# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Sep 20 04:19:55 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: (2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-oxidanyl-propanoic acid
#   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)OC[C@@H](O)C(O)=O)[C@@H](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
 6WI  6WI  "3-(guanosine-5'-diphospho)-D-glycerate"  ligand  53  34  .  2022-09-16  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6WI
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
 6WI  C4    C  CR56  0   0.521  -13.6218  22.0221  35.6450
 6WI  C5    C  CR56  0  -0.084  -12.5057  21.3810  36.1429
 6WI  C6    C  CR6   0   0.510  -11.2409  22.0327  36.0701
 6WI  C8    C  CR15  0   0.080  -14.1407  20.0574  36.4674
 6WI  N1    N  NR16  0  -0.679  -11.3748  23.2876  35.4619
 6WI  N3    N  N     0  -0.522  -13.6969  23.2278  35.0736
 6WI  CBD   C  C     0   0.523  -12.2720  16.8868  36.8951
 6WI  OBG   O  OH1   0  -0.528  -11.8071  17.8798  37.6059
 6WI  CBC   C  CH1   0  -0.078  -12.2389  15.5590  37.6441
 6WI  OBD   O  OH1   0  -0.663  -12.6357  14.5064  36.8195
 6WI  CBE   C  CH2   0  -0.199  -13.1066  15.6735  38.8875
 6WI  O3B   O  O2    0  -0.519  -14.3635  16.2451  38.4923
 6WI  PB    P  P     0   1.386  -15.7541  15.6810  38.9990
 6WI  O2B   O  OH1   0  -0.617  -15.8586  16.2220  40.4869
 6WI  O1B   O  O     0  -0.718  -16.0364  14.2542  38.7862
 6WI  O3A   O  O2    0  -0.704  -16.7385  16.6971  38.2111
 6WI  PA    P  P     0   1.499  -17.1391  16.6396  36.6466
 6WI  O2A   O  OH1   0  -0.738  -18.6121  16.0649  36.7972
 6WI  O1A   O  O     0  -0.615  -16.1916  15.9215  35.7851
 6WI  C5'   C  CH2   0  -0.272  -18.2449  19.0703  36.7660
 6WI  C4'   C  CH1   0   0.003  -18.0649  20.4351  36.1429
 6WI  O4'   O  O2    0  -0.478  -16.8470  21.0315  36.5890
 6WI  C3'   C  CH1   0  -0.085  -18.0269  20.4717  34.6041
 6WI  O3'   O  OH1   0  -0.705  -18.5844  21.6544  34.0961
 6WI  C2'   C  CH1   0   0.010  -16.5209  20.5201  34.3338
 6WI  O2'   O  OH1   0  -0.675  -16.1181  21.1032  33.1362
 6WI  C1'   C  CH1   0   0.177  -16.0415  21.3798  35.5024
 6WI  N9    N  NR5   0  -0.471  -14.6604  21.1637  35.8594
 6WI  C2    C  CR6   0   0.671  -12.5379  23.8408  35.0023
 6WI  O6    O  O     0  -0.558  -10.1551  21.6329  36.4479
 6WI  N7    N  N     0  -0.435  -12.8580  20.1575  36.6531
 6WI  H8    H  HCR5  0   0.281  -14.7465  19.2136  36.7568
 6WI  HN1   H  HNR6  0   0.432  -10.5168  23.8177  35.3676
 6WI  HN21  H  HNH2  0   0.421  -13.3040  25.4792  34.0987
 6WI  HN22  H  HNH2  0   0.407  -11.6030  25.5629  34.3641
 6WI  HBG   H  HOH1  0   0.496  -12.0325  18.7762  37.1907
 6WI  HBC   H  HCH1  0   0.315  -11.2148  15.3706  37.9859
 6WI  HBF   H  HCH2  0   0.259  -12.6487  16.3238  39.6319
 6WI  HBE   H  HCH2  0   0.242  -13.2343  14.6815  39.3262
 6WI  HOB2  H  HOH1  0   0.544  -16.4291  15.6969  41.0663
 6WI  HOA2  H  HOH1  0   0.508  -19.0475  15.8356  35.9630
 6WI  H5''  H  HCH2  0   0.281  -19.2472  18.7084  36.5256
 6WI  H5'   H  HCH2  0   0.231  -18.1575  19.1446  37.8524
 6WI  H4'   H  HCH1  0   0.298  -18.9079  21.0347  36.5061
 6WI  H3'   H  HCH1  0   0.266  -18.4990  19.5821  34.1689
 6WI  HO3'  H  HOH1  0   0.450  -19.5317  21.6449  34.2666
 6WI  H2'   H  HCH1  0   0.282  -16.1192  19.5068  34.4496
 6WI  HO2'  H  HOH1  0   0.458  -16.2347  20.4666  32.4241
 6WI  H1'   H  HCH1  0   0.296  -16.1294  22.4432  35.2520
 6WI  N2    N  NH2   0  -0.843  -12.4673  25.0602  34.4666
 6WI  O5'   O  O2    0  -0.567  -17.2572  18.1715  36.2508
 6WI  HBD   H  HOH1  0   0.454  -13.2183  14.8582  36.1353
 6WI  OBF   O  O     0  -0.549  -12.7142  16.9673  35.7723

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
 6WI  O6   C6    double    1.217  0.020  1.217
 6WI  C6   C5    single    1.425  0.020  1.425
 6WI  C6   N1    single    1.401  0.020  1.401
 6WI  N7   C5    aromatic  1.372  0.020  1.372
 6WI  N7   C8    aromatic  1.300  0.020  1.300
 6WI  C5   C4    aromatic  1.380  0.020  1.380
 6WI  N1   C2    single    1.368  0.020  1.368
 6WI  O1A  PA    double    1.468  0.020  1.468
 6WI  C8   N9    aromatic  1.365  0.020  1.365
 6WI  O2'  C2'   single    1.392  0.020  1.392
 6WI  C4   N9    aromatic  1.364  0.020  1.364
 6WI  C4   N3    single    1.336  0.020  1.336
 6WI  C2   N3    double    1.313  0.020  1.313
 6WI  C2   N2    single    1.334  0.020  1.334
 6WI  N9   C1'   single    1.443  0.020  1.443
 6WI  C2'  C1'   single    1.528  0.020  1.528
 6WI  C2'  C3'   single    1.531  0.020  1.531
 6WI  PA   O5'   single    1.587  0.020  1.587
 6WI  PA   O2A   single    1.588  0.020  1.588
 6WI  PA   O3A   single    1.616  0.020  1.616
 6WI  C1'  O4'   single    1.397  0.020  1.397
 6WI  O5'  C5'   single    1.431  0.020  1.431
 6WI  O1B  PB    double    1.470  0.020  1.470
 6WI  O3A  PB    single    1.619  0.020  1.619
 6WI  C3'  O3'   single    1.403  0.020  1.403
 6WI  C3'  C4'   single    1.540  0.020  1.540
 6WI  O4'  C4'   single    1.428  0.020  1.428
 6WI  PB   O2B   single    1.587  0.020  1.587
 6WI  PB   O3B   single    1.584  0.020  1.584
 6WI  C5'  C4'   single    1.511  0.020  1.511
 6WI  O3B  CBE   single    1.436  0.020  1.436
 6WI  CBE  CBC   single    1.520  0.020  1.520
 6WI  CBC  OBD   single    1.395  0.020  1.395
 6WI  CBC  CBD   single    1.525  0.020  1.525
 6WI  CBD  OBF   double    1.210  0.020  1.210
 6WI  CBD  OBG   single    1.307  0.020  1.307
 6WI  C8   H8    single    0.930  0.020  1.080
 6WI  N1   HN1   single    0.860  0.020  1.020
 6WI  N2   HN21  single    0.860  0.020  1.020
 6WI  N2   HN22  single    0.860  0.020  1.020
 6WI  OBG  HBG   single    0.850  0.020  0.980
 6WI  CBC  HBC   single    0.970  0.020  1.090
 6WI  OBD  HBD   single    0.850  0.020  0.980
 6WI  CBE  HBF   single    0.970  0.020  1.090
 6WI  CBE  HBE   single    0.970  0.020  1.090
 6WI  O2B  HOB2  single    0.850  0.020  0.980
 6WI  O2A  HOA2  single    0.850  0.020  0.980
 6WI  C5'  H5''  single    0.970  0.020  1.090
 6WI  C5'  H5'   single    0.970  0.020  1.090
 6WI  C4'  H4'   single    0.970  0.020  1.090
 6WI  C3'  H3'   single    0.970  0.020  1.090
 6WI  O3'  HO3'  single    0.850  0.020  0.980
 6WI  C2'  H2'   single    0.970  0.020  1.090
 6WI  O2'  HO2'  single    0.850  0.020  0.980
 6WI  C1'  H1'   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
 6WI  N9    C4   N3    126.30  3.000
 6WI  N3    C4   C5    128.23  3.000
 6WI  N9    C4   C5    105.47  3.000
 6WI  N7    C5   C6    130.93  3.000
 6WI  N7    C5   C4    109.93  3.000
 6WI  C6    C5   C4    119.14  3.000
 6WI  O6    C6   N1    120.95  3.000
 6WI  N1    C6   C5    110.31  3.000
 6WI  O6    C6   C5    128.74  3.000
 6WI  H8    C8   N7    125.19  3.000
 6WI  H8    C8   N9    122.67  3.000
 6WI  N7    C8   N9    112.14  3.000
 6WI  HN1   N1   C2    118.52  3.000
 6WI  HN1   N1   C6    115.36  3.000
 6WI  C2    N1   C6    126.13  3.000
 6WI  C2    N3   C4    113.25  3.000
 6WI  CBC   CBD  OBG   112.76  3.000
 6WI  OBG   CBD  OBF   125.76  3.000
 6WI  CBC   CBD  OBF   121.46  3.000
 6WI  HBG   OBG  CBD   111.73  3.000
 6WI  HBC   CBC  CBE   106.93  3.000
 6WI  HBC   CBC  OBD   108.69  3.000
 6WI  CBE   CBC  OBD   112.20  3.000
 6WI  HBC   CBC  CBD   108.86  3.000
 6WI  OBD   CBC  CBD   111.14  3.000
 6WI  CBE   CBC  CBD   108.89  3.000
 6WI  HBD   OBD  CBC   108.41  3.000
 6WI  HBE   CBE  HBF   108.47  3.000
 6WI  HBE   CBE  O3B   111.70  3.000
 6WI  HBF   CBE  O3B   108.56  3.000
 6WI  HBE   CBE  CBC   109.08  3.000
 6WI  HBF   CBE  CBC   111.34  3.000
 6WI  O3B   CBE  CBC   107.72  3.000
 6WI  PB    O3B  CBE   122.59  3.000
 6WI  O3A   PB   O1B   114.96  3.000
 6WI  O3A   PB   O2B   101.67  3.000
 6WI  O1B   PB   O2B   117.01  3.000
 6WI  O2B   PB   O3B   103.67  3.000
 6WI  O3A   PB   O3B    98.89  3.000
 6WI  O1B   PB   O3B   117.90  3.000
 6WI  HOB2  O2B  PB    114.53  3.000
 6WI  PA    O3A  PB    126.83  3.000
 6WI  O5'   PA   O1A   111.95  3.000
 6WI  O5'   PA   O2A   107.70  3.000
 6WI  O1A   PA   O2A   118.50  3.000
 6WI  O2A   PA   O3A    98.69  3.000
 6WI  O5'   PA   O3A   103.04  3.000
 6WI  O1A   PA   O3A   115.18  3.000
 6WI  HOA2  O2A  PA    114.89  3.000
 6WI  H5'   C5'  H5''  108.35  3.000
 6WI  H5'   C5'  C4'   109.82  3.000
 6WI  H5''  C5'  C4'   108.53  3.000
 6WI  H5'   C5'  O5'   110.22  3.000
 6WI  H5''  C5'  O5'   110.23  3.000
 6WI  C4'   C5'  O5'   109.66  3.000
 6WI  H4'   C4'  C3'   109.70  3.000
 6WI  H4'   C4'  O4'   108.90  3.000
 6WI  C3'   C4'  O4'   106.34  3.000
 6WI  H4'   C4'  C5'   105.41  3.000
 6WI  O4'   C4'  C5'   110.49  3.000
 6WI  C3'   C4'  C5'   115.88  3.000
 6WI  C1'   O4'  C4'   110.67  3.000
 6WI  H3'   C3'  C2'   112.27  3.000
 6WI  H3'   C3'  O3'   111.65  3.000
 6WI  C2'   C3'  O3'   107.48  3.000
 6WI  H3'   C3'  C4'   111.50  3.000
 6WI  O3'   C3'  C4'   111.85  3.000
 6WI  C2'   C3'  C4'   101.63  3.000
 6WI  HO3'  O3'  C3'   108.58  3.000
 6WI  H2'   C2'  C1'   108.92  3.000
 6WI  H2'   C2'  O2'   111.85  3.000
 6WI  C1'   C2'  O2'   109.37  3.000
 6WI  H2'   C2'  C3'   108.22  3.000
 6WI  C1'   C2'  C3'   101.03  3.000
 6WI  O2'   C2'  C3'   116.74  3.000
 6WI  HO2'  O2'  C2'   108.94  3.000
 6WI  H1'   C1'  N9    106.18  3.000
 6WI  H1'   C1'  C2'   110.24  3.000
 6WI  N9    C1'  C2'   113.91  3.000
 6WI  H1'   C1'  O4'   111.93  3.000
 6WI  C2'   C1'  O4'   105.89  3.000
 6WI  N9    C1'  O4'   108.79  3.000
 6WI  C1'   N9   C8    126.59  3.000
 6WI  C1'   N9   C4    126.55  3.000
 6WI  C8    N9   C4    106.86  3.000
 6WI  N3    C2   N2    119.69  3.000
 6WI  N2    C2   N1    117.38  3.000
 6WI  N3    C2   N1    122.93  3.000
 6WI  C8    N7   C5    105.61  3.000
 6WI  HN22  N2   HN21  118.03  3.000
 6WI  HN22  N2   C2    122.94  3.000
 6WI  HN21  N2   C2    118.94  3.000
 6WI  C5'   O5'  PA    124.60  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
 6WI  CONST_01  C8    N7   C5   C4      0.00   0.0  0
 6WI  CONST_02  N7    C8   N9   C4      0.00   0.0  0
 6WI  CONST_03  N9    C8   N7   C5      0.00   0.0  0
 6WI  CONST_04  C8    N9   C4   C5      0.00   0.0  0
 6WI  CONST_05  N7    C5   C4   N9      0.00   0.0  0
 6WI  CONST_06  C1'   N9   C4   C5    180.00   0.0  0
 6WI  CONST_07  C1'   N9   C4   N3      0.00   0.0  0
 6WI  CONST_08  N7    C8   N9   C1'   180.00   0.0  0
 6WI  CONST_09  N1    C2   N3   C4      0.00   0.0  0
 6WI  CONST_10  C2    N1   C6   C5      0.00   0.0  0
 6WI  CONST_11  N3    C2   N1   C6      0.00   0.0  0
 6WI  CONST_12  N2    C2   N3   C4    180.00   0.0  0
 6WI  CONST_13  N2    C2   N1   C6    180.00   0.0  0
 6WI  CONST_14  O6    C6   N1   C2    180.00   0.0  0
 6WI  CONST_15  H8    C8   N9   C4    180.00   0.0  0
 6WI  CONST_16  H8    C8   N7   C5    180.00   0.0  0
 6WI  CONST_17  H8    C8   N9   C1'     0.00   0.0  0
 6WI  CONST_18  HN1   N1   C6   C5    180.00   0.0  0
 6WI  CONST_19  HN1   N1   C2   N3    180.00   0.0  0
 6WI  CONST_20  HN21  N2   C2   N1    180.00   0.0  0
 6WI  CONST_21  HN22  N2   C2   N1      0.00   0.0  0
 6WI  CONST_22  HN1   N1   C2   N2      0.00   0.0  0
 6WI  CONST_23  HN21  N2   C2   N3      0.00   0.0  0
 6WI  CONST_24  HN22  N2   C2   N3    180.00   0.0  0
 6WI  CONST_25  HN1   N1   C6   O6      0.00   0.0  0
 6WI  CONST_26  HBG   OBG  CBD  OBF     0.00   0.0  0
 6WI  CONST_27  HBG   OBG  CBD  CBC   180.00   0.0  0
 6WI  Var_01    C4'   C5'  O5'  PA   -178.84  30.0  3
 6WI  Var_02    PB    O3B  CBE  CBC   135.44  30.0  1
 6WI  Var_03    O1B   PB   O3B  CBE   -54.68  30.0  2
 6WI  Var_04    O3A   PB   O3B  CBE  -179.16  30.0  2
 6WI  Var_05    O2B   PB   O3B  CBE    76.44  30.0  2
 6WI  Var_06    PA    O3A  PB   O3B    77.44  30.0  1
 6WI  Var_07    O1A   PA   O3A  PB    -22.60  30.0  2
 6WI  Var_08    O5'   PA   O3A  PB   -144.80  30.0  2
 6WI  Var_09    O2A   PA   O3A  PB    104.64  30.0  2
 6WI  Var_10    PA    O3A  PB   O2B  -176.51  30.0  1
 6WI  Var_11    PA    O3A  PB   O1B   -49.09  30.0  1
 6WI  Var_12    C5'   O5'  PA   O3A   -65.86  30.0  3
 6WI  Var_13    C5'   O5'  PA   O2A    37.82  30.0  3
 6WI  Var_14    C5'   O5'  PA   O1A   169.78  30.0  3
 6WI  Var_15    HBF   CBE  O3B  PB   -103.88  30.0  3
 6WI  Var_16    HBE   CBE  O3B  PB     15.68  30.0  3
 6WI  Var_17    H5''  C5'  O5'  PA    -59.41  30.0  3
 6WI  Var_18    H5'   C5'  O5'  PA     60.14  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
 6WI  chir_01  CBC  CBE  OBD  CBD  negativ
 6WI  chir_04  C4'  C3'  O4'  C5'  positiv
 6WI  chir_05  C3'  O3'  C2'  C4'  negativ
 6WI  chir_06  C2'  O2'  C1'  C3'  negativ
 6WI  chir_07  C1'  O4'  N9   C2'  negativ
 6WI  chir_08  PB   O3A  O2B  O3B  both
 6WI  chir_09  PA   O2A  O5'  O1A  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
 6WI  plan-1  C4    0.020
 6WI  plan-1  C5    0.020
 6WI  plan-1  C6    0.020
 6WI  plan-1  C8    0.020
 6WI  plan-1  N1    0.020
 6WI  plan-1  N3    0.020
 6WI  plan-1  C1'   0.020
 6WI  plan-1  N9    0.020
 6WI  plan-1  C2    0.020
 6WI  plan-1  O6    0.020
 6WI  plan-1  N7    0.020
 6WI  plan-1  H8    0.020
 6WI  plan-1  HN1   0.020
 6WI  plan-1  HN21  0.020
 6WI  plan-1  HN22  0.020
 6WI  plan-1  N2    0.020
 6WI  plan-2  CBD   0.020
 6WI  plan-2  OBG   0.020
 6WI  plan-2  CBC   0.020
 6WI  plan-2  HBG   0.020
 6WI  plan-2  OBF   0.020

