# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun  6 18:17:48 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 5'-S-[(S)-hydroxy{[2-(1H-indol-3-yl)ethyl]amino}phosphoryl]-5'-thioguanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([C@@H]3O[C@H](CS[P](O)(=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
 6CE  6CE  5'-S-[(S)-hydroxy{[2-(1H-indol-3-yl)ethyl]amino}phosphoryl]-5'-thioguanosine  ligand  58  35  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6CE
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
 6CE  C8   C  CH1    0  -0.070   2.4188  -1.7313   0.1930
 6CE  C5   C  CH2    0  -0.587   0.8199  -1.1501   2.7701
 6CE  C6   C  CH1    0  -0.001   0.4293  -1.7895   1.4482
 6CE  C2   C  CH2    0  -0.558  -3.1681   0.3118   0.9697
 6CE  C4   C  CR56   0   0.023  -4.8208   0.1535  -1.0537
 6CE  NE2  N  NH1    0  -0.757  -3.3462  -0.4276   3.3603
 6CE  P1   P  P      0   1.142  -1.9795  -0.9430   4.1905
 6CE  O2   O  OP    -1  -0.783  -2.0917  -0.4249   5.5932
 6CE  O3   O  O      0  -0.770  -1.7179  -2.3877   3.8756
 6CE  S4   S  S2     0  -0.297  -0.3054   0.1594   3.3255
 6CE  C7   C  CH1    0  -0.002   1.5035  -2.7276   0.9127
 6CE  C9   C  CH1    0   0.234   1.4016  -0.7290  -0.3711
 6CE  O10  O  O2     0  -0.481   0.2619  -0.8209   0.4069
 6CE  N11  N  NR5    0  -0.542   1.8972   0.6458  -0.3351
 6CE  C12  C  CR15   0   0.086   1.3608   1.7256   0.3288
 6CE  N13  N  N      0  -0.445   2.0079   2.8265   0.0896
 6CE  C14  C  CR5    0  -0.105   3.0163   2.4768  -0.7703
 6CE  C15  C  CR5    0   0.623   2.9470   1.1348  -1.0298
 6CE  N16  N  NH1    0  -0.740   3.8139   0.4899  -1.8529
 6CE  C17  C  C      0   0.662   4.7851   1.2650  -2.4199
 6CE  N18  N  N      0  -0.540   4.8966   2.5518  -2.2275
 6CE  C19  C  C      0   0.414   4.0559   3.2599  -1.4006
 6CE  N20  N  NH2    0  -0.826   5.6786   0.6250  -3.1903
 6CE  O21  O  O      0  -0.495   4.1989   4.4661  -1.2352
 6CE  O22  O  OH1    0  -0.663   0.9094  -3.6173   0.0068
 6CE  O23  O  OH1    0  -0.661   3.1798  -2.2691  -0.8569
 6CE  C1   C  CH2    0  -0.267  -3.6203  -0.7519   1.9767
 6CE  C3   C  CR5    0   0.002  -3.5472  -0.0501  -0.4277
 6CE  C13  C  CR15   0  -0.087  -2.7769  -0.7014  -1.3502
 6CE  C22  C  CR56   0   0.352  -4.7428  -0.3966  -2.3536
 6CE  N23  N  NR15   0  -0.687  -3.4884  -0.9095  -2.5005
 6CE  C24  C  CR16   0  -0.372  -6.0146   0.7583  -0.6425
 6CE  C25  C  CR16   0  -0.271  -7.0821   0.7989  -1.5184
 6CE  C26  C  CR16   0  -0.286  -6.9837   0.2430  -2.8055
 6CE  C27  C  CR16   0  -0.308  -5.8185  -0.3593  -3.2404
 6CE  H1   H  HCH1   0   0.269   3.0616  -1.2339   0.9279
 6CE  H2   H  HCH2   0   0.280   0.8768  -1.9277   3.5306
 6CE  H3   H  HCH2   0   0.267   1.8079  -0.6860   2.7151
 6CE  H4   H  HCH1   0   0.275  -0.5247  -2.3009   1.5775
 6CE  H5   H  HCH2   0   0.221  -3.6235   1.2700   1.2425
 6CE  H6   H  HCH2   0   0.262  -2.0887   0.4437   1.0513
 6CE  H7   H  HNH1   0   0.367  -3.7049   0.4728   3.6470
 6CE  H9   H  HCH1   0   0.251   2.0321  -3.2513   1.7195
 6CE  H10  H  HCH1   0   0.276   1.1714  -0.9623  -1.4176
 6CE  H11  H  HCR5   0   0.294   0.5045   1.6187   0.9769
 6CE  H12  H  HNH1   0   0.431   3.8150  -0.5220  -1.9304
 6CE  H13  H  HNH2   0   0.411   5.4933  -0.2975  -3.5461
 6CE  H14  H  HNH2   0   0.410   6.3144   1.1919  -3.7248
 6CE  H15  H  HOH1   0   0.451   1.6021  -3.9937  -0.5477
 6CE  H16  H  HOH1   0   0.479   3.9883  -2.6496  -0.4959
 6CE  H17  H  HCH2   0   0.222  -4.6953  -0.9223   1.8536
 6CE  H18  H  HCH2   0   0.226  -3.1377  -1.7016   1.7413
 6CE  H19  H  HCR5   0   0.282  -1.7554  -1.0367  -1.2645
 6CE  H20  H  HNR5   0   0.405  -3.1318  -1.3609  -3.3255
 6CE  H21  H  HCR6   0   0.239  -6.1006   1.1914   0.3474
 6CE  H22  H  HCR6   0   0.243  -8.0102   1.2649  -1.2127
 6CE  H23  H  HCR6   0   0.247  -7.8371   0.2869  -3.4699
 6CE  H24  H  HCR6   0   0.256  -5.7459  -0.7863  -4.2330

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
 6CE  O21  C19  double    1.226  0.020  1.226
 6CE  N18  C19  single    1.376  0.020  1.376
 6CE  N18  C17  double    1.306  0.020  1.306
 6CE  C19  C14  single    1.446  0.020  1.446
 6CE  N20  C17  single    1.342  0.020  1.342
 6CE  C17  N16  single    1.366  0.020  1.366
 6CE  C14  N13  aromatic  1.371  0.020  1.371
 6CE  C14  C15  aromatic  1.369  0.020  1.369
 6CE  N13  C12  aromatic  1.299  0.020  1.299
 6CE  N16  C15  single    1.358  0.020  1.358
 6CE  C15  N11  aromatic  1.351  0.020  1.351
 6CE  C12  N11  aromatic  1.376  0.020  1.376
 6CE  N11  C9   single    1.462  0.020  1.462
 6CE  C9   C8   single    1.535  0.020  1.535
 6CE  C9   O10  single    1.383  0.020  1.383
 6CE  O23  C8   single    1.404  0.020  1.404
 6CE  C8   C7   single    1.532  0.020  1.532
 6CE  O10  C6   single    1.432  0.020  1.432
 6CE  C7   C6   single    1.523  0.020  1.523
 6CE  C7   O22  single    1.402  0.020  1.402
 6CE  C6   C5   single    1.519  0.020  1.519
 6CE  S4   C5   single    1.814  0.020  1.814
 6CE  S4   P1   single    2.183  0.020  2.183
 6CE  C13  N23  aromatic  1.369  0.020  1.369
 6CE  C13  C3   aromatic  1.367  0.020  1.367
 6CE  C2   C3   single    1.493  0.020  1.493
 6CE  C2   C1   single    1.533  0.020  1.533
 6CE  P1   O3   deloc     1.502  0.020  1.502
 6CE  P1   NE2  single    1.680  0.020  1.680
 6CE  P1   O2   deloc     1.500  0.020  1.500
 6CE  N23  C22  aromatic  1.363  0.020  1.363
 6CE  C3   C4   aromatic  1.434  0.020  1.434
 6CE  NE2  C1   single    1.447  0.020  1.447
 6CE  C22  C4   aromatic  1.414  0.020  1.414
 6CE  C22  C27  aromatic  1.395  0.020  1.395
 6CE  C4   C24  aromatic  1.400  0.020  1.400
 6CE  C27  C26  aromatic  1.382  0.020  1.382
 6CE  C24  C25  aromatic  1.381  0.020  1.381
 6CE  C26  C25  aromatic  1.405  0.020  1.405
 6CE  C8   H1   single    0.970  0.020  1.090
 6CE  C5   H2   single    0.970  0.020  1.090
 6CE  C5   H3   single    0.970  0.020  1.090
 6CE  C6   H4   single    0.970  0.020  1.090
 6CE  C2   H5   single    0.970  0.020  1.090
 6CE  C2   H6   single    0.970  0.020  1.090
 6CE  NE2  H7   single    0.890  0.020  1.040
 6CE  C7   H9   single    0.970  0.020  1.090
 6CE  C9   H10  single    0.970  0.020  1.090
 6CE  C12  H11  single    0.930  0.020  1.080
 6CE  N16  H12  single    0.860  0.020  1.020
 6CE  N20  H13  single    0.890  0.020  1.040
 6CE  N20  H14  single    0.890  0.020  1.040
 6CE  O22  H15  single    0.850  0.020  0.980
 6CE  O23  H16  single    0.850  0.020  0.980
 6CE  C1   H17  single    0.970  0.020  1.090
 6CE  C1   H18  single    0.970  0.020  1.090
 6CE  C13  H19  single    0.930  0.020  1.080
 6CE  N23  H20  single    0.860  0.020  1.020
 6CE  C24  H21  single    0.930  0.020  1.080
 6CE  C25  H22  single    0.930  0.020  1.080
 6CE  C26  H23  single    0.930  0.020  1.080
 6CE  C27  H24  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
 6CE  H1   C8   O23  110.95  3.000
 6CE  H1   C8   C9   109.80  3.000
 6CE  O23  C8   C9   109.54  3.000
 6CE  H1   C8   C7   109.30  3.000
 6CE  O23  C8   C7   115.21  3.000
 6CE  C9   C8   C7   101.61  3.000
 6CE  H3   C5   H2   106.92  3.000
 6CE  H3   C5   S4   105.65  3.000
 6CE  H2   C5   S4   109.51  3.000
 6CE  H3   C5   C6   111.55  3.000
 6CE  H2   C5   C6   108.69  3.000
 6CE  S4   C5   C6   114.25  3.000
 6CE  H4   C6   O10  107.53  3.000
 6CE  H4   C6   C7   111.71  3.000
 6CE  O10  C6   C7   104.09  3.000
 6CE  H4   C6   C5   108.61  3.000
 6CE  C7   C6   C5   112.56  3.000
 6CE  O10  C6   C5   112.21  3.000
 6CE  H6   C2   H5   106.68  3.000
 6CE  H6   C2   C3   110.54  3.000
 6CE  H5   C2   C3   109.86  3.000
 6CE  H6   C2   C1   109.07  3.000
 6CE  H5   C2   C1   108.71  3.000
 6CE  C3   C2   C1   111.83  3.000
 6CE  C24  C4   C22  119.03  3.000
 6CE  C24  C4   C3   133.68  3.000
 6CE  C22  C4   C3   107.29  3.000
 6CE  H7   NE2  C1   113.80  3.000
 6CE  H7   NE2  P1   114.95  3.000
 6CE  C1   NE2  P1   123.90  3.000
 6CE  S4   P1   O3   105.61  3.000
 6CE  O3   P1   O2   122.80  3.000
 6CE  S4   P1   O2   104.69  3.000
 6CE  O2   P1   NE2  107.18  3.000
 6CE  O3   P1   NE2  109.46  3.000
 6CE  S4   P1   NE2  105.85  3.000
 6CE  P1   S4   C5   103.45  3.000
 6CE  H9   C7   O22  112.11  3.000
 6CE  H9   C7   C6   112.03  3.000
 6CE  O22  C7   C6   108.61  3.000
 6CE  H9   C7   C8   111.58  3.000
 6CE  O22  C7   C8   111.24  3.000
 6CE  C6   C7   C8   100.71  3.000
 6CE  H10  C9   N11  107.14  3.000
 6CE  H10  C9   O10  110.47  3.000
 6CE  N11  C9   O10  109.15  3.000
 6CE  H10  C9   C8   110.54  3.000
 6CE  O10  C9   C8   107.21  3.000
 6CE  N11  C9   C8   112.35  3.000
 6CE  C9   O10  C6   110.96  3.000
 6CE  C15  N11  C12  105.48  3.000
 6CE  C12  N11  C9   128.14  3.000
 6CE  C15  N11  C9   126.26  3.000
 6CE  H11  C12  N13  126.14  3.000
 6CE  H11  C12  N11  121.41  3.000
 6CE  N13  C12  N11  112.45  3.000
 6CE  C14  N13  C12  105.41  3.000
 6CE  C19  C14  C15  118.99  3.000
 6CE  C15  C14  N13  109.39  3.000
 6CE  C19  C14  N13  131.62  3.000
 6CE  N16  C15  C14  123.24  3.000
 6CE  N16  C15  N11  129.49  3.000
 6CE  C14  C15  N11  107.27  3.000
 6CE  H12  N16  C17  122.23  3.000
 6CE  H12  N16  C15  121.36  3.000
 6CE  C17  N16  C15  115.85  3.000
 6CE  N20  C17  N18  119.84  3.000
 6CE  N20  C17  N16  116.17  3.000
 6CE  N18  C17  N16  123.97  3.000
 6CE  C19  N18  C17  122.93  3.000
 6CE  O21  C19  N18  121.09  3.000
 6CE  N18  C19  C14  115.00  3.000
 6CE  O21  C19  C14  123.91  3.000
 6CE  H14  N20  H13  116.45  3.000
 6CE  H14  N20  C17  117.20  3.000
 6CE  H13  N20  C17  121.18  3.000
 6CE  H15  O22  C7   108.36  3.000
 6CE  H16  O23  C8   109.02  3.000
 6CE  H18  C1   H17  105.93  3.000
 6CE  H18  C1   NE2  108.51  3.000
 6CE  H17  C1   NE2  109.16  3.000
 6CE  H18  C1   C2   109.38  3.000
 6CE  H17  C1   C2   108.88  3.000
 6CE  NE2  C1   C2   114.62  3.000
 6CE  C13  C3   C4   105.88  3.000
 6CE  C4   C3   C2   126.87  3.000
 6CE  C13  C3   C2   127.18  3.000
 6CE  H19  C13  N23  120.79  3.000
 6CE  H19  C13  C3   128.92  3.000
 6CE  N23  C13  C3   110.29  3.000
 6CE  C27  C22  N23  130.64  3.000
 6CE  C27  C22  C4   122.12  3.000
 6CE  N23  C22  C4   107.23  3.000
 6CE  H20  N23  C22  125.70  3.000
 6CE  H20  N23  C13  124.99  3.000
 6CE  C22  N23  C13  109.31  3.000
 6CE  H21  C24  C25  120.40  3.000
 6CE  H21  C24  C4   120.56  3.000
 6CE  C25  C24  C4   119.04  3.000
 6CE  H22  C25  C26  119.26  3.000
 6CE  H22  C25  C24  119.75  3.000
 6CE  C26  C25  C24  120.99  3.000
 6CE  H23  C26  C27  119.29  3.000
 6CE  H23  C26  C25  119.40  3.000
 6CE  C27  C26  C25  121.31  3.000
 6CE  H24  C27  C26  121.12  3.000
 6CE  H24  C27  C22  121.37  3.000
 6CE  C26  C27  C22  117.51  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
 6CE  CONST_01  N23  C13  C3   C4      0.00   0.0  0
 6CE  CONST_02  C13  N23  C22  C4      0.00   0.0  0
 6CE  CONST_03  C26  C27  C22  C4      0.00   0.0  0
 6CE  CONST_04  C26  C25  C24  C4      0.00   0.0  0
 6CE  CONST_05  N13  C14  C15  N11     0.00   0.0  0
 6CE  CONST_06  C14  N13  C12  N11     0.00   0.0  0
 6CE  CONST_07  C15  C14  N13  C12     0.00   0.0  0
 6CE  CONST_08  C14  C15  N11  C12     0.00   0.0  0
 6CE  CONST_09  C15  N11  C12  N13     0.00   0.0  0
 6CE  CONST_10  C22  N23  C13  C3      0.00   0.0  0
 6CE  CONST_11  N23  C22  C4   C3      0.00   0.0  0
 6CE  CONST_12  C27  C22  C4   C3    180.00   0.0  0
 6CE  CONST_13  C25  C24  C4   C3    180.00   0.0  0
 6CE  CONST_14  C27  C22  N23  C13   180.00   0.0  0
 6CE  CONST_15  C22  C4   C3   C13     0.00   0.0  0
 6CE  CONST_16  C24  C4   C3   C13   180.00   0.0  0
 6CE  CONST_17  C25  C24  C4   C22     0.00   0.0  0
 6CE  CONST_18  C25  C26  C27  C22     0.00   0.0  0
 6CE  CONST_19  C24  C4   C22  N23   180.00   0.0  0
 6CE  CONST_20  C26  C27  C22  N23   180.00   0.0  0
 6CE  CONST_21  C27  C22  C4   C24     0.00   0.0  0
 6CE  CONST_22  C27  C26  C25  C24     0.00   0.0  0
 6CE  CONST_23  C14  C15  N11  C9    180.00   0.0  0
 6CE  CONST_24  N16  C15  N11  C9      0.00   0.0  0
 6CE  CONST_25  N13  C12  N11  C9    180.00   0.0  0
 6CE  CONST_26  N18  C17  N16  C15     0.00   0.0  0
 6CE  CONST_27  C19  N18  C17  N16     0.00   0.0  0
 6CE  CONST_28  N23  C13  C3   C2    180.00   0.0  0
 6CE  CONST_29  C22  C4   C3   C2    180.00   0.0  0
 6CE  CONST_30  C24  C4   C3   C2      0.00   0.0  0
 6CE  CONST_31  N20  C17  N16  C15   180.00   0.0  0
 6CE  CONST_32  N20  C17  N18  C19   180.00   0.0  0
 6CE  CONST_33  H19  C13  C3   C4    180.00   0.0  0
 6CE  CONST_34  H20  N23  C22  C4    180.00   0.0  0
 6CE  CONST_35  H24  C27  C22  C4    180.00   0.0  0
 6CE  CONST_36  H22  C25  C24  C4    180.00   0.0  0
 6CE  CONST_37  H11  C12  N11  C9      0.00   0.0  0
 6CE  CONST_38  H21  C24  C4   C3      0.00   0.0  0
 6CE  CONST_39  H23  C26  C27  C22   180.00   0.0  0
 6CE  CONST_40  H12  N16  C17  N18   180.00   0.0  0
 6CE  CONST_42  H14  N20  C17  N16   180.00   0.0  0
 6CE  Var_01    C1   C2   C3   C4     82.28  30.0  2
 6CE  Var_02    C3   C2   C1   NE2  -176.86  30.0  2
 6CE  Var_03    O3   P1   S4   C5     -7.09  30.0  3
 6CE  Var_04    P1   NE2  C1   C2    -94.95  30.0  1
 6CE  Var_05    C1   NE2  P1   O2   -178.65  30.0  3
 6CE  Var_06    H2   C5   S4   P1    -42.60  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
 6CE  chir_01  C8  C9   O23  C7   positiv
 6CE  chir_02  C6  O10  C7   C5   negativ
 6CE  chir_04  C7  C8   C6   O22  negativ
 6CE  chir_05  C9  O10  N11  C8   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
 6CE  plan-1  C9   0.020
 6CE  plan-1  N11  0.020
 6CE  plan-1  C12  0.020
 6CE  plan-1  N13  0.020
 6CE  plan-1  C14  0.020
 6CE  plan-1  C15  0.020
 6CE  plan-1  N16  0.020
 6CE  plan-1  C17  0.020
 6CE  plan-1  N18  0.020
 6CE  plan-1  C19  0.020
 6CE  plan-1  N20  0.020
 6CE  plan-1  O21  0.020
 6CE  plan-1  H11  0.020
 6CE  plan-1  H12  0.020
 6CE  plan-1  H13  0.020
 6CE  plan-1  H14  0.020
 6CE  plan-2  C2   0.020
 6CE  plan-2  C4   0.020
 6CE  plan-2  C3   0.020
 6CE  plan-2  C13  0.020
 6CE  plan-2  C22  0.020
 6CE  plan-2  N23  0.020
 6CE  plan-2  C24  0.020
 6CE  plan-2  C25  0.020
 6CE  plan-2  C26  0.020
 6CE  plan-2  C27  0.020
 6CE  plan-2  H19  0.020
 6CE  plan-2  H20  0.020
 6CE  plan-2  H21  0.020
 6CE  plan-2  H22  0.020
 6CE  plan-2  H23  0.020
 6CE  plan-2  H24  0.020

