# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 11:22:30 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/m/M2G.cif
#   Ligand name: N,N-dimethylguanosine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Aug 17 11:23:28 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
M2G M2G 'N,N-dimethylguanosine 5'-(dihydrogen phosphate)' RNA 42 26 . 
2020-08-17 2020-08-17
;
CIF prepared directly in eLBOW
;
#
data_comp_M2G
#
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
M2G         P      P   P      0   1.222   -0.7315    0.9606   -5.2310
M2G         OP1    O   O      0  -0.905   -2.0390    0.2048   -5.0216
M2G         OP2    O   OP    -1  -0.896   -0.8691    2.4685   -5.3868
M2G         OP3    O   OP    -1  -0.904    0.2245    0.2937   -6.2142
M2G        O5'     O   O2     0  -0.656    0.0673    0.8725   -3.7202
M2G        C5'     C   CH2    0  -0.120    0.2464   -0.3924   -3.1713
M2G        C4'     C   CH1    0   0.003    1.2649   -0.3301   -2.0572
M2G        O4'     O   O2     0  -0.493    0.7855    0.4986   -0.9987
M2G        C3'     C   CH1    0  -0.048    1.5471   -1.6781   -1.3997
M2G        O3'     O   OH1    0  -0.658    2.5382   -2.3670   -2.1119
M2G        C2'     C   CH1    0  -0.035    1.9884   -1.2602    0.0084
M2G        O2'     O   OH1    0  -0.667    3.3285   -0.8478    0.0024
M2G        C1'     C   CH1    0   0.161    1.1196   -0.0242    0.2530
M2G         N9     N   NR5    0  -0.534   -0.0971   -0.3219    0.9878
M2G         C8     C   CR15   0   0.094   -1.2572   -0.8919    0.5233
M2G         N7     N   N      0  -0.443   -2.1603   -1.0233    1.4455
M2G         C5     C   CR56   0  -0.100   -1.5766   -0.5187    2.5787
M2G         C6     C   CR6    0   0.493   -2.0789   -0.3815    3.9034
M2G         O6     O   O      0  -0.477   -3.1685   -0.7052    4.3470
M2G         N1     N   NR16   0  -0.763   -1.1235    0.2143    4.7382
M2G         C2     C   CR6    0   0.799    0.1318    0.6226    4.3720
M2G         N2     N   NT     0  -0.494    0.9137    1.1792    5.3086
M2G         N3     N   N      0  -0.529    0.5863    0.4843    3.1470
M2G         C4     C   CR56   0   0.507   -0.2939   -0.0771    2.3120
M2G         CM1    C   CH3    0  -0.510    2.2474    1.6027    4.9213
M2G         CM2    C   CH3    0  -0.574    0.4321    1.4139    6.6553
M2G        H5'     H   HCH2   0   0.181    0.6194   -1.1179   -3.9095
M2G        H5''    H   HCH2   0   0.171   -0.6930   -0.8086   -2.7746
M2G        H4'     H   HCH1   0   0.229    2.2037    0.0851   -2.4478
M2G        H3'     H   HCH1   0   0.239    0.6241   -2.2695   -1.3396
M2G        HO3'    H   HOH1   0   0.469    2.5007   -3.2994   -1.8744
M2G        H2'     H   HCH1   0   0.255    1.8081   -2.0363    0.7624
M2G        HO2'    H   HOH1   0   0.450    3.7962   -1.3885   -0.6473
M2G        H1'     H   HCH1   0   0.274    1.6608    0.7091    0.8576
M2G         H8     H   HCR5   0   0.284   -1.3855   -1.1758   -0.5100
M2G         HN1    H   HNR6   0   0.437   -1.4201    0.3307    5.6979
M2G        HM11    H   HCH3   0   0.251    2.7655    1.9662    5.8034
M2G        HM12    H   HCH3   0   0.248    2.8197    0.7759    4.5028
M2G        HM13    H   HCH3   0   0.244    2.2192    2.4040    4.1821
M2G        HM21    H   HCH3   0   0.278    1.2074    1.9178    7.2225
M2G        HM22    H   HCH3   0   0.257   -0.4518    2.0558    6.6671
M2G        HM23    H   HCH3   0   0.257    0.1989    0.4831    7.1775
#
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
M2G   P       OP1   deloc         1.525 0.020     1.525
M2G   P       OP2   deloc         1.522 0.020     1.522
M2G   P       OP3   deloc         1.525 0.020     1.525
M2G   P      O5'    single        1.711 0.020     1.711
M2G  O5'     C5'    single        1.390 0.020     1.390
M2G  C5'     C4'    single        1.511 0.020     1.511
M2G  C5'     H5'    single        0.970 0.020     1.090
M2G  C5'     H5''   single        0.970 0.020     1.090
M2G  C4'     O4'    single        1.427 0.020     1.427
M2G  C4'     C3'    single        1.526 0.020     1.526
M2G  C4'     H4'    single        0.970 0.020     1.090
M2G  O4'     C1'    single        1.397 0.020     1.397
M2G  C3'     O3'    single        1.401 0.020     1.401
M2G  C3'     C2'    single        1.534 0.020     1.534
M2G  C3'     H3'    single        0.970 0.020     1.090
M2G  O3'     HO3'   single        0.850 0.020     0.980
M2G  C2'     O2'    single        1.402 0.020     1.402
M2G  C2'     C1'    single        1.531 0.020     1.531
M2G  C2'     H2'    single        0.970 0.020     1.090
M2G  O2'     HO2'   single        0.850 0.020     0.980
M2G  C1'      N9    single        1.452 0.020     1.452
M2G  C1'     H1'    single        0.970 0.020     1.090
M2G   N9      C8    aromatic      1.374 0.020     1.374
M2G   N9      C4    aromatic      1.361 0.020     1.361
M2G   C8      N7    aromatic      1.297 0.020     1.297
M2G   C8      H8    single        0.930 0.020     1.080
M2G   N7      C5    aromatic      1.371 0.020     1.371
M2G   C5      C6    single        1.423 0.020     1.423
M2G   C5      C4    aromatic      1.383 0.020     1.383
M2G   C6      O6    double        1.220 0.020     1.220
M2G   C6      N1    single        1.402 0.020     1.402
M2G   N1      C2    single        1.370 0.020     1.370
M2G   N1      HN1   single        0.860 0.020     1.020
M2G   C2      N2    single        1.341 0.020     1.341
M2G   C2      N3    double        1.314 0.020     1.314
M2G   N2      CM1   single        1.452 0.020     1.452
M2G   N2      CM2   single        1.449 0.020     1.449
M2G   N3      C4    single        1.337 0.020     1.337
M2G   CM1    HM11   single        0.970 0.020     1.090
M2G   CM1    HM12   single        0.970 0.020     1.090
M2G   CM1    HM13   single        0.970 0.020     1.090
M2G   CM2    HM21   single        0.970 0.020     1.090
M2G   CM2    HM22   single        0.970 0.020     1.090
M2G   CM2    HM23   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
M2G  O5'      P       OP3         104.72 3.000
M2G  O5'      P       OP2         100.58 3.000
M2G   OP3     P       OP2         115.08 3.000
M2G  O5'      P       OP1         104.69 3.000
M2G   OP3     P       OP1         114.17 3.000
M2G   OP2     P       OP1         115.31 3.000
M2G  C5'     O5'      P           117.10 3.000
M2G  H5''    C5'     H5'          106.35 3.000
M2G  H5''    C5'     C4'          108.96 3.000
M2G  H5'     C5'     C4'          107.07 3.000
M2G  H5''    C5'     O5'          112.09 3.000
M2G  H5'     C5'     O5'          112.25 3.000
M2G  C4'     C5'     O5'          109.91 3.000
M2G  H4'     C4'     C3'          109.21 3.000
M2G  H4'     C4'     O4'          109.35 3.000
M2G  C3'     C4'     O4'          104.80 3.000
M2G  H4'     C4'     C5'          109.24 3.000
M2G  C3'     C4'     C5'          113.95 3.000
M2G  O4'     C4'     C5'          110.14 3.000
M2G  C1'     O4'     C4'          111.52 3.000
M2G  H3'     C3'     C2'          109.78 3.000
M2G  H3'     C3'     O3'          110.95 3.000
M2G  C2'     C3'     O3'          113.39 3.000
M2G  H3'     C3'     C4'          110.12 3.000
M2G  C2'     C3'     C4'          102.01 3.000
M2G  O3'     C3'     C4'          110.25 3.000
M2G  HO3'    O3'     C3'          108.86 3.000
M2G  H2'     C2'     C1'          111.60 3.000
M2G  H2'     C2'     O2'          111.60 3.000
M2G  C1'     C2'     O2'          107.80 3.000
M2G  H2'     C2'     C3'          113.02 3.000
M2G  C1'     C2'     C3'          101.74 3.000
M2G  O2'     C2'     C3'          110.57 3.000
M2G  HO2'    O2'     C2'          107.51 3.000
M2G  H1'     C1'      N9          105.80 3.000
M2G  H1'     C1'     C2'          110.43 3.000
M2G   N9     C1'     C2'          113.01 3.000
M2G  H1'     C1'     O4'          111.27 3.000
M2G   N9     C1'     O4'          109.25 3.000
M2G  C2'     C1'     O4'          107.14 3.000
M2G   C4      N9      C8          106.35 3.000
M2G   C4      N9     C1'          125.21 3.000
M2G   C8      N9     C1'          128.43 3.000
M2G   H8      C8      N7          124.83 3.000
M2G   H8      C8      N9          122.23 3.000
M2G   N7      C8      N9          112.93 3.000
M2G   C5      N7      C8          104.71 3.000
M2G   C4      C5      C6          118.44 3.000
M2G   C4      C5      N7          110.67 3.000
M2G   C6      C5      N7          130.89 3.000
M2G   N1      C6      O6          120.33 3.000
M2G   N1      C6      C5          110.78 3.000
M2G   O6      C6      C5          128.89 3.000
M2G   HN1     N1      C2          119.22 3.000
M2G   HN1     N1      C6          114.47 3.000
M2G   C2      N1      C6          126.30 3.000
M2G   N3      C2      N2          119.55 3.000
M2G   N3      C2      N1          122.33 3.000
M2G   N2      C2      N1          118.12 3.000
M2G   CM2     N2      CM1         120.39 3.000
M2G   CM2     N2      C2          121.49 3.000
M2G   CM1     N2      C2          118.06 3.000
M2G   C4      N3      C2          113.50 3.000
M2G   N3      C4      C5          128.64 3.000
M2G   N3      C4      N9          126.02 3.000
M2G   C5      C4      N9          105.34 3.000
M2G  HM13     CM1    HM12         108.11 3.000
M2G  HM13     CM1    HM11         108.49 3.000
M2G  HM12     CM1    HM11         108.40 3.000
M2G  HM13     CM1     N2          111.80 3.000
M2G  HM12     CM1     N2          111.33 3.000
M2G  HM11     CM1     N2          108.62 3.000
M2G  HM23     CM2    HM22         108.83 3.000
M2G  HM23     CM2    HM21         107.36 3.000
M2G  HM22     CM2    HM21         107.44 3.000
M2G  HM23     CM2     N2          112.15 3.000
M2G  HM22     CM2     N2          111.97 3.000
M2G  HM21     CM2     N2          108.88 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
M2G CONST_01   C5      N7      C8      N9            0.00   0.0 0
M2G CONST_02   N7      C5      C4      N9            0.00   0.0 0
M2G CONST_03   C5      C4      N9      C8            0.00   0.0 0
M2G CONST_04   C4      C5      N7      C8            0.00   0.0 0
M2G CONST_05   C4      N9      C8      N7            0.00   0.0 0
M2G CONST_06   N7      C8      N9      C1'         180.00   0.0 0
M2G CONST_07   C5      C4      N9      C1'         180.00   0.0 0
M2G CONST_08   N3      C4      N9      C1'           0.00   0.0 0
M2G CONST_09   C2      N1      C6      C5            0.00   0.0 0
M2G CONST_10   N3      C2      N1      C6            0.00   0.0 0
M2G CONST_11   C4      N3      C2      N1            0.00   0.0 0
M2G CONST_12   N2      C2      N1      C6          180.00   0.0 0
M2G CONST_13   C2      N1      C6      O6          180.00   0.0 0
M2G CONST_14   C4      N3      C2      N2          180.00   0.0 0
M2G CONST_15   H8      C8      N9      C1'           0.00   0.0 0
M2G CONST_16   HN1     N1      C6      C5          180.00   0.0 0
M2G CONST_17   CM1     N2      C2      N1          180.00   0.0 0
M2G CONST_18   CM2     N2      C2      N1            0.00   0.0 0
M2G CONST_19   CM1     N2      C2      N3            0.00   0.0 0
M2G CONST_20   CM2     N2      C2      N3          180.00   0.0 0
M2G   Var_01   C4'     C5'     O5'     P           165.00  30.0 3
M2G   Var_02  HM11     CM1     N2      C2         -176.25  30.0 3
M2G   Var_03  HM21     CM2     N2      C2         -176.93  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
M2G plan-1    C1' 0.020
M2G plan-1    N9  0.020
M2G plan-1    C8  0.020
M2G plan-1    N7  0.020
M2G plan-1    C5  0.020
M2G plan-1    C6  0.020
M2G plan-1    O6  0.020
M2G plan-1    N1  0.020
M2G plan-1    C2  0.020
M2G plan-1    N2  0.020
M2G plan-1    N3  0.020
M2G plan-1    C4  0.020
M2G plan-1    CM1 0.020
M2G plan-1    CM2 0.020
M2G plan-1    H8  0.020
M2G plan-1    HN1 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
M2G chir_01   C4'     C5'     O4'     C3'   negativ
M2G chir_02   C3'     O3'     C4'     C2'   positiv
M2G chir_03   C2'     O2'     C3'     C1'   positiv
M2G chir_04   C1'     O4'     N9      C2'   negativ
#
