# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 11:11:34 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/h/H2U.cif
#   Ligand name: 5'-uridylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Aug 17 11:17:03 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
H2U H2U '5'-uridylic acid ' RNA 34 21 . 
2020-08-17 2020-08-17
;
CIF prepared directly in eLBOW and edited for planes
;
#
data_comp_H2U
#
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
H2U         P      P   P      0   1.220   -0.9437    0.2613   -4.1535
H2U         OP1    O   O      0  -0.906   -1.7532   -1.0220   -3.9979
H2U         OP2    O   OP    -1  -0.897   -1.7584    1.5109   -4.4573
H2U         OP3    O   OP    -1  -0.904    0.3247    0.0988   -4.9851
H2U        O5'     O   O2     0  -0.659   -0.3884    0.6225   -2.5782
H2U        C5'     C   CH2    0  -0.131    0.3735   -0.3504   -1.9344
H2U        C4'     C   CR15   0   0.015    1.2370    0.2794   -0.8665
H2U        O4'     O   O      0  -0.498    0.4251    0.7979    0.1729
H2U        C3'     C   CR15   0  -0.031    2.1725   -0.7108   -0.1796
H2U        O3'     O   OH1    0  -0.666    3.3700   -0.8326   -0.9092
H2U        C1'     C   CR15   0   0.223    1.1105    0.7798    1.3991
H2U        C2'     C   CR15   0  -0.050    2.3807   -0.0739    1.2046
H2U        O2'     O   OH1    0  -0.679    3.4867    0.7954    1.1805
H2U         N1     N   NR6    0  -0.527    0.2027    0.3868    2.4528
H2U         C2     C   CR6    0   0.741   -0.3226   -0.8571    2.4709
H2U         O2     O   O      0  -0.484   -0.0445   -1.7411    1.6835
H2U         N3     N   NR16   0  -0.719   -1.2378   -1.1101    3.4920
H2U         C4     C   CR6    0   0.540   -1.9037   -0.1906    4.2606
H2U         O4     O   O      0  -0.439   -2.7613   -0.5274    5.0470
H2U         C5     C   C      0  -0.598   -1.4882    1.2261    3.9994
H2U         C6     C   C      0  -0.303   -0.0377    1.2888    3.5702
H2U        H5'     H   HCH2   0   0.178    1.0481   -0.8720   -2.6281
H2U        H5''    H   HCH2   0   0.173   -0.2526   -1.1216   -1.4611
H2U        H4'     H   HCR5   0   0.211    1.8400    1.0835   -1.3162
H2U        H3'     H   HCR5   0   0.248    1.6780   -1.6779   -0.0685
H2U        HO3'    H   HOH1   0   0.467    3.7479   -1.7008   -0.7397
H2U        H1'     H   HCR5   0   0.244    1.4360    1.7898    1.6692
H2U        H2'     H   HCR5   0   0.238    2.4948   -0.8226    1.9965
H2U        HO2'    H   HOH1   0   0.445    4.0897    0.4547    0.5057
H2U         HN3    H   HNR6   0   0.417   -1.5492   -2.0714    3.5516
H2U         H51    H   H      0   0.293   -1.6531    1.8255    4.8930
H2U         H52    H   H      0   0.297   -2.1341    1.6254    3.2111
H2U         H61    H   H      0   0.262    0.6182    1.0410    4.4099
H2U         H62    H   H      0   0.280    0.2061    2.3009    3.2559
#
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
H2U   P       OP1   deloc         1.525 0.020     1.525
H2U   P       OP2   deloc         1.522 0.020     1.522
H2U   P       OP3   deloc         1.525 0.020     1.525
H2U   P      O5'    single        1.709 0.020     1.709
H2U  O5'     C5'    single        1.393 0.020     1.393
H2U  C5'     C4'    single        1.511 0.020     1.511
H2U  C5'     H5'    single        0.970 0.020     1.090
H2U  C5'     H5''   single        0.970 0.020     1.090
H2U  C4'     O4'    single        1.417 0.020     1.417
H2U  C4'     C3'    single        1.526 0.020     1.526
H2U  C4'     H4'    single        0.970 0.020     1.090
H2U  O4'     C1'    single        1.405 0.020     1.405
H2U  C3'     O3'    single        1.408 0.020     1.408
H2U  C3'     C2'    single        1.538 0.020     1.538
H2U  C3'     H3'    single        0.970 0.020     1.090
H2U  O3'     HO3'   single        0.850 0.020     0.980
H2U  C1'     C2'    single        1.543 0.020     1.543
H2U  C1'      N1    single        1.445 0.020     1.445
H2U  C1'     H1'    single        0.970 0.020     1.090
H2U  C2'     O2'    single        1.407 0.020     1.407
H2U  C2'     H2'    single        0.970 0.020     1.090
H2U  O2'     HO2'   single        0.850 0.020     0.980
H2U   N1      C2    single        1.350 0.020     1.350
H2U   N1      C6    single        1.456 0.020     1.456
H2U   C2      O2    double        1.216 0.020     1.216
H2U   C2      N3    single        1.394 0.020     1.394
H2U   N3      C4    single        1.371 0.020     1.371
H2U   N3      HN3   single        0.860 0.020     1.020
H2U   C4      O4    double        1.211 0.020     1.211
H2U   C4      C5    single        1.499 0.020     1.499
H2U   C5      C6    single        1.514 0.020     1.514
H2U   C5      H51   single        0.970 0.020     1.090
H2U   C5      H52   single        0.970 0.020     1.090
H2U   C6      H61   single        0.970 0.020     1.090
H2U   C6      H62   single        0.970 0.020     1.090
#
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
H2U  O5'      P       OP3         104.77 3.000
H2U  O5'      P       OP2         100.62 3.000
H2U   OP3     P       OP2         115.06 3.000
H2U  O5'      P       OP1         104.85 3.000
H2U   OP3     P       OP1         114.04 3.000
H2U   OP2     P       OP1         115.27 3.000
H2U  C5'     O5'      P           117.13 3.000
H2U  H5''    C5'     H5'          106.74 3.000
H2U  H5''    C5'     C4'          108.26 3.000
H2U  H5'     C5'     C4'          107.04 3.000
H2U  H5''    C5'     O5'          112.14 3.000
H2U  H5'     C5'     O5'          112.04 3.000
H2U  C4'     C5'     O5'          110.37 3.000
H2U  H4'     C4'     C3'          108.79 3.000
H2U  H4'     C4'     O4'          110.25 3.000
H2U  C3'     C4'     O4'          104.98 3.000
H2U  H4'     C4'     C5'          109.19 3.000
H2U  C3'     C4'     C5'          113.46 3.000
H2U  O4'     C4'     C5'          110.09 3.000
H2U  C1'     O4'     C4'          110.85 3.000
H2U  H3'     C3'     C2'          109.66 3.000
H2U  H3'     C3'     O3'          111.19 3.000
H2U  C2'     C3'     O3'          112.78 3.000
H2U  H3'     C3'     C4'          110.06 3.000
H2U  C2'     C3'     C4'          102.68 3.000
H2U  O3'     C3'     C4'          110.15 3.000
H2U  HO3'    O3'     C3'          108.72 3.000
H2U  H1'     C1'      N1          104.94 3.000
H2U  H1'     C1'     C2'          107.27 3.000
H2U   N1     C1'     C2'          117.30 3.000
H2U  H1'     C1'     O4'          110.39 3.000
H2U   N1     C1'     O4'          109.47 3.000
H2U  C2'     C1'     O4'          107.38 3.000
H2U  H2'     C2'     O2'          110.66 3.000
H2U  H2'     C2'     C1'          111.88 3.000
H2U  O2'     C2'     C1'          107.90 3.000
H2U  H2'     C2'     C3'          112.44 3.000
H2U  O2'     C2'     C3'          110.30 3.000
H2U  C1'     C2'     C3'          103.37 3.000
H2U  HO2'    O2'     C2'          106.53 3.000
H2U   C6      N1      C2          119.75 3.000
H2U   C6      N1     C1'          119.65 3.000
H2U   C2      N1     C1'          120.30 3.000
H2U   N3      C2      O2          119.50 3.000
H2U   N3      C2      N1          115.61 3.000
H2U   O2      C2      N1          124.89 3.000
H2U   HN3     N3      C4          117.03 3.000
H2U   HN3     N3      C2          114.67 3.000
H2U   C4      N3      C2          127.42 3.000
H2U   C5      C4      O4          124.89 3.000
H2U   C5      C4      N3          113.67 3.000
H2U   O4      C4      N3          121.42 3.000
H2U   H52     C5      H51         107.51 3.000
H2U   H52     C5      C6          110.25 3.000
H2U   H51     C5      C6          110.80 3.000
H2U   H52     C5      C4          107.86 3.000
H2U   H51     C5      C4          109.59 3.000
H2U   C6      C5      C4          110.73 3.000
H2U   H62     C6      H61         107.35 3.000
H2U   H62     C6      C5          109.59 3.000
H2U   H61     C6      C5          110.34 3.000
H2U   H62     C6      N1          108.52 3.000
H2U   H61     C6      N1          110.47 3.000
H2U   C5      C6      N1          110.49 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
H2U CONST_01   N3      C2      N1      C1'         180.00   0.0 0
H2U CONST_03   C5      C4      N3      C2            0.00   0.0 0
H2U CONST_04   C6      N1      C2      N3            0.00   0.0 0
H2U CONST_05   O2      C2      N1      C1'           0.00   0.0 0
H2U CONST_06   O4      C4      N3      C2          180.00   0.0 0
H2U CONST_09   HN3     N3      C2      N1          180.00   0.0 0
H2U   Var_01   H61     C6      N1      C1'         -95.04  30.0 1
H2U   Var_02   H51     C5      C6      N1          174.61  30.0 1
H2U   Var_03   C4'     C5'     O5'     P           156.77  30.0 3
#
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
H2U plan-1    C1' 0.020
H2U plan-1    N1  0.020
H2U plan-1    C2  0.020
H2U plan-1    O2  0.020
H2U plan-1    N3  0.020
H2U plan-1    C6  0.040
H2U plan-1    HN3 0.020
H2U plan-2    C2  0.040
H2U plan-2    HN3 0.020
H2U plan-2    C5  0.020
H2U plan-2    N3  0.020
H2U plan-2    C4  0.020
H2U plan-2    O4  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
H2U chir_01  C4'     C5'     O4'     C3'    negativ
H2U chir_02  C3'     O3'     C4'     C2'    positiv
H2U chir_03   C1'    O4'      N1     C2'    negativ
H2U chir_04  C2'     O2'      C1'    C3'    negativ
#
