# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul 10 07:51:11 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxo-2-sulfanylethyl)pyridin-4-yl]oxy}phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)nc(CC(S)=O)c(C)c1O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N
#
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
 ZGP  ZGP  5'-O-[(R)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxo-2-sulfanylethyl)pyridin-4-yl]oxy}phosphoryl]guanosine  ligand  59  37  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ZGP
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
 ZGP  O6   O  O      0  -0.477  -3.4149  -4.3067  -0.2055
 ZGP  C6   C  CR6    0   0.497  -3.6206  -3.1322  -0.4647
 ZGP  N1   N  NR16   0  -0.726  -4.5594  -2.7739  -1.4409
 ZGP  C2   C  CR6    0   0.682  -4.8760  -1.5032  -1.8259
 ZGP  N2   N  NH2    0  -0.833  -5.8306  -1.3714  -2.7625
 ZGP  N3   N  N      0  -0.509  -4.3232  -0.4402  -1.2998
 ZGP  C4   C  CR56   0   0.503  -3.4198  -0.7287  -0.3525
 ZGP  C5   C  CR56   0  -0.092  -3.0213  -1.9719   0.1026
 ZGP  N7   N  N      0  -0.448  -2.0598  -1.8467   1.0725
 ZGP  C8   C  CR15   0   0.083  -1.8843  -0.5678   1.2063
 ZGP  N9   N  NR5    0  -0.543  -2.6855   0.1660   0.3629
 ZGP  C1'  C  CH1    0   0.226  -2.7806   1.6005   0.2739
 ZGP  O4'  O  O2     0  -0.484  -1.4972   2.1528   0.2284
 ZGP  C2'  C  CH1    0  -0.047  -3.4645   2.2543   1.4725
 ZGP  O2'  O  OH1    0  -0.653  -4.8510   2.1735   1.3344
 ZGP  C3'  C  CH1    0  -0.038  -2.8834   3.6680   1.3948
 ZGP  O3'  O  OH1    0  -0.669  -3.5049   4.4099   0.3767
 ZGP  C4'  C  CH1    0  -0.022  -1.4458   3.3678   0.9823
 ZGP  C5'  C  CH2    0  -0.170  -0.5382   3.2225   2.1897
 ZGP  O5'  O  O2     0  -0.604   0.7984   2.9772   1.8117
 ZGP  PBK  P  P      0   1.398   1.5218   1.5199   1.9343
 ZGP  OAJ  O  OP    -1  -0.761   0.7137   0.6194   2.8157
 ZGP  OAG  O  O      0  -0.765   2.9745   1.7630   2.1601
 ZGP  OAT  O  O2     0  -0.623   1.3348   0.9798   0.3625
 ZGP  CBA  C  C      0   0.438   2.3766   0.5361  -0.3699
 ZGP  CAX  C  C      0  -0.066   2.5940  -0.8450  -0.4768
 ZGP  CAA  C  CH3    0  -0.761   1.7288  -1.8438   0.2357
 ZGP  CAY  C  C      0  -0.166   3.1754   1.4452  -1.0580
 ZGP  CAB  C  CH3    0  -0.805   2.9569   2.9273  -1.0040
 ZGP  CBB  C  C      0   0.396   4.2081   0.8955  -1.8235
 ZGP  OAE  O  OH1    0  -0.624   5.0663   1.6640  -2.5173
 ZGP  NAR  N  N      0  -0.459   4.4339  -0.3950  -1.9446
 ZGP  CAZ  C  C      0   0.208   3.6432  -1.2438  -1.2952
 ZGP  CAM  C  CH2    0  -0.672   3.9398  -2.7024  -1.4954
 ZGP  CAV  C  C      0   0.238   4.6599  -3.3177  -0.3184
 ZGP  OAD  O  O      0  -0.360   5.3216  -2.7021   0.4703
 ZGP  SAK  S  S2     0  -0.211   4.4512  -5.0837  -0.2509
 ZGP  H1   H  HNR6   0   0.422  -5.0428  -3.5435  -1.8856
 ZGP  H2   H  HNH2   0   0.412  -6.0769  -2.1506  -3.3498
 ZGP  H3   H  HNH2   0   0.410  -5.9367  -0.4616  -3.1791
 ZGP  H4   H  HCR5   0   0.306  -1.1668  -0.1014   1.8687
 ZGP  H5   H  HCH1   0   0.253  -3.3478   1.8128  -0.6396
 ZGP  H6   H  HCH1   0   0.247  -3.1194   1.7744   2.3982
 ZGP  H7   H  HOH1   0   0.468  -5.2584   2.3297   2.1922
 ZGP  H8   H  HCH1   0   0.248  -2.9310   4.1890   2.3605
 ZGP  H9   H  HOH1   0   0.448  -4.4583   4.2957   0.4674
 ZGP  H10  H  HCH1   0   0.255  -1.0543   4.1598   0.3362
 ZGP  H11  H  HCH2   0   0.233  -0.5564   4.1680   2.7389
 ZGP  H12  H  HCH2   0   0.218  -0.9117   2.4473   2.8646
 ZGP  H15  H  HCH3   0   0.243   1.1425  -2.4396  -0.4667
 ZGP  H16  H  HCH3   0   0.234   2.3180  -2.5393   0.8355
 ZGP  H17  H  HCH3   0   0.281   1.0274  -1.3623   0.9105
 ZGP  H18  H  HCH3   0   0.275   3.7108   3.4242  -0.3898
 ZGP  H19  H  HCH3   0   0.264   2.9901   3.3741  -2.0004
 ZGP  H20  H  HCH3   0   0.271   1.9862   3.1752  -0.5852
 ZGP  H21  H  HCH2   0   0.309   3.0383  -3.2754  -1.7262
 ZGP  H22  H  HCH2   0   0.348   4.6062  -2.8179  -2.3555
 ZGP  H23  H  HSH1   0   0.274   5.2657  -5.3022   0.7886
 ZGP  H14  H  HOH1   0   0.499   4.8849   2.6006  -2.3806

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
 ZGP  N2   C2   single    1.344  0.020  1.344
 ZGP  C2   N1   single    1.365  0.020  1.365
 ZGP  C2   N3   double    1.309  0.020  1.309
 ZGP  N1   C6   single    1.401  0.020  1.401
 ZGP  N3   C4   single    1.340  0.020  1.340
 ZGP  O2'  C2'  single    1.396  0.020  1.396
 ZGP  C6   O6   double    1.220  0.020  1.220
 ZGP  C6   C5   single    1.424  0.020  1.424
 ZGP  C4   C5   aromatic  1.383  0.020  1.383
 ZGP  C4   N9   aromatic  1.361  0.020  1.361
 ZGP  C1'  C2'  single    1.527  0.020  1.527
 ZGP  C1'  N9   single    1.440  0.020  1.440
 ZGP  C1'  O4'  single    1.398  0.020  1.398
 ZGP  C2'  C3'  single    1.530  0.020  1.530
 ZGP  C5   N7   aromatic  1.371  0.020  1.371
 ZGP  N9   C8   aromatic  1.375  0.020  1.375
 ZGP  O4'  C4'  single    1.431  0.020  1.431
 ZGP  O3'  C3'  single    1.405  0.020  1.405
 ZGP  C4'  C3'  single    1.525  0.020  1.525
 ZGP  C4'  C5'  single    1.517  0.020  1.517
 ZGP  N7   C8   aromatic  1.298  0.020  1.298
 ZGP  C5'  O5'  single    1.411  0.020  1.411
 ZGP  O5'  PBK  single    1.632  0.020  1.632
 ZGP  OAG  PBK  deloc     1.490  0.020  1.490
 ZGP  PBK  OAJ  deloc     1.497  0.020  1.497
 ZGP  PBK  OAT  single    1.673  0.020  1.673
 ZGP  OAE  CBB  single    1.345  0.020  1.345
 ZGP  CAB  CAY  single    1.499  0.020  1.499
 ZGP  CBB  CAY  aromatic  1.398  0.020  1.398
 ZGP  CBB  NAR  aromatic  1.316  0.020  1.316
 ZGP  CAY  CBA  aromatic  1.392  0.020  1.392
 ZGP  NAR  CAZ  aromatic  1.329  0.020  1.329
 ZGP  CBA  OAT  single    1.349  0.020  1.349
 ZGP  CBA  CAX  aromatic  1.402  0.020  1.402
 ZGP  CAZ  CAX  aromatic  1.389  0.020  1.389
 ZGP  CAZ  CAM  single    1.502  0.020  1.502
 ZGP  CAX  CAA  single    1.501  0.020  1.501
 ZGP  CAM  CAV  single    1.511  0.020  1.511
 ZGP  CAV  OAD  double    1.200  0.020  1.200
 ZGP  CAV  SAK  single    1.780  0.020  1.780
 ZGP  N1   H1   single    0.860  0.020  1.020
 ZGP  N2   H2   single    0.890  0.020  1.040
 ZGP  N2   H3   single    0.890  0.020  1.040
 ZGP  C8   H4   single    0.930  0.020  1.080
 ZGP  C1'  H5   single    0.970  0.020  1.090
 ZGP  C2'  H6   single    0.970  0.020  1.090
 ZGP  O2'  H7   single    0.850  0.020  0.980
 ZGP  C3'  H8   single    0.970  0.020  1.090
 ZGP  O3'  H9   single    0.850  0.020  0.980
 ZGP  C4'  H10  single    0.970  0.020  1.090
 ZGP  C5'  H11  single    0.970  0.020  1.090
 ZGP  C5'  H12  single    0.970  0.020  1.090
 ZGP  CAA  H15  single    0.970  0.020  1.090
 ZGP  CAA  H16  single    0.970  0.020  1.090
 ZGP  CAA  H17  single    0.970  0.020  1.090
 ZGP  CAB  H18  single    0.970  0.020  1.090
 ZGP  CAB  H19  single    0.970  0.020  1.090
 ZGP  CAB  H20  single    0.970  0.020  1.090
 ZGP  CAM  H21  single    0.970  0.020  1.090
 ZGP  CAM  H22  single    0.970  0.020  1.090
 ZGP  SAK  H23  single    1.200  0.020  1.300
 ZGP  OAE  H14  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
 ZGP  C5   C6   N1   110.57  3.000
 ZGP  C5   C6   O6   128.96  3.000
 ZGP  N1   C6   O6   120.48  3.000
 ZGP  H1   N1   C2   118.25  3.000
 ZGP  H1   N1   C6   115.59  3.000
 ZGP  C2   N1   C6   126.16  3.000
 ZGP  N3   C2   N2   120.04  3.000
 ZGP  N3   C2   N1   123.02  3.000
 ZGP  N2   C2   N1   116.91  3.000
 ZGP  H3   N2   H2   115.64  3.000
 ZGP  H3   N2   C2   116.88  3.000
 ZGP  H2   N2   C2   120.31  3.000
 ZGP  C4   N3   C2   113.20  3.000
 ZGP  N9   C4   C5   105.23  3.000
 ZGP  N9   C4   N3   126.42  3.000
 ZGP  C5   C4   N3   128.35  3.000
 ZGP  N7   C5   C4   110.66  3.000
 ZGP  N7   C5   C6   130.64  3.000
 ZGP  C4   C5   C6   118.71  3.000
 ZGP  C8   N7   C5   104.93  3.000
 ZGP  H4   C8   N9   122.12  3.000
 ZGP  H4   C8   N7   125.27  3.000
 ZGP  N9   C8   N7   112.56  3.000
 ZGP  C1'  N9   C8   127.42  3.000
 ZGP  C8   N9   C4   106.62  3.000
 ZGP  C1'  N9   C4   125.92  3.000
 ZGP  H5   C1'  C2'  109.85  3.000
 ZGP  H5   C1'  O4'  111.81  3.000
 ZGP  C2'  C1'  O4'  105.52  3.000
 ZGP  H5   C1'  N9   106.18  3.000
 ZGP  O4'  C1'  N9   109.57  3.000
 ZGP  C2'  C1'  N9   114.05  3.000
 ZGP  C4'  O4'  C1'  110.57  3.000
 ZGP  H6   C2'  C3'  109.09  3.000
 ZGP  H6   C2'  O2'  111.73  3.000
 ZGP  C3'  C2'  O2'  115.19  3.000
 ZGP  H6   C2'  C1'  109.50  3.000
 ZGP  C3'  C2'  C1'  100.70  3.000
 ZGP  O2'  C2'  C1'  110.03  3.000
 ZGP  H7   O2'  C2'  108.84  3.000
 ZGP  H8   C3'  C4'  111.84  3.000
 ZGP  H8   C3'  O3'  111.57  3.000
 ZGP  C4'  C3'  O3'  108.96  3.000
 ZGP  H8   C3'  C2'  112.15  3.000
 ZGP  C4'  C3'  C2'  100.94  3.000
 ZGP  O3'  C3'  C2'  110.90  3.000
 ZGP  H9   O3'  C3'  107.86  3.000
 ZGP  H10  C4'  C5'  108.96  3.000
 ZGP  H10  C4'  C3'  110.75  3.000
 ZGP  C5'  C4'  C3'  111.55  3.000
 ZGP  H10  C4'  O4'  108.44  3.000
 ZGP  C5'  C4'  O4'  111.07  3.000
 ZGP  C3'  C4'  O4'  106.01  3.000
 ZGP  H12  C5'  H11  107.29  3.000
 ZGP  H12  C5'  O5'  111.45  3.000
 ZGP  H11  C5'  O5'  107.50  3.000
 ZGP  H12  C5'  C4'  110.78  3.000
 ZGP  H11  C5'  C4'  107.87  3.000
 ZGP  O5'  C5'  C4'  111.73  3.000
 ZGP  PBK  O5'  C5'  123.73  3.000
 ZGP  OAT  PBK  OAG  107.70  3.000
 ZGP  OAT  PBK  OAJ  107.38  3.000
 ZGP  OAG  PBK  OAJ  122.36  3.000
 ZGP  OAT  PBK  O5'   99.69  3.000
 ZGP  OAJ  PBK  O5'  110.01  3.000
 ZGP  OAG  PBK  O5'  107.33  3.000
 ZGP  CBA  OAT  PBK  122.03  3.000
 ZGP  CAY  CBA  CAX  121.10  3.000
 ZGP  CAX  CBA  OAT  119.03  3.000
 ZGP  CAY  CBA  OAT  119.79  3.000
 ZGP  CAZ  CAX  CAA  121.60  3.000
 ZGP  CAA  CAX  CBA  121.99  3.000
 ZGP  CAZ  CAX  CBA  116.41  3.000
 ZGP  H17  CAA  H16  106.85  3.000
 ZGP  H17  CAA  H15  107.15  3.000
 ZGP  H16  CAA  H15  107.20  3.000
 ZGP  H17  CAA  CAX  111.85  3.000
 ZGP  H16  CAA  CAX  111.95  3.000
 ZGP  H15  CAA  CAX  111.54  3.000
 ZGP  CBB  CAY  CAB  121.07  3.000
 ZGP  CBB  CAY  CBA  115.96  3.000
 ZGP  CAB  CAY  CBA  122.97  3.000
 ZGP  H20  CAB  H19  106.60  3.000
 ZGP  H20  CAB  H18  107.23  3.000
 ZGP  H19  CAB  H18  107.81  3.000
 ZGP  H20  CAB  CAY  111.71  3.000
 ZGP  H19  CAB  CAY  111.53  3.000
 ZGP  H18  CAB  CAY  111.68  3.000
 ZGP  NAR  CBB  OAE  113.80  3.000
 ZGP  NAR  CBB  CAY  124.25  3.000
 ZGP  OAE  CBB  CAY  121.95  3.000
 ZGP  H14  OAE  CBB  111.23  3.000
 ZGP  CAZ  NAR  CBB  118.63  3.000
 ZGP  CAM  CAZ  NAR  115.94  3.000
 ZGP  CAM  CAZ  CAX  120.43  3.000
 ZGP  NAR  CAZ  CAX  123.63  3.000
 ZGP  H22  CAM  H21  106.32  3.000
 ZGP  H22  CAM  CAV  106.21  3.000
 ZGP  H21  CAM  CAV  110.13  3.000
 ZGP  H22  CAM  CAZ  109.13  3.000
 ZGP  H21  CAM  CAZ  111.99  3.000
 ZGP  CAV  CAM  CAZ  112.69  3.000
 ZGP  SAK  CAV  OAD  123.30  3.000
 ZGP  SAK  CAV  CAM  112.20  3.000
 ZGP  OAD  CAV  CAM  124.48  3.000
 ZGP  H23  SAK  CAV   96.90  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
 ZGP  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 ZGP  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 ZGP  CONST_03  C8   N9   C4   C5      0.00   0.0  0
 ZGP  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 ZGP  CONST_05  N9   C4   C5   N7      0.00   0.0  0
 ZGP  CONST_06  NAR  CBB  CAY  CBA     0.00   0.0  0
 ZGP  CONST_07  NAR  CAZ  CAX  CBA     0.00   0.0  0
 ZGP  CONST_08  CBB  CAY  CBA  CAX     0.00   0.0  0
 ZGP  CONST_09  CBB  NAR  CAZ  CAX     0.00   0.0  0
 ZGP  CONST_10  CAZ  NAR  CBB  CAY     0.00   0.0  0
 ZGP  CONST_11  CAZ  CAX  CBA  CAY     0.00   0.0  0
 ZGP  CONST_12  C1'  N9   C4   N3      0.00   0.0  0
 ZGP  CONST_13  C1'  N9   C4   C5    180.00   0.0  0
 ZGP  CONST_14  C1'  N9   C8   N7    180.00   0.0  0
 ZGP  CONST_15  N3   C2   N1   C6      0.00   0.0  0
 ZGP  CONST_16  C4   N3   C2   N1      0.00   0.0  0
 ZGP  CONST_17  C5   C6   N1   C2      0.00   0.0  0
 ZGP  CONST_18  CBB  CAY  CBA  OAT   180.00   0.0  0
 ZGP  CONST_19  CAZ  CAX  CBA  OAT   180.00   0.0  0
 ZGP  CONST_20  OAE  CBB  CAY  CBA   180.00   0.0  0
 ZGP  CONST_21  CAM  CAZ  CAX  CBA   180.00   0.0  0
 ZGP  CONST_22  CAB  CAY  CBA  CAX   180.00   0.0  0
 ZGP  CONST_23  CAY  CBA  CAX  CAA   180.00   0.0  0
 ZGP  CONST_24  NAR  CAZ  CAX  CAA   180.00   0.0  0
 ZGP  CONST_25  NAR  CBB  CAY  CAB   180.00   0.0  0
 ZGP  CONST_26  CAM  CAZ  NAR  CBB   180.00   0.0  0
 ZGP  CONST_27  CAZ  NAR  CBB  OAE   180.00   0.0  0
 ZGP  CONST_28  C2   N1   C6   O6    180.00   0.0  0
 ZGP  CONST_29  N2   C2   N1   C6    180.00   0.0  0
 ZGP  CONST_30  C4   N3   C2   N2    180.00   0.0  0
 ZGP  CONST_31  H4   C8   N9   C4    180.00   0.0  0
 ZGP  CONST_32  H1   N1   C2   N3    180.00   0.0  0
 ZGP  CONST_34  H3   N2   C2   N1    180.00   0.0  0
 ZGP  Var_01    CAY  CBA  OAT  PBK   -84.23  30.0  2
 ZGP  Var_02    CAV  CAM  CAZ  CAX   -77.11  30.0  2
 ZGP  Var_03    H18  CAB  CAY  CBA   105.94  30.0  2
 ZGP  Var_04    H15  CAA  CAX  CBA   113.04  30.0  2
 ZGP  Var_05    OAD  CAV  CAM  CAZ   -23.84  30.0  3
 ZGP  Var_06    OAG  PBK  O5'  C5'  -150.28  30.0  3
 ZGP  Var_07    H11  C5'  O5'  PBK   136.45  30.0  2

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
 ZGP  chir_01  C1'  C2'  N9   O4'  positiv
 ZGP  chir_02  C2'  O2'  C3'  C1'  positiv
 ZGP  chir_03  C3'  O3'  C4'  C2'  positiv
 ZGP  chir_04  C4'  O4'  C3'  C5'  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
 ZGP  plan-1  OAT  0.020
 ZGP  plan-1  CBA  0.020
 ZGP  plan-1  CAX  0.020
 ZGP  plan-1  CAA  0.020
 ZGP  plan-1  CAY  0.020
 ZGP  plan-1  CAB  0.020
 ZGP  plan-1  CBB  0.020
 ZGP  plan-1  OAE  0.020
 ZGP  plan-1  NAR  0.020
 ZGP  plan-1  CAZ  0.020
 ZGP  plan-1  CAM  0.020
 ZGP  plan-2  O6   0.020
 ZGP  plan-2  C6   0.020
 ZGP  plan-2  N1   0.020
 ZGP  plan-2  C2   0.020
 ZGP  plan-2  N2   0.020
 ZGP  plan-2  N3   0.020
 ZGP  plan-2  C4   0.020
 ZGP  plan-2  C5   0.020
 ZGP  plan-2  N7   0.020
 ZGP  plan-2  C8   0.020
 ZGP  plan-2  N9   0.020
 ZGP  plan-2  C1'  0.020
 ZGP  plan-2  H1   0.020
 ZGP  plan-2  H2   0.020
 ZGP  plan-2  H3   0.020
 ZGP  plan-2  H4   0.020
 ZGP  plan-3  CAM  0.020
 ZGP  plan-3  CAV  0.020
 ZGP  plan-3  OAD  0.020
 ZGP  plan-3  SAK  0.020

