# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:59:03 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 5'-O-{[2-(1H-indol-3-yl)ethyl]carbamoyl}guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([C@@H]3O[C@H](COC(=O)NCCc4c[nH]c5ccccc45)[C@@H](O)[C@H]3O)c2N1
#
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
 HHJ  HHJ  5'-O-{[2-(1H-indol-3-yl)ethyl]carbamoyl}guanosine  ligand  57  34  .  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_HHJ
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
 HHJ  O6   O  O     0  -0.493  -6.5928  -4.0290   0.2487
 HHJ  C6   C  CR6   0   0.417  -6.3999  -2.8502  -0.0243
 HHJ  N1   N  N     0  -0.539  -7.4228  -2.0480  -0.4755
 HHJ  C2   C  CR6   0   0.661  -7.2609  -0.7840  -0.7583
 HHJ  N2   N  NH2   0  -0.826  -8.3134  -0.0423  -1.1383
 HHJ  N3   N  NR16  0  -0.741  -6.0665  -0.1272  -0.6652
 HHJ  C4   C  CR56  0   0.624  -5.0152  -0.8712  -0.2362
 HHJ  C5   C  CR56  0  -0.102  -5.1149  -2.1955   0.0897
 HHJ  N7   N  N     0  -0.443  -3.8875  -2.6612   0.4834
 HHJ  C8   C  CR15  0   0.090  -3.0862  -1.6439   0.3938
 HHJ  N9   N  NR5   0  -0.555  -3.7270  -0.5083  -0.0490
 HHJ  C1'  C  CH1   0   0.238  -3.1729   0.8022  -0.3150
 HHJ  O4'  O  O2    0  -0.498  -1.8164   0.7648  -0.0256
 HHJ  C2'  C  CH1   0  -0.043  -3.7721   1.9159   0.5536
 HHJ  O2'  O  OH1   0  -0.662  -4.7922   2.5376  -0.1783
 HHJ  C3'  C  CH1   0  -0.010  -2.5374   2.8143   0.8635
 HHJ  O3'  O  OH1   0  -0.656  -2.6454   4.1327   0.4224
 HHJ  C4'  C  CH1   0  -0.013  -1.3971   2.1126   0.1161
 HHJ  C5'  C  CH2   0  -0.182  -0.0884   2.1661   0.8568
 HHJ  O5'  O  O2    0  -0.489   0.9035   1.5713   0.0314
 HHJ  C1   C  C     0   0.762   2.1628   1.5737   0.4926
 HHJ  O2   O  O     0  -0.523   2.4911   2.0598   1.5566
 HHJ  N4   N  NH1   0  -0.674   2.9958   0.9819  -0.3741
 HHJ  C9   C  CH2   0  -0.232   4.4065   0.8158  -0.0946
 HHJ  C10  C  CH2   0  -0.584   5.1196   0.2623  -1.3254
 HHJ  C12  C  CR5   0   0.009   6.5754   0.0543  -1.0749
 HHJ  C16  C  CR15  0  -0.083   7.6056   0.8366  -1.5145
 HHJ  C17  C  CR56  0   0.029   7.1745  -0.9870  -0.2925
 HHJ  C18  C  CR16  0  -0.376   6.6671  -2.0863   0.4102
 HHJ  C19  C  CR16  0  -0.269   7.5463  -2.9246   1.0671
 HHJ  C20  C  CR16  0  -0.284   8.9310  -2.6873   1.0398
 HHJ  C21  C  CR16  0  -0.305   9.4613  -1.6116   0.3542
 HHJ  C22  C  CR56  0   0.354   8.5703  -0.7689  -0.3091
 HHJ  N23  N  NR15  0  -0.686   8.7976   0.3465  -1.0603
 HHJ  H1   H  HNH2  0   0.410  -9.1668  -0.5313  -1.3472
 HHJ  H2   H  HNH2  0   0.411  -8.1834   0.8409  -1.6024
 HHJ  H3   H  HNR6  0   0.431  -5.9912   0.8800  -0.7710
 HHJ  H4   H  HCR5  0   0.296  -2.0348  -1.6468   0.6289
 HHJ  H5   H  HCH1  0   0.268  -3.3496   1.0400  -1.3750
 HHJ  H6   H  HCH1  0   0.270  -4.1520   1.4889   1.4880
 HHJ  H7   H  HOH1  0   0.472  -5.3089   3.1001   0.4078
 HHJ  H8   H  HCH1  0   0.250  -2.3489   2.7690   1.9421
 HHJ  H9   H  HOH1  0   0.464  -3.0257   4.6674   1.1247
 HHJ  H10  H  HCH1  0   0.254  -1.2882   2.5774  -0.8744
 HHJ  H11  H  HCH2  0   0.249   0.1492   3.2122   1.0656
 HHJ  H12  H  HCH2  0   0.243  -0.1730   1.6375   1.8107
 HHJ  H13  H  HNH1  0   0.403   2.6140   0.5536  -1.2023
 HHJ  H14  H  HCH2  0   0.240   4.8482   1.7767   0.1763
 HHJ  H15  H  HCH2  0   0.235   4.5545   0.1407   0.7537
 HHJ  H16  H  HCH2  0   0.247   4.6501  -0.6835  -1.6163
 HHJ  H17  H  HCH2  0   0.257   4.9820   0.9523  -2.1616
 HHJ  H18  H  HCR5  0   0.282   7.5769   1.7207  -2.1321
 HHJ  H19  H  HCR6  0   0.241   5.6012  -2.2799   0.4387
 HHJ  H20  H  HCR6  0   0.245   7.1668  -3.7795   1.6118
 HHJ  H21  H  HCR6  0   0.249   9.5947  -3.3612   1.5659
 HHJ  H22  H  HCR6  0   0.258  10.5287  -1.4307   0.3334
 HHJ  H23  H  HNR5  0   0.408   9.6974   0.7529  -1.2515

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
 HHJ  N2   C2   single    1.343  0.020  1.343
 HHJ  N1   C2   double    1.305  0.020  1.305
 HHJ  N1   C6   single    1.376  0.020  1.376
 HHJ  C2   N3   single    1.366  0.020  1.366
 HHJ  O6   C6   double    1.225  0.020  1.225
 HHJ  C6   C5   single    1.447  0.020  1.447
 HHJ  N3   C4   single    1.358  0.020  1.358
 HHJ  O2'  C2'  single    1.401  0.020  1.401
 HHJ  C5   C4   aromatic  1.367  0.020  1.367
 HHJ  C5   N7   aromatic  1.371  0.020  1.371
 HHJ  C4   N9   aromatic  1.351  0.020  1.351
 HHJ  C20  C19  aromatic  1.405  0.020  1.405
 HHJ  C20  C21  aromatic  1.382  0.020  1.382
 HHJ  C19  C18  aromatic  1.381  0.020  1.381
 HHJ  N7   C8   aromatic  1.298  0.020  1.298
 HHJ  N9   C8   aromatic  1.377  0.020  1.377
 HHJ  N9   C1'  single    1.447  0.020  1.447
 HHJ  C2'  C1'  single    1.534  0.020  1.534
 HHJ  C2'  C3'  single    1.558  0.020  1.558
 HHJ  C1'  O4'  single    1.388  0.020  1.388
 HHJ  C21  C22  aromatic  1.394  0.020  1.394
 HHJ  C18  C17  aromatic  1.400  0.020  1.400
 HHJ  O3'  C3'  single    1.394  0.020  1.394
 HHJ  C3'  C4'  single    1.533  0.020  1.533
 HHJ  C22  C17  aromatic  1.413  0.020  1.413
 HHJ  C22  N23  aromatic  1.364  0.020  1.364
 HHJ  C17  C12  aromatic  1.434  0.020  1.434
 HHJ  O4'  C4'  single    1.419  0.020  1.419
 HHJ  C4'  C5'  single    1.505  0.020  1.505
 HHJ  N23  C16  aromatic  1.367  0.020  1.367
 HHJ  C12  C10  single    1.492  0.020  1.492
 HHJ  C12  C16  aromatic  1.366  0.020  1.366
 HHJ  C10  C9   single    1.526  0.020  1.526
 HHJ  C5'  O5'  single    1.421  0.020  1.421
 HHJ  C9   N4   single    1.448  0.020  1.448
 HHJ  O5'  C1   single    1.341  0.020  1.341
 HHJ  N4   C1   single    1.340  0.020  1.340
 HHJ  C1   O2   double    1.215  0.020  1.215
 HHJ  N2   H1   single    0.890  0.020  1.040
 HHJ  N2   H2   single    0.890  0.020  1.040
 HHJ  N3   H3   single    0.860  0.020  1.020
 HHJ  C8   H4   single    0.930  0.020  1.080
 HHJ  C1'  H5   single    0.970  0.020  1.090
 HHJ  C2'  H6   single    0.970  0.020  1.090
 HHJ  O2'  H7   single    0.850  0.020  0.980
 HHJ  C3'  H8   single    0.970  0.020  1.090
 HHJ  O3'  H9   single    0.850  0.020  0.980
 HHJ  C4'  H10  single    0.970  0.020  1.090
 HHJ  C5'  H11  single    0.970  0.020  1.090
 HHJ  C5'  H12  single    0.970  0.020  1.090
 HHJ  N4   H13  single    0.860  0.020  1.020
 HHJ  C9   H14  single    0.970  0.020  1.090
 HHJ  C9   H15  single    0.970  0.020  1.090
 HHJ  C10  H16  single    0.970  0.020  1.090
 HHJ  C10  H17  single    0.970  0.020  1.090
 HHJ  C16  H18  single    0.930  0.020  1.080
 HHJ  C18  H19  single    0.930  0.020  1.080
 HHJ  C19  H20  single    0.930  0.020  1.080
 HHJ  C20  H21  single    0.930  0.020  1.080
 HHJ  C21  H22  single    0.930  0.020  1.080
 HHJ  N23  H23  single    0.860  0.020  1.020

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
 HHJ  C5   C6   N1   114.98  3.000
 HHJ  C5   C6   O6   123.89  3.000
 HHJ  N1   C6   O6   121.12  3.000
 HHJ  C2   N1   C6   122.91  3.000
 HHJ  N3   C2   N2   116.04  3.000
 HHJ  N3   C2   N1   124.00  3.000
 HHJ  N2   C2   N1   119.94  3.000
 HHJ  H2   N2   H1   116.16  3.000
 HHJ  H2   N2   C2   120.95  3.000
 HHJ  H1   N2   C2   117.09  3.000
 HHJ  H3   N3   C4   121.27  3.000
 HHJ  H3   N3   C2   122.31  3.000
 HHJ  C4   N3   C2   115.79  3.000
 HHJ  N9   C4   C5   107.26  3.000
 HHJ  N9   C4   N3   129.40  3.000
 HHJ  C5   C4   N3   123.34  3.000
 HHJ  N7   C5   C4   109.40  3.000
 HHJ  N7   C5   C6   131.63  3.000
 HHJ  C4   C5   C6   118.97  3.000
 HHJ  C8   N7   C5   105.47  3.000
 HHJ  H4   C8   N9   121.77  3.000
 HHJ  H4   C8   N7   125.82  3.000
 HHJ  N9   C8   N7   112.41  3.000
 HHJ  C1'  N9   C8   128.87  3.000
 HHJ  C1'  N9   C4   125.64  3.000
 HHJ  C8   N9   C4   105.46  3.000
 HHJ  H5   C1'  C2'  109.01  3.000
 HHJ  H5   C1'  O4'  111.32  3.000
 HHJ  C2'  C1'  O4'  106.45  3.000
 HHJ  H5   C1'  N9   108.13  3.000
 HHJ  O4'  C1'  N9   108.15  3.000
 HHJ  C2'  C1'  N9   113.81  3.000
 HHJ  C4'  O4'  C1'  106.51  3.000
 HHJ  H6   C2'  C3'  109.27  3.000
 HHJ  H6   C2'  O2'  111.47  3.000
 HHJ  C3'  C2'  O2'  115.15  3.000
 HHJ  H6   C2'  C1'  109.60  3.000
 HHJ  C3'  C2'  C1'  102.81  3.000
 HHJ  O2'  C2'  C1'  108.11  3.000
 HHJ  H7   O2'  C2'  109.40  3.000
 HHJ  H8   C3'  C4'  109.44  3.000
 HHJ  H8   C3'  O3'  111.33  3.000
 HHJ  C4'  C3'  O3'  109.64  3.000
 HHJ  H8   C3'  C2'  107.95  3.000
 HHJ  C4'  C3'  C2'  103.21  3.000
 HHJ  O3'  C3'  C2'  114.89  3.000
 HHJ  H9   O3'  C3'  109.00  3.000
 HHJ  H10  C4'  C5'  110.02  3.000
 HHJ  H10  C4'  C3'  108.62  3.000
 HHJ  C5'  C4'  C3'  112.99  3.000
 HHJ  H10  C4'  O4'  109.93  3.000
 HHJ  C5'  C4'  O4'  109.88  3.000
 HHJ  C3'  C4'  O4'  105.29  3.000
 HHJ  H12  C5'  H11  108.23  3.000
 HHJ  H12  C5'  O5'  110.99  3.000
 HHJ  H11  C5'  O5'  111.09  3.000
 HHJ  H12  C5'  C4'  110.17  3.000
 HHJ  H11  C5'  C4'  108.49  3.000
 HHJ  O5'  C5'  C4'  107.84  3.000
 HHJ  C1   O5'  C5'  117.07  3.000
 HHJ  N4   C1   O2   125.11  3.000
 HHJ  O2   C1   O5'  123.75  3.000
 HHJ  N4   C1   O5'  111.13  3.000
 HHJ  H13  N4   C9   118.63  3.000
 HHJ  H13  N4   C1   118.94  3.000
 HHJ  C9   N4   C1   122.11  3.000
 HHJ  H15  C9   H14  107.21  3.000
 HHJ  H15  C9   C10  109.77  3.000
 HHJ  H14  C9   C10  109.29  3.000
 HHJ  H15  C9   N4   110.63  3.000
 HHJ  H14  C9   N4   109.95  3.000
 HHJ  C10  C9   N4   109.95  3.000
 HHJ  H17  C10  H16  106.75  3.000
 HHJ  H17  C10  C12  109.84  3.000
 HHJ  H16  C10  C12  110.03  3.000
 HHJ  H17  C10  C9   109.22  3.000
 HHJ  H16  C10  C9   109.09  3.000
 HHJ  C12  C10  C9   111.78  3.000
 HHJ  C17  C12  C16  106.04  3.000
 HHJ  C16  C12  C10  127.01  3.000
 HHJ  C17  C12  C10  126.92  3.000
 HHJ  H18  C16  N23  120.49  3.000
 HHJ  H18  C16  C12  129.30  3.000
 HHJ  N23  C16  C12  110.21  3.000
 HHJ  C22  C17  C18  119.02  3.000
 HHJ  C22  C17  C12  107.12  3.000
 HHJ  C18  C17  C12  133.85  3.000
 HHJ  H19  C18  C19  120.35  3.000
 HHJ  H19  C18  C17  120.66  3.000
 HHJ  C19  C18  C17  118.99  3.000
 HHJ  H20  C19  C20  119.26  3.000
 HHJ  H20  C19  C18  119.71  3.000
 HHJ  C20  C19  C18  121.03  3.000
 HHJ  H21  C20  C21  119.39  3.000
 HHJ  H21  C20  C19  119.32  3.000
 HHJ  C21  C20  C19  121.30  3.000
 HHJ  H22  C21  C22  121.32  3.000
 HHJ  H22  C21  C20  121.20  3.000
 HHJ  C22  C21  C20  117.48  3.000
 HHJ  N23  C22  C21  130.53  3.000
 HHJ  N23  C22  C17  107.30  3.000
 HHJ  C21  C22  C17  122.17  3.000
 HHJ  H23  N23  C22  125.76  3.000
 HHJ  H23  N23  C16  124.91  3.000
 HHJ  C22  N23  C16  109.33  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
 HHJ  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 HHJ  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 HHJ  CONST_03  C8   N9   C4   C5      0.00   0.0  0
 HHJ  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 HHJ  CONST_05  N9   C4   C5   N7      0.00   0.0  0
 HHJ  CONST_06  C19  C18  C17  C12   180.00   0.0  0
 HHJ  CONST_07  C21  C22  C17  C12   180.00   0.0  0
 HHJ  CONST_08  N23  C22  C17  C12     0.00   0.0  0
 HHJ  CONST_09  C22  N23  C16  C12     0.00   0.0  0
 HHJ  CONST_10  C21  C22  N23  C16   180.00   0.0  0
 HHJ  CONST_11  C17  C22  N23  C16     0.00   0.0  0
 HHJ  CONST_12  C18  C17  C12  C16   180.00   0.0  0
 HHJ  CONST_13  C22  C17  C12  C16     0.00   0.0  0
 HHJ  CONST_14  C20  C19  C18  C17     0.00   0.0  0
 HHJ  CONST_15  C20  C21  C22  C17     0.00   0.0  0
 HHJ  CONST_16  N23  C16  C12  C17     0.00   0.0  0
 HHJ  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 HHJ  CONST_18  C21  C22  C17  C18     0.00   0.0  0
 HHJ  CONST_19  N23  C22  C17  C18   180.00   0.0  0
 HHJ  CONST_20  C22  C21  C20  C19     0.00   0.0  0
 HHJ  CONST_21  C22  C17  C18  C19     0.00   0.0  0
 HHJ  CONST_22  N23  C22  C21  C20   180.00   0.0  0
 HHJ  CONST_23  C1'  N9   C4   N3      0.00   0.0  0
 HHJ  CONST_24  C1'  N9   C4   C5    180.00   0.0  0
 HHJ  CONST_25  C1'  N9   C8   N7    180.00   0.0  0
 HHJ  CONST_26  N3   C2   N1   C6      0.00   0.0  0
 HHJ  CONST_27  C4   N3   C2   N1      0.00   0.0  0
 HHJ  CONST_28  C18  C17  C12  C10     0.00   0.0  0
 HHJ  CONST_29  C22  C17  C12  C10   180.00   0.0  0
 HHJ  CONST_30  N23  C16  C12  C10   180.00   0.0  0
 HHJ  CONST_31  N2   C2   N1   C6    180.00   0.0  0
 HHJ  CONST_32  C4   N3   C2   N2    180.00   0.0  0
 HHJ  CONST_33  H4   C8   N9   C4    180.00   0.0  0
 HHJ  CONST_34  H19  C18  C17  C12     0.00   0.0  0
 HHJ  CONST_35  H23  N23  C16  C12   180.00   0.0  0
 HHJ  CONST_36  H20  C19  C18  C17   180.00   0.0  0
 HHJ  CONST_37  H22  C21  C22  C17   180.00   0.0  0
 HHJ  CONST_38  H18  C16  C12  C17   180.00   0.0  0
 HHJ  CONST_39  H21  C20  C19  C18   180.00   0.0  0
 HHJ  CONST_40  H3   N3   C2   N1    180.00   0.0  0
 HHJ  CONST_41  H1   N2   C2   N1      0.00   0.0  0
 HHJ  Var_01    C17  C12  C10  C9     74.03  30.0  2
 HHJ  Var_02    C12  C10  C9   N4   -179.09  30.0  1
 HHJ  Var_03    N4   C1   O5'  C5'   179.79  30.0  3
 HHJ  Var_04    C9   N4   C1   O5'  -177.99  30.0  1
 HHJ  Var_05    C10  C9   N4   C1   -173.37  30.0  1
 HHJ  Var_06    H11  C5'  O5'  C1     58.40  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
 HHJ  chir_01  C1'  N9   C2'  O4'  negativ
 HHJ  chir_02  C2'  O2'  C3'  C1'  positiv
 HHJ  chir_03  C3'  O3'  C4'  C2'  positiv
 HHJ  chir_04  C4'  O4'  C3'  C5'  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
 HHJ  plan-1  O6   0.020
 HHJ  plan-1  C6   0.020
 HHJ  plan-1  N1   0.020
 HHJ  plan-1  C2   0.020
 HHJ  plan-1  N2   0.020
 HHJ  plan-1  N3   0.020
 HHJ  plan-1  C4   0.020
 HHJ  plan-1  C5   0.020
 HHJ  plan-1  N7   0.020
 HHJ  plan-1  C8   0.020
 HHJ  plan-1  N9   0.020
 HHJ  plan-1  C1'  0.020
 HHJ  plan-1  H1   0.020
 HHJ  plan-1  H2   0.020
 HHJ  plan-1  H3   0.020
 HHJ  plan-1  H4   0.020
 HHJ  plan-2  C10  0.020
 HHJ  plan-2  C12  0.020
 HHJ  plan-2  C16  0.020
 HHJ  plan-2  C17  0.020
 HHJ  plan-2  C18  0.020
 HHJ  plan-2  C19  0.020
 HHJ  plan-2  C20  0.020
 HHJ  plan-2  C21  0.020
 HHJ  plan-2  C22  0.020
 HHJ  plan-2  N23  0.020
 HHJ  plan-2  H18  0.020
 HHJ  plan-2  H19  0.020
 HHJ  plan-2  H20  0.020
 HHJ  plan-2  H21  0.020
 HHJ  plan-2  H22  0.020
 HHJ  plan-2  H23  0.020
 HHJ  plan-3  O5'  0.020
 HHJ  plan-3  C1   0.020
 HHJ  plan-3  O2   0.020
 HHJ  plan-3  N4   0.020

