# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 21:47:17 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CN([C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)C3=C1C(=O)NC(=N3)N
#
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
 MGT  MGT  '7-methylguanosine 5'-(tetrahydrogen triphosphate)'  ligand  53  33  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MGT
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
 MGT  PG    P  P     0   1.455  14.1369  54.2290  75.2886
 MGT  O1G   O  O     0  -0.678  14.8905  53.9482  76.5144
 MGT  O2G   O  OH1   0  -0.764  15.0182  54.4604  74.0089
 MGT  O3G   O  OH1   0  -0.719  13.0339  53.1295  74.9979
 MGT  O3B   O  O2    0  -0.707  13.1881  55.5735  75.3822
 MGT  PB    P  P     0   1.505  13.4790  57.1260  75.6289
 MGT  O1B   O  O     0  -0.644  12.3581  57.8305  76.2533
 MGT  O2B   O  OH1   0  -0.712  14.8977  57.1602  76.3126
 MGT  O3A   O  O2    0  -0.695  13.8476  57.6548  74.1367
 MGT  PA    P  P     0   1.544  13.3026  57.2090  72.6897
 MGT  O1A   O  O     0  -0.695  13.6871  55.8335  72.2888
 MGT  O2A   O  OH1   0  -0.721  11.7569  57.4954  72.8484
 MGT  O5'   O  O2    0  -0.556  13.9399  58.2750  71.7299
 MGT  C5'   C  CH2   0  -0.219  13.7853  59.6987  71.8627
 MGT  C4'   C  CR15  0   0.032  14.0370  60.3402  70.5218
 MGT  O4'   O  O     0  -0.500  15.3284  60.0078  70.0584
 MGT  C3'   C  CR15  0  -0.036  13.0882  59.9208  69.4019
 MGT  O3'   O  OH1   0  -0.660  11.8992  60.6546  69.4796
 MGT  C2'   C  CR15  0  -0.057  13.9378  60.2222  68.1648
 MGT  O2'   O  OH1   0  -0.666  13.9287  61.5957  67.8762
 MGT  C1'   C  CR15  0   0.167  15.3504  59.8624  68.6431
 MGT  N9    N  NR5   0  -0.558  15.7893  58.5579  68.2822
 MGT  C8    C  CH2   0  -0.099  15.0023  57.3397  68.4253
 MGT  N7    N  NR5   0  -0.508  15.9079  56.2700  68.0015
 MGT  CM7   C  CH3   0  -0.542  15.2399  55.2194  67.2631
 MGT  C5    C  CR56  0  -0.009  16.9969  56.9203  67.3732
 MGT  C6    C  CR6   0   0.488  18.1257  56.3814  66.7408
 MGT  O6    O  O     0  -0.517  18.4041  55.2059  66.5005
 MGT  N1    N  NR16  0  -0.722  19.0226  57.3962  66.3420
 MGT  C2    C  CR6   0   0.700  18.8705  58.7160  66.5938
 MGT  N2    N  NH2   0  -0.833  19.8388  59.5475  66.1968
 MGT  N3    N  N     0  -0.528  17.8206  59.1975  67.2261
 MGT  C4    C  CR56  0   0.531  16.9242  58.2771  67.5878
 MGT  HOG2  H  HOH1  0   0.505  14.5782  54.9250  73.2374
 MGT  HOG3  H  HOH1  0   0.503  12.5930  53.1489  74.1374
 MGT  HOB2  H  HOH1  0   0.521  14.9906  57.7893  77.0431
 MGT  HOA2  H  HOH1  0   0.518  11.1778  57.0473  72.2141
 MGT  H5'1  H  HCH2  0   0.263  12.7784  59.9582  72.1979
 MGT  H5'2  H  HCH2  0   0.280  14.4997  60.0587  72.6045
 MGT  H4'   H  HCR5  0   0.249  13.9412  61.4235  70.6820
 MGT  H3'   H  HCR5  0   0.248  12.8934  58.8426  69.4506
 MGT  HO3'  H  HOH1  0   0.469  11.2178  60.1969  68.9766
 MGT  H2'   H  HCR5  0   0.251  13.6384  59.6261  67.2925
 MGT  HO2'  H  HOH1  0   0.450  13.0210  61.9103  67.9671
 MGT  H1'   H  HCR5  0   0.268  16.0756  60.5589  68.2164
 MGT  H81   H  HCH2  0   0.242  14.6720  57.1938  69.4560
 MGT  H82   H  HCH2  0   0.214  14.1055  57.3771  67.7828
 MGT  HM71  H  HCH3  0   0.252  15.9502  54.4369  67.0084
 MGT  HM72  H  HCH3  0   0.240  14.4642  54.7753  67.8869
 MGT  HM73  H  HCH3  0   0.203  14.7686  55.5790  66.3375
 MGT  HN1   H  HNR6  0   0.419  19.8566  57.0808  65.8650
 MGT  HN21  H  HNH2  0   0.417  20.6177  59.2379  65.6424
 MGT  HN22  H  HNH2  0   0.414  19.7045  60.5372  66.3066

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
 MGT  PG   O1G   double  1.466  0.020  1.466
 MGT  PG   O2G   single  1.571  0.020  1.571
 MGT  PG   O3G   single  1.584  0.020  1.584
 MGT  PG   O3B   single  1.648  0.020  1.648
 MGT  O2G  HOG2  single  0.850  0.020  0.980
 MGT  O3G  HOG3  single  0.850  0.020  0.980
 MGT  O3B  PB    single  1.599  0.020  1.599
 MGT  PB   O1B   double  1.464  0.020  1.464
 MGT  PB   O2B   single  1.575  0.020  1.575
 MGT  PB   O3A   single  1.625  0.020  1.625
 MGT  O2B  HOB2  single  0.850  0.020  0.980
 MGT  O3A  PA    single  1.609  0.020  1.609
 MGT  PA   O1A   double  1.483  0.020  1.483
 MGT  PA   O2A   single  1.580  0.020  1.580
 MGT  PA   O5'   single  1.570  0.020  1.570
 MGT  O2A  HOA2  single  0.850  0.020  0.980
 MGT  O5'  C5'   single  1.438  0.020  1.438
 MGT  C5'  C4'   single  1.508  0.020  1.508
 MGT  C5'  H5'1  single  0.970  0.020  1.090
 MGT  C5'  H5'2  single  0.970  0.020  1.090
 MGT  C4'  O4'   single  1.412  0.020  1.412
 MGT  C4'  C3'   single  1.527  0.020  1.527
 MGT  C4'  H4'   single  0.970  0.020  1.090
 MGT  O4'  C1'   single  1.423  0.020  1.423
 MGT  C3'  O3'   single  1.399  0.020  1.399
 MGT  C3'  C2'   single  1.531  0.020  1.531
 MGT  C3'  H3'   single  0.970  0.020  1.090
 MGT  O3'  HO3'  single  0.850  0.020  0.980
 MGT  C2'  O2'   single  1.403  0.020  1.403
 MGT  C2'  C1'   single  1.534  0.020  1.534
 MGT  C2'  H2'   single  0.970  0.020  1.090
 MGT  O2'  HO2'  single  0.850  0.020  0.980
 MGT  C1'  N9    single  1.423  0.020  1.423
 MGT  C1'  H1'   single  0.970  0.020  1.090
 MGT  N9   C8    single  1.457  0.020  1.457
 MGT  N9   C4    single  1.360  0.020  1.360
 MGT  C8   N7    single  1.464  0.020  1.464
 MGT  C8   H81   single  0.970  0.020  1.090
 MGT  C8   H82   single  0.970  0.020  1.090
 MGT  N7   CM7   single  1.447  0.020  1.447
 MGT  N7   C5    single  1.415  0.020  1.415
 MGT  CM7  HM71  single  0.970  0.020  1.090
 MGT  CM7  HM72  single  0.970  0.020  1.090
 MGT  CM7  HM73  single  0.970  0.020  1.090
 MGT  C5   C6    single  1.402  0.020  1.402
 MGT  C5   C4    double  1.376  0.020  1.376
 MGT  C6   O6    double  1.232  0.020  1.232
 MGT  C6   N1    single  1.412  0.020  1.412
 MGT  N1   C2    single  1.352  0.020  1.352
 MGT  N1   HN1   single  0.860  0.020  1.020
 MGT  C2   N2    single  1.337  0.020  1.337
 MGT  C2   N3    double  1.317  0.020  1.317
 MGT  N2   HN21  single  0.860  0.020  1.020
 MGT  N2   HN22  single  0.860  0.020  1.020
 MGT  N3   C4    single  1.335  0.020  1.335

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
 MGT  O3B   PG   O3G   100.12  3.000
 MGT  O3B   PG   O2G   104.42  3.000
 MGT  O3G   PG   O2G   110.08  3.000
 MGT  O3B   PG   O1G   113.87  3.000
 MGT  O3G   PG   O1G   112.24  3.000
 MGT  O2G   PG   O1G   114.90  3.000
 MGT  HOG2  O2G  PG    116.68  3.000
 MGT  HOG3  O3G  PG    117.83  3.000
 MGT  PB    O3B  PG    134.12  3.000
 MGT  O3A   PB   O2B   100.79  3.000
 MGT  O3A   PB   O1B   114.12  3.000
 MGT  O2B   PB   O1B   119.61  3.000
 MGT  O3A   PB   O3B   102.44  3.000
 MGT  O2B   PB   O3B   104.59  3.000
 MGT  O1B   PB   O3B   113.20  3.000
 MGT  HOB2  O2B  PB    115.34  3.000
 MGT  PA    O3A  PB    131.19  3.000
 MGT  O5'   PA   O2A   109.60  3.000
 MGT  O5'   PA   O1A   111.06  3.000
 MGT  O2A   PA   O1A   116.66  3.000
 MGT  O5'   PA   O3A   102.96  3.000
 MGT  O2A   PA   O3A   101.00  3.000
 MGT  O1A   PA   O3A   114.34  3.000
 MGT  HOA2  O2A  PA    115.80  3.000
 MGT  C5'   O5'  PA    124.91  3.000
 MGT  H5'2  C5'  H5'1  108.46  3.000
 MGT  H5'2  C5'  C4'   110.79  3.000
 MGT  H5'1  C5'  C4'   109.01  3.000
 MGT  H5'2  C5'  O5'   108.60  3.000
 MGT  H5'1  C5'  O5'   111.26  3.000
 MGT  C4'   C5'  O5'   108.74  3.000
 MGT  H4'   C4'  C3'   108.87  3.000
 MGT  H4'   C4'  O4'   111.08  3.000
 MGT  C3'   C4'  O4'   105.25  3.000
 MGT  H4'   C4'  C5'   105.98  3.000
 MGT  C3'   C4'  C5'   115.58  3.000
 MGT  O4'   C4'  C5'   110.15  3.000
 MGT  C1'   O4'  C4'   111.39  3.000
 MGT  H3'   C3'  C2'   109.15  3.000
 MGT  H3'   C3'  O3'   111.23  3.000
 MGT  C2'   C3'  O3'   114.41  3.000
 MGT  H3'   C3'  C4'   110.36  3.000
 MGT  C2'   C3'  C4'   101.18  3.000
 MGT  O3'   C3'  C4'   110.08  3.000
 MGT  HO3'  O3'  C3'   108.85  3.000
 MGT  H2'   C2'  C1'   111.80  3.000
 MGT  H2'   C2'  O2'   111.48  3.000
 MGT  C1'   C2'  O2'   107.43  3.000
 MGT  H2'   C2'  C3'   112.57  3.000
 MGT  C1'   C2'  C3'   102.29  3.000
 MGT  O2'   C2'  C3'   110.81  3.000
 MGT  HO2'  O2'  C2'   107.81  3.000
 MGT  H1'   C1'  N9    106.31  3.000
 MGT  H1'   C1'  C2'   109.88  3.000
 MGT  N9    C1'  C2'   114.83  3.000
 MGT  H1'   C1'  O4'   109.49  3.000
 MGT  N9    C1'  O4'   110.53  3.000
 MGT  C2'   C1'  O4'   105.78  3.000
 MGT  C4    N9   C8    109.16  3.000
 MGT  C4    N9   C1'   125.19  3.000
 MGT  C8    N9   C1'   125.09  3.000
 MGT  H82   C8   H81   107.94  3.000
 MGT  H82   C8   N7    111.03  3.000
 MGT  H81   C8   N7    111.26  3.000
 MGT  H82   C8   N9    110.69  3.000
 MGT  H81   C8   N9    111.57  3.000
 MGT  N7    C8   N9    104.38  3.000
 MGT  C5    N7   CM7   117.52  3.000
 MGT  C5    N7   C8    105.58  3.000
 MGT  CM7   N7   C8    113.11  3.000
 MGT  HM73  CM7  HM72  108.06  3.000
 MGT  HM73  CM7  HM71  108.56  3.000
 MGT  HM72  CM7  HM71  107.81  3.000
 MGT  HM73  CM7  N7    112.96  3.000
 MGT  HM72  CM7  N7    109.40  3.000
 MGT  HM71  CM7  N7    109.91  3.000
 MGT  C4    C5   C6    119.48  3.000
 MGT  C4    C5   N7    110.07  3.000
 MGT  C6    C5   N7    130.04  3.000
 MGT  N1    C6   O6    119.16  3.000
 MGT  N1    C6   C5    111.27  3.000
 MGT  O6    C6   C5    129.57  3.000
 MGT  HN1   N1   C2    119.01  3.000
 MGT  HN1   N1   C6    115.66  3.000
 MGT  C2    N1   C6    125.28  3.000
 MGT  N3    C2   N2    119.52  3.000
 MGT  N3    C2   N1    122.41  3.000
 MGT  N2    C2   N1    118.06  3.000
 MGT  HN22  N2   HN21  117.86  3.000
 MGT  HN22  N2   C2    118.91  3.000
 MGT  HN21  N2   C2    122.25  3.000
 MGT  C4    N3   C2    114.42  3.000
 MGT  N3    C4   C5    127.04  3.000
 MGT  N3    C4   N9    123.81  3.000
 MGT  C5    C4   N9    109.11  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
 MGT  CONST_01  C5    C4   N9   C1'   180.00   0.0  0
 MGT  CONST_02  N3    C4   N9   C1'     0.00   0.0  0
 MGT  CONST_03  C2    N3   C4   N9    180.00   0.0  0
 MGT  CONST_04  C5    C4   N9   C8      0.00   0.0  0
 MGT  CONST_05  N3    C4   N9   C8    180.00   0.0  0
 MGT  CONST_06  C2    N1   C6   C5      0.00   0.0  0
 MGT  CONST_07  C2    N3   C4   C5      0.00   0.0  0
 MGT  CONST_08  N3    C2   N1   C6      0.00   0.0  0
 MGT  CONST_09  C4    N3   C2   N1      0.00   0.0  0
 MGT  CONST_10  N2    C2   N1   C6    180.00   0.0  0
 MGT  CONST_11  C2    N1   C6   O6    180.00   0.0  0
 MGT  CONST_12  C4    N3   C2   N2    180.00   0.0  0
 MGT  CONST_13  HN1   N1   C6   C5    180.00   0.0  0
 MGT  CONST_14  HN21  N2   C2   N1      0.00   0.0  0
 MGT  CONST_15  HN22  N2   C2   N1    180.00   0.0  0
 MGT  Var_01    H81   C8   N9   C1'   -56.36  30.0  1
 MGT  Var_02    HM71  CM7  N7   C8   -177.82  30.0  3
 MGT  Var_03    C4'   C5'  O5'  PA   -157.37  30.0  3
 MGT  Var_04    O1B   PB   O3B  PG   -152.15  30.0  3
 MGT  Var_05    O1A   PA   O3A  PB    -67.16  30.0  3

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
 MGT  chir_03  C4'  C5'  O4'  C3'  negativ
 MGT  chir_04  C3'  O3'  C4'  C2'  positiv
 MGT  chir_05  C2'  O2'  C3'  C1'  positiv
 MGT  chir_06  C1'  O4'  N9   C2'  negativ
 MGT  chir_07  PB   O1B  O2B  O3A  both
 MGT  chir_08  PA   O1A  O2A  O5'  both

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
 MGT  plan-1  C1'   0.020
 MGT  plan-1  N9    0.020
 MGT  plan-1  C8    0.020
 MGT  plan-1  N7    0.020
 MGT  plan-1  CM7   0.020
 MGT  plan-1  C5    0.020
 MGT  plan-1  C6    0.020
 MGT  plan-1  O6    0.020
 MGT  plan-1  N1    0.020
 MGT  plan-1  C2    0.020
 MGT  plan-1  N2    0.020
 MGT  plan-1  N3    0.020
 MGT  plan-1  C4    0.020
 MGT  plan-1  HN1   0.020
 MGT  plan-1  HN21  0.020
 MGT  plan-1  HN22  0.020

