# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 18:28:51 2021
#   Inital geometry file: a 147 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)nc(CC=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
 I2C  I2C  5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine  ligand  59  36  .  2021-08-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_I2C
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
 I2C  O8    O  O     0  -0.378  21.0755   6.7117  23.9227
 I2C  C8    C  C1    0   0.196  20.9912   7.6517  24.6716
 I2C  N1    N  N     0  -0.466  19.4564   7.8322  26.8208
 I2C  C2    C  CR6   0   0.433  18.5284   8.1001  27.7117
 I2C  O2    O  OH1   0  -0.603  17.2876   7.7863  27.3195
 I2C  C3    C  CR6   0  -0.149  18.7944   8.6563  28.9696
 I2C  C3M   C  CH3   0  -0.777  17.6783   8.9664  29.9215
 I2C  C7    C  CH2   0  -0.605  21.6922   7.7503  25.9976
 I2C  C6    C  CR6   0   0.194  20.7264   8.1214  27.0879
 I2C  C5    C  CR6   0  -0.036  21.1447   8.6775  28.2932
 I2C  C5M   C  CH3   0  -0.755  22.5827   9.0068  28.5576
 I2C  C4    C  CR6   0   0.387  20.1355   8.8992  29.2330
 I2C  O3P   O  O2    0  -0.603  20.4740   9.4336  30.4534
 I2C  P1    P  P     0   1.490  20.7293   8.5543  31.7882
 I2C  O2P   O  OH1   0  -0.724  19.7409   7.3207  31.7208
 I2C  O1P   O  O     0  -0.672  20.5539   9.4024  32.9758
 I2C  O5'   O  O2    0  -0.586  22.1548   7.8716  31.5990
 I2C  C5'   C  CH2   0  -0.211  23.3701   8.5094  32.0127
 I2C  C4'   C  CH1   0  -0.016  24.0414   7.6442  33.0699
 I2C  O4'   O  O2    0  -0.491  25.3602   8.1542  33.2646
 I2C  C3'   C  CH1   0  -0.056  23.3648   7.6817  34.4418
 I2C  O3'   O  OH1   0  -0.676  23.6715   6.5468  35.2114
 I2C  C2'   C  CH1   0  -0.030  24.0808   8.8595  35.0972
 I2C  O2'   O  OH1   0  -0.650  23.9928   8.9330  36.4810
 I2C  C1'   C  CH1   0   0.188  25.5081   8.6707  34.5631
 I2C  N9A   N  NR5   0  -0.538  26.2775   9.8826  34.5109
 I2C  C4A   C  CR56  0   0.512  27.5058  10.0828  35.0659
 I2C  N3A   N  N     0  -0.515  28.2008   9.1970  35.7885
 I2C  C2A   C  CR6   0   0.699  29.3575   9.6597  36.1979
 I2C  N2A   N  NH2   0  -0.832  30.1786   8.8744  36.9026
 I2C  N1A   N  NR16  0  -0.728  29.7939  10.9226  35.9164
 I2C  C8A   C  CR15  0   0.097  25.9553  11.0482  33.8552
 I2C  N7A   N  N     0  -0.439  26.8715  11.9572  33.9621
 I2C  C5A   C  CR56  0  -0.098  27.8549  11.3746  34.7210
 I2C  C6A   C  CR6   0   0.507  29.1067  11.8872  35.1685
 I2C  O6A   O  O     0  -0.472  29.5945  12.9885  34.9793
 I2C  H8    H  H     0   0.194  20.4095   8.5476  24.3967
 I2C  HO2   H  HOH1  0   0.489  16.6354   7.9905  27.9994
 I2C  H3M   H  HCH3  0   0.270  18.0111   9.5438  30.7793
 I2C  H3MA  H  HCH3  0   0.263  16.9039   9.5640  29.4356
 I2C  H3MB  H  HCH3  0   0.268  17.2065   8.0595  30.3043
 I2C  H7    H  HCH2  0   0.286  22.1930   6.8075  26.2326
 I2C  H7A   H  HCH2  0   0.288  22.4768   8.5065  25.8898
 I2C  H5M   H  HCH3  0   0.259  23.0666   9.3902  27.6608
 I2C  H5MA  H  HCH3  0   0.258  22.6950   9.7707  29.3232
 I2C  H5MB  H  HCH3  0   0.257  23.1472   8.1273  28.8731
 I2C  HO2P  H  HOH1  0   0.509  19.9398   6.5977  31.1097
 I2C  H5'   H  HCH2  0   0.278  24.0173   8.5894  31.1400
 I2C  H5'A  H  HCH2  0   0.242  23.1797   9.5202  32.3841
 I2C  H4'   H  HCH1  0   0.273  24.1066   6.6179  32.6953
 I2C  H3'   H  HCH1  0   0.269  22.2848   7.8464  34.3750
 I2C  HO3'  H  HOH1  0   0.470  23.0895   5.8238  34.9578
 I2C  H2'   H  HCH1  0   0.267  23.6592   9.7905  34.7026
 I2C  HO2'  H  HOH1  0   0.452  24.1077   8.0441  36.8387
 I2C  H1'   H  HCH1  0   0.267  26.0691   7.9804  35.2019
 I2C  HN2A  H  HNH2  0   0.418  31.0018   9.2351  37.3527
 I2C  HN2B  H  HNH2  0   0.415  29.8336   7.9849  37.2196
 I2C  HN1A  H  HNR6  0   0.426  30.6987  11.2063  36.2703
 I2C  H8A   H  HCR5  0   0.288  25.0294  11.1609  33.3113

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
 I2C  O8   C8    double    1.205  0.020  1.205
 I2C  C8   C7    single    1.503  0.020  1.503
 I2C  N1   C2    aromatic  1.314  0.020  1.314
 I2C  N1   C6    aromatic  1.330  0.020  1.330
 I2C  C2   O2    single    1.339  0.020  1.339
 I2C  C2   C3    aromatic  1.401  0.020  1.401
 I2C  C3   C3M   single    1.499  0.020  1.499
 I2C  C3   C4    aromatic  1.388  0.020  1.388
 I2C  C7   C6    single    1.503  0.020  1.503
 I2C  C6   C5    aromatic  1.392  0.020  1.392
 I2C  C5   C5M   single    1.499  0.020  1.499
 I2C  C5   C4    aromatic  1.397  0.020  1.397
 I2C  C4   O3P   single    1.375  0.020  1.375
 I2C  O3P  P1    single    1.619  0.020  1.619
 I2C  P1   O2P   single    1.582  0.020  1.582
 I2C  P1   O1P   double    1.470  0.020  1.470
 I2C  P1   O5'   single    1.592  0.020  1.592
 I2C  O5'  C5'   single    1.433  0.020  1.433
 I2C  C5'  C4'   single    1.522  0.020  1.522
 I2C  C4'  O4'   single    1.427  0.020  1.427
 I2C  C4'  C3'   single    1.530  0.020  1.530
 I2C  O4'  C1'   single    1.405  0.020  1.405
 I2C  C3'  O3'   single    1.405  0.020  1.405
 I2C  C3'  C2'   single    1.526  0.020  1.526
 I2C  C2'  O2'   single    1.388  0.020  1.388
 I2C  C2'  C1'   single    1.536  0.020  1.536
 I2C  C1'  N9A   single    1.436  0.020  1.436
 I2C  N9A  C4A   aromatic  1.363  0.020  1.363
 I2C  N9A  C8A   aromatic  1.376  0.020  1.376
 I2C  C4A  N3A   single    1.338  0.020  1.338
 I2C  C4A  C5A   aromatic  1.382  0.020  1.382
 I2C  N3A  C2A   double    1.311  0.020  1.311
 I2C  C2A  N2A   single    1.337  0.020  1.337
 I2C  C2A  N1A   single    1.366  0.020  1.366
 I2C  N1A  C6A   single    1.401  0.020  1.401
 I2C  C8A  N7A   aromatic  1.295  0.020  1.295
 I2C  N7A  C5A   aromatic  1.372  0.020  1.372
 I2C  C5A  C6A   single    1.425  0.020  1.425
 I2C  C6A  O6A   double    1.219  0.020  1.219
 I2C  C8   H8    single    0.930  0.020  1.080
 I2C  O2   HO2   single    0.850  0.020  0.980
 I2C  C3M  H3M   single    0.970  0.020  1.090
 I2C  C3M  H3MA  single    0.970  0.020  1.090
 I2C  C3M  H3MB  single    0.970  0.020  1.090
 I2C  C7   H7    single    0.970  0.020  1.090
 I2C  C7   H7A   single    0.970  0.020  1.090
 I2C  C5M  H5M   single    0.970  0.020  1.090
 I2C  C5M  H5MA  single    0.970  0.020  1.090
 I2C  C5M  H5MB  single    0.970  0.020  1.090
 I2C  O2P  HO2P  single    0.850  0.020  0.980
 I2C  C5'  H5'   single    0.970  0.020  1.090
 I2C  C5'  H5'A  single    0.970  0.020  1.090
 I2C  C4'  H4'   single    0.970  0.020  1.090
 I2C  C3'  H3'   single    0.970  0.020  1.090
 I2C  O3'  HO3'  single    0.850  0.020  0.980
 I2C  C2'  H2'   single    0.970  0.020  1.090
 I2C  O2'  HO2'  single    0.850  0.020  0.980
 I2C  C1'  H1'   single    0.970  0.020  1.090
 I2C  N2A  HN2A  single    0.860  0.020  1.020
 I2C  N2A  HN2B  single    0.860  0.020  1.020
 I2C  N1A  HN1A  single    0.860  0.020  1.020
 I2C  C8A  H8A   single    0.930  0.020  1.080

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
 I2C  H8    C8   C7    114.36  3.000
 I2C  H8    C8   O8    121.05  3.000
 I2C  C7    C8   O8    124.53  3.000
 I2C  C6    N1   C2    119.60  3.000
 I2C  C3    C2   O2    122.15  3.000
 I2C  C3    C2   N1    123.76  3.000
 I2C  O2    C2   N1    114.09  3.000
 I2C  HO2   O2   C2    111.77  3.000
 I2C  C4    C3   C3M   124.23  3.000
 I2C  C4    C3   C2    115.04  3.000
 I2C  C3M   C3   C2    120.72  3.000
 I2C  H3MB  C3M  H3MA  107.70  3.000
 I2C  H3MB  C3M  H3M   107.29  3.000
 I2C  H3MA  C3M  H3M   106.13  3.000
 I2C  H3MB  C3M  C3    111.87  3.000
 I2C  H3MA  C3M  C3    111.00  3.000
 I2C  H3M   C3M  C3    112.53  3.000
 I2C  H7A   C7   H7    106.77  3.000
 I2C  H7A   C7   C6    111.18  3.000
 I2C  H7    C7   C6    110.58  3.000
 I2C  H7A   C7   C8    107.01  3.000
 I2C  H7    C7   C8    110.29  3.000
 I2C  C6    C7   C8    110.89  3.000
 I2C  C5    C6   C7    122.26  3.000
 I2C  C5    C6   N1    123.23  3.000
 I2C  C7    C6   N1    114.48  3.000
 I2C  C4    C5   C5M   122.66  3.000
 I2C  C4    C5   C6    115.41  3.000
 I2C  C5M   C5   C6    121.93  3.000
 I2C  H5MB  C5M  H5MA  108.00  3.000
 I2C  H5MB  C5M  H5M   106.97  3.000
 I2C  H5MA  C5M  H5M   106.66  3.000
 I2C  H5MB  C5M  C5    111.72  3.000
 I2C  H5MA  C5M  C5    112.19  3.000
 I2C  H5M   C5M  C5    111.01  3.000
 I2C  O3P   C4   C5    118.77  3.000
 I2C  O3P   C4   C3    118.32  3.000
 I2C  C5    C4   C3    122.86  3.000
 I2C  P1    O3P  C4    124.05  3.000
 I2C  O5'   P1   O1P   116.77  3.000
 I2C  O5'   P1   O2P   102.71  3.000
 I2C  O1P   P1   O2P   114.19  3.000
 I2C  O5'   P1   O3P   106.04  3.000
 I2C  O1P   P1   O3P   109.52  3.000
 I2C  O2P   P1   O3P   106.84  3.000
 I2C  HO2P  O2P  P1    118.77  3.000
 I2C  C5'   O5'  P1    122.28  3.000
 I2C  H5'A  C5'  H5'   107.91  3.000
 I2C  H5'A  C5'  C4'   111.48  3.000
 I2C  H5'   C5'  C4'   109.64  3.000
 I2C  H5'A  C5'  O5'   111.21  3.000
 I2C  H5'   C5'  O5'   107.77  3.000
 I2C  C4'   C5'  O5'   108.75  3.000
 I2C  H4'   C4'  C3'   110.87  3.000
 I2C  H4'   C4'  O4'   109.07  3.000
 I2C  C3'   C4'  O4'   106.11  3.000
 I2C  H4'   C4'  C5'   108.76  3.000
 I2C  C3'   C4'  C5'   114.44  3.000
 I2C  O4'   C4'  C5'   107.41  3.000
 I2C  C1'   O4'  C4'   110.77  3.000
 I2C  H3'   C3'  C2'   111.90  3.000
 I2C  H3'   C3'  O3'   111.74  3.000
 I2C  C2'   C3'  O3'   106.60  3.000
 I2C  H3'   C3'  C4'   112.66  3.000
 I2C  C2'   C3'  C4'   101.34  3.000
 I2C  O3'   C3'  C4'   112.01  3.000
 I2C  HO3'  O3'  C3'   109.30  3.000
 I2C  H2'   C2'  C1'   109.68  3.000
 I2C  H2'   C2'  O2'   106.84  3.000
 I2C  C1'   C2'  O2'   114.33  3.000
 I2C  H2'   C2'  C3'   108.70  3.000
 I2C  C1'   C2'  C3'   101.06  3.000
 I2C  O2'   C2'  C3'   116.05  3.000
 I2C  HO2'  O2'  C2'   108.25  3.000
 I2C  H1'   C1'  N9A   106.18  3.000
 I2C  H1'   C1'  C2'   110.53  3.000
 I2C  N9A   C1'  C2'   114.00  3.000
 I2C  H1'   C1'  O4'   111.18  3.000
 I2C  N9A   C1'  O4'   109.44  3.000
 I2C  C2'   C1'  O4'   105.59  3.000
 I2C  C8A   N9A  C4A   106.30  3.000
 I2C  C8A   N9A  C1'   127.35  3.000
 I2C  C4A   N9A  C1'   126.30  3.000
 I2C  C5A   C4A  N3A   128.50  3.000
 I2C  C5A   C4A  N9A   105.28  3.000
 I2C  N3A   C4A  N9A   126.22  3.000
 I2C  C2A   N3A  C4A   113.15  3.000
 I2C  N1A   C2A  N2A   117.11  3.000
 I2C  N1A   C2A  N3A   122.95  3.000
 I2C  N2A   C2A  N3A   119.93  3.000
 I2C  HN2B  N2A  HN2A  117.22  3.000
 I2C  HN2B  N2A  C2A   118.37  3.000
 I2C  HN2A  N2A  C2A   121.88  3.000
 I2C  HN1A  N1A  C6A   115.61  3.000
 I2C  HN1A  N1A  C2A   118.21  3.000
 I2C  C6A   N1A  C2A   126.17  3.000
 I2C  H8A   C8A  N7A   125.10  3.000
 I2C  H8A   C8A  N9A   121.97  3.000
 I2C  N7A   C8A  N9A   112.93  3.000
 I2C  C5A   N7A  C8A   104.76  3.000
 I2C  C6A   C5A  N7A   130.59  3.000
 I2C  C6A   C5A  C4A   118.68  3.000
 I2C  N7A   C5A  C4A   110.72  3.000
 I2C  O6A   C6A  C5A   128.89  3.000
 I2C  O6A   C6A  N1A   120.57  3.000
 I2C  C5A   C6A  N1A   110.54  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
 I2C  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 I2C  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 I2C  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 I2C  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 I2C  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 I2C  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 I2C  CONST_07  N7A   C5A  C4A  N9A     0.00   0.0  0
 I2C  CONST_08  C5A   N7A  C8A  N9A     0.00   0.0  0
 I2C  CONST_09  N7A   C8A  N9A  C4A     0.00   0.0  0
 I2C  CONST_10  C8A   N7A  C5A  C4A     0.00   0.0  0
 I2C  CONST_11  C5A   C4A  N9A  C8A     0.00   0.0  0
 I2C  CONST_12  N3A   C4A  N9A  C1'     0.00   0.0  0
 I2C  CONST_13  C5A   C4A  N9A  C1'   180.00   0.0  0
 I2C  CONST_14  N7A   C8A  N9A  C1'   180.00   0.0  0
 I2C  CONST_15  N1A   C2A  N3A  C4A     0.00   0.0  0
 I2C  CONST_16  C6A   N1A  C2A  N3A     0.00   0.0  0
 I2C  CONST_17  C5A   C6A  N1A  C2A     0.00   0.0  0
 I2C  CONST_18  C3M   C3   C2   N1    180.00   0.0  0
 I2C  CONST_19  C5M   C5   C6   N1    180.00   0.0  0
 I2C  CONST_20  C7    C6   N1   C2    180.00   0.0  0
 I2C  CONST_21  O3P   C4   C3   C2    180.00   0.0  0
 I2C  CONST_22  C6    N1   C2   O2    180.00   0.0  0
 I2C  CONST_23  C4    C3   C2   O2    180.00   0.0  0
 I2C  CONST_24  C5M   C5   C4   C3    180.00   0.0  0
 I2C  CONST_25  C5    C4   C3   C3M   180.00   0.0  0
 I2C  CONST_26  C4    C5   C6   C7    180.00   0.0  0
 I2C  CONST_27  O3P   C4   C5   C6    180.00   0.0  0
 I2C  CONST_28  N2A   C2A  N3A  C4A   180.00   0.0  0
 I2C  CONST_29  O6A   C6A  N1A  C2A   180.00   0.0  0
 I2C  CONST_30  C6A   N1A  C2A  N2A   180.00   0.0  0
 I2C  CONST_31  H8A   C8A  N9A  C1'     0.00   0.0  0
 I2C  CONST_32  HN1A  N1A  C2A  N3A   180.00   0.0  0
 I2C  CONST_33  HN2A  N2A  C2A  N3A   180.00   0.0  0
 I2C  CONST_34  HN2B  N2A  C2A  N3A     0.00   0.0  0
 I2C  Var_01    N1    C6   C7   C8     22.68  30.0  2
 I2C  Var_02    H3M   C3M  C3   C2   -170.24  30.0  2
 I2C  Var_03    H5M   C5M  C5   C6     37.48  30.0  2
 I2C  Var_04    C6    C7   C8   O8   -129.19  30.0  3
 I2C  Var_05    O2P   P1   O3P  C4    -34.06  30.0  3
 I2C  Var_06    C4'   C5'  O5'  P1    118.71  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
 I2C  chir_02  C4'  C5'  O4'  C3'  negativ
 I2C  chir_03  C3'  O3'  C4'  C2'  positiv
 I2C  chir_04  C2'  O2'  C3'  C1'  positiv
 I2C  chir_05  C1'  O4'  N9A  C2'  negativ
 I2C  chir_06  P1   O2P  O1P  O5'  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
 I2C  plan-1  N1    0.020
 I2C  plan-1  C2    0.020
 I2C  plan-1  O2    0.020
 I2C  plan-1  C3    0.020
 I2C  plan-1  C3M   0.020
 I2C  plan-1  C7    0.020
 I2C  plan-1  C6    0.020
 I2C  plan-1  C5    0.020
 I2C  plan-1  C5M   0.020
 I2C  plan-1  C4    0.020
 I2C  plan-1  O3P   0.020
 I2C  plan-2  C1'   0.020
 I2C  plan-2  N9A   0.020
 I2C  plan-2  C4A   0.020
 I2C  plan-2  N3A   0.020
 I2C  plan-2  C2A   0.020
 I2C  plan-2  N2A   0.020
 I2C  plan-2  N1A   0.020
 I2C  plan-2  C8A   0.020
 I2C  plan-2  N7A   0.020
 I2C  plan-2  C5A   0.020
 I2C  plan-2  C6A   0.020
 I2C  plan-2  O6A   0.020
 I2C  plan-2  HN2A  0.020
 I2C  plan-2  HN2B  0.020
 I2C  plan-2  HN1A  0.020
 I2C  plan-2  H8A   0.020
 I2C  plan-3  O8    0.020
 I2C  plan-3  C8    0.020
 I2C  plan-3  C7    0.020
 I2C  plan-3  H8    0.020

