# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 13:40:08 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  50  34  .  2022-09-16  2022-09-16
;
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   0.505  -13.8059  22.7214  34.5590
 6WI  C5    C  CR56   0  -0.097  -12.7653  22.1441  33.8575
 6WI  C6    C  CR6    0   0.500  -11.6676  22.9624  33.4627
 6WI  C8    C  CR15   0   0.088  -14.1409  20.5806  34.2280
 6WI  N1    N  NR16   0  -0.728  -11.8578  24.2834  33.8937
 6WI  N3    N  N      0  -0.512  -13.9432  23.9980  34.9408
 6WI  CBD   C  C      0   0.390  -11.9531  14.9360  40.0346
 6WI  OBG   O  OC    -1  -0.590  -11.3113  15.9708  39.8030
 6WI  CBC   C  CH1    0  -0.104  -13.4740  15.0765  40.2885
 6WI  OBD   O  OH1    0  -0.695  -14.0226  13.8140  40.5619
 6WI  CBE   C  CH2    0  -0.165  -14.1686  15.7462  39.1176
 6WI  O3B   O  O2     0  -0.617  -13.8907  15.0453  37.9185
 6WI  PB    P  P      0   1.337  -15.0782  14.7190  36.8428
 6WI  O2B   O  OP    -1  -0.795  -16.2541  14.1058  37.5351
 6WI  O1B   O  O      0  -0.786  -14.4158  14.0397  35.6880
 6WI  O3A   O  O2     0  -0.762  -15.4270  16.2849  36.4390
 6WI  PA    P  P      0   1.362  -16.4644  16.8798  35.3131
 6WI  O2A   O  OP    -1  -0.793  -17.8459  16.3638  35.5638
 6WI  O1A   O  O      0  -0.781  -15.8421  16.8208  33.9557
 6WI  C5'   C  CH2    0  -0.168  -16.8205  18.9057  37.0096
 6WI  C4'   C  CH1    0  -0.024  -17.0494  20.4031  36.9913
 6WI  O4'   O  O2     0  -0.491  -15.8307  21.0978  36.7189
 6WI  C3'   C  CH1    0  -0.044  -18.0588  20.9056  35.9493
 6WI  O3'   O  OH1    0  -0.666  -18.7017  22.0841  36.3672
 6WI  C2'   C  CH1    0  -0.020  -17.1423  21.2715  34.7823
 6WI  O2'   O  OH1    0  -0.654  -17.6137  22.2371  33.8936
 6WI  C1'   C  CH1    0   0.207  -15.9242  21.8212  35.5250
 6WI  N9    N  NR5    0  -0.543  -14.6913  21.7113  34.7880
 6WI  C2    C  CR6    0   0.690  -12.9352  24.7565  34.5874
 6WI  O6    O  O      0  -0.465  -10.6655  22.6535  32.8415
 6WI  N7    N  N      0  -0.442  -12.9961  20.8056  33.6630
 6WI  H8    H  HCR5   0   0.291  -14.6354  19.6220  34.2767
 6WI  HN1   H  HNR6   0   0.424  -11.1108  24.9260  33.6606
 6WI  HN21  H  HNH2   0   0.411  -13.7669  26.4379  35.3214
 6WI  HN22  H  HNH2   0   0.414  -12.2775  26.7012  34.5201
 6WI  HBC   H  HCH1   0   0.193  -13.6068  15.7474  41.1521
 6WI  HBF   H  HCH2   0   0.199  -13.8127  16.7774  39.0333
 6WI  HBE   H  HCH2   0   0.206  -15.2446  15.7933  39.3162
 6WI  H5''  H  HCH2   0   0.212  -17.7629  18.4252  37.2958
 6WI  H5'   H  HCH2   0   0.223  -16.0879  18.6699  37.7902
 6WI  H4'   H  HCH1   0   0.252  -17.3913  20.6767  37.9970
 6WI  H3'   H  HCH1   0   0.247  -18.7818  20.1241  35.6836
 6WI  HO3'  H  HOH1   0   0.453  -19.2373  21.8806  37.1403
 6WI  H2'   H  HCH1   0   0.252  -16.8712  20.3448  34.2663
 6WI  HO2'  H  HOH1   0   0.459  -18.2665  21.8318  33.3146
 6WI  H1'   H  HCH1   0   0.253  -16.0615  22.8906  35.7201
 6WI  N2    N  NH2    0  -0.831  -12.9211  26.0507  34.9384
 6WI  OBF   O  O      0  -0.605  -11.5231  13.7617  40.1005
 6WI  O5'   O  O2     0  -0.616  -16.3675  18.4649  35.7528
 6WI  HBD   H  HOH1   0   0.423  -13.2431  13.2347  40.4658

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    1.219  0.020  1.219
 6WI  C6   C5    single    1.425  0.020  1.425
 6WI  C6   N1    single    1.402  0.020  1.402
 6WI  N7   C5    aromatic  1.372  0.020  1.372
 6WI  N7   C8    aromatic  1.296  0.020  1.296
 6WI  C5   C4    aromatic  1.381  0.020  1.381
 6WI  N1   C2    single    1.366  0.020  1.366
 6WI  O1A  PA    deloc     1.494  0.020  1.494
 6WI  C8   N9    aromatic  1.377  0.020  1.377
 6WI  O2'  C2'   single    1.394  0.020  1.394
 6WI  C4   N9    aromatic  1.363  0.020  1.363
 6WI  C4   N3    single    1.340  0.020  1.340
 6WI  C2   N3    double    1.310  0.020  1.310
 6WI  C2   N2    single    1.341  0.020  1.341
 6WI  N9   C1'   single    1.441  0.020  1.441
 6WI  C2'  C1'   single    1.529  0.020  1.529
 6WI  C2'  C3'   single    1.528  0.020  1.528
 6WI  PA   O5'   single    1.648  0.020  1.648
 6WI  PA   O2A   deloc     1.496  0.020  1.496
 6WI  PA   O3A   single    1.642  0.020  1.642
 6WI  C1'  O4'   single    1.399  0.020  1.399
 6WI  O5'  C5'   single    1.407  0.020  1.407
 6WI  O1B  PB    deloc     1.495  0.020  1.495
 6WI  O3A  PB    single    1.654  0.020  1.654
 6WI  C3'  O3'   single    1.406  0.020  1.406
 6WI  C3'  C4'   single    1.535  0.020  1.535
 6WI  O4'  C4'   single    1.429  0.020  1.429
 6WI  PB   O2B   deloc     1.496  0.020  1.496
 6WI  PB   O3B   single    1.635  0.020  1.635
 6WI  C5'  C4'   single    1.515  0.020  1.515
 6WI  O3B  CBE   single    1.416  0.020  1.416
 6WI  CBE  CBC   single    1.517  0.020  1.517
 6WI  CBC  OBD   single    1.403  0.020  1.403
 6WI  CBC  CBD   single    1.548  0.020  1.548
 6WI  CBD  OBF   deloc     1.252  0.020  1.252
 6WI  CBD  OBG   deloc     1.239  0.020  1.239
 6WI  C8   H8    single    0.930  0.020  1.080
 6WI  N1   HN1   single    0.860  0.020  1.020
 6WI  N2   HN21  single    0.890  0.020  1.040
 6WI  N2   HN22  single    0.890  0.020  1.040
 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  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    128.33  3.000
 6WI  N9    C4   C5    105.37  3.000
 6WI  N7    C5   C6    130.58  3.000
 6WI  N7    C5   C4    110.67  3.000
 6WI  C6    C5   C4    118.75  3.000
 6WI  O6    C6   N1    120.46  3.000
 6WI  N1    C6   C5    110.57  3.000
 6WI  O6    C6   C5    128.98  3.000
 6WI  H8    C8   N7    125.32  3.000
 6WI  H8    C8   N9    121.86  3.000
 6WI  N7    C8   N9    112.82  3.000
 6WI  HN1   N1   C2    118.62  3.000
 6WI  HN1   N1   C6    115.27  3.000
 6WI  C2    N1   C6    126.11  3.000
 6WI  C2    N3   C4    113.33  3.000
 6WI  CBC   CBD  OBG   117.61  3.000
 6WI  OBG   CBD  OBF   127.95  3.000
 6WI  CBC   CBD  OBF   114.44  3.000
 6WI  HBC   CBC  CBE   106.32  3.000
 6WI  HBC   CBC  OBD   110.37  3.000
 6WI  CBE   CBC  OBD   111.62  3.000
 6WI  HBC   CBC  CBD   107.60  3.000
 6WI  OBD   CBC  CBD   109.53  3.000
 6WI  CBE   CBC  CBD   111.30  3.000
 6WI  HBD   OBD  CBC   101.68  3.000
 6WI  HBE   CBE  HBF   107.04  3.000
 6WI  HBE   CBE  O3B   111.57  3.000
 6WI  HBF   CBE  O3B   109.72  3.000
 6WI  HBE   CBE  CBC   109.20  3.000
 6WI  HBF   CBE  CBC   109.05  3.000
 6WI  O3B   CBE  CBC   110.19  3.000
 6WI  PB    O3B  CBE   120.88  3.000
 6WI  O3A   PB   O1B   109.58  3.000
 6WI  O3A   PB   O2B   109.58  3.000
 6WI  O1B   PB   O2B   121.31  3.000
 6WI  O2B   PB   O3B   110.38  3.000
 6WI  O3A   PB   O3B    97.17  3.000
 6WI  O1B   PB   O3B   106.09  3.000
 6WI  PA    O3A  PB    130.04  3.000
 6WI  O5'   PA   O1A   104.83  3.000
 6WI  O5'   PA   O2A   109.96  3.000
 6WI  O1A   PA   O2A   121.55  3.000
 6WI  O2A   PA   O3A   110.09  3.000
 6WI  O5'   PA   O3A    97.37  3.000
 6WI  O1A   PA   O3A   110.20  3.000
 6WI  H5'   C5'  H5''  107.13  3.000
 6WI  H5'   C5'  C4'   108.80  3.000
 6WI  H5''  C5'  C4'   107.85  3.000
 6WI  H5'   C5'  O5'   110.71  3.000
 6WI  H5''  C5'  O5'   111.89  3.000
 6WI  C4'   C5'  O5'   110.34  3.000
 6WI  H4'   C4'  C3'   109.62  3.000
 6WI  H4'   C4'  O4'   108.62  3.000
 6WI  C3'   C4'  O4'   105.80  3.000
 6WI  H4'   C4'  C5'   106.41  3.000
 6WI  O4'   C4'  C5'   110.73  3.000
 6WI  C3'   C4'  C5'   115.53  3.000
 6WI  C1'   O4'  C4'   110.92  3.000
 6WI  H3'   C3'  C2'   112.38  3.000
 6WI  H3'   C3'  O3'   111.57  3.000
 6WI  C2'   C3'  O3'   107.49  3.000
 6WI  H3'   C3'  C4'   111.37  3.000
 6WI  O3'   C3'  C4'   111.91  3.000
 6WI  C2'   C3'  C4'   101.68  3.000
 6WI  HO3'  O3'  C3'   108.43  3.000
 6WI  H2'   C2'  C1'   109.63  3.000
 6WI  H2'   C2'  O2'   111.69  3.000
 6WI  C1'   C2'  O2'   109.26  3.000
 6WI  H2'   C2'  C3'   107.80  3.000
 6WI  C1'   C2'  C3'   101.12  3.000
 6WI  O2'   C2'  C3'   116.73  3.000
 6WI  HO2'  O2'  C2'   108.73  3.000
 6WI  H1'   C1'  N9    105.83  3.000
 6WI  H1'   C1'  C2'   109.73  3.000
 6WI  N9    C1'  C2'   113.95  3.000
 6WI  H1'   C1'  O4'   111.17  3.000
 6WI  C2'   C1'  O4'   106.37  3.000
 6WI  N9    C1'  O4'   109.87  3.000
 6WI  C1'   N9   C8    127.80  3.000
 6WI  C1'   N9   C4    125.84  3.000
 6WI  C8    N9   C4    106.31  3.000
 6WI  N3    C2   N2    119.75  3.000
 6WI  N2    C2   N1    117.32  3.000
 6WI  N3    C2   N1    122.91  3.000
 6WI  C8    N7   C5    104.84  3.000
 6WI  HN22  N2   HN21  116.57  3.000
 6WI  HN22  N2   C2    121.46  3.000
 6WI  HN21  N2   C2    117.54  3.000
 6WI  C5'   O5'  PA    121.39  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_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  Var_01    C4'   C5'  O5'  PA   -161.19  30.0  3
 6WI  Var_02    PB    O3B  CBE  CBC   135.55  30.0  1
 6WI  Var_03    O1B   PB   O3B  CBE   177.27  30.0  1
 6WI  Var_04    O3A   PB   O3B  CBE    64.46  30.0  1
 6WI  Var_05    O2B   PB   O3B  CBE   -49.56  30.0  1
 6WI  Var_06    PA    O3A  PB   O3B   175.32  30.0  2
 6WI  Var_07    O1A   PA   O3A  PB    -79.93  30.0  1
 6WI  Var_08    O5'   PA   O3A  PB    171.25  30.0  1
 6WI  Var_09    O2A   PA   O3A  PB     56.80  30.0  1
 6WI  Var_10    PA    O3A  PB   O2B   -70.02  30.0  2
 6WI  Var_11    PA    O3A  PB   O1B    65.37  30.0  2
 6WI  Var_12    C5'   O5'  PA   O3A   -64.65  30.0  3
 6WI  Var_13    C5'   O5'  PA   O2A    49.90  30.0  3
 6WI  Var_14    C5'   O5'  PA   O1A  -177.89  30.0  3
 6WI  Var_15    HBF   CBE  O3B  PB   -104.37  30.0  3
 6WI  Var_16    HBE   CBE  O3B  PB     14.08  30.0  3
 6WI  Var_17    H5''  C5'  O5'  PA    -41.11  30.0  3
 6WI  Var_18    H5'   C5'  O5'  PA     78.31  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

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  OBF   0.020

