# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 19:30:28 2021
#   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  60  37  .  2022-07-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.473  -1.2344   9.1615   2.2054
 ZGP  C6   C  CR6   0   0.505  -0.1800   8.9131   1.6458
 ZGP  N1   N  NR16  0  -0.727   0.0870   9.4228   0.3684
 ZGP  C2   C  CR6   0   0.686   1.2239   9.2210  -0.3608
 ZGP  N2   N  NH2   0  -0.831   1.2707   9.7761  -1.5802
 ZGP  N3   N  N     0  -0.515   2.2277   8.4964   0.0689
 ZGP  C4   C  CR56  0   0.505   2.0167   7.9804   1.2878
 ZGP  C5   C  CR56  0  -0.087   0.9150   8.1278   2.1092
 ZGP  N7   N  N     0  -0.443   1.0929   7.4432   3.2824
 ZGP  C8   C  CR15  0   0.083   2.2662   6.8983   3.1745
 ZGP  N9   N  NR5   0  -0.532   2.8787   7.1895   1.9791
 ZGP  C1'  C  CR15  0   0.175   4.1810   6.7581   1.4929
 ZGP  O4'  O  O     0  -0.495   4.6053   5.6667   2.2593
 ZGP  C2'  C  CR15  0  -0.045   5.2405   7.8548   1.6470
 ZGP  O2'  O  OH1   0  -0.661   6.1960   7.6553   0.6414
 ZGP  C3'  C  CR15  0  -0.024   5.7782   7.5208   3.0340
 ZGP  O3'  O  OH1   0  -0.671   7.0111   8.1108   3.2915
 ZGP  C4'  C  CR15  0   0.026   5.7986   5.9924   2.9661
 ZGP  C5'  C  CH2   0  -0.237   5.8719   5.2452   4.2745
 ZGP  O5'  O  O2    0  -0.587   4.9092   5.7129   5.2306
 ZGP  PBK  P  P     0   1.500   5.3036   6.7036   6.4125
 ZGP  OAJ  O  OH1   0  -0.706   3.9521   7.4495   6.7497
 ZGP  OAG  O  O     0  -0.682   6.4991   7.5332   6.1434
 ZGP  OAT  O  O2    0  -0.594   5.3932   5.7681   7.7206
 ZGP  CBA  C  CR6   0   0.395   5.9584   4.5116   7.6977
 ZGP  CAX  C  CR6   0  -0.056   7.3148   4.3801   8.0164
 ZGP  CAA  C  CH3   0  -0.751   8.1616   5.5477   8.4293
 ZGP  CAY  C  CR6   0  -0.112   5.1405   3.4305   7.4151
 ZGP  CAB  C  CH3   0  -0.719   3.6717   3.5205   7.1383
 ZGP  CBB  C  CR6   0   0.431   5.7902   2.1895   7.4236
 ZGP  OAE  O  OH1   0  -0.610   5.0626   1.1077   7.1329
 ZGP  NAR  N  N     0  -0.476   7.0634   2.0227   7.6978
 ZGP  CAZ  C  CR6   0   0.240   7.8108   3.0814   7.9995
 ZGP  CAM  C  CH2   0  -0.672   9.2476   2.7922   8.3228
 ZGP  CAV  C  C     0   0.243   9.5543   2.9373   9.7955
 ZGP  OAD  O  O     0  -0.355   8.7270   2.9346  10.6641
 ZGP  SAK  S  S2    0  -0.184  11.2996   3.0801  10.1046
 ZGP  H1   H  HNR6  0   0.426  -0.6448   9.9929  -0.0363
 ZGP  H2   H  HNH2  0   0.413   2.1584   9.7845  -2.0536
 ZGP  H3   H  HNH2  0   0.415   0.6203  10.4972  -1.8431
 ZGP  H4   H  HCR5  0   0.287   2.7309   6.2733   3.9191
 ZGP  H5   H  HCR5  0   0.285   4.0585   6.4731   0.4441
 ZGP  H6   H  HCR5  0   0.268   4.7987   8.8569   1.5991
 ZGP  H7   H  HOH1  0   0.461   6.9647   8.2026   0.8359
 ZGP  H8   H  HCR5  0   0.222   5.0133   7.8470   3.7522
 ZGP  H9   H  HOH1  0   0.463   7.1598   8.0639   4.2463
 ZGP  H10  H  HCR5  0   0.255   6.6736   5.6675   2.3887
 ZGP  H11  H  HCH2  0   0.284   5.6643   4.1864   4.1199
 ZGP  H12  H  HCH2  0   0.259   6.8905   5.3250   4.6588
 ZGP  H13  H  HOH1  0   0.514   3.9341   8.3866   6.5099
 ZGP  H15  H  HCH3  0   0.259   8.1283   5.6853   9.5118
 ZGP  H16  H  HCH3  0   0.249   9.2052   5.4062   8.1526
 ZGP  H17  H  HCH3  0   0.265   7.8438   6.4812   7.9756
 ZGP  H18  H  HCH3  0   0.257   3.1295   2.7677   7.7097
 ZGP  H19  H  HCH3  0   0.247   3.2585   4.4890   7.4065
 ZGP  H20  H  HCH3  0   0.257   3.4524   3.3457   6.0838
 ZGP  H21  H  HCH2  0   0.334   9.4725   1.7561   8.0544
 ZGP  H22  H  HCH2  0   0.305   9.9317   3.4128   7.7390
 ZGP  H23  H  HSH1  0   0.258  11.2217   3.0962  11.4406
 ZGP  H14  H  HOH1  0   0.475   5.6294   0.3270   7.1917

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    1.341  0.020  1.341
 ZGP  C2   N1   single    1.366  0.020  1.366
 ZGP  C2   N3   double    1.310  0.020  1.310
 ZGP  N1   C6   single    1.401  0.020  1.401
 ZGP  N3   C4   single    1.340  0.020  1.340
 ZGP  O2'  C2'  single    1.401  0.020  1.401
 ZGP  C6   O6   double    1.219  0.020  1.219
 ZGP  C6   C5   single    1.425  0.020  1.425
 ZGP  C4   C5   aromatic  1.382  0.020  1.382
 ZGP  C4   N9   aromatic  1.359  0.020  1.359
 ZGP  C1'  C2'  single    1.533  0.020  1.533
 ZGP  C1'  N9   single    1.456  0.020  1.456
 ZGP  C1'  O4'  single    1.399  0.020  1.399
 ZGP  C2'  C3'  single    1.525  0.020  1.525
 ZGP  C5   N7   aromatic  1.370  0.020  1.370
 ZGP  N9   C8   aromatic  1.374  0.020  1.374
 ZGP  O4'  C4'  single    1.425  0.020  1.425
 ZGP  O3'  C3'  single    1.391  0.020  1.391
 ZGP  C4'  C3'  single    1.530  0.020  1.530
 ZGP  C4'  C5'  single    1.508  0.020  1.508
 ZGP  N7   C8   aromatic  1.298  0.020  1.298
 ZGP  C5'  O5'  single    1.435  0.020  1.435
 ZGP  O5'  PBK  single    1.592  0.020  1.592
 ZGP  OAG  PBK  double    1.480  0.020  1.480
 ZGP  PBK  OAJ  single    1.580  0.020  1.580
 ZGP  PBK  OAT  single    1.611  0.020  1.611
 ZGP  OAE  CBB  single    1.336  0.020  1.336
 ZGP  CAB  CAY  single    1.497  0.020  1.497
 ZGP  CBB  CAY  aromatic  1.401  0.020  1.401
 ZGP  CBB  NAR  aromatic  1.313  0.020  1.313
 ZGP  CAY  CBA  aromatic  1.385  0.020  1.385
 ZGP  NAR  CAZ  aromatic  1.331  0.020  1.331
 ZGP  CBA  OAT  single    1.378  0.020  1.378
 ZGP  CBA  CAX  aromatic  1.400  0.020  1.400
 ZGP  CAZ  CAX  aromatic  1.390  0.020  1.390
 ZGP  CAZ  CAM  single    1.501  0.020  1.501
 ZGP  CAX  CAA  single    1.500  0.020  1.500
 ZGP  CAM  CAV  single    1.511  0.020  1.511
 ZGP  CAV  OAD  double    1.200  0.020  1.200
 ZGP  CAV  SAK  single    1.778  0.020  1.778
 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  OAJ  H13  single    0.850  0.020  0.980
 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   110.52  3.000
 ZGP  C5   C6   O6   128.87  3.000
 ZGP  N1   C6   O6   120.61  3.000
 ZGP  H1   N1   C2   118.15  3.000
 ZGP  H1   N1   C6   115.57  3.000
 ZGP  C2   N1   C6   126.28  3.000
 ZGP  N3   C2   N2   120.03  3.000
 ZGP  N3   C2   N1   122.98  3.000
 ZGP  N2   C2   N1   116.97  3.000
 ZGP  H3   N2   H2   116.20  3.000
 ZGP  H3   N2   C2   120.79  3.000
 ZGP  H2   N2   C2   117.53  3.000
 ZGP  C4   N3   C2   112.98  3.000
 ZGP  N9   C4   C5   105.39  3.000
 ZGP  N9   C4   N3   125.93  3.000
 ZGP  C5   C4   N3   128.68  3.000
 ZGP  N7   C5   C4   110.62  3.000
 ZGP  N7   C5   C6   130.82  3.000
 ZGP  C4   C5   C6   118.56  3.000
 ZGP  C8   N7   C5   104.83  3.000
 ZGP  H4   C8   N9   122.13  3.000
 ZGP  H4   C8   N7   125.15  3.000
 ZGP  N9   C8   N7   112.72  3.000
 ZGP  C1'  N9   C8   128.79  3.000
 ZGP  C8   N9   C4   106.45  3.000
 ZGP  C1'  N9   C4   124.76  3.000
 ZGP  H5   C1'  C2'  111.12  3.000
 ZGP  H5   C1'  O4'  110.85  3.000
 ZGP  C2'  C1'  O4'  107.06  3.000
 ZGP  H5   C1'  N9   107.30  3.000
 ZGP  O4'  C1'  N9   108.63  3.000
 ZGP  C2'  C1'  N9   111.89  3.000
 ZGP  C4'  O4'  C1'  110.33  3.000
 ZGP  H6   C2'  C3'  112.47  3.000
 ZGP  H6   C2'  O2'  111.94  3.000
 ZGP  C3'  C2'  O2'  112.40  3.000
 ZGP  H6   C2'  C1'  111.79  3.000
 ZGP  C3'  C2'  C1'  100.28  3.000
 ZGP  O2'  C2'  C1'  107.29  3.000
 ZGP  H7   O2'  C2'  108.56  3.000
 ZGP  H8   C3'  C4'  109.57  3.000
 ZGP  H8   C3'  O3'  111.72  3.000
 ZGP  C4'  C3'  O3'  114.85  3.000
 ZGP  H8   C3'  C2'  106.50  3.000
 ZGP  C4'  C3'  C2'  100.55  3.000
 ZGP  O3'  C3'  C2'  112.84  3.000
 ZGP  H9   O3'  C3'  107.37  3.000
 ZGP  H10  C4'  C5'  105.72  3.000
 ZGP  H10  C4'  C3'  109.25  3.000
 ZGP  C5'  C4'  C3'  117.19  3.000
 ZGP  H10  C4'  O4'  109.82  3.000
 ZGP  C5'  C4'  O4'  110.96  3.000
 ZGP  C3'  C4'  O4'  103.84  3.000
 ZGP  H12  C5'  H11  107.38  3.000
 ZGP  H12  C5'  O5'  111.56  3.000
 ZGP  H11  C5'  O5'  106.46  3.000
 ZGP  H12  C5'  C4'  108.33  3.000
 ZGP  H11  C5'  C4'  110.42  3.000
 ZGP  O5'  C5'  C4'  112.57  3.000
 ZGP  PBK  O5'  C5'  122.10  3.000
 ZGP  OAT  PBK  OAG  115.36  3.000
 ZGP  OAT  PBK  OAJ   98.54  3.000
 ZGP  OAG  PBK  OAJ  117.72  3.000
 ZGP  OAT  PBK  O5'  104.79  3.000
 ZGP  OAJ  PBK  O5'  103.91  3.000
 ZGP  OAG  PBK  O5'  114.46  3.000
 ZGP  H13  OAJ  PBK  114.85  3.000
 ZGP  CBA  OAT  PBK  122.61  3.000
 ZGP  CAY  CBA  CAX  123.06  3.000
 ZGP  CAX  CBA  OAT  118.65  3.000
 ZGP  CAY  CBA  OAT  118.23  3.000
 ZGP  CAZ  CAX  CAA  121.94  3.000
 ZGP  CAA  CAX  CBA  122.45  3.000
 ZGP  CAZ  CAX  CBA  115.51  3.000
 ZGP  H17  CAA  H16  106.63  3.000
 ZGP  H17  CAA  H15  107.28  3.000
 ZGP  H16  CAA  H15  107.31  3.000
 ZGP  H17  CAA  CAX  112.89  3.000
 ZGP  H16  CAA  CAX  111.71  3.000
 ZGP  H15  CAA  CAX  110.72  3.000
 ZGP  CBB  CAY  CAB  120.62  3.000
 ZGP  CBB  CAY  CBA  114.61  3.000
 ZGP  CAB  CAY  CBA  124.76  3.000
 ZGP  H20  CAB  H19  107.75  3.000
 ZGP  H20  CAB  H18  107.23  3.000
 ZGP  H19  CAB  H18  107.29  3.000
 ZGP  H20  CAB  CAY  111.48  3.000
 ZGP  H19  CAB  CAY  112.39  3.000
 ZGP  H18  CAB  CAY  110.46  3.000
 ZGP  NAR  CBB  OAE  118.08  3.000
 ZGP  NAR  CBB  CAY  124.30  3.000
 ZGP  OAE  CBB  CAY  117.61  3.000
 ZGP  H14  OAE  CBB  108.76  3.000
 ZGP  CAZ  NAR  CBB  119.40  3.000
 ZGP  CAM  CAZ  NAR  115.67  3.000
 ZGP  CAM  CAZ  CAX  121.26  3.000
 ZGP  NAR  CAZ  CAX  123.07  3.000
 ZGP  H22  CAM  H21  106.15  3.000
 ZGP  H22  CAM  CAV  109.82  3.000
 ZGP  H21  CAM  CAV  106.76  3.000
 ZGP  H22  CAM  CAZ  112.01  3.000
 ZGP  H21  CAM  CAZ  109.06  3.000
 ZGP  CAV  CAM  CAZ  112.69  3.000
 ZGP  SAK  CAV  OAD  123.45  3.000
 ZGP  SAK  CAV  CAM  112.11  3.000
 ZGP  OAD  CAV  CAM  124.43  3.000
 ZGP  H23  SAK  CAV   96.74  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_33  H2   N2   C2   N1    180.00   0.0  0
 ZGP  Var_01    CAY  CBA  OAT  PBK   -90.00  30.0  2
 ZGP  Var_02    CAV  CAM  CAZ  CAX    73.10  30.0  2
 ZGP  Var_03    H18  CAB  CAY  CBA  -133.20  30.0  2
 ZGP  Var_04    H15  CAA  CAX  CBA    89.60  30.0  2
 ZGP  Var_05    OAD  CAV  CAM  CAZ    18.43  30.0  3
 ZGP  Var_06    OAG  PBK  O5'  C5'    24.75  30.0  3
 ZGP  Var_07    H11  C5'  O5'  PBK   138.29  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
 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
 ZGP  chir_05  PBK  OAG  OAJ  OAT  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
 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

