# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 18:23:32 2021
#   Inital geometry file: a 136 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)c2N1
#
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
 BKP  BKP  5'-O-[(S)-hydroxy{[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine  ligand  53  36  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BKP
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
 BKP  PB   P  P     0   1.470   7.0832  16.4425  -15.8252
 BKP  O1B  O  O     0  -0.664   8.3300  15.7982  -15.3939
 BKP  O2B  O  OH1   0  -0.705   6.0544  16.9380  -14.7397
 BKP  O3B  O  O2    0  -0.668   7.2277  17.7513  -16.7486
 BKP  O3A  O  O2    0  -0.688   6.2050  15.5416  -16.8267
 BKP  PA   P  P     0   1.500   6.6594  14.1054  -17.4726
 BKP  O1A  O  O     0  -0.658   7.7595  14.2173  -18.4354
 BKP  O2A  O  OH1   0  -0.732   6.8387  13.1504  -16.2204
 BKP  O5'  O  O2    0  -0.566   5.2924  13.6327  -18.0994
 BKP  C5'  C  CH2   0  -0.193   4.0738  13.4833  -17.3602
 BKP  C4'  C  CH1   0  -0.026   2.9329  13.9357  -18.2587
 BKP  O4'  O  O2    0  -0.482   1.7140  13.6534  -17.5695
 BKP  C3'  C  CH1   0  -0.036   2.9227  15.4342  -18.5489
 BKP  O3'  O  OH1   0  -0.663   2.2694  15.6287  -19.7747
 BKP  C2'  C  CH1   0  -0.025   2.0880  15.9571  -17.3826
 BKP  O2'  O  OH1   0  -0.649   1.5573  17.2143  -17.6461
 BKP  C1'  C  CH1   0   0.182   1.0366  14.8442  -17.2712
 BKP  N9   N  NR5   0  -0.536   0.4260  14.7363  -15.9721
 BKP  C8   C  CR15  0   0.098   1.0728  14.6464  -14.7560
 BKP  N7   N  N     0  -0.433   0.2554  14.4937  -13.7649
 BKP  C5   C  CR56  0  -0.114  -0.9968  14.4692  -14.3261
 BKP  C6   C  CR6   0   0.420  -2.3064  14.3274  -13.7269
 BKP  O6   O  O     0  -0.491  -2.4948  14.2009  -12.5231
 BKP  N1   N  N     0  -0.538  -3.3549  14.3446  -14.6145
 BKP  C2   C  CR6   0   0.676  -3.1894  14.4682  -15.9037
 BKP  N2   N  NH2   0  -0.827  -4.2475  14.4368  -16.7202
 BKP  N3   N  NR16  0  -0.737  -1.9682  14.6126  -16.5058
 BKP  C4   C  CR56  0   0.644  -0.8918  14.6074  -15.6818
 BKP  PD   P  P     0   1.467   6.0195  21.1814  -14.9804
 BKP  PG   P  P     0   1.520   7.6781  19.2564  -16.3574
 BKP  O1G  O  OH1   0  -0.732   8.4775  19.1223  -14.9995
 BKP  O2G  O  O     0  -0.642   8.3043  19.9335  -17.4935
 BKP  O3G  O  O2    0  -0.685   6.2679  19.8251  -15.8554
 BKP  O4A  O  O     0  -0.685   7.1235  22.1473  -15.0827
 BKP  O4B  O  OH1   0  -0.715   5.7073  20.5231  -13.5773
 BKP  O4G  O  OH1   0  -0.712   4.5860  21.6305  -15.4797
 BKP  H1   H  HOH1  0   0.519   6.0819  16.4661  -13.8942
 BKP  H2   H  HOH1  0   0.508   7.7181  13.1455  -15.8155
 BKP  H3   H  HCH2  0   0.232   4.0933  14.0635  -16.4338
 BKP  H4   H  HCH2  0   0.289   3.9503  12.4325  -17.0970
 BKP  H5   H  HCH1  0   0.283   2.9605  13.3622  -19.1896
 BKP  H6   H  HCH1  0   0.265   3.9296  15.8662  -18.5534
 BKP  H7   H  HOH1  0   0.460   2.1873  16.5750  -19.9350
 BKP  H8   H  HCH1  0   0.235   2.7138  15.9650  -16.4793
 BKP  H9   H  HOH1  0   0.470   1.2833  17.6261  -16.8210
 BKP  H10  H  HCH1  0   0.258   0.2367  15.0352  -17.9947
 BKP  H11  H  HCR5  0   0.291   2.1480  14.6973  -14.6785
 BKP  H12  H  HNH2  0   0.414  -5.1659  14.4327  -16.3115
 BKP  H13  H  HNH2  0   0.416  -4.1755  14.6567  -17.6984
 BKP  H14  H  HNR6  0   0.441  -1.8863  14.6679  -17.5111
 BKP  H15  H  HOH1  0   0.518   9.4423  19.1064  -15.0880
 BKP  H16  H  HOH1  0   0.513   5.7985  21.1226  -12.8231
 BKP  H17  H  HOH1  0   0.511   4.5865  22.1921  -16.2681

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
 BKP  O3'  C3'  single    1.403  0.020  1.403
 BKP  O1A  PA   double    1.466  0.020  1.466
 BKP  N2   C2   single    1.337  0.020  1.337
 BKP  O2G  PG   double    1.463  0.020  1.463
 BKP  O2'  C2'  single    1.390  0.020  1.390
 BKP  C3'  C4'  single    1.526  0.020  1.526
 BKP  C3'  C2'  single    1.527  0.020  1.527
 BKP  C4'  O4'  single    1.428  0.020  1.428
 BKP  C4'  C5'  single    1.521  0.020  1.521
 BKP  PA   O5'  single    1.576  0.020  1.576
 BKP  PA   O2A  single    1.585  0.020  1.585
 BKP  PA   O3A  single    1.639  0.020  1.639
 BKP  N3   C2   single    1.369  0.020  1.369
 BKP  N3   C4   single    1.356  0.020  1.356
 BKP  C2   N1   double    1.306  0.020  1.306
 BKP  O5'  C5'  single    1.433  0.020  1.433
 BKP  C2'  C1'  single    1.535  0.020  1.535
 BKP  C1'  O4'  single    1.402  0.020  1.402
 BKP  C1'  N9   single    1.440  0.020  1.440
 BKP  O3B  PG   single    1.619  0.020  1.619
 BKP  O3B  PB   single    1.608  0.020  1.608
 BKP  PG   O1G  single    1.581  0.020  1.581
 BKP  PG   O3G  single    1.601  0.020  1.601
 BKP  O3A  PB   single    1.608  0.020  1.608
 BKP  N1   C6   single    1.374  0.020  1.374
 BKP  C4   N9   aromatic  1.356  0.020  1.356
 BKP  C4   C5   aromatic  1.367  0.020  1.367
 BKP  O1B  PB   double    1.468  0.020  1.468
 BKP  PB   O2B  single    1.576  0.020  1.576
 BKP  N9   C8   aromatic  1.380  0.020  1.380
 BKP  O3G  PD   single    1.633  0.020  1.633
 BKP  O4A  PD   double    1.470  0.020  1.470
 BKP  C6   C5   single    1.447  0.020  1.447
 BKP  C6   O6   double    1.225  0.020  1.225
 BKP  C5   N7   aromatic  1.372  0.020  1.372
 BKP  PD   O4G  single    1.583  0.020  1.583
 BKP  PD   O4B  single    1.581  0.020  1.581
 BKP  C8   N7   aromatic  1.294  0.020  1.294
 BKP  O2B  H1   single    0.850  0.020  0.980
 BKP  O2A  H2   single    0.850  0.020  0.980
 BKP  C5'  H3   single    0.970  0.020  1.090
 BKP  C5'  H4   single    0.970  0.020  1.090
 BKP  C4'  H5   single    0.970  0.020  1.090
 BKP  C3'  H6   single    0.970  0.020  1.090
 BKP  O3'  H7   single    0.850  0.020  0.980
 BKP  C2'  H8   single    0.970  0.020  1.090
 BKP  O2'  H9   single    0.850  0.020  0.980
 BKP  C1'  H10  single    0.970  0.020  1.090
 BKP  C8   H11  single    0.930  0.020  1.080
 BKP  N2   H12  single    0.860  0.020  1.020
 BKP  N2   H13  single    0.860  0.020  1.020
 BKP  N3   H14  single    0.860  0.020  1.020
 BKP  O1G  H15  single    0.850  0.020  0.980
 BKP  O4B  H16  single    0.850  0.020  0.980
 BKP  O4G  H17  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
 BKP  O3A  PB   O3B   98.48  3.000
 BKP  O3A  PB   O2B  104.40  3.000
 BKP  O3B  PB   O2B  101.44  3.000
 BKP  O2B  PB   O1B  119.35  3.000
 BKP  O3A  PB   O1B  113.64  3.000
 BKP  O3B  PB   O1B  116.71  3.000
 BKP  H1   O2B  PB   115.45  3.000
 BKP  PG   O3B  PB   130.00  3.000
 BKP  PA   O3A  PB   125.79  3.000
 BKP  O5'  PA   O2A  103.39  3.000
 BKP  O2A  PA   O1A  118.68  3.000
 BKP  O5'  PA   O1A  114.35  3.000
 BKP  O2A  PA   O3A  104.36  3.000
 BKP  O5'  PA   O3A  100.31  3.000
 BKP  O1A  PA   O3A  113.57  3.000
 BKP  H2   O2A  PA   115.86  3.000
 BKP  C5'  O5'  PA   124.30  3.000
 BKP  H4   C5'  H3   107.99  3.000
 BKP  H4   C5'  C4'  110.14  3.000
 BKP  H3   C5'  C4'  110.86  3.000
 BKP  H4   C5'  O5'  108.74  3.000
 BKP  H3   C5'  O5'  111.51  3.000
 BKP  C4'  C5'  O5'  107.59  3.000
 BKP  H5   C4'  C3'  110.68  3.000
 BKP  H5   C4'  O4'  109.18  3.000
 BKP  C3'  C4'  O4'  106.27  3.000
 BKP  H5   C4'  C5'  109.14  3.000
 BKP  O4'  C4'  C5'  107.23  3.000
 BKP  C3'  C4'  C5'  114.16  3.000
 BKP  C1'  O4'  C4'  110.31  3.000
 BKP  H6   C3'  C2'  111.75  3.000
 BKP  H6   C3'  O3'  111.71  3.000
 BKP  C2'  C3'  O3'  111.44  3.000
 BKP  H6   C3'  C4'  112.44  3.000
 BKP  C2'  C3'  C4'  101.23  3.000
 BKP  O3'  C3'  C4'  107.78  3.000
 BKP  H7   O3'  C3'  108.75  3.000
 BKP  H8   C2'  C1'  109.61  3.000
 BKP  H8   C2'  O2'  111.52  3.000
 BKP  C1'  C2'  O2'  114.08  3.000
 BKP  H8   C2'  C3'  108.61  3.000
 BKP  C1'  C2'  C3'  100.46  3.000
 BKP  O2'  C2'  C3'  111.95  3.000
 BKP  H9   O2'  C2'  109.47  3.000
 BKP  H10  C1'  N9   107.42  3.000
 BKP  H10  C1'  C2'  109.01  3.000
 BKP  N9   C1'  C2'  114.22  3.000
 BKP  H10  C1'  O4'  111.13  3.000
 BKP  N9   C1'  O4'  109.47  3.000
 BKP  C2'  C1'  O4'  105.63  3.000
 BKP  C4   N9   C8   105.11  3.000
 BKP  C8   N9   C1'  126.96  3.000
 BKP  C4   N9   C1'  127.79  3.000
 BKP  H11  C8   N7   125.45  3.000
 BKP  H11  C8   N9   121.81  3.000
 BKP  N7   C8   N9   112.74  3.000
 BKP  C5   N7   C8   105.39  3.000
 BKP  C4   C5   C6   119.35  3.000
 BKP  C6   C5   N7   131.16  3.000
 BKP  C4   C5   N7   109.50  3.000
 BKP  N1   C6   O6   121.25  3.000
 BKP  O6   C6   C5   123.79  3.000
 BKP  N1   C6   C5   114.96  3.000
 BKP  C2   N1   C6   122.84  3.000
 BKP  N3   C2   N2   116.09  3.000
 BKP  N3   C2   N1   123.87  3.000
 BKP  N2   C2   N1   120.04  3.000
 BKP  H13  N2   H12  117.51  3.000
 BKP  H13  N2   C2   122.18  3.000
 BKP  H12  N2   C2   118.35  3.000
 BKP  H14  N3   C4   122.74  3.000
 BKP  H14  N3   C2   121.05  3.000
 BKP  C4   N3   C2   116.13  3.000
 BKP  N3   C4   C5   122.85  3.000
 BKP  C5   C4   N9   107.26  3.000
 BKP  N3   C4   N9   129.89  3.000
 BKP  O4G  PD   O4B  102.67  3.000
 BKP  O4B  PD   O4A  118.92  3.000
 BKP  O4G  PD   O4A  118.14  3.000
 BKP  O4B  PD   O3G   99.19  3.000
 BKP  O4G  PD   O3G  101.79  3.000
 BKP  O4A  PD   O3G  113.20  3.000
 BKP  O3G  PG   O2G  117.12  3.000
 BKP  O3G  PG   O1G  101.90  3.000
 BKP  O2G  PG   O1G  119.31  3.000
 BKP  O3G  PG   O3B   99.27  3.000
 BKP  O1G  PG   O3B  105.62  3.000
 BKP  O2G  PG   O3B  111.20  3.000
 BKP  H15  O1G  PG   115.23  3.000
 BKP  PG   O3G  PD   126.65  3.000
 BKP  H16  O4B  PD   114.53  3.000
 BKP  H17  O4G  PD   114.90  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
 BKP  CONST_01  N7   C5   C4   N9     0.00   0.0  0
 BKP  CONST_02  C5   N7   C8   N9     0.00   0.0  0
 BKP  CONST_03  C5   C4   N9   C8     0.00   0.0  0
 BKP  CONST_04  C4   C5   N7   C8     0.00   0.0  0
 BKP  CONST_05  C4   N9   C8   N7     0.00   0.0  0
 BKP  CONST_06  N3   C4   N9   C1'    0.00   0.0  0
 BKP  CONST_07  C5   C4   N9   C1'  180.00   0.0  0
 BKP  CONST_08  N7   C8   N9   C1'  180.00   0.0  0
 BKP  CONST_09  N3   C2   N1   C6     0.00   0.0  0
 BKP  CONST_10  C4   N3   C2   N1     0.00   0.0  0
 BKP  CONST_11  N2   C2   N1   C6   180.00   0.0  0
 BKP  CONST_12  C4   N3   C2   N2   180.00   0.0  0
 BKP  CONST_13  H11  C8   N9   C1'    0.00   0.0  0
 BKP  CONST_14  H14  N3   C2   N1   180.00   0.0  0
 BKP  CONST_15  H12  N2   C2   N1     0.00   0.0  0
 BKP  CONST_16  H13  N2   C2   N1   180.00   0.0  0
 BKP  Var_01    C4'  C5'  O5'  PA   142.63  30.0  3
 BKP  Var_02    O2G  PG   O3B  PB   151.62  30.0  3
 BKP  Var_03    O1A  PA   O3A  PB   -68.08  30.0  2
 BKP  Var_04    O4A  PD   O3G  PG    21.74  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
 BKP  chir_03  C4'  C3'  O4'  C5'  positiv
 BKP  chir_04  C3'  O3'  C2'  C4'  negativ
 BKP  chir_05  C2'  O2'  C1'  C3'  negativ
 BKP  chir_06  C1'  O4'  N9   C2'  negativ
 BKP  chir_07  PB   O3A  O1B  O2B  both
 BKP  chir_08  PA   O2A  O5'  O1A  both
 BKP  chir_09  PG   O1G  O3B  O2G  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
 BKP  plan-1  C1'  0.020
 BKP  plan-1  N9   0.020
 BKP  plan-1  C8   0.020
 BKP  plan-1  N7   0.020
 BKP  plan-1  C5   0.020
 BKP  plan-1  C6   0.020
 BKP  plan-1  O6   0.020
 BKP  plan-1  N1   0.020
 BKP  plan-1  C2   0.020
 BKP  plan-1  N2   0.020
 BKP  plan-1  N3   0.020
 BKP  plan-1  C4   0.020
 BKP  plan-1  H11  0.020
 BKP  plan-1  H12  0.020
 BKP  plan-1  H13  0.020
 BKP  plan-1  H14  0.020

