# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 17:16:16 2020
#   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  58  37  .  2021-08-09  2021-08-09  
;
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  -0.461   1.3258  -1.8554  -1.0902
 FEG  C2    C  CR6    0   0.406   0.7705  -0.9152  -1.8184
 FEG  O2    O  OH1    0  -0.624  -0.1732  -1.3703  -2.6710
 FEG  C3    C  CR6    0  -0.162   1.1038   0.4396  -1.7523
 FEG  C3M   C  CH3    0  -0.761   0.4878   1.4346  -2.6903
 FEG  C4    C  CR6    0   0.423   2.0863   0.7682  -0.8209
 FEG  C5    C  CR6    0  -0.049   2.7242  -0.2143  -0.0595
 FEG  C5M   C  CH3    0  -0.748   3.8522   0.1050   0.8770
 FEG  C6    C  CR6    0   0.262   2.2818  -1.5246  -0.2255
 FEG  C7    C  CH2    0  -0.700   2.8467  -2.6479   0.5822
 FEG  C8    C  C      0   0.417   4.1195  -3.2942  -0.0099
 FEG  O28   O  O      0  -0.602   4.5775  -2.8150  -1.0638
 FEG  O18   O  OC    -1  -0.626   4.5807  -4.2602   0.6312
 FEG  O3P   O  O2     0  -0.640   2.4904   2.0634  -0.7329
 FEG  P1    P  P      0   1.365   2.1080   3.0888   0.5159
 FEG  O1P   O  O      0  -0.762   1.8010   2.3251   1.7633
 FEG  O2P   O  OP    -1  -0.773   3.1768   4.1303   0.4646
 FEG  O5S   O  O2     0  -0.609   0.7294   3.7408  -0.0925
 FEG  C5S   C  CH2    0  -0.156  -0.4042   3.9571   0.7172
 FEG  C4S   C  CH1    0  -0.022  -1.6504   3.4213   0.0358
 FEG  C3S   C  CH1    0  -0.036  -2.8537   3.4630   0.9709
 FEG  O3S   O  OH1    0  -0.670  -4.0239   3.6074   0.2081
 FEG  C2S   C  CH1    0  -0.056  -2.7794   2.0708   1.6059
 FEG  O2S   O  OH1    0  -0.656  -3.9896   1.5873   2.1084
 FEG  C1S   C  CH1    0   0.225  -2.3305   1.2290   0.4125
 FEG  O4S   O  O2     0  -0.469  -1.4815   2.0544  -0.3291
 FEG  N9A   N  NR5    0  -0.543  -1.6481   0.0172   0.7699
 FEG  C8A   C  CR15   0   0.096  -0.5343  -0.1173   1.5684
 FEG  N7A   N  N      0  -0.438  -0.1810  -1.3533   1.7283
 FEG  C5A   C  CR56   0  -0.071  -1.0777  -2.0758   0.9850
 FEG  C4A   C  CR56   0   0.511  -1.9872  -1.2388   0.3701
 FEG  C6A   C  CR6    0   0.517  -1.1382  -3.4683   0.7068
 FEG  O6A   O  O      0  -0.485  -0.4352  -4.3729   1.1303
 FEG  N1A   N  NR16   0  -0.727  -2.1828  -3.7485  -0.1842
 FEG  C2A   C  CR6    0   0.680  -3.0441  -2.8400  -0.7261
 FEG  N3A   N  N      0  -0.515  -2.9860  -1.5607  -0.4645
 FEG  N2A   N  NH2    0  -0.835  -4.0129  -3.3211  -1.5269
 FEG  H3M   H  HCH3   0   0.238  -0.6024   1.3995  -2.6732
 FEG  H3MA  H  HCH3   0   0.263   0.7579   2.4517  -2.4288
 FEG  H3MB  H  HCH3   0   0.238   0.8108   1.2564  -3.7193
 FEG  H5M   H  HCH3   0   0.238   3.5168   0.1490   1.9139
 FEG  H5MA  H  HCH3   0   0.234   4.6337  -0.6506   0.8087
 FEG  H5MB  H  HCH3   0   0.233   4.3116   1.0648   0.6495
 FEG  H7    H  HCH2   0   0.236   3.0655  -2.3166   1.6010
 FEG  H7A   H  HCH2   0   0.260   2.0762  -3.4161   0.6796
 FEG  H5S   H  HCH2   0   0.215  -0.2782   3.4993   1.7022
 FEG  H5SA  H  HCH2   0   0.224  -0.5422   5.0323   0.8761
 FEG  H4S   H  HCH1   0   0.251  -1.8451   4.0000  -0.8730
 FEG  H3S   H  HCH1   0   0.248  -2.7607   4.2588   1.7222
 FEG  HO3S  H  HOH1   0   0.448  -4.7657   3.3090   0.7471
 FEG  H2S   H  HCH1   0   0.249  -1.9971   2.0737   2.3758
 FEG  HO2S  H  HOH1   0   0.469  -4.0969   1.8988   3.0127
 FEG  H8A   H  HCR5   0   0.293  -0.0046   0.7401   1.9582
 FEG  HN1A  H  HNR6   0   0.420  -2.2921  -4.7225  -0.4348
 FEG  HN2A  H  HNH2   0   0.410  -3.9246  -4.2363  -1.9360
 FEG  HN2B  H  HNH2   0   0.408  -4.5272  -2.6494  -2.0716
 FEG  H23   H  HCH1   0   0.249  -3.2041   0.9202  -0.1731
 FEG  H25   H  HOH1   0   0.472  -0.6091  -0.6380  -3.1190

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  1.313  0.020  1.313
 FEG  N1   C6    aromatic  1.331  0.020  1.331
 FEG  C2   O2    single    1.351  0.020  1.351
 FEG  C2   C3    aromatic  1.397  0.020  1.397
 FEG  C3   C3M   single    1.500  0.020  1.500
 FEG  C3   C4    aromatic  1.393  0.020  1.393
 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  1.397  0.020  1.397
 FEG  C4   O3P   single    1.360  0.020  1.360
 FEG  C5   C5M   single    1.501  0.020  1.501
 FEG  C5   C6    aromatic  1.393  0.020  1.393
 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    1.494  0.020  1.494
 FEG  C7   C8    single    1.545  0.020  1.545
 FEG  C7   H7    single    0.970  0.020  1.090
 FEG  C7   H7A   single    0.970  0.020  1.090
 FEG  C8   O28   deloc     1.245  0.020  1.245
 FEG  C8   O18   deloc     1.248  0.020  1.248
 FEG  O3P  P1    single    1.660  0.020  1.660
 FEG  P1   O1P   deloc     1.494  0.020  1.494
 FEG  P1   O2P   deloc     1.493  0.020  1.493
 FEG  P1   O5S   single    1.642  0.020  1.642
 FEG  O5S  C5S   single    1.410  0.020  1.410
 FEG  C5S  C4S   single    1.518  0.020  1.518
 FEG  C5S  H5S   single    0.970  0.020  1.090
 FEG  C5S  H5SA  single    0.970  0.020  1.090
 FEG  C4S  C3S   single    1.525  0.020  1.525
 FEG  C4S  O4S   single    1.425  0.020  1.425
 FEG  C4S  H4S   single    0.970  0.020  1.090
 FEG  C3S  O3S   single    1.404  0.020  1.404
 FEG  C3S  C2S   single    1.532  0.020  1.532
 FEG  C3S  H3S   single    0.970  0.020  1.090
 FEG  O3S  HO3S  single    0.850  0.020  0.980
 FEG  C2S  O2S   single    1.397  0.020  1.397
 FEG  C2S  C1S   single    1.528  0.020  1.528
 FEG  C2S  H2S   single    0.970  0.020  1.090
 FEG  O2S  HO2S  single    0.850  0.020  0.980
 FEG  C1S  O4S   single    1.397  0.020  1.397
 FEG  C1S  N9A   single    1.436  0.020  1.436
 FEG  C1S  H23   single    0.970  0.020  1.090
 FEG  N9A  C8A   aromatic  1.377  0.020  1.377
 FEG  N9A  C4A   aromatic  1.361  0.020  1.361
 FEG  C8A  N7A   aromatic  1.295  0.020  1.295
 FEG  C8A  H8A   single    0.930  0.020  1.080
 FEG  N7A  C5A   aromatic  1.371  0.020  1.371
 FEG  C5A  C4A   aromatic  1.381  0.020  1.381
 FEG  C5A  C6A   single    1.421  0.020  1.421
 FEG  C4A  N3A   single    1.341  0.020  1.341
 FEG  C6A  O6A   double    1.221  0.020  1.221
 FEG  C6A  N1A   single    1.401  0.020  1.401
 FEG  N1A  C2A   single    1.364  0.020  1.364
 FEG  N1A  HN1A  single    0.860  0.020  1.020
 FEG  C2A  N3A   double    1.307  0.020  1.307
 FEG  C2A  N2A   single    1.346  0.020  1.346
 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    119.10  3.000
 FEG  C3    C2   O2    121.56  3.000
 FEG  C3    C2   N1    124.58  3.000
 FEG  O2    C2   N1    113.86  3.000
 FEG  H25   O2   C2    110.71  3.000
 FEG  C4    C3   C3M   123.46  3.000
 FEG  C4    C3   C2    115.39  3.000
 FEG  C3M   C3   C2    121.06  3.000
 FEG  H3MB  C3M  H3MA  107.83  3.000
 FEG  H3MB  C3M  H3M   107.75  3.000
 FEG  H3MA  C3M  H3M   105.98  3.000
 FEG  H3MB  C3M  C3    111.05  3.000
 FEG  H3MA  C3M  C3    111.67  3.000
 FEG  H3M   C3M  C3    112.30  3.000
 FEG  O3P   C4   C5    119.93  3.000
 FEG  O3P   C4   C3    118.53  3.000
 FEG  C5    C4   C3    121.36  3.000
 FEG  C6    C5   C5M   120.88  3.000
 FEG  C6    C5   C4    116.85  3.000
 FEG  C5M   C5   C4    122.26  3.000
 FEG  H5MB  C5M  H5MA  107.21  3.000
 FEG  H5MB  C5M  H5M   107.04  3.000
 FEG  H5MA  C5M  H5M   107.95  3.000
 FEG  H5MB  C5M  C5    112.00  3.000
 FEG  H5MA  C5M  C5    110.65  3.000
 FEG  H5M   C5M  C5    111.76  3.000
 FEG  C7    C6   C5    121.51  3.000
 FEG  C7    C6   N1    115.84  3.000
 FEG  C5    C6   N1    122.64  3.000
 FEG  H7A   C7   H7    105.73  3.000
 FEG  H7A   C7   C8    108.72  3.000
 FEG  H7    C7   C8    108.59  3.000
 FEG  H7A   C7   C6    108.07  3.000
 FEG  H7    C7   C6    110.57  3.000
 FEG  C8    C7   C6    114.75  3.000
 FEG  O18   C8   O28   126.65  3.000
 FEG  O18   C8   C7    115.55  3.000
 FEG  O28   C8   C7    117.79  3.000
 FEG  P1    O3P  C4    124.65  3.000
 FEG  O5S   P1   O2P   108.14  3.000
 FEG  O5S   P1   O1P   109.86  3.000
 FEG  O2P   P1   O1P   122.15  3.000
 FEG  O5S   P1   O3P    99.20  3.000
 FEG  O2P   P1   O3P   103.89  3.000
 FEG  O1P   P1   O3P   111.07  3.000
 FEG  C5S   O5S  P1    121.55  3.000
 FEG  H5SA  C5S  H5S   107.14  3.000
 FEG  H5SA  C5S  C4S   107.95  3.000
 FEG  H5S   C5S  C4S   110.56  3.000
 FEG  H5SA  C5S  O5S   109.58  3.000
 FEG  H5S   C5S  O5S   111.13  3.000
 FEG  C4S   C5S  O5S   110.37  3.000
 FEG  H4S   C4S  O4S   108.40  3.000
 FEG  H4S   C4S  C3S   110.75  3.000
 FEG  O4S   C4S  C3S   106.08  3.000
 FEG  H4S   C4S  C5S   109.39  3.000
 FEG  O4S   C4S  C5S   110.87  3.000
 FEG  C3S   C4S  C5S   111.28  3.000
 FEG  H3S   C3S  C2S   111.77  3.000
 FEG  H3S   C3S  O3S   111.57  3.000
 FEG  C2S   C3S  O3S   111.04  3.000
 FEG  H3S   C3S  C4S   111.87  3.000
 FEG  C2S   C3S  C4S   101.01  3.000
 FEG  O3S   C3S  C4S   109.11  3.000
 FEG  HO3S  O3S  C3S   107.79  3.000
 FEG  H2S   C2S  C1S   109.87  3.000
 FEG  H2S   C2S  O2S   111.47  3.000
 FEG  C1S   C2S  O2S   110.17  3.000
 FEG  H2S   C2S  C3S   108.84  3.000
 FEG  C1S   C2S  C3S   101.03  3.000
 FEG  O2S   C2S  C3S   114.94  3.000
 FEG  HO2S  O2S  C2S   108.82  3.000
 FEG  H23   C1S  N9A   105.90  3.000
 FEG  H23   C1S  O4S   111.54  3.000
 FEG  N9A   C1S  O4S   109.99  3.000
 FEG  H23   C1S  C2S   109.78  3.000
 FEG  N9A   C1S  C2S   114.22  3.000
 FEG  O4S   C1S  C2S   105.52  3.000
 FEG  C1S   O4S  C4S   111.02  3.000
 FEG  C4A   N9A  C8A   106.36  3.000
 FEG  C4A   N9A  C1S   125.96  3.000
 FEG  C8A   N9A  C1S   127.67  3.000
 FEG  H8A   C8A  N7A   125.37  3.000
 FEG  H8A   C8A  N9A   121.88  3.000
 FEG  N7A   C8A  N9A   112.67  3.000
 FEG  C5A   N7A  C8A   104.92  3.000
 FEG  C6A   C5A  C4A   118.61  3.000
 FEG  C6A   C5A  N7A   130.58  3.000
 FEG  C4A   C5A  N7A   110.67  3.000
 FEG  N3A   C4A  C5A   128.49  3.000
 FEG  N3A   C4A  N9A   126.16  3.000
 FEG  C5A   C4A  N9A   105.34  3.000
 FEG  N1A   C6A  O6A   120.10  3.000
 FEG  N1A   C6A  C5A   110.62  3.000
 FEG  O6A   C6A  C5A   129.29  3.000
 FEG  HN1A  N1A  C2A   118.33  3.000
 FEG  HN1A  N1A  C6A   115.51  3.000
 FEG  C2A   N1A  C6A   126.16  3.000
 FEG  N2A   C2A  N3A   120.07  3.000
 FEG  N2A   C2A  N1A   116.92  3.000
 FEG  N3A   C2A  N1A   122.98  3.000
 FEG  C2A   N3A  C4A   113.12  3.000
 FEG  HN2B  N2A  HN2A  115.59  3.000
 FEG  HN2B  N2A  C2A   116.83  3.000
 FEG  HN2A  N2A  C2A   120.26  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_34  HN2B  N2A  C2A  N1A   180.00   0.0  0
 FEG  Var_01    C8    C7   C6   N1     93.95  30.0  2
 FEG  Var_02    H3M   C3M  C3   C2     54.11  30.0  2
 FEG  Var_03    H5M   C5M  C5   C4    101.12  30.0  2
 FEG  Var_04    O1P   P1   O3P  C4     24.57  30.0  3
 FEG  Var_05    O28   C8   C7   C6      1.84  30.0  3
 FEG  Var_06    C4S   C5S  O5S  P1   -131.88  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

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

