# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:12:59 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)N=C(N)Nc23
#
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
 G5J  G5J  5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine  ligand  48  33  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G5J
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
 G5J  C2   C  CR6    0   0.671  -5.4057  -2.4150  -1.2016
 G5J  N2   N  NH2    0  -0.829  -6.6917  -2.3832  -1.5734
 G5J  C4   C  CR56   0   0.630  -3.5055  -1.2311  -0.6180
 G5J  C5   C  CR56   0  -0.122  -2.8285  -2.3957  -0.3862
 G5J  C6   C  CR6    0   0.411  -3.5035  -3.6582  -0.5884
 G5J  O6   O  O      0  -0.496  -2.9763  -4.7512  -0.4143
 G5J  O2'  O  OH1    0  -0.655  -3.7719   1.7560   1.7359
 G5J  O3'  O  OH1    0  -0.668  -3.7964   3.9322   0.0031
 G5J  O4'  O  O2     0  -0.486  -2.0829   1.7957  -1.3672
 G5J  O5'  O  O2     0  -0.625   0.4146   2.9749  -1.9187
 G5J  C1'  C  CH1    0   0.215  -2.9287   1.1977  -0.4325
 G5J  C2'  C  CH1    0  -0.041  -2.6973   1.9560   0.8695
 G5J  C3'  C  CH1    0  -0.047  -2.5469   3.3815   0.3312
 G5J  C3G  C  CH3    0  -0.403   4.9998  -3.4270   0.6126
 G5J  C4'  C  CH1    0  -0.031  -1.7627   3.1336  -0.9547
 G5J  C5'  C  CH2    0  -0.172  -0.2759   3.2873  -0.7271
 G5J  C8   C  CR15   0   0.053  -1.4709  -0.8139   0.0361
 G5J  N1   N  N      0  -0.540  -4.8123  -3.5603  -1.0012
 G5J  N3   N  NR16   0  -0.737  -4.7979  -1.2019  -1.0318
 G5J  N7   N  N      0  -0.427  -1.5500  -2.1075   0.0225
 G5J  N9   N  NR5    0  -0.537  -2.6549  -0.2131  -0.3500
 G5J  O1A  O  OP    -1  -0.788   2.5090   2.6937  -3.2471
 G5J  O1B  O  OP    -1  -0.789   3.7041   0.8325   0.6337
 G5J  O1G  O  O      0  -0.814   2.4989  -2.0828   1.9972
 G5J  O2A  O  O      0  -0.804   2.6325   3.5801  -0.7846
 G5J  O2B  O  O      0  -0.774   1.1437   0.8475   1.0593
 G5J  O2G  O  OP    -1  -0.793   1.9505  -3.5274  -0.0957
 G5J  O3A  O  O2     0  -0.746   2.0593   1.1333  -1.3327
 G5J  O3B  O  O2     0  -0.736   2.2091  -1.0289  -0.3407
 G5J  O3G  O  O2     0  -0.615   4.2190  -2.3636   0.1098
 G5J  PA   P  P      0   1.368   2.0318   2.6970  -1.8314
 G5J  PB   P  P      0   1.374   2.3165   0.5300   0.1760
 G5J  PG   P  P      0   1.364   2.6257  -2.3485   0.5292
 G5J  H1   H  HNH2   0   0.412  -7.1382  -3.2509  -1.8136
 G5J  H2   H  HNH2   0   0.415  -7.1446  -1.5331  -1.8617
 G5J  H3   H  HOH1   0   0.470  -3.4856   1.9397   2.6358
 G5J  H4   H  HOH1   0   0.450  -4.3698   3.8554   0.7742
 G5J  H5   H  HCH1   0   0.237  -3.9827   1.3027  -0.7207
 G5J  H6   H  HCH1   0   0.255  -1.7453   1.6389   1.3144
 G5J  H7   H  HCH1   0   0.253  -1.9924   4.0234   1.0283
 G5J  H8   H  HCH3   0   0.204   4.9963  -3.4618   1.7062
 G5J  H9   H  HCH3   0   0.205   4.6620  -4.3992   0.2418
 G5J  H10  H  HCH3   0   0.225   6.0283  -3.2779   0.2837
 G5J  H11  H  HCH1   0   0.254  -2.0872   3.8239  -1.7405
 G5J  H12  H  HCH2   0   0.234   0.0473   2.6513   0.1011
 G5J  H13  H  HCH2   0   0.210  -0.0937   4.3271  -0.4337
 G5J  H14  H  HCR5   0   0.325  -0.5997  -0.2326   0.3157
 G5J  H15  H  HNR6   0   0.439  -5.2929  -0.3409  -1.2132

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
 G5J  N2   C2   single    1.339  0.020  1.339
 G5J  C2   N1   double    1.305  0.020  1.305
 G5J  C2   N3   single    1.367  0.020  1.367
 G5J  N1   C6   single    1.376  0.020  1.376
 G5J  N3   C4   single    1.357  0.020  1.357
 G5J  C6   O6   double    1.226  0.020  1.226
 G5J  C6   C5   single    1.446  0.020  1.446
 G5J  C4   C5   aromatic  1.367  0.020  1.367
 G5J  C4   N9   aromatic  1.353  0.020  1.353
 G5J  O2'  C2'  single    1.395  0.020  1.395
 G5J  C5   N7   aromatic  1.373  0.020  1.373
 G5J  C2'  C1'  single    1.524  0.020  1.524
 G5J  C2'  C3'  single    1.531  0.020  1.531
 G5J  N9   C1'  single    1.439  0.020  1.439
 G5J  N9   C8   aromatic  1.383  0.020  1.383
 G5J  C1'  O4'  single    1.395  0.020  1.395
 G5J  N7   C8   aromatic  1.296  0.020  1.296
 G5J  O3'  C3'  single    1.404  0.020  1.404
 G5J  C3'  C4'  single    1.526  0.020  1.526
 G5J  O4'  C4'  single    1.436  0.020  1.436
 G5J  C4'  C5'  single    1.512  0.020  1.512
 G5J  O5'  C5'  single    1.412  0.020  1.412
 G5J  O5'  PA   single    1.643  0.020  1.643
 G5J  O2B  PB   deloc     1.502  0.020  1.502
 G5J  O2A  PA   deloc     1.496  0.020  1.496
 G5J  PA   O1A  deloc     1.494  0.020  1.494
 G5J  PA   O3A  single    1.642  0.020  1.642
 G5J  PB   O3A  single    1.645  0.020  1.645
 G5J  PB   O1B  deloc     1.492  0.020  1.492
 G5J  PB   O3B  single    1.646  0.020  1.646
 G5J  O3B  PG   single    1.635  0.020  1.635
 G5J  PG   O1G  deloc     1.497  0.020  1.497
 G5J  PG   O2G  deloc     1.495  0.020  1.495
 G5J  PG   O3G  single    1.648  0.020  1.648
 G5J  O3G  C3G  single    1.412  0.020  1.412
 G5J  N2   H1   single    0.860  0.020  1.020
 G5J  N2   H2   single    0.860  0.020  1.020
 G5J  O2'  H3   single    0.850  0.020  0.980
 G5J  O3'  H4   single    0.850  0.020  0.980
 G5J  C1'  H5   single    0.970  0.020  1.090
 G5J  C2'  H6   single    0.970  0.020  1.090
 G5J  C3'  H7   single    0.970  0.020  1.090
 G5J  C3G  H8   single    0.970  0.020  1.090
 G5J  C3G  H9   single    0.970  0.020  1.090
 G5J  C3G  H10  single    0.970  0.020  1.090
 G5J  C4'  H11  single    0.970  0.020  1.090
 G5J  C5'  H12  single    0.970  0.020  1.090
 G5J  C5'  H13  single    0.970  0.020  1.090
 G5J  C8   H14  single    0.930  0.020  1.080
 G5J  N3   H15  single    0.860  0.020  1.020

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
 G5J  N3   C2   N1   123.86  3.000
 G5J  N3   C2   N2   116.13  3.000
 G5J  N1   C2   N2   120.00  3.000
 G5J  H2   N2   H1   117.48  3.000
 G5J  H2   N2   C2   122.16  3.000
 G5J  H1   N2   C2   118.20  3.000
 G5J  N9   C4   N3   129.99  3.000
 G5J  N9   C4   C5   107.21  3.000
 G5J  N3   C4   C5   122.79  3.000
 G5J  N7   C5   C6   131.28  3.000
 G5J  N7   C5   C4   109.44  3.000
 G5J  C6   C5   C4   119.27  3.000
 G5J  N1   C6   O6   121.01  3.000
 G5J  O6   C6   C5   123.91  3.000
 G5J  N1   C6   C5   115.09  3.000
 G5J  H3   O2'  C2'  108.93  3.000
 G5J  H4   O3'  C3'  108.13  3.000
 G5J  C4'  O4'  C1'  110.00  3.000
 G5J  PA   O5'  C5'  118.28  3.000
 G5J  H5   C1'  N9   106.94  3.000
 G5J  H5   C1'  C2'  108.81  3.000
 G5J  N9   C1'  C2'  114.19  3.000
 G5J  H5   C1'  O4'  111.41  3.000
 G5J  N9   C1'  O4'  110.07  3.000
 G5J  C2'  C1'  O4'  105.48  3.000
 G5J  H6   C2'  C3'  109.04  3.000
 G5J  H6   C2'  C1'  109.53  3.000
 G5J  C3'  C2'  C1'  100.24  3.000
 G5J  H6   C2'  O2'  112.02  3.000
 G5J  C3'  C2'  O2'  115.31  3.000
 G5J  C1'  C2'  O2'  110.02  3.000
 G5J  H7   C3'  C4'  111.74  3.000
 G5J  H7   C3'  C2'  111.76  3.000
 G5J  C4'  C3'  C2'  101.27  3.000
 G5J  H7   C3'  O3'  111.62  3.000
 G5J  C4'  C3'  O3'  108.90  3.000
 G5J  C2'  C3'  O3'  111.09  3.000
 G5J  H10  C3G  H9   108.10  3.000
 G5J  H10  C3G  H8   108.00  3.000
 G5J  H9   C3G  H8   108.03  3.000
 G5J  H10  C3G  O3G  108.14  3.000
 G5J  H9   C3G  O3G  112.21  3.000
 G5J  H8   C3G  O3G  112.22  3.000
 G5J  H11  C4'  C5'  109.59  3.000
 G5J  H11  C4'  C3'  110.48  3.000
 G5J  C5'  C4'  C3'  111.21  3.000
 G5J  H11  C4'  O4'  108.37  3.000
 G5J  C5'  C4'  O4'  110.92  3.000
 G5J  C3'  C4'  O4'  106.18  3.000
 G5J  H13  C5'  H12  107.47  3.000
 G5J  H13  C5'  C4'  107.47  3.000
 G5J  H12  C5'  C4'  110.23  3.000
 G5J  H13  C5'  O5'  110.77  3.000
 G5J  H12  C5'  O5'  111.47  3.000
 G5J  C4'  C5'  O5'  109.35  3.000
 G5J  H14  C8   N9   121.81  3.000
 G5J  H14  C8   N7   125.95  3.000
 G5J  N9   C8   N7   112.24  3.000
 G5J  C6   N1   C2   122.75  3.000
 G5J  H15  N3   C4   122.68  3.000
 G5J  H15  N3   C2   121.08  3.000
 G5J  C4   N3   C2   116.24  3.000
 G5J  C8   N7   C5   105.64  3.000
 G5J  C8   N9   C1'  127.21  3.000
 G5J  C8   N9   C4   105.47  3.000
 G5J  C1'  N9   C4   127.32  3.000
 G5J  PB   O3A  PA   129.09  3.000
 G5J  PG   O3B  PB   125.52  3.000
 G5J  PG   O3G  C3G  116.81  3.000
 G5J  O3A  PA   O2A  110.07  3.000
 G5J  O3A  PA   O1A  106.28  3.000
 G5J  O2A  PA   O1A  122.43  3.000
 G5J  O3A  PA   O5'  101.17  3.000
 G5J  O1A  PA   O5'  105.33  3.000
 G5J  O2A  PA   O5'  109.43  3.000
 G5J  O3B  PB   O3A   92.82  3.000
 G5J  O3B  PB   O2B  109.50  3.000
 G5J  O3A  PB   O2B  109.86  3.000
 G5J  O3B  PB   O1B  110.43  3.000
 G5J  O3A  PB   O1B  110.63  3.000
 G5J  O2B  PB   O1B  120.19  3.000
 G5J  O3G  PG   O3B   96.80  3.000
 G5J  O3G  PG   O2G  108.85  3.000
 G5J  O3B  PG   O2G  107.39  3.000
 G5J  O3G  PG   O1G  109.46  3.000
 G5J  O2G  PG   O1G  120.75  3.000
 G5J  O3B  PG   O1G  110.92  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
 G5J  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 G5J  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 G5J  CONST_03  C8   N9   C4   C5      0.00   0.0  0
 G5J  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 G5J  CONST_05  N9   C4   C5   N7      0.00   0.0  0
 G5J  CONST_06  C1'  N9   C4   C5    180.00   0.0  0
 G5J  CONST_07  N3   C4   N9   C1'     0.00   0.0  0
 G5J  CONST_08  N7   C8   N9   C1'   180.00   0.0  0
 G5J  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 G5J  CONST_10  N3   C2   N1   C6      0.00   0.0  0
 G5J  CONST_11  C6   N1   C2   N2    180.00   0.0  0
 G5J  CONST_12  C4   N3   C2   N2    180.00   0.0  0
 G5J  CONST_13  H14  C8   N9   C4    180.00   0.0  0
 G5J  CONST_14  H15  N3   C2   N1    180.00   0.0  0
 G5J  CONST_15  H1   N2   C2   N1      0.00   0.0  0
 G5J  CONST_16  H2   N2   C2   N1    180.00   0.0  0
 G5J  Var_01    O3B  PG   O3G  C3G  -177.22  30.0  1
 G5J  Var_02    O2A  PA   O5'  C5'   -34.74  30.0  3
 G5J  Var_03    H12  C5'  O5'  PA    -42.61  30.0  3
 G5J  Var_04    H8   C3G  O3G  PG    -58.82  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
 G5J  chir_01  C1'  C2'  N9   O4'  positiv
 G5J  chir_02  C2'  O2'  C3'  C1'  positiv
 G5J  chir_03  C3'  O3'  C4'  C2'  positiv
 G5J  chir_04  C4'  O4'  C3'  C5'  negativ

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
 G5J  plan-1  C2   0.020
 G5J  plan-1  N2   0.020
 G5J  plan-1  C4   0.020
 G5J  plan-1  C5   0.020
 G5J  plan-1  C6   0.020
 G5J  plan-1  O6   0.020
 G5J  plan-1  C1'  0.020
 G5J  plan-1  C8   0.020
 G5J  plan-1  N1   0.020
 G5J  plan-1  N3   0.020
 G5J  plan-1  N7   0.020
 G5J  plan-1  N9   0.020
 G5J  plan-1  H1   0.020
 G5J  plan-1  H2   0.020
 G5J  plan-1  H14  0.020
 G5J  plan-1  H15  0.020

