# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 11:50:05 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/5/5MU.cif
#   Ligand name: 5-methyluridine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)NC1=O
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Aug 17 11:50:29 2020
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
5MU 5MU '5-methyluridine 5'-(dihydrogen phosphate)' RNA 35 22 . 
2020-08-17 2020-08-17
;
CIF prepared directly in eLBOW
;
#
data_comp_5MU
#
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
5MU         N1     N   NT     0  -0.570   -0.2935   -0.2134    2.2518
5MU         C2     C   C      0   0.742    0.2420    1.0522    2.1886
5MU         N3     N   NH1    0  -0.734    1.1094    1.3550    3.2047
5MU         C4     C   C      0   0.560    1.4999    0.5523    4.2611
5MU         C5     C   C      0  -0.186    0.9070   -0.7697    4.2561
5MU         C5M    C   CH3    0  -0.705    1.2672   -1.7265    5.3444
5MU         C6     C   C1     0   0.062    0.0579   -1.0745    3.2603
5MU         O2     O   O      0  -0.473   -0.0284    1.8499    1.3157
5MU         O4     O   O      0  -0.454    2.2811    0.9655    5.0984
5MU        C1'     C   CH1    0   0.207   -1.1837   -0.6793    1.1943
5MU        C2'     C   CH1    0  -0.049   -2.4366    0.1770    0.9321
5MU        O2'     O   OH1    0  -0.676   -3.5483   -0.6820    0.9335
5MU        C3'     C   CH1    0  -0.032   -2.1932    0.7355   -0.4823
5MU        C4'     C   CH1    0   0.012   -1.2358   -0.2848   -1.0917
5MU        O3'     O   OH1    0  -0.665   -3.3739    0.8039   -1.2441
5MU        O4'     O   O2     0  -0.491   -0.4680   -0.7753   -0.0009
5MU        C5'     C   CH2    0  -0.131   -0.3239    0.2990   -2.1453
5MU        O5'     O   O2     0  -0.660    0.4553   -0.7022   -2.7204
5MU         P      P   P      0   1.220    1.0810   -0.3987   -4.2829
5MU         OP1    O   O      0  -0.905    1.8796    0.8923   -4.1372
5MU         OP2    O   OP    -1  -0.897    1.9104   -1.6563   -4.5012
5MU         OP3    O   OP    -1  -0.903   -0.1495   -0.2726   -5.1753
5MU         HN3    H   HNH1   0   0.426    1.5019    2.2879    3.1715
5MU         H71    H   HCH3   0   0.247    2.3432   -1.9014    5.3783
5MU         H72    H   HCH3   0   0.247    0.9703   -1.3469    6.3230
5MU         H73    H   HCH3   0   0.247    0.7774   -2.6874    5.1955
5MU         H6     H   H      0   0.317   -0.4083   -2.0491    3.2099
5MU        H1'     H   HCH1   0   0.256   -1.5190   -1.6663    1.5278
5MU        H2'     H   HCH1   0   0.246   -2.5566    0.9672    1.6811
5MU        HO2'    H   HOH1   0   0.447   -4.1238   -0.3864    0.2141
5MU        H3'     H   HCH1   0   0.255   -1.7108    1.7119   -0.4149
5MU        H4'     H   HCH1   0   0.219   -1.8234   -1.1040   -1.5325
5MU        HO3'    H   HOH1   0   0.468   -3.7534    1.6828   -1.1482
5MU        H5'     H   HCH2   0   0.179   -0.9669    0.7987   -2.8840
5MU        H5''    H   HCH2   0   0.175    0.2874    1.0843   -1.6769
#
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
5MU   N1      C2    single        1.376 0.020     1.376
5MU   N1      C6    single        1.372 0.020     1.372
5MU   N1     C1'    single        1.459 0.020     1.459
5MU   C2      N3    single        1.370 0.020     1.370
5MU   C2      O2    double        1.213 0.020     1.213
5MU   N3      C4    single        1.383 0.020     1.383
5MU   N3      HN3   single        0.860 0.020     1.020
5MU   C4      C5    single        1.449 0.020     1.449
5MU   C4      O4    double        1.217 0.020     1.217
5MU   C5      C5M   single        1.493 0.020     1.493
5MU   C5      C6    double        1.344 0.020     1.344
5MU   C5M     H71   single        0.970 0.020     1.090
5MU   C5M     H72   single        0.970 0.020     1.090
5MU   C5M     H73   single        0.970 0.020     1.090
5MU   C6      H6    single        0.930 0.020     1.080
5MU  C1'     C2'    single        1.540 0.020     1.540
5MU  C1'     O4'    single        1.396 0.020     1.396
5MU  C1'     H1'    single        0.970 0.020     1.090
5MU  C2'     O2'    single        1.405 0.020     1.405
5MU  C2'     C3'    single        1.540 0.020     1.540
5MU  C2'     H2'    single        0.970 0.020     1.090
5MU  O2'     HO2'   single        0.850 0.020     0.980
5MU  C3'     C4'    single        1.526 0.020     1.526
5MU  C3'     O3'    single        1.407 0.020     1.407
5MU  C3'     H3'    single        0.970 0.020     1.090
5MU  C4'     O4'    single        1.421 0.020     1.421
5MU  C4'     C5'    single        1.511 0.020     1.511
5MU  C4'     H4'    single        0.970 0.020     1.090
5MU  O3'     HO3'   single        0.850 0.020     0.980
5MU  C5'     O5'    single        1.393 0.020     1.393
5MU  C5'     H5'    single        0.970 0.020     1.090
5MU  C5'     H5''   single        0.970 0.020     1.090
5MU  O5'      P     single        1.710 0.020     1.710
5MU   P       OP1   deloc         1.525 0.020     1.525
5MU   P       OP2   deloc         1.522 0.020     1.522
5MU   P       OP3   deloc         1.525 0.020     1.525
#
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
5MU  C1'      N1      C6          119.26 3.000
5MU  C1'      N1      C2          119.87 3.000
5MU   C6      N1      C2          120.77 3.000
5MU   O2      C2      N3          121.97 3.000
5MU   O2      C2      N1          123.46 3.000
5MU   N3      C2      N1          114.57 3.000
5MU   HN3     N3      C4          116.77 3.000
5MU   HN3     N3      C2          115.14 3.000
5MU   C4      N3      C2          128.10 3.000
5MU   O4      C4      C5          125.07 3.000
5MU   O4      C4      N3          120.63 3.000
5MU   C5      C4      N3          114.30 3.000
5MU   C6      C5      C5M         123.17 3.000
5MU   C6      C5      C4          117.91 3.000
5MU   C5M     C5      C4          118.91 3.000
5MU   H73     C5M     H72         107.91 3.000
5MU   H73     C5M     H71         107.85 3.000
5MU   H72     C5M     H71         107.24 3.000
5MU   H73     C5M     C5          110.94 3.000
5MU   H72     C5M     C5          111.42 3.000
5MU   H71     C5M     C5          111.31 3.000
5MU   H6      C6      C5          120.75 3.000
5MU   H6      C6      N1          114.90 3.000
5MU   C5      C6      N1          124.35 3.000
5MU  H1'     C1'     O4'          110.84 3.000
5MU  H1'     C1'     C2'          107.70 3.000
5MU  O4'     C1'     C2'          108.03 3.000
5MU  H1'     C1'      N1          104.72 3.000
5MU  O4'     C1'      N1          109.25 3.000
5MU  C2'     C1'      N1          116.26 3.000
5MU  H2'     C2'     C3'          112.56 3.000
5MU  H2'     C2'     O2'          110.71 3.000
5MU  C3'     C2'     O2'          110.35 3.000
5MU  H2'     C2'     C1'          111.95 3.000
5MU  C3'     C2'     C1'          103.27 3.000
5MU  O2'     C2'     C1'          107.68 3.000
5MU  HO2'    O2'     C2'          106.45 3.000
5MU  H3'     C3'     O3'          111.16 3.000
5MU  H3'     C3'     C4'          110.21 3.000
5MU  O3'     C3'     C4'          110.05 3.000
5MU  H3'     C3'     C2'          109.74 3.000
5MU  O3'     C3'     C2'          112.48 3.000
5MU  C4'     C3'     C2'          102.91 3.000
5MU  H4'     C4'     C5'          109.31 3.000
5MU  H4'     C4'     O4'          109.82 3.000
5MU  C5'     C4'     O4'          110.03 3.000
5MU  H4'     C4'     C3'          108.83 3.000
5MU  C5'     C4'     C3'          113.50 3.000
5MU  O4'     C4'     C3'          105.26 3.000
5MU  HO3'    O3'     C3'          108.75 3.000
5MU  C4'     O4'     C1'          110.87 3.000
5MU  H5''    C5'     H5'          106.66 3.000
5MU  H5''    C5'     O5'          112.22 3.000
5MU  H5'     C5'     O5'          112.11 3.000
5MU  H5''    C5'     C4'          108.32 3.000
5MU  H5'     C5'     C4'          106.93 3.000
5MU  O5'     C5'     C4'          110.35 3.000
5MU   P      O5'     C5'          117.02 3.000
5MU   OP3     P       OP2         115.08 3.000
5MU   OP3     P       OP1         114.11 3.000
5MU   OP2     P       OP1         115.32 3.000
5MU   OP3     P      O5'          104.72 3.000
5MU   OP2     P      O5'          100.59 3.000
5MU   OP1     P      O5'          104.75 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
5MU CONST_01   C4      N3      C2      N1            0.00   0.0 0
5MU CONST_02   C5      C4      N3      C2            0.00   0.0 0
5MU CONST_03   C6      N1      C2      N3            0.00   0.0 0
5MU CONST_04   C1'     N1      C2      N3          180.00   0.0 0
5MU CONST_05   O4      C4      N3      C2          180.00   0.0 0
5MU CONST_06   O2      C2      N3      C4          180.00   0.0 0
5MU CONST_07   O2      C2      N1      C6          180.00   0.0 0
5MU CONST_08   C1'     N1      C2      O2            0.00   0.0 0
5MU CONST_09   HN3     N3      C2      N1          180.00   0.0 0
5MU   Var_01   H71     C5M     C5      C4          -57.92  30.0 3
5MU   Var_02   OP1     P       O5'     C5'          56.89  30.0 3
5MU   Var_03   H5'     C5'     O5'     P            37.87  30.0 1
#
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
5MU plan-1    N1  0.020
5MU plan-1    C2  0.020
5MU plan-1    N3  0.020
5MU plan-1    C4  0.020
5MU plan-1    C5  0.020
5MU plan-1    C5M 0.020
5MU plan-1    C6  0.020
5MU plan-1    O2  0.020
5MU plan-1    O4  0.020
5MU plan-1    C1' 0.020
5MU plan-1    HN3 0.020
5MU 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
5MU chir_01   C1'     N1      C2'     O4'   negativ
5MU chir_02   C2'     O2'     C3'     C1'   positiv
5MU chir_03   C3'     O3'     C4'     C2'   positiv
5MU chir_04   C4'     O4'     C3'     C5'   negativ
#
