# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 09:28:28 2020
#   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  58  36  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.375   8.4366   0.5673   1.2828
 I2C  C8    C  C1     0   0.188   7.4132   1.1607   1.5119
 I2C  N1    N  N      0  -0.456   4.3102   2.2223   1.2768
 I2C  C2    C  CR6    0   0.411   3.0608   1.8932   1.5096
 I2C  O2    O  OH1    0  -0.611   2.3530   2.8480   2.1358
 I2C  C3    C  CR6    0  -0.153   2.4855   0.6664   1.1521
 I2C  C3M   C  CH3    0  -0.796   1.0539   0.3698   1.4820
 I2C  C7    C  CH2    0  -0.646   6.5339   1.7985   0.4715
 I2C  C6    C  CR6    0   0.177   5.1047   1.3512   0.6539
 I2C  C5    C  CR6    0  -0.096   4.6720   0.1005   0.2336
 I2C  C5M   C  CH3    0  -0.729   5.5498  -0.9014  -0.4589
 I2C  C4    C  CR6    0   0.457   3.3311  -0.2207   0.5015
 I2C  O3P   O  O2     0  -0.628   2.9003  -1.4574   0.1649
 I2C  P1    P  P      0   1.363   2.0541  -1.7646  -1.2385
 I2C  O2P   O  OP    -1  -0.757   2.8841  -2.6539  -2.1040
 I2C  O1P   O  O      0  -0.760   1.4875  -0.4849  -1.7637
 I2C  O5'   O  O2     0  -0.607   0.9063  -2.6538  -0.4809
 I2C  C5'   C  CH2    0  -0.154  -0.1785  -3.1257  -1.2490
 I2C  C4'   C  CH1    0  -0.043  -1.3916  -3.2578  -0.3471
 I2C  O4'   O  O2     0  -0.484  -1.6861  -2.0154   0.2969
 I2C  C3'   C  CH1    0  -0.031  -2.6419  -3.6263  -1.1334
 I2C  O3'   O  OH1    0  -0.668  -3.5271  -4.3108  -0.2863
 I2C  C2'   C  CH1    0  -0.052  -3.1831  -2.2375  -1.4853
 I2C  O2'   O  OH1    0  -0.652  -4.5530  -2.1883  -1.7485
 I2C  C1'   C  CH1    0   0.223  -2.8695  -1.4652  -0.2031
 I2C  N9A   N  NR5    0  -0.540  -2.6940  -0.0485  -0.4062
 I2C  C4A   C  CR56   0   0.506  -3.5900   0.9211  -0.0770
 I2C  N3A   N  N      0  -0.513  -4.7686   0.7394   0.5328
 I2C  C2A   C  CR6    0   0.694  -5.4271   1.8555   0.7257
 I2C  N2A   N  NH2    0  -0.834  -6.6371   1.8270   1.2974
 I2C  N1A   N  NR16   0  -0.728  -4.9512   3.0763   0.3400
 I2C  C8A   C  CR15   0   0.072  -1.6291   0.5861  -1.0023
 I2C  N7A   N  N      0  -0.450  -1.7894   1.8724  -1.0688
 I2C  C5A   C  CR56   0  -0.100  -3.0149   2.1057  -0.4989
 I2C  C6A   C  CR6    0   0.501  -3.7258   3.3222  -0.2929
 I2C  O6A   O  O      0  -0.476  -3.3995   4.4600  -0.5895
 I2C  H8    H  H      0   0.201   7.0449   1.2790   2.5468
 I2C  HO2   H  HOH1   0   0.485   1.4384   2.5752   2.2688
 I2C  H3M   H  HCH3   0   0.256   0.3735   1.0317   0.9410
 I2C  H3MA  H  HCH3   0   0.278   0.7683  -0.6434   1.2201
 I2C  H3MB  H  HCH3   0   0.251   0.8585   0.4910   2.5505
 I2C  H7    H  HCH2   0   0.302   6.5733   2.8785   0.6409
 I2C  H7A   H  HCH2   0   0.280   6.9211   1.5984  -0.5273
 I2C  H5M   H  HCH3   0   0.247   5.7072  -1.7863   0.1602
 I2C  H5MA  H  HCH3   0   0.253   5.1041  -1.2434  -1.3923
 I2C  H5MB  H  HCH3   0   0.244   6.5294  -0.4969  -0.6981
 I2C  H5'   H  HCH2   0   0.211  -0.4022  -2.4539  -2.0863
 I2C  H5'A  H  HCH2   0   0.235   0.0468  -4.1092  -1.6757
 I2C  H4'   H  HCH1   0   0.264  -1.1847  -4.0030   0.4269
 I2C  H3'   H  HCH1   0   0.252  -2.4032  -4.2115  -2.0317
 I2C  HO3'  H  HOH1   0   0.449  -4.4162  -4.2173  -0.6483
 I2C  H2'   H  HCH1   0   0.249  -2.5981  -1.8237  -2.3166
 I2C  HO2'  H  HOH1   0   0.469  -4.7008  -2.4102  -2.6734
 I2C  H1'   H  HCH1   0   0.259  -3.6967  -1.5721   0.5071
 I2C  HN2A  H  HNH2   0   0.413  -6.9524   0.9625   1.7025
 I2C  HN2B  H  HNH2   0   0.416  -7.1043   2.6680   1.5881
 I2C  HN1A  H  HNR6   0   0.425  -5.5225   3.8929   0.5183
 I2C  H8A   H  HCR5   0   0.311  -0.7475   0.0535  -1.3321

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    1.504  0.020  1.504
 I2C  N1   C2    aromatic  1.313  0.020  1.313
 I2C  N1   C6    aromatic  1.334  0.020  1.334
 I2C  C2   O2    single    1.343  0.020  1.343
 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    1.509  0.020  1.509
 I2C  C6   C5    aromatic  1.388  0.020  1.388
 I2C  C5   C5M   single    1.501  0.020  1.501
 I2C  C5   C4    aromatic  1.405  0.020  1.405
 I2C  C4   O3P   single    1.352  0.020  1.352
 I2C  O3P  P1    single    1.667  0.020  1.667
 I2C  P1   O2P   deloc     1.493  0.020  1.493
 I2C  P1   O1P   deloc     1.495  0.020  1.495
 I2C  P1   O5'   single    1.638  0.020  1.638
 I2C  O5'  C5'   single    1.410  0.020  1.410
 I2C  C5'  C4'   single    1.517  0.020  1.517
 I2C  C4'  O4'   single    1.430  0.020  1.430
 I2C  C4'  C3'   single    1.522  0.020  1.522
 I2C  O4'  C1'   single    1.398  0.020  1.398
 I2C  C3'  O3'   single    1.404  0.020  1.404
 I2C  C3'  C2'   single    1.531  0.020  1.531
 I2C  C2'  O2'   single    1.396  0.020  1.396
 I2C  C2'  C1'   single    1.529  0.020  1.529
 I2C  C1'  N9A   single    1.442  0.020  1.442
 I2C  N9A  C4A   aromatic  1.361  0.020  1.361
 I2C  N9A  C8A   aromatic  1.375  0.020  1.375
 I2C  C4A  N3A   single    1.339  0.020  1.339
 I2C  C4A  C5A   aromatic  1.383  0.020  1.383
 I2C  N3A  C2A   double    1.310  0.020  1.310
 I2C  C2A  N2A   single    1.339  0.020  1.339
 I2C  C2A  N1A   single    1.366  0.020  1.366
 I2C  N1A  C6A   single    1.401  0.020  1.401
 I2C  C8A  N7A   aromatic  1.298  0.020  1.298
 I2C  N7A  C5A   aromatic  1.372  0.020  1.372
 I2C  C5A  C6A   single    1.424  0.020  1.424
 I2C  C6A  O6A   double    1.220  0.020  1.220
 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  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    114.05  3.000
 I2C  H8    C8   O8    120.92  3.000
 I2C  C7    C8   O8    125.02  3.000
 I2C  C6    N1   C2    119.08  3.000
 I2C  C3    C2   O2    121.66  3.000
 I2C  C3    C2   N1    124.40  3.000
 I2C  O2    C2   N1    113.94  3.000
 I2C  HO2   O2   C2    111.29  3.000
 I2C  C4    C3   C3M   123.97  3.000
 I2C  C4    C3   C2    115.42  3.000
 I2C  C3M   C3   C2    120.61  3.000
 I2C  H3MB  C3M  H3MA  107.01  3.000
 I2C  H3MB  C3M  H3M   107.79  3.000
 I2C  H3MA  C3M  H3M   106.40  3.000
 I2C  H3MB  C3M  C3    111.35  3.000
 I2C  H3MA  C3M  C3    112.53  3.000
 I2C  H3M   C3M  C3    111.47  3.000
 I2C  H7A   C7   H7    108.08  3.000
 I2C  H7A   C7   C6    113.14  3.000
 I2C  H7    C7   C6    107.95  3.000
 I2C  H7A   C7   C8    110.38  3.000
 I2C  H7    C7   C8    106.89  3.000
 I2C  C6    C7   C8    110.15  3.000
 I2C  C5    C6   C7    121.72  3.000
 I2C  C5    C6   N1    122.96  3.000
 I2C  C7    C6   N1    115.29  3.000
 I2C  C4    C5   C5M   119.57  3.000
 I2C  C4    C5   C6    116.47  3.000
 I2C  C5M   C5   C6    123.95  3.000
 I2C  H5MB  C5M  H5MA  107.28  3.000
 I2C  H5MB  C5M  H5M   107.27  3.000
 I2C  H5MA  C5M  H5M   106.89  3.000
 I2C  H5MB  C5M  C5    112.35  3.000
 I2C  H5MA  C5M  C5    111.44  3.000
 I2C  H5M   C5M  C5    111.33  3.000
 I2C  O3P   C4   C5    117.76  3.000
 I2C  O3P   C4   C3    120.49  3.000
 I2C  C5    C4   C3    121.66  3.000
 I2C  P1    O3P  C4    122.67  3.000
 I2C  O5'   P1   O1P   111.20  3.000
 I2C  O5'   P1   O2P   109.54  3.000
 I2C  O1P   P1   O2P   121.13  3.000
 I2C  O5'   P1   O3P    93.81  3.000
 I2C  O1P   P1   O3P   109.29  3.000
 I2C  O2P   P1   O3P   108.39  3.000
 I2C  C5'   O5'  P1    117.95  3.000
 I2C  H5'A  C5'  H5'   107.13  3.000
 I2C  H5'A  C5'  C4'   108.53  3.000
 I2C  H5'   C5'  C4'   110.13  3.000
 I2C  H5'A  C5'  O5'   110.75  3.000
 I2C  H5'   C5'  O5'   111.58  3.000
 I2C  C4'   C5'  O5'   108.68  3.000
 I2C  H4'   C4'  C3'   110.85  3.000
 I2C  H4'   C4'  O4'   108.18  3.000
 I2C  C3'   C4'  O4'   105.89  3.000
 I2C  H4'   C4'  C5'   109.19  3.000
 I2C  C3'   C4'  C5'   111.76  3.000
 I2C  O4'   C4'  C5'   110.89  3.000
 I2C  C1'   O4'  C4'   110.81  3.000
 I2C  H3'   C3'  C2'   111.85  3.000
 I2C  H3'   C3'  O3'   111.77  3.000
 I2C  C2'   C3'  O3'   110.98  3.000
 I2C  H3'   C3'  C4'   111.89  3.000
 I2C  C2'   C3'  C4'   100.92  3.000
 I2C  O3'   C3'  C4'   108.92  3.000
 I2C  HO3'  O3'  C3'   107.91  3.000
 I2C  H2'   C2'  C1'   109.59  3.000
 I2C  H2'   C2'  O2'   111.53  3.000
 I2C  C1'   C2'  O2'   109.97  3.000
 I2C  H2'   C2'  C3'   109.12  3.000
 I2C  C1'   C2'  C3'   101.12  3.000
 I2C  O2'   C2'  C3'   114.97  3.000
 I2C  HO2'  O2'  C2'   108.89  3.000
 I2C  H1'   C1'  N9A   106.20  3.000
 I2C  H1'   C1'  C2'   109.84  3.000
 I2C  N9A   C1'  C2'   113.77  3.000
 I2C  H1'   C1'  O4'   111.66  3.000
 I2C  N9A   C1'  O4'   109.52  3.000
 I2C  C2'   C1'  O4'   105.95  3.000
 I2C  C8A   N9A  C4A   106.61  3.000
 I2C  C8A   N9A  C1'   127.49  3.000
 I2C  C4A   N9A  C1'   125.87  3.000
 I2C  C5A   C4A  N3A   128.40  3.000
 I2C  C5A   C4A  N9A   105.24  3.000
 I2C  N3A   C4A  N9A   126.36  3.000
 I2C  C2A   N3A  C4A   113.19  3.000
 I2C  N1A   C2A  N2A   117.04  3.000
 I2C  N1A   C2A  N3A   123.00  3.000
 I2C  N2A   C2A  N3A   119.95  3.000
 I2C  HN2B  N2A  HN2A  117.21  3.000
 I2C  HN2B  N2A  C2A   121.73  3.000
 I2C  HN2A  N2A  C2A   118.28  3.000
 I2C  HN1A  N1A  C6A   115.57  3.000
 I2C  HN1A  N1A  C2A   118.33  3.000
 I2C  C6A   N1A  C2A   126.10  3.000
 I2C  H8A   C8A  N7A   124.97  3.000
 I2C  H8A   C8A  N9A   122.41  3.000
 I2C  N7A   C8A  N9A   112.57  3.000
 I2C  C5A   N7A  C8A   104.93  3.000
 I2C  C6A   C5A  N7A   130.65  3.000
 I2C  C6A   C5A  C4A   118.69  3.000
 I2C  N7A   C5A  C4A   110.65  3.000
 I2C  O6A   C6A  C5A   128.90  3.000
 I2C  O6A   C6A  N1A   120.49  3.000
 I2C  C5A   C6A  N1A   110.61  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     0.00   0.0  0
 I2C  CONST_34  HN2B  N2A  C2A  N3A   180.00   0.0  0
 I2C  Var_01    N1    C6   C7   C8    100.53  30.0  2
 I2C  Var_02    H3M   C3M  C3   C2     65.29  30.0  2
 I2C  Var_03    H5M   C5M  C5   C6    113.70  30.0  2
 I2C  Var_04    C6    C7   C8   O8    129.00  30.0  3
 I2C  Var_05    O2P   P1   O3P  C4    115.32  30.0  3
 I2C  Var_06    C4'   C5'  O5'  P1   -151.07  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

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

