# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 08:39:33 2021
#   Inital geometry file: a 153 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ccccc1C(=O)O[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO[P](O)(=O)O[P](O)(O)=O)n3cnc4C(=O)NC(=Nc34)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
 BGO  BGO  '3'-O-[2-(methylamino)benzoyl]guanosine 5'-(trihydrogen diphosphate)'  ligand  60  38  .  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_BGO
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
 BGO  C'    C  C     0   0.649  21.3957   -4.6400  -70.5619
 BGO  N1    N  NR16  0  -0.728  18.6772  -10.0118  -64.6819
 BGO  C2    C  CR6   0   0.698  19.1594   -9.9494  -65.9578
 BGO  N2    N  NH2   0  -0.833  18.9502  -11.0151  -66.7397
 BGO  N3    N  N     0  -0.514  19.8259   -8.9190  -66.4190
 BGO  C4    C  CR56  0   0.512  19.9846   -7.9466  -65.5132
 BGO  C5    C  CR56  0  -0.097  19.5410   -7.9103  -64.2051
 BGO  C6    C  CR6   0   0.506  18.8124   -9.0241  -63.6980
 BGO  O6    O  O     0  -0.473  18.3361   -9.1852  -62.5872
 BGO  N7    N  N     0  -0.440  19.9077   -6.7352  -63.6000
 BGO  C8    C  CR15  0   0.096  20.5503   -6.0780  -64.5127
 BGO  N9    N  NR5   0  -0.545  20.6301   -6.7619  -65.7053
 BGO  PA    P  P     0   1.512  22.6042   -2.0649  -64.8762
 BGO  PB    P  P     0   1.466  24.8857   -0.6593  -63.7652
 BGO  C1'   C  CR6   0  -0.203  21.5159   -5.4735  -71.7623
 BGO  O1'   O  O     0  -0.478  20.8143   -3.5745  -70.5026
 BGO  O1A   O  O     0  -0.666  21.4915   -1.9700  -63.9238
 BGO  C1B   C  CH1   0   0.205  21.2795   -6.3351  -66.9136
 BGO  O1B   O  OH1   0  -0.712  26.0052   -1.2901  -62.8431
 BGO  C2'   C  CR6   0   0.396  20.9851   -5.0322  -73.0098
 BGO  N2'   N  NH1   0  -0.688  20.3453   -3.8553  -73.1513
 BGO  O2'   O  OH1   0  -0.644  19.5932   -5.3330  -68.2633
 BGO  O2A   O  OH1   0  -0.742  22.7128   -0.9482  -66.0043
 BGO  C2B   C  CH1   0  -0.007  20.7137   -5.0387  -67.4952
 BGO  O2B   O  O     0  -0.688  23.9795    0.3593  -63.2131
 BGO  C3'   C  CR16  0  -0.359  21.1564   -5.8806  -74.1271
 BGO  O3'   O  O2    0  -0.479  22.0332   -5.1552  -69.5091
 BGO  O3A   O  O2    0  -0.703  24.0971   -1.9978  -64.2663
 BGO  C3B   C  CH1   0  -0.089  21.9295   -4.4960  -68.2549
 BGO  O3B   O  OH1   0  -0.722  25.7627   -0.2658  -65.0241
 BGO  C4'   C  CR16  0  -0.233  21.8017   -7.0908  -74.0158
 BGO  O4'   O  O2    0  -0.489  22.6336   -6.0883  -66.6511
 BGO  C4B   C  CH1   0  -0.002  23.1057   -4.9738  -67.4014
 BGO  C5'   C  CR16  0  -0.284  22.3120   -7.5274  -72.7928
 BGO  C5B   C  CH2   0  -0.207  23.6687   -3.9260  -66.4702
 BGO  C6'   C  CR16  0  -0.273  22.1634   -6.7154  -71.6906
 BGO  CM'   C  CH3   0  -0.534  19.8152   -3.3670  -74.3956
 BGO  HN1   H  HNR6  0   0.426  18.1705  -10.8419  -64.4015
 BGO  HN2   H  HNH2  0   0.414  19.1805  -10.9394  -67.7156
 BGO  HN2A  H  HNH2  0   0.417  18.3054  -11.7416  -66.4791
 BGO  H8    H  HCR5  0   0.287  20.9904   -5.1017  -64.3808
 BGO  H1B   H  HCH1  0   0.267  21.1520   -7.1495  -67.6359
 BGO  HO1B  H  HOH1  0   0.512  25.6955   -1.6230  -61.9890
 BGO  HN2'  H  HNH1  0   0.407  20.2329   -3.2917  -72.3257
 BGO  HO2'  H  HOH1  0   0.468  19.0942   -4.5239  -68.4125
 BGO  HO2A  H  HOH1  0   0.510  21.8697   -0.5521  -66.2660
 BGO  H2B   H  HCH1  0   0.259  20.4799   -4.3392  -66.6842
 BGO  H3'   H  HCR6  0   0.274  20.7745   -5.5774  -75.0920
 BGO  H3B   H  HCH1  0   0.295  21.9135   -3.4127  -68.3847
 BGO  HO3B  H  HOH1  0   0.511  25.5791    0.6170  -65.3733
 BGO  H4'   H  HCR6  0   0.261  21.9105   -7.7087  -74.8985
 BGO  H4B   H  HCH1  0   0.285  23.9322   -5.2884  -68.0469
 BGO  H5'   H  HCR6  0   0.252  22.8152   -8.4807  -72.7097
 BGO  H5B   H  HCH2  0   0.277  24.4756   -4.3541  -65.8731
 BGO  H5BA  H  HCH2  0   0.259  24.0796   -3.1079  -67.0664
 BGO  H6'   H  HCR6  0   0.262  22.5571   -7.0510  -70.7416
 BGO  HM'   H  HCH3  0   0.262  19.3590   -2.3979  -74.2132
 BGO  HM'A  H  HCH3  0   0.233  20.5906   -3.2345  -75.1548
 BGO  HM'B  H  HCH3  0   0.233  19.0479   -4.0262  -74.8097
 BGO  O5'   O  O2    0  -0.580  22.6274   -3.4766  -65.6001

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
 BGO  C'   C1'   single    1.466  0.020  1.466
 BGO  C'   O1'   double    1.215  0.020  1.215
 BGO  C'   O3'   single    1.334  0.020  1.334
 BGO  N1   C2    single    1.365  0.020  1.365
 BGO  N1   C6    single    1.401  0.020  1.401
 BGO  C2   N2    single    1.338  0.020  1.338
 BGO  C2   N3    double    1.311  0.020  1.311
 BGO  N3   C4    single    1.338  0.020  1.338
 BGO  C4   C5    aromatic  1.382  0.020  1.382
 BGO  C4   N9    aromatic  1.363  0.020  1.363
 BGO  C5   C6    single    1.424  0.020  1.424
 BGO  C5   N7    aromatic  1.372  0.020  1.372
 BGO  C6   O6    double    1.219  0.020  1.219
 BGO  N7   C8    aromatic  1.295  0.020  1.295
 BGO  C8   N9    aromatic  1.377  0.020  1.377
 BGO  N9   C1B   single    1.437  0.020  1.437
 BGO  PA   O1A   double    1.468  0.020  1.468
 BGO  PA   O2A   single    1.591  0.020  1.591
 BGO  PA   O3A   single    1.614  0.020  1.614
 BGO  PA   O5'   single    1.587  0.020  1.587
 BGO  PB   O1B   single    1.582  0.020  1.582
 BGO  PB   O2B   double    1.471  0.020  1.471
 BGO  PB   O3A   single    1.632  0.020  1.632
 BGO  PB   O3B   single    1.584  0.020  1.584
 BGO  C1'  C2'   aromatic  1.426  0.020  1.426
 BGO  C1'  C6'   aromatic  1.402  0.020  1.402
 BGO  C1B  C2B   single    1.529  0.020  1.529
 BGO  C1B  O4'   single    1.401  0.020  1.401
 BGO  C2'  N2'   single    1.347  0.020  1.347
 BGO  C2'  C3'   aromatic  1.413  0.020  1.413
 BGO  N2'  CM'   single    1.438  0.020  1.438
 BGO  O2'  C2B   single    1.390  0.020  1.390
 BGO  C2B  C3B   single    1.533  0.020  1.533
 BGO  C3'  C4'   aromatic  1.376  0.020  1.376
 BGO  O3'  C3B   single    1.421  0.020  1.421
 BGO  C3B  C4B   single    1.530  0.020  1.530
 BGO  C4'  C5'   aromatic  1.395  0.020  1.395
 BGO  O4'  C4B   single    1.424  0.020  1.424
 BGO  C4B  C5B   single    1.511  0.020  1.511
 BGO  C5'  C6'   aromatic  1.377  0.020  1.377
 BGO  O5'  C5B   single    1.429  0.020  1.429
 BGO  N1   HN1   single    0.860  0.020  1.020
 BGO  N2   HN2   single    0.890  0.020  1.040
 BGO  N2   HN2A  single    0.890  0.020  1.040
 BGO  C8   H8    single    0.930  0.020  1.080
 BGO  C1B  H1B   single    0.970  0.020  1.090
 BGO  O1B  HO1B  single    0.850  0.020  0.980
 BGO  N2'  HN2'  single    0.860  0.020  1.020
 BGO  O2'  HO2'  single    0.850  0.020  0.980
 BGO  O2A  HO2A  single    0.850  0.020  0.980
 BGO  C2B  H2B   single    0.970  0.020  1.090
 BGO  C3'  H3'   single    0.930  0.020  1.080
 BGO  C3B  H3B   single    0.970  0.020  1.090
 BGO  O3B  HO3B  single    0.850  0.020  0.980
 BGO  C4'  H4'   single    0.930  0.020  1.080
 BGO  C4B  H4B   single    0.970  0.020  1.090
 BGO  C5'  H5'   single    0.930  0.020  1.080
 BGO  C5B  H5B   single    0.970  0.020  1.090
 BGO  C5B  H5BA  single    0.970  0.020  1.090
 BGO  C6'  H6'   single    0.930  0.020  1.080
 BGO  CM'  HM'   single    0.970  0.020  1.090
 BGO  CM'  HM'A  single    0.970  0.020  1.090
 BGO  CM'  HM'B  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
 BGO  O3'   C'   O1'   121.92  3.000
 BGO  O3'   C'   C1'   112.78  3.000
 BGO  O1'   C'   C1'   125.28  3.000
 BGO  HN1   N1   C6    115.59  3.000
 BGO  HN1   N1   C2    118.24  3.000
 BGO  C6    N1   C2    126.16  3.000
 BGO  N3    C2   N2    119.99  3.000
 BGO  N3    C2   N1    122.97  3.000
 BGO  N2    C2   N1    117.03  3.000
 BGO  HN2A  N2   HN2   116.92  3.000
 BGO  HN2A  N2   C2    121.61  3.000
 BGO  HN2   N2   C2    118.12  3.000
 BGO  C4    N3   C2    113.16  3.000
 BGO  N9    C4   C5    105.23  3.000
 BGO  N9    C4   N3    126.33  3.000
 BGO  C5    C4   N3    128.45  3.000
 BGO  N7    C5   C6    130.51  3.000
 BGO  N7    C5   C4    110.75  3.000
 BGO  C6    C5   C4    118.73  3.000
 BGO  O6    C6   C5    128.86  3.000
 BGO  O6    C6   N1    120.61  3.000
 BGO  C5    C6   N1    110.53  3.000
 BGO  C8    N7   C5    104.85  3.000
 BGO  H8    C8   N9    122.11  3.000
 BGO  H8    C8   N7    125.11  3.000
 BGO  N9    C8   N7    112.77  3.000
 BGO  C1B   N9   C8    127.38  3.000
 BGO  C1B   N9   C4    126.22  3.000
 BGO  C8    N9   C4    106.39  3.000
 BGO  O5'   PA   O3A   101.30  3.000
 BGO  O5'   PA   O2A   107.45  3.000
 BGO  O3A   PA   O2A   100.11  3.000
 BGO  O5'   PA   O1A   111.38  3.000
 BGO  O3A   PA   O1A   116.96  3.000
 BGO  O2A   PA   O1A   117.81  3.000
 BGO  O3B   PB   O3A   103.14  3.000
 BGO  O3B   PB   O2B   117.87  3.000
 BGO  O3A   PB   O2B   112.67  3.000
 BGO  O3B   PB   O1B    99.82  3.000
 BGO  O3A   PB   O1B   101.18  3.000
 BGO  O2B   PB   O1B   119.56  3.000
 BGO  C6'   C1'  C2'   119.39  3.000
 BGO  C6'   C1'  C'    119.96  3.000
 BGO  C2'   C1'  C'    120.65  3.000
 BGO  H1B   C1B  O4'   111.52  3.000
 BGO  H1B   C1B  C2B   109.65  3.000
 BGO  O4'   C1B  C2B   106.23  3.000
 BGO  H1B   C1B  N9    106.32  3.000
 BGO  O4'   C1B  N9    109.37  3.000
 BGO  C2B   C1B  N9    113.85  3.000
 BGO  HO1B  O1B  PB    115.17  3.000
 BGO  C3'   C2'  N2'   119.93  3.000
 BGO  C3'   C2'  C1'   117.44  3.000
 BGO  N2'   C2'  C1'   122.63  3.000
 BGO  HN2'  N2'  CM'   118.60  3.000
 BGO  HN2'  N2'  C2'   117.16  3.000
 BGO  CM'   N2'  C2'   124.24  3.000
 BGO  HO2'  O2'  C2B   109.01  3.000
 BGO  HO2A  O2A  PA    114.81  3.000
 BGO  H2B   C2B  C3B   108.05  3.000
 BGO  H2B   C2B  O2'   111.84  3.000
 BGO  C3B   C2B  O2'   116.13  3.000
 BGO  H2B   C2B  C1B   109.79  3.000
 BGO  C3B   C2B  C1B   101.25  3.000
 BGO  O2'   C2B  C1B   109.20  3.000
 BGO  H3'   C3'  C4'   118.98  3.000
 BGO  H3'   C3'  C2'   119.63  3.000
 BGO  C4'   C3'  C2'   121.39  3.000
 BGO  C3B   O3'  C'    118.85  3.000
 BGO  PB    O3A  PA    126.65  3.000
 BGO  H3B   C3B  C4B   112.81  3.000
 BGO  H3B   C3B  O3'   110.90  3.000
 BGO  C4B   C3B  O3'   106.95  3.000
 BGO  H3B   C3B  C2B   113.51  3.000
 BGO  C4B   C3B  C2B   102.87  3.000
 BGO  O3'   C3B  C2B   109.34  3.000
 BGO  HO3B  O3B  PB    114.13  3.000
 BGO  H4'   C4'  C5'   119.95  3.000
 BGO  H4'   C4'  C3'   118.88  3.000
 BGO  C5'   C4'  C3'   121.17  3.000
 BGO  C4B   O4'  C1B   111.07  3.000
 BGO  H4B   C4B  C5B   106.35  3.000
 BGO  H4B   C4B  O4'   109.63  3.000
 BGO  C5B   C4B  O4'   109.97  3.000
 BGO  H4B   C4B  C3B   109.95  3.000
 BGO  C5B   C4B  C3B   114.45  3.000
 BGO  O4'   C4B  C3B   106.47  3.000
 BGO  H5'   C5'  C6'   120.58  3.000
 BGO  H5'   C5'  C4'   120.89  3.000
 BGO  C6'   C5'  C4'   118.53  3.000
 BGO  H5BA  C5B  H5B   108.31  3.000
 BGO  H5BA  C5B  O5'   111.76  3.000
 BGO  H5B   C5B  O5'   109.21  3.000
 BGO  H5BA  C5B  C4B   108.85  3.000
 BGO  H5B   C5B  C4B   109.92  3.000
 BGO  O5'   C5B  C4B   108.77  3.000
 BGO  H6'   C6'  C5'   118.71  3.000
 BGO  H6'   C6'  C1'   119.21  3.000
 BGO  C5'   C6'  C1'   122.08  3.000
 BGO  HM'B  CM'  HM'A  107.93  3.000
 BGO  HM'B  CM'  HM'   107.87  3.000
 BGO  HM'A  CM'  HM'   107.83  3.000
 BGO  HM'B  CM'  N2'   112.45  3.000
 BGO  HM'A  CM'  N2'   112.37  3.000
 BGO  HM'   CM'  N2'   108.20  3.000
 BGO  C5B   O5'  PA    124.61  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
 BGO  CONST_01  C8    N7   C5   C4      0.00   0.0  0
 BGO  CONST_02  N7    C8   N9   C4      0.00   0.0  0
 BGO  CONST_03  C8    N9   C4   C5      0.00   0.0  0
 BGO  CONST_04  N9    C8   N7   C5      0.00   0.0  0
 BGO  CONST_05  N9    C4   C5   N7      0.00   0.0  0
 BGO  CONST_06  C4'   C3'  C2'  C1'     0.00   0.0  0
 BGO  CONST_07  C4'   C5'  C6'  C1'     0.00   0.0  0
 BGO  CONST_08  C5'   C6'  C1'  C2'     0.00   0.0  0
 BGO  CONST_09  C5'   C4'  C3'  C2'     0.00   0.0  0
 BGO  CONST_10  C6'   C1'  C2'  C3'     0.00   0.0  0
 BGO  CONST_11  C6'   C5'  C4'  C3'     0.00   0.0  0
 BGO  CONST_12  C1B   N9   C4   N3      0.00   0.0  0
 BGO  CONST_13  C1B   N9   C4   C5    180.00   0.0  0
 BGO  CONST_14  C1B   N9   C8   N7    180.00   0.0  0
 BGO  CONST_15  C4    N3   C2   N1      0.00   0.0  0
 BGO  CONST_16  C5    C6   N1   C2      0.00   0.0  0
 BGO  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 BGO  CONST_18  C3'   C2'  C1'  C'    180.00   0.0  0
 BGO  CONST_19  C5'   C6'  C1'  C'    180.00   0.0  0
 BGO  CONST_20  C6'   C1'  C2'  N2'   180.00   0.0  0
 BGO  CONST_21  C4'   C3'  C2'  N2'   180.00   0.0  0
 BGO  CONST_22  O6    C6   N1   C2    180.00   0.0  0
 BGO  CONST_23  C6    N1   C2   N2    180.00   0.0  0
 BGO  CONST_24  C4    N3   C2   N2    180.00   0.0  0
 BGO  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 BGO  CONST_26  H3'   C3'  C2'  C1'   180.00   0.0  0
 BGO  CONST_27  H5'   C5'  C6'  C1'   180.00   0.0  0
 BGO  CONST_28  H6'   C6'  C1'  C2'   180.00   0.0  0
 BGO  CONST_29  H4'   C4'  C3'  C2'   180.00   0.0  0
 BGO  CONST_30  HN1   N1   C2   N3    180.00   0.0  0
 BGO  CONST_31  CM'   N2'  C2'  C1'   180.00   0.0  0
 BGO  CONST_32  CM'   N2'  C2'  C3'     0.00   0.0  0
 BGO  CONST_33  HN2'  N2'  C2'  C1'     0.00   0.0  0
 BGO  CONST_34  HN2   N2   C2   N1    180.00   0.0  0
 BGO  CONST_35  HN2A  N2   C2   N1      0.00   0.0  0
 BGO  Var_01    C2'   C1'  C'   O1'     3.13  30.0  2
 BGO  Var_02    C4B   C5B  O5'  PA   -155.70  30.0  3
 BGO  Var_03    HM'   CM'  N2'  C2'  -179.81  30.0  3
 BGO  Var_04    O1B   PB   O3A  PA    160.66  30.0  1
 BGO  Var_05    O1A   PA   O3A  PB    -77.36  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
 BGO  chir_02  C1B  N9   C2B  O4'  negativ
 BGO  chir_03  C2B  O2'  C3B  C1B  positiv
 BGO  chir_04  C3B  O3'  C4B  C2B  positiv
 BGO  chir_05  C4B  O4'  C3B  C5B  negativ
 BGO  chir_06  PA   O2A  O3A  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
 BGO  plan-1  C'    0.020
 BGO  plan-1  C1'   0.020
 BGO  plan-1  C2'   0.020
 BGO  plan-1  N2'   0.020
 BGO  plan-1  C3'   0.020
 BGO  plan-1  C4'   0.020
 BGO  plan-1  C5'   0.020
 BGO  plan-1  C6'   0.020
 BGO  plan-1  H3'   0.020
 BGO  plan-1  H4'   0.020
 BGO  plan-1  H5'   0.020
 BGO  plan-1  H6'   0.020
 BGO  plan-2  N1    0.020
 BGO  plan-2  C2    0.020
 BGO  plan-2  N2    0.020
 BGO  plan-2  N3    0.020
 BGO  plan-2  C4    0.020
 BGO  plan-2  C5    0.020
 BGO  plan-2  C6    0.020
 BGO  plan-2  O6    0.020
 BGO  plan-2  N7    0.020
 BGO  plan-2  C8    0.020
 BGO  plan-2  N9    0.020
 BGO  plan-2  C1B   0.020
 BGO  plan-2  HN1   0.020
 BGO  plan-2  HN2   0.020
 BGO  plan-2  HN2A  0.020
 BGO  plan-2  H8    0.020
 BGO  plan-3  C2'   0.020
 BGO  plan-3  N2'   0.020
 BGO  plan-3  CM'   0.020
 BGO  plan-3  HN2'  0.020
 BGO  plan-4  C'    0.020
 BGO  plan-4  C1'   0.020
 BGO  plan-4  O1'   0.020
 BGO  plan-4  O3'   0.020

