# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug 17 11:44:41 2020
#
#   Final geometry file: /net/cci/nigel/work/qm/PBEh-3c.None.CPCM/7/7MG.cif
#   Ligand name: 7-methylguanosine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C3=C1C(=O)NC(=N3)N
#
# Restraints Editor Exclusively Ligands (REEL)
#   - a module of PHENIX
#   - file written: Mon Aug 17 11:46:11 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
7MG 7MG '7-methylguanosine 5'-(dihydrogen phosphate)' RNA 41 25 . 
2020-08-17 2020-08-17
;
CIF prepared directly in eLBOW
;
#
data_comp_7MG
#
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
7MG         P      P   P      0   1.222    1.2144   -1.3628   -3.8381
7MG         OP1    O   O      0  -0.907    2.4482   -0.8447   -3.1065
7MG         OP2    O   OP    -1  -0.898    1.1729   -2.8696   -4.0533
7MG         OP3    O   OP    -1  -0.906    0.8110   -0.5259   -5.0476
7MG        O5'     O   O2     0  -0.658   -0.0681   -1.1718   -2.7245
7MG        C5'     C   CH2    0  -0.124   -0.2913    0.1067   -2.2197
7MG        C4'     C   CR15   0   0.011   -1.5295    0.1164   -1.3540
7MG        O4'     O   O      0  -0.502   -1.3302   -0.7054   -0.2184
7MG        C3'     C   CR15   0  -0.030   -1.8546    1.4903   -0.7772
7MG        O3'     O   OH1    0  -0.667   -2.6019    2.2474   -1.6972
7MG        C2'     C   CR15   0  -0.040   -2.6439    1.1434    0.4966
7MG        O2'     O   OH1    0  -0.680   -4.0171    1.0320    0.2120
7MG        C1'     C   CR15   0   0.184   -2.1154   -0.2538    0.8692
7MG         N9     N   NR5    0  -0.548   -1.3713   -0.3342    2.0881
7MG         C8     C   CH2    0  -0.098   -1.2839   -1.6249    2.7672
7MG         N7     N   NR5    0  -0.503   -0.2823   -1.4094    3.8065
7MG         C5     C   CR56   0   0.004    0.4926   -0.3288    3.3222
7MG         C6     C   CR6    0   0.486    1.6958    0.2163    3.8025
7MG         O6     O   O      0  -0.511    2.4190   -0.1682    4.7209
7MG         N1     N   NR16   0  -0.717    2.0677    1.3593    3.0661
7MG         C2     C   CR6    0   0.688    1.3455    1.9149    2.0674
7MG         N2     N   NH2    0  -0.831    1.8112    3.0402    1.5002
7MG         N3     N   N      0  -0.516    0.1975    1.4167    1.6681
7MG         C4     C   CR56   0   0.503   -0.1825    0.3097    2.3094
7MG         CM7    C   CH3    0  -0.543    0.4062   -2.6246    4.1828
7MG        H5'     H   HCH2   0   0.174   -0.4440    0.8465   -3.0201
7MG        H5''    H   HCH2   0   0.170    0.5557    0.4672   -1.6165
7MG        H4'     H   HCR5   0   0.208   -2.3907   -0.2421   -1.9399
7MG        H3'     H   HCR5   0   0.247   -0.9283    1.9964   -0.4926
7MG        HO3'    H   HOH1   0   0.466   -2.4707    3.1815   -1.5076
7MG        H2'     H   HCR5   0   0.235   -2.4696    1.8674    1.3001
7MG        HO2'    H   HOH1   0   0.444   -4.1982    1.6287   -0.5263
7MG        H1'     H   HCR5   0   0.247   -2.9797   -0.9143    1.0076
7MG         H81    H   HCH2   0   0.204   -0.9650   -2.4156    2.0626
7MG         H82    H   HCH2   0   0.247   -2.2492   -1.9147    3.1872
7MG         HN1    H   HNR6   0   0.420    2.9386    1.7935    3.3436
7MG        HN21    H   HNH2   0   0.410    1.3623    3.3407    0.6516
7MG        HN22    H   HNH2   0   0.412    2.7764    3.3038    1.6041
7MG        HM71    H   HCH3   0   0.252    1.1345   -2.4167    4.9621
7MG        HM72    H   HCH3   0   0.239   -0.3149   -3.3381    4.5823
7MG        HM73    H   HCH3   0   0.203    0.9249   -3.1006    3.3389
#
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
7MG   P       OP1   deloc         1.525 0.020     1.525
7MG   P       OP2   deloc         1.523 0.020     1.523
7MG   P       OP3   deloc         1.525 0.020     1.525
7MG   P      O5'    single        1.709 0.020     1.709
7MG  O5'     C5'    single        1.393 0.020     1.393
7MG  C5'     C4'    single        1.511 0.020     1.511
7MG  C5'     H5'    single        0.970 0.020     1.090
7MG  C5'     H5''   single        0.970 0.020     1.090
7MG  C4'     O4'    single        1.416 0.020     1.416
7MG  C4'     C3'    single        1.525 0.020     1.525
7MG  C4'     H4'    single        0.970 0.020     1.090
7MG  O4'     C1'    single        1.415 0.020     1.415
7MG  C3'     O3'    single        1.406 0.020     1.406
7MG  C3'     C2'    single        1.538 0.020     1.538
7MG  C3'     H3'    single        0.970 0.020     1.090
7MG  O3'     HO3'   single        0.850 0.020     0.980
7MG  C2'     O2'    single        1.407 0.020     1.407
7MG  C2'     C1'    single        1.540 0.020     1.540
7MG  C2'     H2'    single        0.970 0.020     1.090
7MG  O2'     HO2'   single        0.850 0.020     0.980
7MG  C1'      N9    single        1.430 0.020     1.430
7MG  C1'     H1'    single        0.970 0.020     1.090
7MG   N9      C8    single        1.461 0.020     1.461
7MG   N9      C4    single        1.370 0.020     1.370
7MG   C8      N7    single        1.459 0.020     1.459
7MG   C8      H81   single        0.970 0.020     1.090
7MG   C8      H82   single        0.970 0.020     1.090
7MG   N7      C5    single        1.415 0.020     1.415
7MG   N7      CM7   single        1.447 0.020     1.447
7MG   C5      C6    single        1.406 0.020     1.406
7MG   C5      C4    double        1.375 0.020     1.375
7MG   C6      O6    double        1.231 0.020     1.231
7MG   C6      N1    single        1.410 0.020     1.410
7MG   N1      C2    single        1.352 0.020     1.352
7MG   N1      HN1   single        0.860 0.020     1.020
7MG   C2      N2    single        1.344 0.020     1.344
7MG   C2      N3    double        1.314 0.020     1.314
7MG   N2     HN21   single        0.890 0.020     1.040
7MG   N2     HN22   single        0.890 0.020     1.040
7MG   N3      C4    single        1.335 0.020     1.335
7MG   CM7    HM71   single        0.970 0.020     1.090
7MG   CM7    HM72   single        0.970 0.020     1.090
7MG   CM7    HM73   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
7MG  O5'      P       OP3         104.89 3.000
7MG  O5'      P       OP2         100.50 3.000
7MG   OP3     P       OP2         115.07 3.000
7MG  O5'      P       OP1         104.87 3.000
7MG   OP3     P       OP1         114.08 3.000
7MG   OP2     P       OP1         115.21 3.000
7MG  C5'     O5'      P           117.32 3.000
7MG  H5''    C5'     H5'          106.57 3.000
7MG  H5''    C5'     C4'          108.33 3.000
7MG  H5'     C5'     C4'          107.38 3.000
7MG  H5''    C5'     O5'          112.09 3.000
7MG  H5'     C5'     O5'          112.07 3.000
7MG  C4'     C5'     O5'          110.18 3.000
7MG  H4'     C4'     C3'          109.13 3.000
7MG  H4'     C4'     O4'          110.35 3.000
7MG  C3'     C4'     O4'          104.45 3.000
7MG  H4'     C4'     C5'          109.50 3.000
7MG  C3'     C4'     C5'          113.40 3.000
7MG  O4'     C4'     C5'          109.91 3.000
7MG  C1'     O4'     C4'          110.67 3.000
7MG  H3'     C3'     C2'          108.88 3.000
7MG  H3'     C3'     O3'          111.79 3.000
7MG  C2'     C3'     O3'          112.99 3.000
7MG  H3'     C3'     C4'          109.56 3.000
7MG  C2'     C3'     C4'          102.68 3.000
7MG  O3'     C3'     C4'          110.54 3.000
7MG  HO3'    O3'     C3'          108.75 3.000
7MG  H2'     C2'     C1'          111.57 3.000
7MG  H2'     C2'     O2'          110.86 3.000
7MG  C1'     C2'     O2'          108.19 3.000
7MG  H2'     C2'     C3'          112.13 3.000
7MG  C1'     C2'     C3'          103.24 3.000
7MG  O2'     C2'     C3'          110.56 3.000
7MG  HO2'    O2'     C2'          106.77 3.000
7MG  H1'     C1'      N9          105.58 3.000
7MG  H1'     C1'     C2'          107.86 3.000
7MG   N9     C1'     C2'          115.83 3.000
7MG  H1'     C1'     O4'          110.00 3.000
7MG   N9     C1'     O4'          110.38 3.000
7MG  C2'     C1'     O4'          107.10 3.000
7MG   C4      N9      C8          106.75 3.000
7MG   C4      N9     C1'          124.24 3.000
7MG   C8      N9     C1'          118.48 3.000
7MG   H82     C8      H81         108.07 3.000
7MG   H82     C8      N7          111.84 3.000
7MG   H81     C8      N7          111.19 3.000
7MG   H82     C8      N9          111.12 3.000
7MG   H81     C8      N9          110.65 3.000
7MG   N7      C8      N9          103.98 3.000
7MG   CM7     N7      C5          118.03 3.000
7MG   CM7     N7      C8          112.82 3.000
7MG   C5      N7      C8          104.17 3.000
7MG   C4      C5      C6          119.48 3.000
7MG   C4      C5      N7          109.75 3.000
7MG   C6      C5      N7          130.38 3.000
7MG   N1      C6      O6          119.22 3.000
7MG   N1      C6      C5          111.21 3.000
7MG   O6      C6      C5          129.57 3.000
7MG   HN1     N1      C2          119.08 3.000
7MG   HN1     N1      C6          115.58 3.000
7MG   C2      N1      C6          125.32 3.000
7MG   N3      C2      N2          119.49 3.000
7MG   N3      C2      N1          122.38 3.000
7MG   N2      C2      N1          118.10 3.000
7MG  HN22     N2     HN21         115.91 3.000
7MG  HN22     N2      C2          120.56 3.000
7MG  HN21     N2      C2          116.85 3.000
7MG   C4      N3      C2          114.67 3.000
7MG   N3      C4      C5          126.84 3.000
7MG   N3      C4      N9          124.01 3.000
7MG   C5      C4      N9          109.08 3.000
7MG  HM73     CM7    HM72         108.07 3.000
7MG  HM73     CM7    HM71         108.49 3.000
7MG  HM72     CM7    HM71         107.80 3.000
7MG  HM73     CM7     N7          112.88 3.000
7MG  HM72     CM7     N7          109.29 3.000
7MG  HM71     CM7     N7          110.17 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
7MG CONST_01   C5      C4      N9      C1'         180.00   0.0 0
7MG CONST_02   N3      C4      N9      C1'           0.00   0.0 0
7MG CONST_03   C2      N3      C4      N9          180.00   0.0 0
7MG CONST_04   C5      C4      N9      C8            0.00   0.0 0
7MG CONST_05   N3      C4      N9      C8          180.00   0.0 0
7MG CONST_06   C2      N1      C6      C5            0.00   0.0 0
7MG CONST_07   C2      N3      C4      C5            0.00   0.0 0
7MG CONST_08   N3      C2      N1      C6            0.00   0.0 0
7MG CONST_09   C4      N3      C2      N1            0.00   0.0 0
7MG CONST_10   N2      C2      N1      C6          180.00   0.0 0
7MG CONST_11   C2      N1      C6      O6          180.00   0.0 0
7MG CONST_12   C4      N3      C2      N2          180.00   0.0 0
7MG CONST_13   HN1     N1      C6      C5          180.00   0.0 0
7MG CONST_14  HN21     N2      C2      N1          180.00   0.0 0
7MG CONST_15  HN22     N2      C2      N1            0.00   0.0 0
7MG   Var_01   H81     C8      N9      C1'          50.71  30.0 1
7MG   Var_02  HM71     CM7     N7      C8         -179.57  30.0 3
7MG   Var_03   C4'     C5'     O5'     P           174.93  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
7MG plan-1    C1' 0.020
7MG plan-1    N9  0.020
7MG plan-1    C8  0.020
7MG plan-1    N7  0.020
7MG plan-1    C5  0.020
7MG plan-1    C6  0.020
7MG plan-1    O6  0.020
7MG plan-1    N1  0.020
7MG plan-1    C2  0.020
7MG plan-1    N2  0.020
7MG plan-1    N3  0.020
7MG plan-1    C4  0.020
7MG plan-1    CM7 0.020
7MG plan-1    HN1 0.020
7MG plan-1   HN21 0.020
7MG 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
7MG chir_01   C4'     C5'     O4'     C3'   negativ
7MG chir_02   C3'     O3'     C4'     C2'   positiv
7MG chir_03   C2'     O2'     C3'     C1'   positiv
7MG chir_04   C1'     O4'     N9      C2'   negativ
#
