# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 10:26:58 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 7-methylguanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1cn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c3N=C(N)NC(=O)c13
#
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
 MG7  MG7  '7-methylguanosine        '  ligand  37  21  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MG7
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
 MG7  N9    N  NR5   0  -0.544   0.0523   0.2448   0.4815
 MG7  C8    C  CR15  0   0.250   0.0887   1.5646   0.2587
 MG7  N7    N  NR5   1  -0.468  -1.0989   1.9915  -0.1087
 MG7  C5    C  CR56  0   0.095  -1.9541   0.9132  -0.1178
 MG7  C6    C  CR6   0   0.563  -3.3418   0.7835  -0.4253
 MG7  O6    O  O     0  -0.440  -4.1188   1.6456  -0.7808
 MG7  N1    N  NR16  0  -0.733  -3.7364  -0.5439  -0.2614
 MG7  C2    C  CR6   0   0.725  -2.9409  -1.5839   0.1324
 MG7  N2    N  NH2   0  -0.822  -3.5050  -2.7796   0.2340
 MG7  N3    N  N     0  -0.509  -1.6594  -1.4389   0.4063
 MG7  C4    C  CR56  0   0.518  -1.2302  -0.1903   0.2633
 MG7  O5'   O  OH1   0  -0.666   4.4583   1.9813   0.9071
 MG7  C5'   C  CH2   0  -0.152   3.8640   1.3522  -0.1988
 MG7  C4'   C  CH1   0   0.003   3.2991   0.0238   0.2368
 MG7  O4'   O  O2    0  -0.491   2.2590   0.2112   1.2065
 MG7  C1'   C  CH1   0   0.175   1.1704  -0.6035   0.9409
 MG7  CN7   C  CH3   0  -0.523  -1.4368   3.3651  -0.4436
 MG7  C2'   C  CH1   0  -0.041   1.5938  -1.5864  -0.1486
 MG7  O2'   O  OH1   0  -0.660   2.1856  -2.6776   0.4958
 MG7  C3'   C  CH1   0  -0.042   2.6393  -0.7528  -0.8991
 MG7  O3'   O  OH1   0  -0.653   3.5913  -1.5223  -1.5735
 MG7  H8    H  HCR5  0   0.370   0.9523   2.1967   0.3753
 MG7  HN1   H  HNR6  0   0.441  -4.7118  -0.7330  -0.4597
 MG7  HN21  H  HNH2  0   0.427  -2.9452  -3.5629   0.5251
 MG7  HN22  H  HNH2  0   0.429  -4.4808  -2.9383   0.0496
 MG7  HO5'  H  HOH1  0   0.461   4.8267   2.8200   0.6150
 MG7  H5'1  H  HCH2  0   0.222   4.5875   1.1509  -0.9996
 MG7  H5'2  H  HCH2  0   0.195   3.0661   1.9634  -0.6427
 MG7  H1'   H  HCH1  0   0.309   0.8245  -1.1076   1.8463
 MG7  H71   H  HCH3  0   0.286  -1.7575   3.4200  -1.4795
 MG7  H72   H  HCH3  0   0.286  -2.2319   3.7141   0.2079
 MG7  H73   H  HCH3  0   0.283  -0.5558   3.9820  -0.3032
 MG7  H2'   H  HCH1  0   0.272   0.7580  -1.8913  -0.7883
 MG7  HO2'  H  HOH1  0   0.455   2.8664  -3.0334  -0.0893
 MG7  H3'   H  HCH1  0   0.249   2.1265  -0.0597  -1.5805
 MG7  HO3'  H  HOH1  0   0.471   3.2364  -1.7780  -2.4314
 MG7  H4'   H  HCH1  0   0.258   4.0944  -0.5805   0.6881

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
 MG7  N9   C8    aromatic  1.339  0.020  1.339
 MG7  N9   C4    aromatic  1.372  0.020  1.372
 MG7  N9   C1'   single    1.477  0.020  1.477
 MG7  C8   N7    aromatic  1.314  0.020  1.314
 MG7  C8   H8    single    0.930  0.020  1.080
 MG7  N7   C5    aromatic  1.376  0.020  1.376
 MG7  N7   CN7   single    1.454  0.020  1.454
 MG7  C5   C6    single    1.427  0.020  1.427
 MG7  C5   C4    aromatic  1.374  0.020  1.374
 MG7  C6   O6    double    1.214  0.020  1.214
 MG7  C6   N1    single    1.395  0.020  1.395
 MG7  N1   C2    single    1.367  0.020  1.367
 MG7  N1   HN1   single    0.860  0.020  1.020
 MG7  C2   N2    single    1.326  0.020  1.326
 MG7  C2   N3    double    1.318  0.020  1.318
 MG7  N2   HN21  single    0.860  0.020  1.020
 MG7  N2   HN22  single    0.860  0.020  1.020
 MG7  N3   C4    single    1.328  0.020  1.328
 MG7  O5'  C5'   single    1.404  0.020  1.404
 MG7  O5'  HO5'  single    0.850  0.020  0.980
 MG7  C5'  C4'   single    1.508  0.020  1.508
 MG7  C5'  H5'1  single    0.970  0.020  1.090
 MG7  C5'  H5'2  single    0.970  0.020  1.090
 MG7  C4'  O4'   single    1.434  0.020  1.434
 MG7  C4'  C3'   single    1.526  0.020  1.526
 MG7  C4'  H4'   single    0.970  0.020  1.090
 MG7  O4'  C1'   single    1.385  0.020  1.385
 MG7  C1'  C2'   single    1.527  0.020  1.527
 MG7  C1'  H1'   single    0.970  0.020  1.090
 MG7  CN7  H71   single    0.970  0.020  1.090
 MG7  CN7  H72   single    0.970  0.020  1.090
 MG7  CN7  H73   single    0.970  0.020  1.090
 MG7  C2'  O2'   single    1.399  0.020  1.399
 MG7  C2'  C3'   single    1.533  0.020  1.533
 MG7  C2'  H2'   single    0.970  0.020  1.090
 MG7  O2'  HO2'  single    0.850  0.020  0.980
 MG7  C3'  O3'   single    1.398  0.020  1.398
 MG7  C3'  H3'   single    0.970  0.020  1.090
 MG7  O3'  HO3'  single    0.850  0.020  0.980

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
 MG7  C1'   N9   C4    125.11  3.000
 MG7  C1'   N9   C8    126.69  3.000
 MG7  C4    N9   C8    108.15  3.000
 MG7  H8    C8   N7    124.36  3.000
 MG7  H8    C8   N9    125.63  3.000
 MG7  N7    C8   N9    110.01  3.000
 MG7  CN7   N7   C5    126.47  3.000
 MG7  CN7   N7   C8    125.54  3.000
 MG7  C5    N7   C8    107.99  3.000
 MG7  C4    C5   C6    119.94  3.000
 MG7  C4    C5   N7    107.47  3.000
 MG7  C6    C5   N7    132.59  3.000
 MG7  N1    C6   O6    121.96  3.000
 MG7  N1    C6   C5    109.65  3.000
 MG7  O6    C6   C5    128.39  3.000
 MG7  HN1   N1   C2    118.33  3.000
 MG7  HN1   N1   C6    115.28  3.000
 MG7  C2    N1   C6    126.39  3.000
 MG7  N3    C2   N2    119.79  3.000
 MG7  N3    C2   N1    122.80  3.000
 MG7  N2    C2   N1    117.41  3.000
 MG7  HN22  N2   HN21  118.04  3.000
 MG7  HN22  N2   C2    122.76  3.000
 MG7  HN21  N2   C2    119.19  3.000
 MG7  C4    N3   C2    113.28  3.000
 MG7  N3    C4   C5    127.94  3.000
 MG7  N3    C4   N9    125.68  3.000
 MG7  C5    C4   N9    106.38  3.000
 MG7  HO5'  O5'  C5'   108.29  3.000
 MG7  H5'2  C5'  H5'1  106.61  3.000
 MG7  H5'2  C5'  C4'   109.56  3.000
 MG7  H5'1  C5'  C4'   107.22  3.000
 MG7  H5'2  C5'  O5'   112.10  3.000
 MG7  H5'1  C5'  O5'   112.19  3.000
 MG7  C4'   C5'  O5'   109.01  3.000
 MG7  H4'   C4'  C3'   109.86  3.000
 MG7  H4'   C4'  O4'   108.65  3.000
 MG7  C3'   C4'  O4'   104.85  3.000
 MG7  H4'   C4'  C5'   109.44  3.000
 MG7  C3'   C4'  C5'   113.28  3.000
 MG7  O4'   C4'  C5'   110.60  3.000
 MG7  C1'   O4'  C4'   111.30  3.000
 MG7  H1'   C1'  C2'   112.46  3.000
 MG7  H1'   C1'  O4'   111.18  3.000
 MG7  C2'   C1'  O4'   107.30  3.000
 MG7  H1'   C1'  N9    106.45  3.000
 MG7  C2'   C1'  N9    110.96  3.000
 MG7  O4'   C1'  N9    108.47  3.000
 MG7  H73   CN7  H72   109.54  3.000
 MG7  H73   CN7  H71   109.55  3.000
 MG7  H72   CN7  H71   109.88  3.000
 MG7  H73   CN7  N7    108.59  3.000
 MG7  H72   CN7  N7    109.62  3.000
 MG7  H71   CN7  N7    109.65  3.000
 MG7  H2'   C2'  C3'   112.68  3.000
 MG7  H2'   C2'  O2'   112.00  3.000
 MG7  C3'   C2'  O2'   111.17  3.000
 MG7  H2'   C2'  C1'   112.59  3.000
 MG7  C3'   C2'  C1'   100.85  3.000
 MG7  O2'   C2'  C1'   106.90  3.000
 MG7  HO2'  O2'  C2'   107.85  3.000
 MG7  H3'   C3'  O3'   111.47  3.000
 MG7  H3'   C3'  C2'   109.16  3.000
 MG7  O3'   C3'  C2'   113.66  3.000
 MG7  H3'   C3'  C4'   110.02  3.000
 MG7  O3'   C3'  C4'   110.17  3.000
 MG7  C2'   C3'  C4'   101.96  3.000
 MG7  HO3'  O3'  C3'   108.97  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
 MG7  CONST_01  C5    N7   C8  N9    0.00   0.0  0
 MG7  CONST_02  N7    C5   C4  N9    0.00   0.0  0
 MG7  CONST_03  C5    C4   N9  C8    0.00   0.0  0
 MG7  CONST_04  C4    C5   N7  C8    0.00   0.0  0
 MG7  CONST_05  C4    N9   C8  N7    0.00   0.0  0
 MG7  CONST_06  C1'   N9   C8  N7  180.00   0.0  0
 MG7  CONST_07  C1'   N9   C4  C5  180.00   0.0  0
 MG7  CONST_08  C1'   N9   C4  N3    0.00   0.0  0
 MG7  CONST_09  C2    N1   C6  C5    0.00   0.0  0
 MG7  CONST_10  N3    C2   N1  C6    0.00   0.0  0
 MG7  CONST_11  C4    N3   C2  N1    0.00   0.0  0
 MG7  CONST_12  CN7   N7   C8  N9  180.00   0.0  0
 MG7  CONST_13  CN7   N7   C5  C6    0.00   0.0  0
 MG7  CONST_14  CN7   N7   C5  C4  180.00   0.0  0
 MG7  CONST_15  N2    C2   N1  C6  180.00   0.0  0
 MG7  CONST_16  C2    N1   C6  O6  180.00   0.0  0
 MG7  CONST_17  C4    N3   C2  N2  180.00   0.0  0
 MG7  CONST_18  H8    C8   N7  C5  180.00   0.0  0
 MG7  CONST_19  HN1   N1   C6  C5  180.00   0.0  0
 MG7  CONST_20  HN21  N2   C2  N1  180.00   0.0  0
 MG7  CONST_21  HN22  N2   C2  N1    0.00   0.0  0
 MG7  Var_01    H71   CN7  N7  C8  117.55  30.0  2

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
 MG7  chir_01  C4'  C5'  O4'  C3'  negativ
 MG7  chir_02  C1'  O4'  N9   C2'  negativ
 MG7  chir_03  C2'  O2'  C1'  C3'  negativ
 MG7  chir_04  C3'  O3'  C4'  C2'  positiv

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
 MG7  plan-1  N9    0.020
 MG7  plan-1  C8    0.020
 MG7  plan-1  N7    0.020
 MG7  plan-1  C5    0.020
 MG7  plan-1  C6    0.020
 MG7  plan-1  O6    0.020
 MG7  plan-1  N1    0.020
 MG7  plan-1  C2    0.020
 MG7  plan-1  N2    0.020
 MG7  plan-1  N3    0.020
 MG7  plan-1  C4    0.020
 MG7  plan-1  C1'   0.020
 MG7  plan-1  CN7   0.020
 MG7  plan-1  H8    0.020
 MG7  plan-1  HN1   0.020
 MG7  plan-1  HN21  0.020
 MG7  plan-1  HN22  0.020

