# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 14:43:10 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)nc(CC(O)=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
 FEG  FEG  5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine  ligand  60  37  .  2021-08-09  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FEG
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
 FEG  N1    N  N     0  -0.474  19.6677   8.5715  26.3436
 FEG  C2    C  CR6   0   0.428  20.9309   8.7987  26.6248
 FEG  O2    O  OH1   0  -0.611  21.8536   8.3676  25.7594
 FEG  C3    C  CR6   0  -0.110  21.3759   9.4526  27.7794
 FEG  C3M   C  CH3   0  -0.731  22.8349   9.6892  28.0163
 FEG  C4    C  CR6   0   0.366  20.3682   9.8589  28.6387
 FEG  C5    C  CR6   0  -0.040  19.0088   9.7018  28.3452
 FEG  C5M   C  CH3   0  -0.752  17.9190  10.2548  29.2172
 FEG  C6    C  CR6   0   0.228  18.7251   9.0126  27.1719
 FEG  C7    C  CH2   0  -0.688  17.3149   8.6924  26.7816
 FEG  C8    C  C     0   0.557  16.7667   7.5243  27.5668
 FEG  O28   O  O     0  -0.431  17.3683   6.9228  28.4191
 FEG  O18   O  OH1   0  -0.590  15.5277   7.2305  27.1948
 FEG  O3P   O  O2    0  -0.597  20.7184  10.4775  29.8170
 FEG  P1    P  P     0   1.493  20.8400   9.6735  31.2159
 FEG  O1P   O  O     0  -0.673  20.8279  10.6212  32.3385
 FEG  O2P   O  OH1   0  -0.724  19.6562   8.6214  31.2502
 FEG  O5S   O  O2    0  -0.587  22.1265   8.7454  31.0725
 FEG  C5S   C  CH2   0  -0.209  23.4248   9.1570  31.5184
 FEG  C4S   C  CR15  0  -0.017  23.8942   8.1891  32.5954
 FEG  C3S   C  CR15  0  -0.055  23.1638   8.3260  33.9328
 FEG  O3S   O  OH1   0  -0.676  23.2364   7.1474  34.6950
 FEG  C2S   C  CR15  0  -0.027  24.0327   9.3568  34.6458
 FEG  O2S   O  OH1   0  -0.649  23.8881   9.4302  36.0244
 FEG  C1S   C  CR15  0   0.186  25.4338   8.9345  34.1776
 FEG  O4S   O  O     0  -0.492  25.2675   8.4708  32.8621
 FEG  N9A   N  NR5   0  -0.536  26.3955  10.0024  34.1889
 FEG  C8A   C  CR15  0   0.096  26.3368  11.1793  33.4803
 FEG  N7A   N  N     0  -0.440  27.3578  11.9473  33.6925
 FEG  C5A   C  CR56  0  -0.097  28.1356  11.2550  34.5851
 FEG  C4A   C  CR56  0   0.511  27.5553  10.0414  34.9020
 FEG  C6A   C  CR6   0   0.506  29.3826  11.5950  35.1849
 FEG  O6A   O  O     0  -0.471  30.0540  12.6015  35.0383
 FEG  N1A   N  NR16  0  -0.728  29.8109  10.5704  36.0397
 FEG  C2A   C  CR6   0   0.696  29.1553   9.3983  36.2853
 FEG  N3A   N  N     0  -0.514  28.0107   9.0903  35.7268
 FEG  N2A   N  NH2   0  -0.832  29.7177   8.5594  37.1652
 FEG  H3M   H  HCH3  0   0.261  23.3244  10.0230  27.1023
 FEG  H3MA  H  HCH3  0   0.251  23.0055  10.4538  28.7700
 FEG  H3MB  H  HCH3  0   0.256  23.3433   8.7783  28.3382
 FEG  H5M   H  HCH3  0   0.259  18.2966  10.9589  29.9538
 FEG  H5MA  H  HCH3  0   0.256  17.1855  10.7935  28.6170
 FEG  H5MB  H  HCH3  0   0.255  17.3841   9.4736  29.7571
 FEG  H7    H  HCH2  0   0.307  16.6462   9.5469  26.9156
 FEG  H7A   H  HCH2  0   0.318  17.2770   8.4399  25.7195
 FEG  H5S   H  HCH2  0   0.277  24.1008   9.1140  30.6646
 FEG  H5SA  H  HCH2  0   0.242  23.4084  10.1882  31.8809
 FEG  H4S   H  HCR5  0   0.272  23.8077   7.1683  32.2095
 FEG  H3S   H  HCR5  0   0.266  22.1313   8.6697  33.8164
 FEG  HO3S  H  HOH1  0   0.469  22.6005   6.5100  34.3559
 FEG  H2S   H  HCR5  0   0.269  23.8011  10.3500  34.2472
 FEG  HO2S  H  HOH1  0   0.452  23.8423   8.5318  36.3730
 FEG  H8A   H  HCR5  0   0.289  25.5162  11.4059  32.8164
 FEG  HN1A  H  HNR6  0   0.426  30.6905  10.7367  36.5113
 FEG  HN2A  H  HNH2  0   0.416  30.6688   8.6782  37.4687
 FEG  HN2B  H  HNH2  0   0.414  29.3258   7.6376  37.2542
 FEG  H20   H  HOH1  0   0.483  15.1967   6.4760  27.7050
 FEG  H23   H  HCR5  0   0.267  25.8382   8.1506  34.8273
 FEG  H24   H  HOH1  0   0.503  19.6728   7.8767  30.6334
 FEG  H25   H  HOH1  0   0.474  21.4058   7.9360  25.0199

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
 FEG  N1   C2    aromatic  1.314  0.020  1.314
 FEG  N1   C6    aromatic  1.330  0.020  1.330
 FEG  C2   O2    single    1.336  0.020  1.336
 FEG  C2   C3    aromatic  1.400  0.020  1.400
 FEG  C3   C3M   single    1.497  0.020  1.497
 FEG  C3   C4    aromatic  1.385  0.020  1.385
 FEG  C3M  H3M   single    0.970  0.020  1.090
 FEG  C3M  H3MA  single    0.970  0.020  1.090
 FEG  C3M  H3MB  single    0.970  0.020  1.090
 FEG  C4   C5    aromatic  1.400  0.020  1.400
 FEG  C4   O3P   single    1.376  0.020  1.376
 FEG  C5   C5M   single    1.501  0.020  1.501
 FEG  C5   C6    aromatic  1.390  0.020  1.390
 FEG  C5M  H5M   single    0.970  0.020  1.090
 FEG  C5M  H5MA  single    0.970  0.020  1.090
 FEG  C5M  H5MB  single    0.970  0.020  1.090
 FEG  C6   C7    single    1.498  0.020  1.498
 FEG  C7   C8    single    1.510  0.020  1.510
 FEG  C7   H7    single    0.970  0.020  1.090
 FEG  C7   H7A   single    0.970  0.020  1.090
 FEG  C8   O28   double    1.204  0.020  1.204
 FEG  C8   O18   single    1.327  0.020  1.327
 FEG  O18  H20   single    0.850  0.020  0.980
 FEG  O3P  P1    single    1.618  0.020  1.618
 FEG  P1   O1P   double    1.469  0.020  1.469
 FEG  P1   O2P   single    1.584  0.020  1.584
 FEG  P1   O5S   single    1.593  0.020  1.593
 FEG  O2P  H24   single    0.850  0.020  0.980
 FEG  O5S  C5S   single    1.433  0.020  1.433
 FEG  C5S  C4S   single    1.522  0.020  1.522
 FEG  C5S  H5S   single    0.970  0.020  1.090
 FEG  C5S  H5SA  single    0.970  0.020  1.090
 FEG  C4S  C3S   single    1.530  0.020  1.530
 FEG  C4S  O4S   single    1.427  0.020  1.427
 FEG  C4S  H4S   single    0.970  0.020  1.090
 FEG  C3S  O3S   single    1.405  0.020  1.405
 FEG  C3S  C2S   single    1.525  0.020  1.525
 FEG  C3S  H3S   single    0.970  0.020  1.090
 FEG  O3S  HO3S  single    0.850  0.020  0.980
 FEG  C2S  O2S   single    1.388  0.020  1.388
 FEG  C2S  C1S   single    1.536  0.020  1.536
 FEG  C2S  H2S   single    0.970  0.020  1.090
 FEG  O2S  HO2S  single    0.850  0.020  0.980
 FEG  C1S  O4S   single    1.405  0.020  1.405
 FEG  C1S  N9A   single    1.437  0.020  1.437
 FEG  C1S  H23   single    0.970  0.020  1.090
 FEG  N9A  C8A   aromatic  1.375  0.020  1.375
 FEG  N9A  C4A   aromatic  1.362  0.020  1.362
 FEG  C8A  N7A   aromatic  1.295  0.020  1.295
 FEG  C8A  H8A   single    0.930  0.020  1.080
 FEG  N7A  C5A   aromatic  1.372  0.020  1.372
 FEG  C5A  C4A   aromatic  1.382  0.020  1.382
 FEG  C5A  C6A   single    1.425  0.020  1.425
 FEG  C4A  N3A   single    1.339  0.020  1.339
 FEG  C6A  O6A   double    1.219  0.020  1.219
 FEG  C6A  N1A   single    1.401  0.020  1.401
 FEG  N1A  C2A   single    1.365  0.020  1.365
 FEG  N1A  HN1A  single    0.860  0.020  1.020
 FEG  C2A  N3A   double    1.310  0.020  1.310
 FEG  C2A  N2A   single    1.339  0.020  1.339
 FEG  N2A  HN2A  single    0.890  0.020  1.040
 FEG  N2A  HN2B  single    0.890  0.020  1.040
 FEG  O2   H25   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
 FEG  C6    N1   C2    119.39  3.000
 FEG  C3    C2   O2    117.73  3.000
 FEG  C3    C2   N1    124.27  3.000
 FEG  O2    C2   N1    118.00  3.000
 FEG  H25   O2   C2    108.64  3.000
 FEG  C4    C3   C3M   124.37  3.000
 FEG  C4    C3   C2    114.68  3.000
 FEG  C3M   C3   C2    120.95  3.000
 FEG  H3MB  C3M  H3MA  108.01  3.000
 FEG  H3MB  C3M  H3M   107.09  3.000
 FEG  H3MA  C3M  H3M   107.20  3.000
 FEG  H3MB  C3M  C3    111.64  3.000
 FEG  H3MA  C3M  C3    111.95  3.000
 FEG  H3M   C3M  C3    110.71  3.000
 FEG  O3P   C4   C5    118.51  3.000
 FEG  O3P   C4   C3    118.55  3.000
 FEG  C5    C4   C3    122.92  3.000
 FEG  C6    C5   C5M   121.65  3.000
 FEG  C6    C5   C4    115.53  3.000
 FEG  C5M   C5   C4    122.81  3.000
 FEG  H5MB  C5M  H5MA  107.26  3.000
 FEG  H5MB  C5M  H5M   107.40  3.000
 FEG  H5MA  C5M  H5M   106.67  3.000
 FEG  H5MB  C5M  C5    112.33  3.000
 FEG  H5MA  C5M  C5    110.53  3.000
 FEG  H5M   C5M  C5    112.35  3.000
 FEG  C7    C6   C5    121.21  3.000
 FEG  C7    C6   N1    115.72  3.000
 FEG  C5    C6   N1    123.05  3.000
 FEG  H7A   C7   H7    106.17  3.000
 FEG  H7A   C7   C8    108.31  3.000
 FEG  H7    C7   C8    108.58  3.000
 FEG  H7A   C7   C6    109.60  3.000
 FEG  H7    C7   C6    112.14  3.000
 FEG  C8    C7   C6    111.82  3.000
 FEG  O18   C8   O28   123.67  3.000
 FEG  O18   C8   C7    111.38  3.000
 FEG  O28   C8   C7    124.95  3.000
 FEG  H20   O18  C8    110.11  3.000
 FEG  P1    O3P  C4    122.41  3.000
 FEG  O5S   P1   O2P   102.63  3.000
 FEG  O5S   P1   O1P   116.83  3.000
 FEG  O2P   P1   O1P   113.94  3.000
 FEG  O5S   P1   O3P   105.81  3.000
 FEG  O2P   P1   O3P   107.01  3.000
 FEG  O1P   P1   O3P   109.84  3.000
 FEG  H24   O2P  P1    119.00  3.000
 FEG  C5S   O5S  P1    122.44  3.000
 FEG  H5SA  C5S  H5S   107.84  3.000
 FEG  H5SA  C5S  C4S   111.70  3.000
 FEG  H5S   C5S  C4S   109.75  3.000
 FEG  H5SA  C5S  O5S   111.14  3.000
 FEG  H5S   C5S  O5S   107.87  3.000
 FEG  C4S   C5S  O5S   108.47  3.000
 FEG  H4S   C4S  O4S   109.02  3.000
 FEG  H4S   C4S  C3S   110.72  3.000
 FEG  O4S   C4S  C3S   106.16  3.000
 FEG  H4S   C4S  C5S   108.61  3.000
 FEG  O4S   C4S  C5S   107.67  3.000
 FEG  C3S   C4S  C5S   114.48  3.000
 FEG  H3S   C3S  C2S   112.03  3.000
 FEG  H3S   C3S  O3S   111.70  3.000
 FEG  C2S   C3S  O3S   106.49  3.000
 FEG  H3S   C3S  C4S   112.68  3.000
 FEG  C2S   C3S  C4S   101.37  3.000
 FEG  O3S   C3S  C4S   111.98  3.000
 FEG  HO3S  O3S  C3S   109.29  3.000
 FEG  H2S   C2S  C1S   109.35  3.000
 FEG  H2S   C2S  O2S   106.95  3.000
 FEG  C1S   C2S  O2S   114.35  3.000
 FEG  H2S   C2S  C3S   108.80  3.000
 FEG  C1S   C2S  C3S   101.03  3.000
 FEG  O2S   C2S  C3S   116.15  3.000
 FEG  HO2S  O2S  C2S   108.33  3.000
 FEG  H23   C1S  N9A   106.26  3.000
 FEG  H23   C1S  O4S   111.27  3.000
 FEG  N9A   C1S  O4S   109.38  3.000
 FEG  H23   C1S  C2S   110.65  3.000
 FEG  N9A   C1S  C2S   113.81  3.000
 FEG  O4S   C1S  C2S   105.56  3.000
 FEG  C1S   O4S  C4S   110.74  3.000
 FEG  C4A   N9A  C8A   106.36  3.000
 FEG  C4A   N9A  C1S   126.53  3.000
 FEG  C8A   N9A  C1S   127.11  3.000
 FEG  H8A   C8A  N7A   125.14  3.000
 FEG  H8A   C8A  N9A   121.93  3.000
 FEG  N7A   C8A  N9A   112.92  3.000
 FEG  C5A   N7A  C8A   104.74  3.000
 FEG  C6A   C5A  C4A   118.72  3.000
 FEG  C6A   C5A  N7A   130.53  3.000
 FEG  C4A   C5A  N7A   110.75  3.000
 FEG  N3A   C4A  C5A   128.48  3.000
 FEG  N3A   C4A  N9A   126.29  3.000
 FEG  C5A   C4A  N9A   105.23  3.000
 FEG  N1A   C6A  O6A   120.58  3.000
 FEG  N1A   C6A  C5A   110.47  3.000
 FEG  O6A   C6A  C5A   128.94  3.000
 FEG  HN1A  N1A  C2A   118.34  3.000
 FEG  HN1A  N1A  C6A   115.46  3.000
 FEG  C2A   N1A  C6A   126.20  3.000
 FEG  N2A   C2A  N3A   119.97  3.000
 FEG  N2A   C2A  N1A   117.02  3.000
 FEG  N3A   C2A  N1A   122.99  3.000
 FEG  C2A   N3A  C4A   113.13  3.000
 FEG  HN2B  N2A  HN2A  116.76  3.000
 FEG  HN2B  N2A  C2A   117.94  3.000
 FEG  HN2A  N2A  C2A   121.43  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
 FEG  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 FEG  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 FEG  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 FEG  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 FEG  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 FEG  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 FEG  CONST_07  C5A   N7A  C8A  N9A     0.00   0.0  0
 FEG  CONST_08  N7A   C5A  C4A  N9A     0.00   0.0  0
 FEG  CONST_09  C5A   C4A  N9A  C8A     0.00   0.0  0
 FEG  CONST_10  C4A   C5A  N7A  C8A     0.00   0.0  0
 FEG  CONST_11  C4A   N9A  C8A  N7A     0.00   0.0  0
 FEG  CONST_12  N7A   C8A  N9A  C1S   180.00   0.0  0
 FEG  CONST_13  C5A   C4A  N9A  C1S   180.00   0.0  0
 FEG  CONST_14  N3A   C4A  N9A  C1S     0.00   0.0  0
 FEG  CONST_15  C2A   N1A  C6A  C5A     0.00   0.0  0
 FEG  CONST_16  N1A   C2A  N3A  C4A     0.00   0.0  0
 FEG  CONST_17  N3A   C2A  N1A  C6A     0.00   0.0  0
 FEG  CONST_18  C3M   C3   C2   N1    180.00   0.0  0
 FEG  CONST_19  C5M   C5   C6   N1    180.00   0.0  0
 FEG  CONST_20  C7    C6   N1   C2    180.00   0.0  0
 FEG  CONST_21  O3P   C4   C3   C2    180.00   0.0  0
 FEG  CONST_22  C6    N1   C2   O2    180.00   0.0  0
 FEG  CONST_23  C4    C3   C2   O2    180.00   0.0  0
 FEG  CONST_24  C5M   C5   C4   C3    180.00   0.0  0
 FEG  CONST_25  C5    C4   C3   C3M   180.00   0.0  0
 FEG  CONST_26  C7    C6   C5   C4    180.00   0.0  0
 FEG  CONST_27  O3P   C4   C5   C6    180.00   0.0  0
 FEG  CONST_28  N2A   C2A  N3A  C4A   180.00   0.0  0
 FEG  CONST_29  N2A   C2A  N1A  C6A   180.00   0.0  0
 FEG  CONST_30  C2A   N1A  C6A  O6A   180.00   0.0  0
 FEG  CONST_31  H8A   C8A  N9A  C1S     0.00   0.0  0
 FEG  CONST_32  HN1A  N1A  C6A  C5A   180.00   0.0  0
 FEG  CONST_33  HN2A  N2A  C2A  N1A     0.00   0.0  0
 FEG  CONST_34  HN2B  N2A  C2A  N1A   180.00   0.0  0
 FEG  CONST_35  H20   O18  C8   C7    180.00   0.0  0
 FEG  Var_01    C8    C7   C6   N1    101.25  30.0  2
 FEG  Var_02    H3M   C3M  C3   C2     42.85  30.0  2
 FEG  Var_03    H5M   C5M  C5   C4     12.67  30.0  2
 FEG  Var_04    O1P   P1   O3P  C4   -163.20  30.0  3
 FEG  Var_05    O28   C8   C7   C6      0.94  30.0  3
 FEG  Var_06    C4S   C5S  O5S  P1    118.82  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
 FEG  chir_02  C4S  C5S  C3S  O4S  positiv
 FEG  chir_03  C3S  O3S  C2S  C4S  negativ
 FEG  chir_04  C2S  O2S  C1S  C3S  negativ
 FEG  chir_05  C1S  O4S  N9A  C2S  negativ
 FEG  chir_06  P1   O1P  O2P  O5S  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
 FEG  plan-1  N1    0.020
 FEG  plan-1  C2    0.020
 FEG  plan-1  O2    0.020
 FEG  plan-1  C3    0.020
 FEG  plan-1  C3M   0.020
 FEG  plan-1  C4    0.020
 FEG  plan-1  C5    0.020
 FEG  plan-1  C5M   0.020
 FEG  plan-1  C6    0.020
 FEG  plan-1  C7    0.020
 FEG  plan-1  O3P   0.020
 FEG  plan-2  C1S   0.020
 FEG  plan-2  N9A   0.020
 FEG  plan-2  C8A   0.020
 FEG  plan-2  N7A   0.020
 FEG  plan-2  C5A   0.020
 FEG  plan-2  C4A   0.020
 FEG  plan-2  C6A   0.020
 FEG  plan-2  O6A   0.020
 FEG  plan-2  N1A   0.020
 FEG  plan-2  C2A   0.020
 FEG  plan-2  N3A   0.020
 FEG  plan-2  N2A   0.020
 FEG  plan-2  H8A   0.020
 FEG  plan-2  HN1A  0.020
 FEG  plan-2  HN2A  0.020
 FEG  plan-2  HN2B  0.020
 FEG  plan-3  C7    0.020
 FEG  plan-3  C8    0.020
 FEG  plan-3  O28   0.020
 FEG  plan-3  O18   0.020
 FEG  plan-3  H20   0.020

