "O3'" "C3'" "C4'" 109.470 3.000
VDM "H3'" "C3'" "C2'" 108.340 3.000
VDM "H3'" "C3'" "C4'" 108.340 3.000
VDM "C2'" "C3'" "C4'" 111.000 3.000
VDM "C3'" "C2'" "H2'" 108.340 3.000
VDM "C3'" "C2'" "O2'" 109.470 3.000
VDM "C3'" "C2'" "C1'" 111.000 3.000
VDM "H2'" "C2'" "O2'" 109.470 3.000
VDM "H2'" "C2'" "C1'" 108.340 3.000
VDM "O2'" "C2'" "C1'" 109.470 3.000
VDM "C2'" "O2'" HE 109.470 3.000
VDM "C3'" "C4'" "H4'" 108.340 3.000
VDM "C3'" "C4'" "O4'" 109.470 3.000
VDM "C3'" "C4'" "C5'" 111.000 3.000
VDM "H4'" "C4'" "O4'" 109.470 3.000
VDM "H4'" "C4'" "C5'" 108.340 3.000
VDM "O4'" "C4'" "C5'" 109.470 3.000
VDM "C4'" "O4'" HF 109.470 3.000
VDM "C4'" "C5'" "H5'" 108.340 3.000
VDM "C4'" "C5'" "C7'" 111.000 3.000
VDM "C4'" "C5'" "C6'" 111.000 3.000
VDM "H5'" "C5'" "C7'" 108.340 3.000
VDM "H5'" "C5'" "C6'" 108.340 3.000
VDM "C7'" "C5'" "C6'" 109.470 3.000
VDM "C5'" "C7'" "H7'1" 109.470 3.000
VDM "C5'" "C7'" "H7'2" 109.470 3.000
VDM "C5'" "C7'" "O7'" 109.470 3.000
VDM "H7'1" "C7'" "H7'2" 107.900 3.000
VDM "H7'1" "C7'" "O7'" 109.470 3.000
VDM "H7'2" "C7'" "O7'" 109.470 3.000
VDM "C7'" "O7'" "H7'" 109.470 3.000
VDM "C5'" "C6'" "H6'1" 109.470 3.000
VDM "C5'" "C6'" "H6'2" 109.470 3.000
VDM "C5'" "C6'" "C1'" 111.000 3.000
VDM "H6'1" "C6'" "H6'2" 107.900 3.000
VDM "H6'1" "C6'" "C1'" 109.470 3.000
VDM "H6'2" "C6'" "C1'" 109.470 3.000
VDM "C6'" "C1'" HD 108.340 3.000
VDM "C6'" "C1'" "N1'" 110.000 3.000
VDM "C6'" "C1'" "C2'" 111.000 3.000
VDM HD "C1'" "N1'" 108.550 3.000
VDM HD "C1'" "C2'" 108.340 3.000
VDM "N1'" "C1'" "C2'" 110.000 3.000
VDM "C1'" "N1'" "H1'" 118.500 3.000
VDM "C1'" "N1'" C1 120.000 3.000
VDM "H1'" "N1'" C1 118.500 3.000
VDM "N1'" C1 H1 108.550 3.000
VDM "N1'" C1 C6 111.600 3.000
VDM "N1'" C1 C2 110.000 3.000
VDM H1 C1 C6 108.810 3.000
VDM H1 C1 C2 108.340 3.000
VDM C6 C1 C2 109.470 3.000
VDM C1 C6 H6 120.000 3.000
VDM C1 C6 C5 120.500 3.000
VDM H6 C6 C5 120.000 3.000
VDM C1 C2 H2 108.340 3.000
VDM C1 C2 O2 109.470 3.000
VDM C1 C2 C3 111.000 3.000
VDM H2 C2 O2 109.470 3.000
VDM H2 C2 C3 108.340 3.000
VDM O2 C2 C3 109.470 3.000
VDM C2 O2 HC 109.470 3.000
VDM C2 C3 H3 108.340 3.000
VDM C2 C3 O3 109.470 3.000
VDM C2 C3 C4 111.000 3.000
VDM H3 C3 O3 109.470 3.000
VDM H3 C3 C4 108.340 3.000
VDM O3 C3 C4 109.470 3.000
VDM C3 O3 HB 109.470 3.000
VDM C3 C4 H4 108.340 3.000
VDM C3 C4 O4 109.470 3.000
VDM C3 C4 C5 109.470 3.000
VDM H4 C4 O4 109.470 3.000
VDM H4 C4 C5 108.810 3.000
VDM O4 C4 C5 109.470 3.000
VDM C4 O4 HA 109.470 3.000
VDM C4 C5 C7 120.000 3.000
VDM C4 C5 C6 120.000 3.000
VDM C7 C5 C6 120.000 3.000
VDM C5 C7 H7C1 109.470 3.000
VDM C5 C7 H7C2 109.470 3.000
VDM C5 C7 O7 109.500 3.000
VDM H7C1 C7 H7C2 107.900 3.000
VDM H7C1 C7 O7 109.470 3.000
VDM H7C2 C7 O7 109.470 3.000
VDM C7 O7 H7 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
VDM var_1 HG "O3'" "C3'" "C4'" -92.424 20.000 1
VDM var_2 "O3'" "C3'" "C2'" "O2'" 60.000 20.000 3
VDM var_3 "C3'" "C2'" "O2'" HE -45.323 20.000 1
VDM var_4 "O3'" "C3'" "C4'" "C5'" 180.000 20.000 3
VDM var_5 "C3'" "C4'" "O4'" HF -53.116 20.000 1
VDM var_6 "C3'" "C4'" "C5'" "C6'" -60.000 20.000 3
VDM var_7 "C4'" "C5'" "C7'" "O7'" -56.701 20.000 3
VDM var_8 "C5'" "C7'" "O7'" "H7'" -33.670 20.000 1
VDM var_9 "C4'" "C5'" "C6'" "C1'" 60.000 20.000 3
VDM var_10 "C5'" "C6'" "C1'" "N1'" 60.000 20.000 3
VDM var_11 "C6'" "C1'" "C2'" "C3'" 60.000 20.000 3
VDM var_12 "C6'" "C1'" "N1'" C1 60.472 20.000 3
VDM var_13 "C1'" "N1'" C1 C2 -175.964 20.000 3
VDM var_14 "N1'" C1 C6 C5 120.000 20.000 1
VDM var_15 "N1'" C1 C2 C3 -90.000 20.000 3
VDM var_16 C1 C2 O2 HC 150.667 20.000 1
VDM var_17 C1 C2 C3 C4 -60.000 20.000 3
VDM var_18 C2 C3 O3 HB -107.596 20.000 1
VDM var_19 C2 C3 C4 C5 30.000 20.000 3
VDM var_20 C3 C4 O4 HA -60.274 20.000 1
VDM var_21 C3 C4 C5 C7 180.000 20.000 3
VDM var_22 C4 C5 C6 C1 0.000 20.000 1
VDM var_23 C4 C5 C7 O7 58.941 20.000 3
VDM var_24 C5 C7 O7 H7 -71.258 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
VDM chir_01 C4 C5 O4 C3 negativ
VDM chir_02 C3 C4 O3 C2 positiv
VDM chir_03 C2 C3 O2 C1 negativ
VDM chir_04 C1 C6 C2 "N1'" negativ
VDM chir_05 "C1'" "N1'" "C2'" "C6'" positiv
VDM chir_06 "C2'" "C1'" "O2'" "C3'" positiv
VDM chir_07 "C5'" "C6'" "C7'" "C4'" positiv
VDM chir_08 "C4'" "C5'" "O4'" "C3'" negativ
VDM chir_09 "C3'" "C2'" "C4'" "O3'" 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
VDM plan-1 C5 0.020
VDM plan-1 C7 0.020
VDM plan-1 C6 0.020
VDM plan-1 C4 0.020
VDM plan-1 H6 0.020
VDM plan-2 C6 0.020
VDM plan-2 C5 0.020
VDM plan-2 C1 0.020
VDM plan-2 H6 0.020
VDM plan-3 "N1'" 0.020
VDM plan-3 C1 0.020
VDM plan-3 "C1'" 0.020
VDM plan-3 "H1'" 0.020
# ------------------------------------------------------
|
