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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
UDP UDP 'uridine 5'-(trihydrogen diphosphate)' RNA 36 25 . 
2015-12-24 2015-12-24
;
CIF prepared directly in eLBOW
;
#
data_comp_UDP
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
UDP         N1     N   NR6   0     .          0.5149   -1.8836    0.6717
UDP         C2     C   CR6   0     .          1.3609   -2.9117    0.1848
UDP         N3     N   NR16  0     .          2.5313   -3.1195    0.9291
UDP         C4     C   CR6   0     .          2.9631   -2.3566    2.0246
UDP         C5     C   CR16  0     .          2.0829   -1.2721    2.4033
UDP         C6     C   CR16  0     .          0.9055   -1.0643    1.7173
UDP         O2     O   O     0     .          1.0463   -3.6409   -0.7179
UDP         O4     O   O     0     .          4.0719   -2.6170    2.5605
UDP         C1'    C   CR15  0     .         -0.7579   -1.6518   -0.0321
UDP         C2'    C   CR15  0     .         -1.8093   -1.3707    0.8229
UDP         O2'    O   OH1   0     .         -2.4121   -2.5083    1.2439
UDP         C3'    C   CR15  0     .         -2.6424   -0.5983    0.0048
UDP         C4'    C   CR15  0     .         -1.7316    0.1682   -0.7177
UDP         O4'    O   O     0     .         -0.6169   -0.5992   -0.7988
UDP         O3'    O   OH1   0     .         -3.4034   -1.3661   -0.8198
UDP         C5'    C   CH2   0     .         -1.3887    1.4488   -0.1128
UDP         O5'    O   O2    0     .         -0.8292    2.3133   -1.1284
UDP         PA     P   P     0     .          0.6313    2.8361   -1.0270
UDP         O1A    O   O     0     .          0.6459    3.9175    0.0002
UDP         O2A    O   OP    -1    .          1.6122    1.7002   -0.7926
UDP         O3A    O   O2    0     .          0.9669    3.4468   -2.5189
UDP         PB     P   P     0     .          1.7318    4.8200   -2.7557
UDP         O1B    O   O     0     .          3.1993    4.4490   -2.5074
UDP         O2B    O   OP    -1    .          1.2334    5.6861   -1.6356
UDP         O3B    O   OP    -1    .          1.4690    5.3916   -4.1366
UDP         HN3    H   HNR6  0     .          3.0411   -3.7921    0.6870
UDP         H5     H   HCR6  0     .          2.3061   -0.7233    3.1240
UDP         H6     H   HCR6  0     .          0.3469   -0.3530    1.9761
UDP         H1'    H   HCR5  0     .         -0.9845   -2.4340   -0.5855
UDP         H2'    H   HCR5  0     .         -1.4941   -0.8391    1.5874
UDP        HO2'    H   HOH1  0     .         -3.2484   -2.3660    1.3508
UDP         H3'    H   HCR5  0     .         -3.2075   -0.0228    0.5517
UDP         H4'    H   HCR5  0     .         -2.0863    0.3188   -1.6233
UDP        HO3'    H   HOH1  0     .         -3.1300   -2.1766   -0.7877
UDP        H5'1    H   HCH2  0     .         -2.1884    1.8601    0.2580
UDP        H5'2    H   HCH2  0     .         -0.7298    1.3107    0.5994
#
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
_chem_comp_bond.value_dist_neutron
UDP   N1      C2    single        1.379 0.02   1.379
UDP   N1      C6    single        1.375 0.01   1.375
UDP   N1      C1'   single        1.471 0.016   1.471
UDP   C2      N3    single        1.375 0.017   1.375
UDP   C2      O2    double        1.223 0.011   1.223
UDP   N3      C4    single        1.383 0.012   1.383
UDP   N3      HN3   single        0.860 0.018   1.02
UDP   C4      C5    single        1.433 0.018   1.433
UDP   C4      O4    double        1.241 0.014   1.241
UDP   C5      C6    double        1.343 0.016   1.343
UDP   C5      H5    single        0.930 0.014   1.08
UDP   C6      H6    single        0.930 0.014   1.08
UDP   C1'     C2'   single        1.530 0.014   1.53
UDP   C1'     O4'   single        1.415 0.014   1.415
UDP   C1'     H1'   single        0.970 0.011   1.09
UDP   C2'     O2'   single        1.423 0.011   1.423
UDP   C2'     C3'   single        1.530 0.013   1.53
UDP   C2'     H2'   single        0.970 0.013   1.09
UDP   O2'    HO2'   single        0.850 0.013   0.98
UDP   C3'     C4'   single        1.526 0.013   1.526
UDP   C3'     O3'   single        1.423 0.014   1.423
UDP   C3'     H3'   single        0.970 0.013   1.09
UDP   C4'     O4'   single        1.444 0.013   1.444
UDP   C4'     C5'   single        1.508 0.011   1.508
UDP   C4'     H4'   single        0.970 0.012   1.09
UDP   O3'    HO3'   single        0.850 0.012   0.98
UDP   C5'     O5'   single        1.443 0.012   1.443
UDP   C5'    H5'1   single        0.970 0.015   1.09
UDP   C5'    H5'2   single        0.970 0.015   1.09
UDP   O5'     PA    single        1.581 0.015   1.581
UDP   PA      O1A   deloc         1.482 0.01   1.482
UDP   PA      O2A   deloc         1.527 0.018   1.527
UDP   PA      O3A   single        1.585 0.03   1.585
UDP   O3A     PB    single        1.584 0.01   1.584
UDP   PB      O1B   deloc         1.530 0.01   1.53
UDP   PB      O2B   deloc         1.530 0.035   1.53
UDP   PB      O3B   deloc         1.494 0.035   1.494
#
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
UDP   C1'     N1      C6          120.85 1.621
UDP   C1'     N1      C2          117.63 1.608
UDP   C6      N1      C2          121.03 1.0
UDP   O2      C2      N3          121.95 1.172
UDP   O2      C2      N1          122.87 1.0
UDP   N3      C2      N1          114.79 1.0
UDP   HN3     N3      C4          120.13 3.0
UDP   HN3     N3      C2          120.09 3.0
UDP   C4      N3      C2          126.93 1.0
UDP   O4      C4      C5          125.34 1.176
UDP   O4      C4      N3          119.33 1.18
UDP   C5      C4      N3          114.70 1.0
UDP   H5      C5      C6          120.00 3.0
UDP   H5      C5      C4          119.76 3.0
UDP   C6      C5      C4          119.74 1.0
UDP   H6      C6      C5          119.72 3.0
UDP   H6      C6      N1          119.89 3.0
UDP   C5      C6      N1          121.65 1.267
UDP   H1'     C1'     O4'         110.05 3.0
UDP   H1'     C1'     C2'         109.98 3.0
UDP   O4'     C1'     C2'         106.49 1.166
UDP   H1'     C1'     N1          110.44 3.0
UDP   O4'     C1'     N1          108.31 1.184
UDP   C2'     C1'     N1          113.44 1.735
UDP   H2'     C2'     C3'         110.11 3.0
UDP   H2'     C2'     O2'         110.60 3.0
UDP   C3'     C2'     O2'         111.95 2.626
UDP   H2'     C2'     C1'         110.15 3.0
UDP   C3'     C2'     C1'         101.51 1.172
UDP   O2'     C2'     C1'         110.58 2.795
UDP  HO2'     O2'     C2'         109.54 3.0
UDP   H3'     C3'     O3'         110.57 3.0
UDP   H3'     C3'     C4'         110.33 3.0
UDP   O3'     C3'     C4'         111.00 2.583
UDP   H3'     C3'     C2'         110.18 3.0
UDP   O3'     C3'     C2'         111.95 2.626
UDP   C4'     C3'     C2'         102.47 1.0
UDP   H4'     C4'     C5'         110.58 3.0
UDP   H4'     C4'     O4'         110.05 3.0
UDP   C5'     C4'     O4'         109.55 1.502
UDP   H4'     C4'     C3'         110.06 3.0
UDP   C5'     C4'     C3'         115.29 1.773
UDP   O4'     C4'     C3'         105.26 1.283
UDP   C4'     O4'     C1'         109.51 1.444
UDP  HO3'     O3'     C3'         109.40 3.0
UDP  H5'2     C5'    H5'1         109.48 3.0
UDP  H5'2     C5'     O5'         109.49 3.0
UDP  H5'1     C5'     O5'         109.32 3.0
UDP  H5'2     C5'     C4'         109.57 3.0
UDP  H5'1     C5'     C4'         109.53 3.0
UDP   O5'     C5'     C4'         109.05 2.309
UDP   PA      O5'     C5'         121.27 1.0
UDP   O3A     PA      O2A         105.97 1.0
UDP   O3A     PA      O1A         109.95 1.0
UDP   O2A     PA      O1A         113.21 3.603
UDP   O3A     PA      O5'         104.35 1.0
UDP   O2A     PA      O5'         110.83 1.0
UDP   O1A     PA      O5'         106.70 1.0
UDP   PB      O3A     PA          123.40 3.0
UDP   O3B     PB      O2B         113.26 2.659
UDP   O3B     PB      O1B         113.26 2.659
UDP   O2B     PB      O1B         109.07 3.13
UDP   O3B     PB      O3A         112.01 1.0
UDP   O2B     PB      O3A         102.95 1.0
UDP   O1B     PB      O3A         102.95 1.0
#
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
UDP CONST_01   C4      N3      C2      N1            0.00   0.0 0
UDP CONST_02   C5      C4      N3      C2            0.00   0.0 0
UDP CONST_03   C6      N1      C2      N3            0.00   0.0 0
UDP CONST_04   C6      N1      C2      N3            0.00   0.0 0
UDP CONST_05   C1'     N1      C2      N3          180.00   0.0 0
UDP CONST_06   C1'     N1      C2      N3          180.00   0.0 0
UDP CONST_07   O4      C4      N3      C2          180.00   0.0 0
UDP CONST_08   O2      C2      N3      C4          180.00   0.0 0
UDP CONST_09   O2      C2      N1      C6          180.00   0.0 0
UDP CONST_10   O2      C2      N1      C6          180.00   0.0 0
UDP CONST_11   C1'     N1      C2      O2            0.00   0.0 0
UDP CONST_12   C1'     N1      C2      O2            0.00   0.0 0
UDP CONST_13   HN3     N3      C2      N1          180.00   0.0 0
#UDP   Var_01   O1A     PA      O5'     C5'         -74.16  30.0 3
#UDP   Var_02   O1B     PB      O3A     PA           78.51  30.0 3
#UDP   Var_03  H5'1     C5'     O5'     PA          122.92  30.0 2
#
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
UDP plan-1    N1  0.020
UDP plan-1    C2  0.020
UDP plan-1    N3  0.020
UDP plan-1    C4  0.020
UDP plan-1    C5  0.020
UDP plan-1    C6  0.020
UDP plan-1    O2  0.020
UDP plan-1    O4  0.020
UDP plan-1    C1' 0.020
UDP plan-1    HN3 0.020
UDP plan-1    H5  0.020
UDP plan-1    H6  0.020
#
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
UDP chir_01   C1'     N1      C2'     O4'   negativ
UDP chir_02   C2'     O2'     C3'     C1'   positiv
UDP chir_03   C3'     O3'     C2'     C4'   negativ
UDP chir_04   C4'     O4'     C3'     C5'   negativ
#
