# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 16:45:48 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H]3O
#
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
 G3D  G3D  'guanosine 3'-(dihydrogen phosphate) 5'-(trihydrogen diphosphate)'  ligand  48  32  .  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_G3D
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
 G3D  PB    P  P     0   1.476   6.4236  18.6593  -0.4338
 G3D  O1B   O  O     0  -0.676   7.0025  17.4665   0.1899
 G3D  O2B   O  OH1   0  -0.733   5.4928  19.4670   0.5666
 G3D  O3B   O  OH1   0  -0.718   7.5159  19.6240  -1.0497
 G3D  PA    P  P     0   1.509   4.0297  17.6651  -1.7508
 G3D  O3A   O  O2    0  -0.707   5.4839  18.3696  -1.7335
 G3D  O1A   O  O     0  -0.673   3.6990  16.8463  -0.5782
 G3D  O2A   O  OH1   0  -0.726   3.1472  18.9502  -2.0511
 G3D  O5'   O  O2    0  -0.578   4.0805  16.7961  -3.0762
 G3D  C5'   C  CH2   0  -0.206   4.4465  17.2908  -4.3667
 G3D  C4'   C  CH1   0  -0.002   4.1227  16.2337  -5.3960
 G3D  O4'   O  O2    0  -0.487   4.9027  15.0669  -5.1582
 G3D  C3'   C  CH1   0  -0.074   2.6581  15.7805  -5.4045
 G3D  O3'   O  O2    0  -0.590   2.2655  15.4548  -6.7362
 G3D  C2'   C  CH1   0  -0.005   2.7007  14.4838  -4.6080
 G3D  O2'   O  OH1   0  -0.644   1.6486  13.6331  -4.9221
 G3D  C1'   C  CH1   0   0.185   4.0813  13.9404  -5.0026
 G3D  N9    N  NR5   0  -0.547   4.6687  13.0599  -4.0325
 G3D  C8    C  CR15  0   0.099   4.9688  13.3377  -2.7175
 G3D  N7    N  N     0  -0.439   5.5560  12.3513  -2.1178
 G3D  C5    C  CR56  0  -0.096   5.6600  11.3705  -3.0718
 G3D  C6    C  CR6   0   0.507   6.2250  10.0638  -3.0030
 G3D  O6    O  O     0  -0.471   6.7495   9.5057  -2.0545
 G3D  N1    N  NR16  0  -0.728   6.1166   9.4159  -4.2406
 G3D  C2    C  CR6   0   0.696   5.5580   9.9319  -5.3745
 G3D  N2    N  NH2   0  -0.831   5.5841   9.1647  -6.4718
 G3D  N3    N  N     0  -0.514   5.0388  11.1340  -5.4296
 G3D  C4    C  CR56  0   0.511   5.1197  11.7957  -4.2697
 G3D  P1    P  P     0   1.455   1.3492  16.3854  -7.6423
 G3D  O4P   O  OH1   0  -0.747   2.0922  17.7951  -7.5070
 G3D  O5P   O  OH1   0  -0.742   0.0203  16.4787  -6.7611
 G3D  O6P   O  O     0  -0.692   1.1893  15.8609  -9.0097
 G3D  HOB2  H  HOH1  0   0.504   5.1498  20.3241   0.2784
 G3D  HOB3  H  HOH1  0   0.507   7.2150  20.4131  -1.5210
 G3D  HOA2  H  HOH1  0   0.510   2.1953  18.8272  -1.9282
 G3D  H5'1  H  HCH2  0   0.260   3.8980  18.2040  -4.6098
 G3D  H5'2  H  HCH2  0   0.275   5.5150  17.5131  -4.3889
 G3D  H4'   H  HCH1  0   0.286   4.3890  16.6576  -6.3690
 G3D  H3'   H  HCH1  0   0.300   1.9849  16.5163  -4.9587
 G3D  H2'   H  HCH1  0   0.265   2.7060  14.7510  -3.5454
 G3D  HO2'  H  HOH1  0   0.467   1.5000  13.0384  -4.1810
 G3D  H1'   H  HCH1  0   0.268   4.0030  13.3644  -5.9312
 G3D  H8    H  HCR5  0   0.284   4.7326  14.2897  -2.2667
 G3D  HN1   H  HNR6  0   0.426   6.5055   8.4820  -4.2796
 G3D  HN21  H  HNH2  0   0.414   5.0426   9.4640  -7.2651
 G3D  HN22  H  HNH2  0   0.416   5.7920   8.1824  -6.4150
 G3D  HO4P  H  HOH1  0   0.503   1.7534  18.4950  -8.0813
 G3D  HO5P  H  HOH1  0   0.502  -0.6986  16.9878  -7.1590

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
 G3D  PB   O1B   double    1.465  0.020  1.465
 G3D  PB   O2B   single    1.587  0.020  1.587
 G3D  PB   O3B   single    1.582  0.020  1.582
 G3D  PB   O3A   single    1.630  0.020  1.630
 G3D  O2B  HOB2  single    0.850  0.020  0.980
 G3D  O3B  HOB3  single    0.850  0.020  0.980
 G3D  PA   O3A   single    1.616  0.020  1.616
 G3D  PA   O1A   double    1.468  0.020  1.468
 G3D  PA   O2A   single    1.588  0.020  1.588
 G3D  PA   O5'   single    1.586  0.020  1.586
 G3D  O2A  HOA2  single    0.850  0.020  0.980
 G3D  O5'  C5'   single    1.430  0.020  1.430
 G3D  C5'  C4'   single    1.510  0.020  1.510
 G3D  C5'  H5'1  single    0.970  0.020  1.090
 G3D  C5'  H5'2  single    0.970  0.020  1.090
 G3D  C4'  O4'   single    1.424  0.020  1.424
 G3D  C4'  C3'   single    1.533  0.020  1.533
 G3D  C4'  H4'   single    0.970  0.020  1.090
 G3D  O4'  C1'   single    1.403  0.020  1.403
 G3D  C3'  O3'   single    1.426  0.020  1.426
 G3D  C3'  C2'   single    1.522  0.020  1.522
 G3D  C3'  H3'   single    0.970  0.020  1.090
 G3D  O3'  P1    single    1.590  0.020  1.590
 G3D  C2'  O2'   single    1.389  0.020  1.389
 G3D  C2'  C1'   single    1.535  0.020  1.535
 G3D  C2'  H2'   single    0.970  0.020  1.090
 G3D  O2'  HO2'  single    0.850  0.020  0.980
 G3D  C1'  N9    single    1.436  0.020  1.436
 G3D  C1'  H1'   single    0.970  0.020  1.090
 G3D  N9   C8    aromatic  1.377  0.020  1.377
 G3D  N9   C4    aromatic  1.363  0.020  1.363
 G3D  C8   N7    aromatic  1.295  0.020  1.295
 G3D  C8   H8    single    0.930  0.020  1.080
 G3D  N7   C5    aromatic  1.372  0.020  1.372
 G3D  C5   C6    single    1.425  0.020  1.425
 G3D  C5   C4    aromatic  1.381  0.020  1.381
 G3D  C6   O6    double    1.219  0.020  1.219
 G3D  C6   N1    single    1.401  0.020  1.401
 G3D  N1   C2    single    1.365  0.020  1.365
 G3D  N1   HN1   single    0.860  0.020  1.020
 G3D  C2   N2    single    1.339  0.020  1.339
 G3D  C2   N3    double    1.311  0.020  1.311
 G3D  N2   HN21  single    0.890  0.020  1.040
 G3D  N2   HN22  single    0.890  0.020  1.040
 G3D  N3   C4    single    1.338  0.020  1.338
 G3D  P1   O4P   single    1.599  0.020  1.599
 G3D  P1   O5P   single    1.597  0.020  1.597
 G3D  P1   O6P   double    1.473  0.020  1.473
 G3D  O4P  HO4P  single    0.850  0.020  0.980
 G3D  O5P  HO5P  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
 G3D  O3A   PB   O3B   101.30  3.000
 G3D  O3A   PB   O2B   104.77  3.000
 G3D  O3B   PB   O2B   109.88  3.000
 G3D  O3A   PB   O1B   114.99  3.000
 G3D  O3B   PB   O1B   112.91  3.000
 G3D  O2B   PB   O1B   112.19  3.000
 G3D  HOB2  O2B  PB    118.10  3.000
 G3D  HOB3  O3B  PB    118.19  3.000
 G3D  O5'   PA   O2A   107.66  3.000
 G3D  O5'   PA   O1A   111.66  3.000
 G3D  O2A   PA   O1A   118.51  3.000
 G3D  O5'   PA   O3A   102.65  3.000
 G3D  O2A   PA   O3A    98.59  3.000
 G3D  O1A   PA   O3A   115.94  3.000
 G3D  PA    O3A  PB    127.22  3.000
 G3D  HOA2  O2A  PA    114.83  3.000
 G3D  C5'   O5'  PA    124.96  3.000
 G3D  H5'2  C5'  H5'1  108.46  3.000
 G3D  H5'2  C5'  C4'   109.78  3.000
 G3D  H5'1  C5'  C4'   109.01  3.000
 G3D  H5'2  C5'  O5'   109.83  3.000
 G3D  H5'1  C5'  O5'   111.19  3.000
 G3D  C4'   C5'  O5'   108.55  3.000
 G3D  H4'   C4'  C3'   110.00  3.000
 G3D  H4'   C4'  O4'   109.43  3.000
 G3D  C3'   C4'  O4'   106.38  3.000
 G3D  H4'   C4'  C5'   106.42  3.000
 G3D  C3'   C4'  C5'   114.55  3.000
 G3D  O4'   C4'  C5'   110.02  3.000
 G3D  C1'   O4'  C4'   110.85  3.000
 G3D  H3'   C3'  C2'   112.17  3.000
 G3D  H3'   C3'  O3'   111.43  3.000
 G3D  C2'   C3'  O3'   107.56  3.000
 G3D  H3'   C3'  C4'   112.79  3.000
 G3D  C2'   C3'  C4'   102.83  3.000
 G3D  O3'   C3'  C4'   109.62  3.000
 G3D  P1    O3'  C3'   123.87  3.000
 G3D  H2'   C2'  C1'   109.35  3.000
 G3D  H2'   C2'  O2'   111.86  3.000
 G3D  C1'   C2'  O2'   113.97  3.000
 G3D  H2'   C2'  C3'   107.45  3.000
 G3D  C1'   C2'  C3'   101.08  3.000
 G3D  O2'   C2'  C3'   112.47  3.000
 G3D  HO2'  O2'  C2'   108.75  3.000
 G3D  H1'   C1'  N9    106.23  3.000
 G3D  H1'   C1'  C2'   109.86  3.000
 G3D  N9    C1'  C2'   114.29  3.000
 G3D  H1'   C1'  O4'   111.72  3.000
 G3D  N9    C1'  O4'   109.14  3.000
 G3D  C2'   C1'  O4'   105.71  3.000
 G3D  C4    N9   C8    106.33  3.000
 G3D  C4    N9   C1'   125.92  3.000
 G3D  C8    N9   C1'   127.63  3.000
 G3D  H8    C8   N7    125.28  3.000
 G3D  H8    C8   N9    121.93  3.000
 G3D  N7    C8   N9    112.79  3.000
 G3D  C5    N7   C8    104.88  3.000
 G3D  C4    C5   C6    118.63  3.000
 G3D  C4    C5   N7    110.69  3.000
 G3D  C6    C5   N7    130.68  3.000
 G3D  N1    C6   O6    120.59  3.000
 G3D  N1    C6   C5    110.53  3.000
 G3D  O6    C6   C5    128.89  3.000
 G3D  HN1   N1   C2    118.29  3.000
 G3D  HN1   N1   C6    115.52  3.000
 G3D  C2    N1   C6    126.19  3.000
 G3D  N3    C2   N2    119.92  3.000
 G3D  N3    C2   N1    122.93  3.000
 G3D  N2    C2   N1    117.13  3.000
 G3D  HN22  N2   HN21  116.52  3.000
 G3D  HN22  N2   C2    121.16  3.000
 G3D  HN21  N2   C2    117.72  3.000
 G3D  C4    N3   C2    113.16  3.000
 G3D  N3    C4   C5    128.56  3.000
 G3D  N3    C4   N9    126.13  3.000
 G3D  C5    C4   N9    105.31  3.000
 G3D  O6P   P1   O5P   116.27  3.000
 G3D  O6P   P1   O4P   116.28  3.000
 G3D  O5P   P1   O4P   106.76  3.000
 G3D  O6P   P1   O3'   112.54  3.000
 G3D  O5P   P1   O3'   101.49  3.000
 G3D  O4P   P1   O3'   101.54  3.000
 G3D  HO4P  O4P  P1    115.16  3.000
 G3D  HO5P  O5P  P1    114.99  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
 G3D  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 G3D  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 G3D  CONST_03  C5    C4   N9   C8      0.00   0.0  0
 G3D  CONST_04  C4    C5   N7   C8      0.00   0.0  0
 G3D  CONST_05  C4    N9   C8   N7      0.00   0.0  0
 G3D  CONST_06  N7    C8   N9   C1'   180.00   0.0  0
 G3D  CONST_07  C5    C4   N9   C1'   180.00   0.0  0
 G3D  CONST_08  N3    C4   N9   C1'     0.00   0.0  0
 G3D  CONST_09  C2    N1   C6   C5      0.00   0.0  0
 G3D  CONST_10  N3    C2   N1   C6      0.00   0.0  0
 G3D  CONST_11  C4    N3   C2   N1      0.00   0.0  0
 G3D  CONST_12  N2    C2   N1   C6    180.00   0.0  0
 G3D  CONST_13  C2    N1   C6   O6    180.00   0.0  0
 G3D  CONST_14  C4    N3   C2   N2    180.00   0.0  0
 G3D  CONST_15  H8    C8   N9   C1'     0.00   0.0  0
 G3D  CONST_16  HN1   N1   C6   C5    180.00   0.0  0
 G3D  CONST_17  HN21  N2   C2   N1    180.00   0.0  0
 G3D  CONST_18  HN22  N2   C2   N1      0.00   0.0  0
 G3D  Var_01    C4'   C5'  O5'  PA   -169.49  30.0  3
 G3D  Var_02    O4P   P1   O3'  C3'    50.30  30.0  3
 G3D  Var_03    O1A   PA   O3A  PB    -20.10  30.0  1

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
 G3D  chir_02  C4'  C5'  O4'  C3'  negativ
 G3D  chir_03  C3'  O3'  C2'  C4'  negativ
 G3D  chir_04  C2'  O2'  C1'  C3'  negativ
 G3D  chir_05  C1'  O4'  N9   C2'  negativ
 G3D  chir_06  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
 G3D  plan-1  C1'   0.020
 G3D  plan-1  N9    0.020
 G3D  plan-1  C8    0.020
 G3D  plan-1  N7    0.020
 G3D  plan-1  C5    0.020
 G3D  plan-1  C6    0.020
 G3D  plan-1  O6    0.020
 G3D  plan-1  N1    0.020
 G3D  plan-1  C2    0.020
 G3D  plan-1  N2    0.020
 G3D  plan-1  N3    0.020
 G3D  plan-1  C4    0.020
 G3D  plan-1  H8    0.020
 G3D  plan-1  HN1   0.020
 G3D  plan-1  HN21  0.020
 G3D  plan-1  HN22  0.020

