# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 11:25:59 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/o/OMG.cif
#   Ligand name: 2'-O-methylguanosine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1n2cnc3C(=O)NC(=Nc23)N
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Aug 17 11:26:51 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
OMG OMG '2'-O-methylguanosine 5'-(dihydrogen phosphate)' RNA 39 25 . 
2020-08-17 2020-08-17
;
CIF prepared directly in eLBOW
;
#
data_comp_OMG
#
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
OMG         P      P   P      0   1.232   -1.8302    0.1791    3.6698
OMG         OP1    O   O      0  -0.868   -2.3337    0.7926    2.3607
OMG         OP2    O   OP    -1  -0.890   -2.6496   -0.9952    4.1825
OMG         OP3    O   OP    -1  -0.898   -1.4312    1.2118    4.7168
OMG        O5'     O   O2     0  -0.656   -0.3749   -0.6056    3.2512
OMG        C5'     C   CH2    0  -0.123    0.6595    0.1854    2.7621
OMG        C4'     C   CH1    0  -0.058    1.5477   -0.6528    1.8590
OMG        O4'     O   O2     0  -0.495    0.7934   -1.2437    0.7934
OMG        C3'     C   CH1    0  -0.037    2.6401    0.1666    1.1750
OMG        O3'     O   OH1    0  -0.671    3.7306   -0.6138    0.7572
OMG        C2'     C   CH1    0  -0.011    1.8979    0.6300   -0.0793
OMG        O2'     O   O2     0  -0.478    2.6793    0.9729   -1.1747
OMG         CM2    C   CH3    0  -0.411    3.3796    2.1846   -1.0105
OMG        C1'     C   CH1    0   0.228    1.0561   -0.6039   -0.4162
OMG         N9     N   NR5    0  -0.539   -0.1890   -0.2855   -1.0799
OMG         C8     C   CR15   0   0.025   -1.3432    0.2047   -0.5105
OMG         N7     N   N      0  -0.458   -2.2682    0.4334   -1.3961
OMG         C5     C   CR5    0  -0.098   -1.7068    0.0880   -2.5982
OMG         C6     C   C      0   0.497   -2.2428    0.1227   -3.9165
OMG         O6     O   O      0  -0.479   -3.3488    0.4838   -4.2861
OMG         N1     N   NH1    0  -0.726   -1.2997   -0.3370   -4.8452
OMG         C2     C   C      0   0.681   -0.0371   -0.7719   -4.5604
OMG         N2     N   NH2    0  -0.833    0.7288   -1.1404   -5.6015
OMG         N3     N   N      0  -0.509    0.4503   -0.8029   -3.3470
OMG         C4     C   CR5    0   0.501   -0.4126   -0.3642   -2.4185
OMG        H5'     H   HCH2   0   0.189    1.2927    0.5836    3.5698
OMG        H5''    H   HCH2   0   0.175    0.2886    1.0580    2.2064
OMG        H4'     H   HCH1   0   0.247    1.9803   -1.4703    2.4460
OMG        H3'     H   HCH1   0   0.251    2.9613    1.0057    1.8056
OMG        HO3'    H   HOH1   0   0.456    4.1865   -0.9394    1.5395
OMG        H2'     H   HCH1   0   0.240    1.2325    1.4612    0.2005
OMG        HM21    H   HCH3   0   0.239    3.9148    2.3814   -1.9380
OMG        HM22    H   HCH3   0   0.212    2.7013    3.0233   -0.8166
OMG        HM23    H   HCH3   0   0.216    4.1084    2.1376   -0.1960
OMG        H1'     H   HCH1   0   0.255    1.6088   -1.2552   -1.1026
OMG         H8     H   HCR5   0   0.347   -1.4707    0.3513    0.5623
OMG         HN1    H   HNH1   0   0.423   -1.5988   -0.3297   -5.8121
OMG        HN21    H   HNH2   0   0.410    1.5842   -1.6260   -5.3901
OMG        HN22    H   HNH2   0   0.412    0.3102   -1.3554   -6.4906
#
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
OMG   P       OP1   deloc         1.531 0.020     1.531
OMG   P       OP2   deloc         1.521 0.020     1.521
OMG   P       OP3   deloc         1.524 0.020     1.524
OMG   P      O5'    single        1.705 0.020     1.705
OMG  O5'     C5'    single        1.391 0.020     1.391
OMG  C5'     C4'    single        1.519 0.020     1.519
OMG  C5'     H5'    single        0.970 0.020     1.090
OMG  C5'     H5''   single        0.970 0.020     1.090
OMG  C4'     O4'    single        1.433 0.020     1.433
OMG  C4'     C3'    single        1.527 0.020     1.527
OMG  C4'     H4'    single        0.970 0.020     1.090
OMG  O4'     C1'    single        1.393 0.020     1.393
OMG  C3'     O3'    single        1.405 0.020     1.405
OMG  C3'     C2'    single        1.529 0.020     1.529
OMG  C3'     H3'    single        0.970 0.020     1.090
OMG  O3'     HO3'   single        0.850 0.020     0.980
OMG  C2'     O2'    single        1.389 0.020     1.389
OMG  C2'     C1'    single        1.531 0.020     1.531
OMG  C2'     H2'    single        0.970 0.020     1.090
OMG  O2'      CM2   single        1.409 0.020     1.409
OMG   CM2    HM21   single        0.970 0.020     1.090
OMG   CM2    HM22   single        0.970 0.020     1.090
OMG   CM2    HM23   single        0.970 0.020     1.090
OMG  C1'      N9    single        1.446 0.020     1.446
OMG  C1'     H1'    single        0.970 0.020     1.090
OMG   N9      C8    aromatic      1.377 0.020     1.377
OMG   N9      C4    aromatic      1.359 0.020     1.359
OMG   C8      N7    aromatic      1.301 0.020     1.301
OMG   C8      H8    single        0.930 0.020     1.080
OMG   N7      C5    aromatic      1.371 0.020     1.371
OMG   C5      C6    single        1.424 0.020     1.424
OMG   C5      C4    aromatic      1.383 0.020     1.383
OMG   C6      O6    double        1.221 0.020     1.221
OMG   C6      N1    single        1.401 0.020     1.401
OMG   N1      C2    single        1.365 0.020     1.365
OMG   N1      HN1   single        0.860 0.020     1.020
OMG   C2      N2    single        1.344 0.020     1.344
OMG   C2      N3    double        1.308 0.020     1.308
OMG   N2     HN21   single        0.890 0.020     1.040
OMG   N2     HN22   single        0.890 0.020     1.040
OMG   N3      C4    single        1.341 0.020     1.341
#
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
OMG  O5'      P       OP3         104.90 3.000
OMG  O5'      P       OP2         100.79 3.000
OMG   OP3     P       OP2         115.64 3.000
OMG  O5'      P       OP1         104.79 3.000
OMG   OP3     P       OP1         113.71 3.000
OMG   OP2     P       OP1         114.86 3.000
OMG  C5'     O5'      P           117.34 3.000
OMG  H5''    C5'     H5'          106.13 3.000
OMG  H5''    C5'     C4'          109.56 3.000
OMG  H5'     C5'     C4'          107.43 3.000
OMG  H5''    C5'     O5'          112.23 3.000
OMG  H5'     C5'     O5'          112.05 3.000
OMG  C4'     C5'     O5'          109.28 3.000
OMG  H4'     C4'     C3'          110.98 3.000
OMG  H4'     C4'     O4'          107.37 3.000
OMG  C3'     C4'     O4'          105.35 3.000
OMG  H4'     C4'     C5'          108.91 3.000
OMG  C3'     C4'     C5'          112.86 3.000
OMG  O4'     C4'     C5'          111.21 3.000
OMG  C1'     O4'     C4'          110.91 3.000
OMG  H3'     C3'     C2'          112.43 3.000
OMG  H3'     C3'     O3'          111.62 3.000
OMG  C2'     C3'     O3'          107.53 3.000
OMG  H3'     C3'     C4'          111.23 3.000
OMG  C2'     C3'     C4'          100.53 3.000
OMG  O3'     C3'     C4'          112.98 3.000
OMG  HO3'    O3'     C3'          108.30 3.000
OMG  H2'     C2'     C1'          109.40 3.000
OMG  H2'     C2'     O2'          110.74 3.000
OMG  C1'     C2'     O2'          109.56 3.000
OMG  H2'     C2'     C3'          108.28 3.000
OMG  C1'     C2'     C3'          101.72 3.000
OMG  O2'     C2'     C3'          116.66 3.000
OMG   CM2    O2'     C2'          113.59 3.000
OMG  HM23     CM2    HM22         108.27 3.000
OMG  HM23     CM2    HM21         108.33 3.000
OMG  HM22     CM2    HM21         108.46 3.000
OMG  HM23     CM2    O2'          112.39 3.000
OMG  HM22     CM2    O2'          111.78 3.000
OMG  HM21     CM2    O2'          107.48 3.000
OMG  H1'     C1'      N9          106.11 3.000
OMG  H1'     C1'     C2'          109.84 3.000
OMG   N9     C1'     C2'          113.37 3.000
OMG  H1'     C1'     O4'          111.47 3.000
OMG   N9     C1'     O4'          109.71 3.000
OMG  C2'     C1'     O4'          106.42 3.000
OMG   C4      N9      C8          106.85 3.000
OMG   C4      N9     C1'          125.50 3.000
OMG   C8      N9     C1'          127.59 3.000
OMG   H8      C8      N7          124.27 3.000
OMG   H8      C8      N9          123.55 3.000
OMG   N7      C8      N9          112.15 3.000
OMG   C5      N7      C8          105.16 3.000
OMG   C4      C5      C6          118.74 3.000
OMG   C4      C5      N7          110.60 3.000
OMG   C6      C5      N7          130.67 3.000
OMG   N1      C6      O6          120.41 3.000
OMG   N1      C6      C5          110.63 3.000
OMG   O6      C6      C5          128.96 3.000
OMG   HN1     N1      C2          118.35 3.000
OMG   HN1     N1      C6          115.59 3.000
OMG   C2      N1      C6          126.06 3.000
OMG   N3      C2      N2          119.99 3.000
OMG   N3      C2      N1          123.07 3.000
OMG   N2      C2      N1          116.92 3.000
OMG  HN22     N2     HN21         115.87 3.000
OMG  HN22     N2      C2          120.41 3.000
OMG  HN21     N2      C2          117.00 3.000
OMG   C4      N3      C2          113.24 3.000
OMG   N3      C4      C5          128.26 3.000
OMG   N3      C4      N9          126.49 3.000
OMG   C5      C4      N9          105.25 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
OMG CONST_01   C5      N7      C8      N9            0.00   0.0 0
OMG CONST_02   N7      C5      C4      N9            0.00   0.0 0
OMG CONST_03   C5      C4      N9      C8            0.00   0.0 0
OMG CONST_04   C4      C5      N7      C8            0.00   0.0 0
OMG CONST_05   C4      N9      C8      N7            0.00   0.0 0
OMG CONST_06   N7      C8      N9      C1'         180.00   0.0 0
OMG CONST_07   C5      C4      N9      C1'         180.00   0.0 0
OMG CONST_08   N3      C4      N9      C1'           0.00   0.0 0
OMG CONST_09   C2      N1      C6      C5            0.00   0.0 0
OMG CONST_10   N3      C2      N1      C6            0.00   0.0 0
OMG CONST_11   C4      N3      C2      N1            0.00   0.0 0
OMG CONST_12   N2      C2      N1      C6          180.00   0.0 0
OMG CONST_13   C2      N1      C6      O6          180.00   0.0 0
OMG CONST_14   C4      N3      C2      N2          180.00   0.0 0
OMG CONST_15   H8      C8      N9      C1'           0.00   0.0 0
OMG CONST_16   HN1     N1      C6      C5          180.00   0.0 0
OMG CONST_17  HN21     N2      C2      N1          180.00   0.0 0
OMG CONST_18  HN22     N2      C2      N1            0.00   0.0 0
OMG   Var_01   C4'     C5'     O5'     P          -153.01  30.0 3
OMG   Var_02  HM21     CM2     O2'     C2'        -177.19  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
OMG plan-1    C1' 0.020
OMG plan-1    N9  0.020
OMG plan-1    C8  0.020
OMG plan-1    N7  0.020
OMG plan-1    C5  0.020
OMG plan-1    C6  0.020
OMG plan-1    O6  0.020
OMG plan-1    N1  0.020
OMG plan-1    C2  0.020
OMG plan-1    N2  0.020
OMG plan-1    N3  0.020
OMG plan-1    C4  0.020
OMG plan-1    H8  0.020
OMG plan-1    HN1 0.020
OMG plan-1   HN21 0.020
OMG plan-1   HN22 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
OMG chir_01   C4'     C5'     O4'     C3'   negativ
OMG chir_02   C3'     O3'     C2'     C4'   negativ
OMG chir_03   C2'     O2'     C1'     C3'   negativ
OMG chir_04   C1'     O4'     N9      C2'   negativ
#
