# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 15 10:35:16 2020
#
#   Inital geometry file: a 94 line input string
#   Ligand name: 2'-Se-methyl-2'-selenouridine 5'-(dihydrogen phosphate)
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: C[Se][C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O
#
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
UMS        UMS '2'-Se-methyl-2'-selenouridine 5'-(dihydrogen phosphate)' RNA 35 22 .
2020-10-15 2020-10-15
;
CIF prepared directly in eLBOW
;
#
data_comp_UMS
#
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
UMS         OP3    O   OP    -1    .      -4.7620    1.9950    0.8210
UMS         P      P   P      0    .      -4.7940    0.7250   -0.1680
UMS         OP1    O   O      0    .      -5.5770   -0.3660    0.4540
UMS         OP2    O   OP    -1    .      -5.4780    1.1480   -1.5630
UMS        O5'     O   O2     0    .      -3.2900    0.2170   -0.4400
UMS        C5'     C   CH2    0    .      -2.4550   -0.3250    0.5850
UMS        C4'     C   CH1    0    .      -1.0980   -0.7050   -0.0110
UMS        O4'     O   O2     0    .      -0.3840    0.4740   -0.4420
UMS        C3'     C   CH1    0    .      -0.1740   -1.3090    1.0770
UMS        O3'     O   OH1    0    .      -0.3970   -2.7140    1.2120
UMS        C2'     C   CH1    0    .       1.2350   -1.0260    0.5000
UMS        SE2'    SE  SE     0    .       1.9300   -2.6110   -0.4200
UMS        C1'     C   CH1    0    .       1.0080    0.1230   -0.5020
UMS        CA'     C   CH3    0    .       1.9900   -3.9020    1.0530
UMS         N1     N   NT     0    .       1.8290    1.2780   -0.1280
UMS         C2     C   C      0    .       2.8070    1.6940   -0.9530
UMS         O2     O   O      0    .       2.9980    1.1070   -2.0010
UMS         N3     N   NH1    0    .       3.5760    2.7520   -0.6360
UMS         C4     C   C      0    .       3.3770    3.4140    0.5220
UMS         O4     O   O      0    .       4.0720    4.3720    0.8100
UMS         C5     C   C1     0    .       2.3510    2.9860    1.3990
UMS         C6     C   C1     0    .       1.5910    1.9250    1.0530
UMS        H5'     H   HCH2   0    .      -2.3120    0.4190    1.3690
UMS        H5'2    H   HCH2   0    .      -2.9270   -1.2120    1.0070
UMS        H4'     H   HCH1   0    .      -1.2250   -1.4010   -0.8400
UMS        H3'     H   HCH1   0    .      -0.3130   -0.8020    2.0310
UMS        HO3'    H   HOH1   0    .      -1.2950   -2.9460    1.4850
UMS        H2'     H   HCH1   0    .       1.9160   -0.7160    1.2920
UMS        H1'     H   HCH1   0    .       1.2650   -0.2070   -1.5080
UMS        HA'     H   HCH3   0    .       2.6500   -3.5290    1.8370
UMS        HA'2    H   HCH3   0    .       0.9880   -4.0390    1.4580
UMS        HA'3    H   HCH3   0    .       2.3670   -4.8560    0.6850
UMS         H3     H   HNH1   0    .       4.2770    3.0390   -1.2420
UMS         H5     H   H      0    .       2.1770    3.5040    2.3310
UMS         H6     H   H      0    .       0.8010    1.5870    1.7070
#
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
UMS   OP3     P     deloc         1.533 0.020     1.533
UMS   P       OP1   deloc         1.491 0.028     1.491
UMS   P       OP2   deloc         1.533 0.032     1.533
UMS   P      O5'    single        1.601 0.028     1.601
UMS  O5'     C5'    single        1.443 0.032     1.443
UMS  C5'     C4'    single        1.508 0.015     1.508
UMS  C5'     H5'    single        0.970 0.011     1.090
UMS  C5'     H5'2   single        0.970 0.011     1.090
UMS  C4'     O4'    single        1.444 0.011     1.444
UMS  C4'     C3'    single        1.526 0.011     1.526
UMS  C4'     H4'    single        0.970 0.013     1.090
UMS  O4'     C1'    single        1.416 0.013     1.416
UMS  C3'     O3'    single        1.423 0.011     1.423
UMS  C3'     C2'    single        1.528 0.012     1.528
UMS  C3'     H3'    single        0.970 0.010     1.090
UMS  O3'     HO3'   single        0.850 0.010     0.980
UMS  C2'     SE2'   single        1.960 0.010     1.960
UMS  C2'     C1'    single        1.524 0.010     1.524
UMS  C2'     H2'    single        0.970 0.010     1.090
UMS  SE2'    CA'    single        1.949 0.010     1.949
UMS  C1'      N1    single        1.471 0.010     1.471
UMS  C1'     H1'    single        0.970 0.017     1.090
UMS  CA'     HA'    single        0.970 0.017     1.090
UMS  CA'     HA'2   single        0.970 0.017     1.090
UMS  CA'     HA'3   single        0.970 0.017     1.090
UMS   N1      C2    single        1.379 0.017     1.379
UMS   N1      C6    single        1.375 0.010     1.375
UMS   C2      O2    double        1.223 0.016     1.223
UMS   C2      N3    single        1.374 0.012     1.374
UMS   N3      C4    single        1.383 0.010     1.383
UMS   N3      H3    single        0.860 0.016     1.020
UMS   C4      O4    double        1.240 0.016     1.240
UMS   C4      C5    single        1.436 0.016     1.436
UMS   C5      C6    double        1.345 0.015     1.345
UMS   C5      H5    single        0.930 0.012     1.080
UMS   C6      H6    single        0.930 0.012     1.080
#
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
UMS  O5'      P       OP2         106.53 2.580
UMS  O5'      P       OP1         106.57 2.496
UMS   OP2     P       OP1         113.32 2.534
UMS  O5'      P       OP3         106.53 2.580
UMS   OP2     P       OP3         108.70 2.785
UMS   OP1     P       OP3         113.32 2.534
UMS  C5'     O5'      P           117.05 1.000
UMS  H5'2    C5'     H5'          109.50 3.000
UMS  H5'2    C5'     C4'          109.44 3.000
UMS  H5'     C5'     C4'          109.47 3.000
UMS  H5'2    C5'     O5'          109.48 3.000
UMS  H5'     C5'     O5'          109.49 3.000
UMS  C4'     C5'     O5'          108.83 2.328
UMS  H4'     C4'     C3'          127.39 3.000
UMS  H4'     C4'     O4'          127.39 3.000
UMS  C3'     C4'     O4'          105.22 1.298
UMS  H4'     C4'     C5'          127.39 3.000
UMS  C3'     C4'     C5'          115.19 1.760
UMS  O4'     C4'     C5'          109.53 1.437
UMS  C1'     O4'     C4'          109.40 1.607
UMS  H3'     C3'     C2'          124.48 3.000
UMS  H3'     C3'     O3'          124.48 3.000
UMS  C2'     C3'     O3'          111.03 1.000
UMS  H3'     C3'     C4'          124.48 3.000
UMS  C2'     C3'     C4'           95.89 1.000
UMS  O3'     C3'     C4'          111.06 2.498
UMS  HO3'    O3'     C3'          114.05 3.000
UMS  H2'     C2'     C1'          128.88 3.000
UMS  H2'     C2'     SE2'         128.88 3.000
UMS  C1'     C2'     SE2'         110.48 3.000
UMS  H2'     C2'     C3'          128.88 3.000
UMS  C1'     C2'     C3'          102.25 1.000
UMS  SE2'    C2'     C3'          110.47 3.000
UMS  CA'     SE2'    C2'          101.00 3.000
UMS  H1'     C1'      N1          122.46 3.000
UMS  H1'     C1'     C2'          122.46 3.000
UMS   N1     C1'     C2'          115.08 3.181
UMS  H1'     C1'     O4'          122.46 3.000
UMS   N1     C1'     O4'          108.36 1.137
UMS  C2'     C1'     O4'          106.18 1.158
UMS  HA'3    CA'     HA'2         109.49 3.000
UMS  HA'3    CA'     HA'          109.44 3.000
UMS  HA'2    CA'     HA'          109.41 3.000
UMS  HA'3    CA'     SE2'         109.48 3.000
UMS  HA'2    CA'     SE2'         109.52 3.000
UMS  HA'     CA'     SE2'         109.49 3.000
UMS   C6      N1      C2          121.09 1.000
UMS   C6      N1     C1'          120.77 1.575
UMS   C2      N1     C1'          117.48 1.676
UMS   N3      C2      O2          121.99 1.083
UMS   N3      C2      N1          114.83 1.000
UMS   O2      C2      N1          122.84 1.000
UMS   H3      N3      C4          116.53 3.000
UMS   H3      N3      C2          116.53 3.000
UMS   C4      N3      C2          126.94 1.000
UMS   C5      C4      O4          125.07 1.333
UMS   C5      C4      N3          114.76 1.000
UMS   O4      C4      N3          119.28 1.186
UMS   H5      C5      C6          120.15 3.000
UMS   H5      C5      C4          120.15 3.000
UMS   C6      C5      C4          119.71 1.000
UMS   H6      C6      C5          119.10 3.000
UMS   H6      C6      N1          119.10 3.000
UMS   C5      C6      N1          121.80 1.181
#
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
UMS CONST_01       N3      C2      N1      C1'         179.96   0.0 0
UMS CONST_02       C4      N3      C2      N1            0.08   0.0 0
UMS CONST_03       C5      C4      N3      C2           -0.07   0.0 0
UMS CONST_04       C6      N1      C2      N3            0.19   0.0 0
UMS CONST_05       O2      C2      N1      C1'           0.06   0.0 0
UMS CONST_06       O4      C4      N3      C2         -179.98   0.0 0
UMS CONST_07       C6      N1      C2      O2         -179.71   0.0 0
UMS CONST_08       C4      N3      C2      O2          179.98   0.0 0
UMS CONST_09       H3      N3      C2      N1          180.00   0.0 0
UMS Var_01        C4'     C5'     O5'      P          -179.97  30.0 3
UMS Var_02        HA'     CA'     SE2'    C2'          -59.97  30.0 3
#
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
UMS chir_01  C4'     C5'     O4'     C3'    negativ
UMS chir_02  C3'     O3'     C2'     C4'    negativ
UMS chir_03  C2'     SE2'     C1'    C3'    negativ
UMS chir_04   C1'    O4'      N1     C2'    negativ
#
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
UMS plan-1    C1' 0.020
UMS plan-1     N1 0.020
UMS plan-1     C2 0.020
UMS plan-1     O2 0.020
UMS plan-1     N3 0.020
UMS plan-1     C4 0.020
UMS plan-1     O4 0.020
UMS plan-1     C5 0.020
UMS plan-1     C6 0.020
UMS plan-1     H3 0.020
UMS plan-1     H5 0.020
UMS plan-1     H6 0.020
