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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
VMS VMS '5'O-[N-(L-VALYL)SULPHAMOYL]ADENOSINE' non-polymer 53 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VMS
#
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
VMS OBC O OS 0.000 0.000 0.000 0.000
VMS SBD S ST 0.000 -1.004 0.463 0.892
VMS OAZ O OS 0.000 -0.820 1.447 1.900
VMS NAS N NH1 0.000 -1.567 -0.883 1.676
VMS HAS H H 0.000 -1.669 -0.877 2.680
VMS C C C 0.000 -1.888 -1.987 0.972
VMS O O O 0.000 -1.765 -1.994 -0.235
VMS CA C CH1 0.000 -2.400 -3.212 1.685
VMS HA H H 0.000 -3.086 -2.909 2.488
VMS N N NH2 0.000 -3.113 -4.072 0.730
VMS H2 H H 0.000 -4.090 -4.296 0.875
VMS H H H 0.000 -2.632 -4.446 -0.079
VMS CB C CH1 0.000 -1.222 -3.984 2.284
VMS HB H H 0.000 -0.536 -4.287 1.481
VMS CG1 C CH3 0.000 -1.742 -5.227 3.007
VMS HG13 H H 0.000 -2.256 -5.847 2.319
VMS HG12 H H 0.000 -0.927 -5.762 3.422
VMS HG11 H H 0.000 -2.403 -4.936 3.782
VMS CG2 C CH3 0.000 -0.480 -3.088 3.278
VMS HG23 H H 0.000 -1.140 -2.795 4.052
VMS HG22 H H 0.000 0.336 -3.620 3.694
VMS HG21 H H 0.000 -0.119 -2.226 2.777
VMS "O5'" O O2 0.000 -2.132 0.981 0.011
VMS "C5'" C CH2 0.000 -3.075 1.616 0.877
VMS "H5'1" H H 0.000 -2.587 2.437 1.406
VMS "H5'2" H H 0.000 -3.449 0.889 1.601
VMS "C4'" C CH1 0.000 -4.241 2.161 0.050
VMS "H4'" H H 0.000 -3.860 2.815 -0.747
VMS "C3'" C CH1 0.000 -5.205 2.949 0.959
VMS "H3'" H H 0.000 -4.871 2.902 2.005
VMS "O3'" O OH1 0.000 -5.310 4.308 0.528
VMS "HO3'" H H 0.000 -5.963 4.768 1.073
VMS "C2'" C CH1 0.000 -6.562 2.219 0.789
VMS H1 H H 0.000 -6.727 1.503 1.606
VMS "O2'" O OH1 0.000 -7.638 3.156 0.707
VMS "H2'" H H 0.000 -7.741 3.603 1.558
VMS "C1'" C CH1 0.000 -6.368 1.481 -0.560
VMS "H1'" H H 0.000 -6.549 2.162 -1.403
VMS "O4'" O O2 0.000 -4.984 1.074 -0.525
VMS N9 N NR5 0.000 -7.248 0.312 -0.644
VMS C4 C CR56 0.000 -8.530 0.295 -1.131
VMS N3 N NRD6 0.000 -9.349 1.203 -1.654
VMS C2 C CR16 0.000 -10.559 0.868 -2.049
VMS H3 H H 0.000 -11.201 1.633 -2.466
VMS N1 N NRD6 0.000 -11.018 -0.367 -1.956
VMS C6 C CR6 0.000 -10.271 -1.344 -1.451
VMS N6 N NH2 0.000 -10.761 -2.634 -1.356
VMS HN62 H H 0.000 -11.701 -2.852 -1.672
VMS HN61 H H 0.000 -10.187 -3.376 -0.970
VMS C5 C CR56 0.000 -8.971 -1.034 -1.015
VMS N7 N NRD5 0.000 -7.956 -1.745 -0.466
VMS C8 C CR15 0.000 -6.945 -0.956 -0.248
VMS H8 H H 0.000 -6.000 -1.262 0.185
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
VMS OBC n/a SBD START
VMS SBD OBC "O5'" .
VMS OAZ SBD . .
VMS NAS SBD C .
VMS HAS NAS . .
VMS C NAS CA .
VMS O C . .
VMS CA C CB .
VMS HA CA . .
VMS N CA H .
VMS H2 N . .
VMS H N . .
VMS CB CA CG2 .
VMS HB CB . .
VMS CG1 CB HG11 .
VMS HG13 CG1 . .
VMS HG12 CG1 . .
VMS HG11 CG1 . .
VMS CG2 CB HG21 .
VMS HG23 CG2 . .
VMS HG22 CG2 . .
VMS HG21 CG2 . .
VMS "O5'" SBD "C5'" .
VMS "C5'" "O5'" "C4'" .
VMS "H5'1" "C5'" . .
VMS "H5'2" "C5'" . .
VMS "C4'" "C5'" "C3'" .
VMS "H4'" "C4'" . .
VMS "C3'" "C4'" "C2'" .
VMS "H3'" "C3'" . .
VMS "O3'" "C3'" "HO3'" .
VMS "HO3'" "O3'" . .
VMS "C2'" "C3'" "C1'" .
VMS H1 "C2'" . .
VMS "O2'" "C2'" "H2'" .
VMS "H2'" "O2'" . .
VMS "C1'" "C2'" N9 .
VMS "H1'" "C1'" . .
VMS "O4'" "C1'" . .
VMS N9 "C1'" C4 .
VMS C4 N9 N3 .
VMS N3 C4 C2 .
VMS C2 N3 N1 .
VMS H3 C2 . .
VMS N1 C2 C6 .
VMS C6 N1 C5 .
VMS N6 C6 HN61 .
VMS HN62 N6 . .
VMS HN61 N6 . .
VMS C5 C6 N7 .
VMS N7 C5 C8 .
VMS C8 N7 H8 .
VMS H8 C8 . END
VMS "C4'" "O4'" . ADD
VMS N9 C8 . ADD
VMS C5 C4 . 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
VMS CG2 CB single 1.524 0.020
VMS HG21 CG2 single 1.059 0.020
VMS HG22 CG2 single 1.059 0.020
VMS HG23 CG2 single 1.059 0.020
VMS CG1 CB single 1.524 0.020
VMS CB CA single 1.524 0.020
VMS HB CB single 1.099 0.020
VMS HG11 CG1 single 1.059 0.020
VMS HG12 CG1 single 1.059 0.020
VMS HG13 CG1 single 1.059 0.020
VMS N CA single 1.450 0.020
VMS CA C single 1.500 0.020
VMS HA CA single 1.099 0.020
VMS H N single 1.010 0.020
VMS H2 N single 1.010 0.020
VMS O C double 1.220 0.020
VMS C NAS single 1.330 0.020
VMS NAS SBD single 1.600 0.020
VMS HAS NAS single 1.010 0.020
VMS OAZ SBD double 1.436 0.020
VMS SBD OBC double 1.436 0.020
VMS "O5'" SBD single 1.535 0.020
VMS "C5'" "O5'" single 1.426 0.020
VMS "C4'" "C5'" single 1.524 0.020
VMS "H5'1" "C5'" single 1.092 0.020
VMS "H5'2" "C5'" single 1.092 0.020
VMS "C4'" "O4'" single 1.426 0.020
VMS "C3'" "C4'" single 1.524 0.020
VMS "H4'" "C4'" single 1.099 0.020
VMS "O4'" "C1'" single 1.426 0.020
VMS "O3'" "C3'" single 1.432 0.020
VMS "C2'" "C3'" single 1.524 0.020
VMS "H3'" "C3'" single 1.099 0.020
VMS "HO3'" "O3'" single 0.967 0.020
VMS "O2'" "C2'" single 1.432 0.020
VMS "C1'" "C2'" single 1.524 0.020
VMS H1 "C2'" single 1.099 0.020
VMS "H2'" "O2'" single 0.967 0.020
VMS N9 "C1'" single 1.485 0.020
VMS "H1'" "C1'" single 1.099 0.020
VMS N9 C8 single 1.337 0.020
VMS C4 N9 single 1.337 0.020
VMS C8 N7 double 1.350 0.020
VMS H8 C8 single 1.083 0.020
VMS N7 C5 single 1.350 0.020
VMS C5 C4 double 1.490 0.020
VMS C5 C6 single 1.490 0.020
VMS N3 C4 single 1.355 0.020
VMS C2 N3 double 1.337 0.020
VMS N1 C2 single 1.337 0.020
VMS H3 C2 single 1.083 0.020
VMS C6 N1 double 1.350 0.020
VMS N6 C6 single 1.355 0.020
VMS HN61 N6 single 1.010 0.020
VMS HN62 N6 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
VMS OBC SBD OAZ 109.500 3.000
VMS OBC SBD NAS 109.500 3.000
VMS OBC SBD "O5'" 109.500 3.000
VMS OAZ SBD NAS 109.500 3.000
VMS OAZ SBD "O5'" 109.500 3.000
VMS NAS SBD "O5'" 109.500 3.000
VMS SBD NAS HAS 120.000 3.000
VMS SBD NAS C 120.000 3.000
VMS HAS NAS C 120.000 3.000
VMS NAS C O 123.000 3.000
VMS NAS C CA 116.500 3.000
VMS O C CA 120.500 3.000
VMS C CA HA 108.810 3.000
VMS C CA N 109.470 3.000
VMS C CA CB 109.470 3.000
VMS HA CA N 109.470 3.000
VMS HA CA CB 108.340 3.000
VMS N CA CB 109.470 3.000
VMS CA N H2 120.000 3.000
VMS CA N H 120.000 3.000
VMS H2 N H 120.000 3.000
VMS CA CB HB 108.340 3.000
VMS CA CB CG1 111.000 3.000
VMS CA CB CG2 111.000 3.000
VMS HB CB CG1 108.340 3.000
VMS HB CB CG2 108.340 3.000
VMS CG1 CB CG2 111.000 3.000
VMS CB CG1 HG13 109.470 3.000
VMS CB CG1 HG12 109.470 3.000
VMS CB CG1 HG11 109.470 3.000
VMS HG13 CG1 HG12 109.470 3.000
VMS HG13 CG1 HG11 109.470 3.000
VMS HG12 CG1 HG11 109.470 3.000
VMS CB CG2 HG23 109.470 3.000
VMS CB CG2 HG22 109.470 3.000
VMS CB CG2 HG21 109.470 3.000
VMS HG23 CG2 HG22 109.470 3.000
VMS HG23 CG2 HG21 109.470 3.000
VMS HG22 CG2 HG21 109.470 3.000
VMS SBD "O5'" "C5'" 120.000 3.000
VMS "O5'" "C5'" "H5'1" 109.470 3.000
VMS "O5'" "C5'" "H5'2" 109.470 3.000
VMS "O5'" "C5'" "C4'" 109.470 3.000
VMS "H5'1" "C5'" "H5'2" 107.900 3.000
VMS "H5'1" "C5'" "C4'" 109.470 3.000
VMS "H5'2" "C5'" "C4'" 109.470 3.000
VMS "C5'" "C4'" "H4'" 108.340 3.000
VMS "C5'" "C4'" "C3'" 111.000 3.000
VMS "C5'" "C4'" "O4'" 109.470 3.000
VMS "H4'" "C4'" "C3'" 108.340 3.000
VMS "H4'" "C4'" "O4'" 109.470 3.000
VMS "C3'" "C4'" "O4'" 109.470 3.000
VMS "C4'" "C3'" "H3'" 108.340 3.000
VMS "C4'" "C3'" "O3'" 109.470 3.000
VMS "C4'" "C3'" "C2'" 111.000 3.000
VMS "H3'" "C3'" "O3'" 109.470 3.000
VMS "H3'" "C3'" "C2'" 108.340 3.000
VMS "O3'" "C3'" "C2'" 109.470 3.000
VMS "C3'" "O3'" "HO3'" 109.470 3.000
VMS "C3'" "C2'" H1 108.340 3.000
VMS "C3'" "C2'" "O2'" 109.470 3.000
VMS "C3'" "C2'" "C1'" 111.000 3.000
VMS H1 "C2'" "O2'" 109.470 3.000
VMS H1 "C2'" "C1'" 108.340 3.000
VMS "O2'" "C2'" "C1'" 109.470 3.000
VMS "C2'" "O2'" "H2'" 109.470 3.000
VMS "C2'" "C1'" "H1'" 108.340 3.000
VMS "C2'" "C1'" "O4'" 109.470 3.000
VMS "C2'" "C1'" N9 109.470 3.000
VMS "H1'" "C1'" "O4'" 109.470 3.000
VMS "H1'" "C1'" N9 109.470 3.000
VMS "O4'" "C1'" N9 109.470 3.000
VMS "C1'" "O4'" "C4'" 111.800 3.000
VMS "C1'" N9 C4 126.000 3.000
VMS "C1'" N9 C8 126.000 3.000
VMS C4 N9 C8 108.000 3.000
VMS N9 C4 N3 132.000 3.000
VMS N9 C4 C5 108.000 3.000
VMS N3 C4 C5 120.000 3.000
VMS C4 N3 C2 120.000 3.000
VMS N3 C2 H3 120.000 3.000
VMS N3 C2 N1 120.000 3.000
VMS H3 C2 N1 120.000 3.000
VMS C2 N1 C6 120.000 3.000
VMS N1 C6 N6 120.000 3.000
VMS N1 C6 C5 120.000 3.000
VMS N6 C6 C5 120.000 3.000
VMS C6 N6 HN62 120.000 3.000
VMS C6 N6 HN61 120.000 3.000
VMS HN62 N6 HN61 120.000 3.000
VMS C6 C5 N7 132.000 3.000
VMS C6 C5 C4 120.000 3.000
VMS N7 C5 C4 108.000 3.000
VMS C5 N7 C8 108.000 3.000
VMS N7 C8 H8 126.000 3.000
VMS N7 C8 N9 108.000 3.000
VMS H8 C8 N9 126.000 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
VMS var_1 OBC SBD NAS C -47.614 20.000 1
VMS CONST_1 SBD NAS C CA 180.000 0.000 0
VMS var_2 NAS C CA CB -79.965 20.000 3
VMS var_3 C CA N H 60.040 20.000 1
VMS var_4 C CA CB CG2 59.977 20.000 3
VMS var_5 CA CB CG1 HG11 -60.038 20.000 3
VMS var_6 CA CB CG2 HG21 -59.983 20.000 3
VMS var_7 OBC SBD "O5'" "C5'" -172.368 20.000 1
VMS var_8 SBD "O5'" "C5'" "C4'" -179.966 20.000 1
VMS var_9 "O5'" "C5'" "C4'" "C3'" -175.305 20.000 3
VMS var_10 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
VMS var_11 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
VMS var_12 "C4'" "C3'" "O3'" "HO3'" 176.190 20.000 1
VMS var_13 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
VMS var_14 "C3'" "C2'" "O2'" "H2'" -67.279 20.000 1
VMS var_15 "C3'" "C2'" "C1'" N9 150.000 20.000 3
VMS var_16 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
VMS var_17 "C2'" "C1'" N9 C4 89.105 20.000 1
VMS CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
VMS CONST_3 "C1'" N9 C4 N3 0.000 0.000 0
VMS CONST_4 N9 C4 N3 C2 180.000 0.000 0
VMS CONST_5 C4 N3 C2 N1 0.000 0.000 0
VMS CONST_6 N3 C2 N1 C6 0.000 0.000 0
VMS CONST_7 C2 N1 C6 C5 0.000 0.000 0
VMS CONST_8 N1 C6 N6 HN61 179.996 0.000 0
VMS CONST_9 N1 C6 C5 N7 180.000 0.000 0
VMS CONST_10 C6 C5 C4 N9 180.000 0.000 0
VMS CONST_11 C6 C5 N7 C8 180.000 0.000 0
VMS CONST_12 C5 N7 C8 N9 0.000 0.000 0
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
VMS chir_01 CB CG2 CG1 CA negativ
VMS chir_02 CA CB N C positiv
VMS chir_03 SBD NAS OAZ OBC negativ
VMS chir_04 "C4'" "C5'" "O4'" "C3'" negativ
VMS chir_05 "C3'" "C4'" "O3'" "C2'" negativ
VMS chir_06 "C2'" "C3'" "O2'" "C1'" negativ
VMS chir_07 "C1'" "O4'" "C2'" N9 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
VMS plan-1 N 0.020
VMS plan-1 CA 0.020
VMS plan-1 H 0.020
VMS plan-1 H2 0.020
VMS plan-2 C 0.020
VMS plan-2 CA 0.020
VMS plan-2 O 0.020
VMS plan-2 NAS 0.020
VMS plan-2 HAS 0.020
VMS plan-3 NAS 0.020
VMS plan-3 C 0.020
VMS plan-3 SBD 0.020
VMS plan-3 HAS 0.020
VMS plan-4 N9 0.020
VMS plan-4 "C1'" 0.020
VMS plan-4 C8 0.020
VMS plan-4 C4 0.020
VMS plan-4 N7 0.020
VMS plan-4 H8 0.020
VMS plan-4 C5 0.020
VMS plan-4 C6 0.020
VMS plan-4 N3 0.020
VMS plan-4 C2 0.020
VMS plan-4 N1 0.020
VMS plan-4 H3 0.020
VMS plan-4 N6 0.020
VMS plan-4 HN62 0.020
VMS plan-4 HN61 0.020
VMS plan-5 N6 0.020
VMS plan-5 C6 0.020
VMS plan-5 HN61 0.020
VMS plan-5 HN62 0.020
# ------------------------------------------------------
|
