# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 17:37:49 2021
#   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  51  33  .  2021-08-10  2022-11-17
;
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   0.668  21.1602  67.0059  22.4609
 G5J  N2   N  NH2   0  -0.826  21.4881  66.7657  21.1842
 G5J  C4   C  CR56  0   0.628  21.7826  66.9540  24.6891
 G5J  C5   C  CR56  0  -0.104  20.5402  67.3856  25.0647
 G5J  C6   C  CR6   0   0.415  19.5451  67.6477  24.0485
 G5J  O6   O  O     0  -0.493  18.4081  68.0348  24.2909
 G5J  O2'  O  OH1   0  -0.660  25.9742  66.6607  24.8217
 G5J  O3'  O  OH1   0  -0.655  26.4843  68.7707  26.5294
 G5J  O4'  O  O2    0  -0.492  24.2345  66.1328  27.2304
 G5J  O5'  O  O2    0  -0.577  23.8796  68.2300  29.1843
 G5J  C1'  C  CH1   0   0.170  23.8948  66.3264  25.8937
 G5J  C2'  C  CH1   0  -0.066  24.8720  67.3592  25.3255
 G5J  C3'  C  CH1   0  -0.030  25.2360  68.1463  26.5900
 G5J  C3G  C  CH3   0  -0.424  20.1804  63.7954  34.2566
 G5J  C4'  C  CH1   0   0.017  25.2619  67.0331  27.6326
 G5J  C5'  C  CH2   0  -0.210  25.0771  67.4553  29.0657
 G5J  C8   C  CR15  0   0.083  21.6608  67.1264  26.8498
 G5J  N1   N  N     0  -0.537  19.9633  67.4338  22.7564
 G5J  N3   N  NR16  0  -0.740  22.1306  66.7496  23.3911
 G5J  N7   N  N     0  -0.443  20.4859  67.4839  26.4298
 G5J  N9   N  NR5   0  -0.533  22.5115  66.7969  25.8177
 G5J  O1A  O  OH1   0  -0.722  24.4545  69.3709  31.3035
 G5J  O1B  O  OH1   0  -0.724  20.7451  67.2011  32.3768
 G5J  O1G  O  O     0  -0.671  23.3364  63.6919  33.9642
 G5J  O2A  O  O     0  -0.669  21.9932  69.4626  30.3539
 G5J  O2B  O  O     0  -0.649  21.2022  66.0445  30.0696
 G5J  O2G  O  OH1   0  -0.723  23.0392  66.2771  34.3783
 G5J  O3A  O  O2    0  -0.704  23.0295  67.3369  31.4089
 G5J  O3B  O  O2    0  -0.685  22.2508  65.1551  32.2174
 G5J  O3G  O  O2    0  -0.573  21.0678  64.9075  34.4515
 G5J  PA   P  P     0   1.517  23.2372  68.7085  30.5439
 G5J  PB   P  P     0   1.497  21.7059  66.4195  31.3955
 G5J  PG   P  P     0   1.501  22.5119  64.8977  33.8120
 G5J  H1   H  HNH2  0   0.412  20.8421  67.0640  20.4739
 G5J  H2   H  HNH2  0   0.414  22.4432  66.6285  20.9006
 G5J  H3   H  HOH1  0   0.456  26.7474  67.2344  24.8930
 G5J  H4   H  HOH1  0   0.472  26.3824  69.6378  26.1239
 G5J  H5   H  HCH1  0   0.294  23.9505  65.3789  25.3483
 G5J  H6   H  HCH1  0   0.268  24.4081  67.9979  24.5625
 G5J  H7   H  HCH1  0   0.259  24.4324  68.8600  26.8046
 G5J  H8   H  HCH3  0   0.265  19.2671  64.0342  34.7924
 G5J  H9   H  HCH3  0   0.244  19.9469  63.6559  33.2012
 G5J  H10  H  HCH3  0   0.251  20.6075  62.8790  34.6605
 G5J  H11  H  HCH1  0   0.265  26.2335  66.5236  27.5942
 G5J  H12  H  HCH2  0   0.272  25.0321  66.5751  29.7115
 G5J  H13  H  HCH2  0   0.268  25.9422  68.0513  29.3618
 G5J  H14  H  HCR5  0   0.294  21.9641  67.0572  27.8793
 G5J  H15  H  HNR6  0   0.438  23.0201  66.3594  23.1150
 G5J  H16  H  HOH1  0   0.515  24.2415  69.8094  32.1398
 G5J  H17  H  HOH1  0   0.515  19.8039  67.1489  32.1575
 G5J  H18  H  HOH1  0   0.514  24.0020  66.3745  34.3722

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    1.340  0.020  1.340
 G5J  C2   N1   double    1.305  0.020  1.305
 G5J  C2   N3   single    1.368  0.020  1.368
 G5J  N1   C6   single    1.375  0.020  1.375
 G5J  N3   C4   single    1.359  0.020  1.359
 G5J  C6   O6   double    1.225  0.020  1.225
 G5J  C6   C5   single    1.446  0.020  1.446
 G5J  C4   C5   aromatic  1.368  0.020  1.368
 G5J  C4   N9   aromatic  1.353  0.020  1.353
 G5J  O2'  C2'  single    1.399  0.020  1.399
 G5J  C5   N7   aromatic  1.370  0.020  1.370
 G5J  C2'  C1'  single    1.531  0.020  1.531
 G5J  C2'  C3'  single    1.533  0.020  1.533
 G5J  N9   C1'  single    1.463  0.020  1.463
 G5J  N9   C8   aromatic  1.377  0.020  1.377
 G5J  C1'  O4'  single    1.393  0.020  1.393
 G5J  N7   C8   aromatic  1.298  0.020  1.298
 G5J  O3'  C3'  single    1.397  0.020  1.397
 G5J  C3'  C4'  single    1.525  0.020  1.525
 G5J  O4'  C4'  single    1.424  0.020  1.424
 G5J  C4'  C5'  single    1.505  0.020  1.505
 G5J  O5'  C5'  single    1.431  0.020  1.431
 G5J  O5'  PA   single    1.578  0.020  1.578
 G5J  O2B  PB   double    1.467  0.020  1.467
 G5J  O2A  PA   double    1.467  0.020  1.467
 G5J  PA   O1A  single    1.580  0.020  1.580
 G5J  PA   O3A  single    1.635  0.020  1.635
 G5J  PB   O3A  single    1.611  0.020  1.611
 G5J  PB   O1B  single    1.580  0.020  1.580
 G5J  PB   O3B  single    1.604  0.020  1.604
 G5J  O3B  PG   single    1.636  0.020  1.636
 G5J  PG   O1G  double    1.469  0.020  1.469
 G5J  PG   O2G  single    1.582  0.020  1.582
 G5J  PG   O3G  single    1.579  0.020  1.579
 G5J  O3G  C3G  single    1.436  0.020  1.436
 G5J  N2   H1   single    0.890  0.020  1.040
 G5J  N2   H2   single    0.890  0.020  1.040
 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
 G5J  O1A  H16  single    0.850  0.020  0.980
 G5J  O1B  H17  single    0.850  0.020  0.980
 G5J  O2G  H18  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
 G5J  N3   C2   N1   123.91  3.000
 G5J  N3   C2   N2   116.14  3.000
 G5J  N1   C2   N2   119.93  3.000
 G5J  H2   N2   H1   116.84  3.000
 G5J  H2   N2   C2   121.70  3.000
 G5J  H1   N2   C2   117.57  3.000
 G5J  N9   C4   N3   129.89  3.000
 G5J  N9   C4   C5   107.27  3.000
 G5J  N3   C4   C5   122.84  3.000
 G5J  N7   C5   C6   131.30  3.000
 G5J  N7   C5   C4   109.42  3.000
 G5J  C6   C5   C4   119.29  3.000
 G5J  N1   C6   O6   121.15  3.000
 G5J  O6   C6   C5   123.83  3.000
 G5J  N1   C6   C5   115.02  3.000
 G5J  H3   O2'  C2'  107.93  3.000
 G5J  H4   O3'  C3'  109.04  3.000
 G5J  C4'  O4'  C1'  111.05  3.000
 G5J  PA   O5'  C5'  125.18  3.000
 G5J  H5   C1'  N9   107.49  3.000
 G5J  H5   C1'  C2'  111.50  3.000
 G5J  N9   C1'  C2'  111.54  3.000
 G5J  H5   C1'  O4'  110.21  3.000
 G5J  N9   C1'  O4'  108.97  3.000
 G5J  C2'  C1'  O4'  107.12  3.000
 G5J  H6   C2'  C3'  112.01  3.000
 G5J  H6   C2'  C1'  112.37  3.000
 G5J  C3'  C2'  C1'  101.05  3.000
 G5J  H6   C2'  O2'  111.92  3.000
 G5J  C3'  C2'  O2'  111.49  3.000
 G5J  C1'  C2'  O2'  107.44  3.000
 G5J  H7   C3'  C4'  110.72  3.000
 G5J  H7   C3'  C2'  108.77  3.000
 G5J  C4'  C3'  C2'  101.13  3.000
 G5J  H7   C3'  O3'  111.88  3.000
 G5J  C4'  C3'  O3'  109.91  3.000
 G5J  C2'  C3'  O3'  113.94  3.000
 G5J  H10  C3G  H9   109.60  3.000
 G5J  H10  C3G  H8   109.40  3.000
 G5J  H9   C3G  H8   109.02  3.000
 G5J  H10  C3G  O3G  111.05  3.000
 G5J  H9   C3G  O3G  111.28  3.000
 G5J  H8   C3G  O3G  106.42  3.000
 G5J  H11  C4'  C5'  105.79  3.000
 G5J  H11  C4'  C3'  109.26  3.000
 G5J  C5'  C4'  C3'  116.35  3.000
 G5J  H11  C4'  O4'  109.59  3.000
 G5J  C5'  C4'  O4'  110.96  3.000
 G5J  C3'  C4'  O4'  104.83  3.000
 G5J  H13  C5'  H12  108.19  3.000
 G5J  H13  C5'  C4'  108.31  3.000
 G5J  H12  C5'  C4'  109.98  3.000
 G5J  H13  C5'  O5'  110.20  3.000
 G5J  H12  C5'  O5'  110.65  3.000
 G5J  C4'  C5'  O5'  109.48  3.000
 G5J  H14  C8   N9   121.84  3.000
 G5J  H14  C8   N7   125.65  3.000
 G5J  N9   C8   N7   112.49  3.000
 G5J  C6   N1   C2   122.88  3.000
 G5J  H15  N3   C4   123.01  3.000
 G5J  H15  N3   C2   120.73  3.000
 G5J  C4   N3   C2   116.06  3.000
 G5J  C8   N7   C5   105.47  3.000
 G5J  C8   N9   C1'  128.46  3.000
 G5J  C8   N9   C4   105.34  3.000
 G5J  C1'  N9   C4   126.16  3.000
 G5J  H16  O1A  PA   115.82  3.000
 G5J  H17  O1B  PB   115.08  3.000
 G5J  H18  O2G  PG   114.66  3.000
 G5J  PB   O3A  PA   125.30  3.000
 G5J  PG   O3B  PB   132.68  3.000
 G5J  PG   O3G  C3G  120.35  3.000
 G5J  O3A  PA   O2A  113.09  3.000
 G5J  O3A  PA   O1A  101.26  3.000
 G5J  O2A  PA   O1A  119.99  3.000
 G5J  O3A  PA   O5'  104.67  3.000
 G5J  O1A  PA   O5'  103.16  3.000
 G5J  O2A  PA   O5'  112.92  3.000
 G5J  O3B  PB   O3A   99.53  3.000
 G5J  O3B  PB   O2B  112.23  3.000
 G5J  O3A  PB   O2B  115.80  3.000
 G5J  O3B  PB   O1B  106.16  3.000
 G5J  O3A  PB   O1B  102.29  3.000
 G5J  O2B  PB   O1B  118.62  3.000
 G5J  O3G  PG   O3B  104.34  3.000
 G5J  O3G  PG   O2G   98.89  3.000
 G5J  O3B  PG   O2G  105.36  3.000
 G5J  O3G  PG   O1G  118.46  3.000
 G5J  O2G  PG   O1G  119.46  3.000
 G5J  O3B  PG   O1G  108.65  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    73.74  30.0  1
 G5J  Var_02    O2A  PA   O5'  C5'  -178.74  30.0  3
 G5J  Var_03    H12  C5'  O5'  PA     50.66  30.0  3
 G5J  Var_04    H8   C3G  O3G  PG    179.59  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
 G5J  chir_05  PA   O2A  O1A  O3A  both
 G5J  chir_06  PB   O1B  O3A  O2B  both
 G5J  chir_07  PG   O1G  O2G  O3G  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
 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

