# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 07:16:21 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-butyl-3-[(~{E})-3-oxidanylprop-1-enyl]-8-[(1~{R},5~{S})-3-tricyclo[3.3.1.0^{3,7}]nonanyl]-7~{H}-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN1C(=O)N(/C=C/CO)c2nc([nH]c2C1=O)C34C[C@H]5C[C@H](CC3C5)C4
#
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
 8JN  8JN  1-butyl-3-[(~{E})-3-oxidanylprop-1-enyl]-8-[(1~{R},5~{S})-3-tricyclo[3.3.1.0^{3,7}]nonanyl]-7~{H}-purine-2,6-dione  ligand  56  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8JN
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
 8JN  C10  C  C1    0  -0.308  -0.0821  -3.2903   0.3395
 8JN  C13  C  CR56  0   0.461   0.3589  -0.3683  -0.1682
 8JN  C14  C  CR56  0   0.102   0.6685   0.9422  -0.4176
 8JN  C16  C  CR5   0   0.575  -1.4782   0.6863  -0.1053
 8JN  C18  C  CT    0  -0.201  -2.9196   0.9901   0.0534
 8JN  C21  C  CH2   0  -0.416  -4.7858  -0.6128   0.1612
 8JN  C22  C  CH1   0  -0.244  -3.8666   0.0870  -0.8471
 8JN  C23  C  CH2   0  -0.416  -4.7157   1.1030  -1.6211
 8JN  C24  C  CH1   0  -0.253  -4.8189   2.2298  -0.5952
 8JN  C25  C  CH2   0  -0.438  -3.3344   2.4298  -0.2924
 8JN  C26  C  CH2   0  -0.420  -5.5538   1.7284   0.6627
 8JN  C27  C  CR6   0   0.543   1.9844   1.4177  -0.6484
 8JN  C01  C  CH3   0  -0.661   7.2872   1.7157   1.4572
 8JN  C02  C  CH2   0  -0.428   6.5248   1.3997   0.1782
 8JN  C03  C  CH2   0  -0.423   5.0666   1.0460   0.4433
 8JN  N05  N  NR6   0  -0.627   2.9195   0.3767  -0.6230
 8JN  C06  C  CR6   0   0.779   2.6601  -0.9574  -0.3486
 8JN  O07  O  O     0  -0.480   3.5582  -1.7729  -0.3106
 8JN  N08  N  NR6   0  -0.658   1.3369  -1.3356  -0.1237
 8JN  C09  C  C1    0  -0.044   1.0938  -2.6908   0.1712
 8JN  C11  C  CH2   0  -0.201  -0.1507  -4.7541   0.6273
 8JN  O12  O  OH1   0  -0.672  -0.8052  -4.9394   1.8679
 8JN  N15  N  NR15  0  -0.686  -0.5334   1.5985  -0.3688
 8JN  N17  N  N     0  -0.479  -0.9588  -0.5284   0.0243
 8JN  C19  C  CH2   0  -0.408  -3.4152   0.7195   1.4925
 8JN  C20  C  CH1   0  -0.259  -4.8976   0.4618   1.2413
 8JN  H1   H  H     0   0.288  -1.0161  -2.7521   0.2632
 8JN  H2   H  HCH2  0   0.231  -5.7422  -0.8968  -0.2828
 8JN  H3   H  HCH2  0   0.235  -4.3278  -1.5175   0.5689
 8JN  H4   H  HCH1  0   0.240  -3.3188  -0.6037  -1.4875
 8JN  H5   H  HCH2  0   0.235  -4.2100   1.4544  -2.5242
 8JN  H6   H  HCH2  0   0.233  -5.6795   0.6878  -1.9233
 8JN  H7   H  HCH1  0   0.230  -5.2966   3.1322  -0.9821
 8JN  H8   H  HCH2  0   0.249  -3.1352   3.1300   0.5222
 8JN  H9   H  HCH2  0   0.240  -2.8269   2.8038  -1.1868
 8JN  H10  H  HCH2  0   0.231  -5.5602   2.5165   1.4218
 8JN  H11  H  HCH2  0   0.231  -6.5994   1.5222   0.4162
 8JN  H12  H  HCH3  0   0.229   8.3321   1.9494   1.2511
 8JN  H13  H  HCH3  0   0.218   6.8524   2.5725   1.9752
 8JN  H14  H  HCH3  0   0.219   7.2663   0.8694   2.1456
 8JN  H15  H  HCH2  0   0.219   6.5752   2.2565  -0.5006
 8JN  H16  H  HCH2  0   0.218   7.0116   0.5694  -0.3421
 8JN  H17  H  HCH2  0   0.228   5.0154   0.1858   1.1159
 8JN  H18  H  HCH2  0   0.226   4.5751   1.8784   0.9556
 8JN  H19  H  HCH2  0   0.262   4.3391   1.5972  -1.5088
 8JN  H20  H  HCH2  0   0.263   4.8033  -0.0848  -1.3802
 8JN  H21  H  H     0   0.287   2.0074  -3.2602   0.2551
 8JN  H22  H  HCH2  0   0.209  -0.7035  -5.2489  -0.1816
 8JN  H23  H  HCH2  0   0.203   0.8586  -5.1858   0.6312
 8JN  H24  H  HOH1  0   0.454  -1.0026  -5.8760   1.9609
 8JN  H25  H  HNR5  0   0.436  -0.6739   2.5889  -0.5022
 8JN  H27  H  HCH2  0   0.245  -2.9397  -0.1676   1.9172
 8JN  H28  H  HCH2  0   0.242  -3.2102   1.5607   2.1587
 8JN  H29  H  HCH1  0   0.229  -5.4288   0.1292   2.1360
 8JN  O28  O  O     0  -0.462   2.3050   2.5745  -0.8518
 8JN  C04  C  CH2   0  -0.305   4.3237   0.7337  -0.8477

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
 8JN  O12  C11  single    1.415  0.020  1.415
 8JN  C11  C10  single    1.493  0.020  1.493
 8JN  C10  C09  double    1.331  0.020  1.331
 8JN  C01  C02  single    1.522  0.020  1.522
 8JN  C09  N08  single    1.408  0.020  1.408
 8JN  C25  C24  single    1.528  0.020  1.528
 8JN  C25  C18  single    1.538  0.020  1.538
 8JN  C02  C03  single    1.524  0.020  1.524
 8JN  C24  C26  single    1.541  0.020  1.541
 8JN  C24  C23  single    1.527  0.020  1.527
 8JN  C26  C20  single    1.539  0.020  1.539
 8JN  C19  C18  single    1.546  0.020  1.546
 8JN  C19  C20  single    1.525  0.020  1.525
 8JN  N08  C13  single    1.376  0.020  1.376
 8JN  N08  C06  single    1.394  0.020  1.394
 8JN  N17  C13  aromatic  1.341  0.020  1.341
 8JN  N17  C16  aromatic  1.327  0.020  1.327
 8JN  O07  C06  double    1.214  0.020  1.214
 8JN  C13  C14  aromatic  1.369  0.020  1.369
 8JN  C06  N05  single    1.386  0.020  1.386
 8JN  C18  C16  single    1.482  0.020  1.482
 8JN  C18  C22  single    1.588  0.020  1.588
 8JN  C16  N15  aromatic  1.339  0.020  1.339
 8JN  C03  C04  single    1.522  0.020  1.522
 8JN  C20  C21  single    1.528  0.020  1.528
 8JN  C14  N15  aromatic  1.370  0.020  1.370
 8JN  C14  C27  single    1.418  0.020  1.418
 8JN  N05  C27  single    1.400  0.020  1.400
 8JN  N05  C04  single    1.466  0.020  1.466
 8JN  C23  C22  single    1.534  0.020  1.534
 8JN  C27  O28  double    1.218  0.020  1.218
 8JN  C22  C21  single    1.533  0.020  1.533
 8JN  C10  H1   single    0.930  0.020  1.080
 8JN  C21  H2   single    0.970  0.020  1.090
 8JN  C21  H3   single    0.970  0.020  1.090
 8JN  C22  H4   single    0.970  0.020  1.090
 8JN  C23  H5   single    0.970  0.020  1.090
 8JN  C23  H6   single    0.970  0.020  1.090
 8JN  C24  H7   single    0.970  0.020  1.090
 8JN  C25  H8   single    0.970  0.020  1.090
 8JN  C25  H9   single    0.970  0.020  1.090
 8JN  C26  H10  single    0.970  0.020  1.090
 8JN  C26  H11  single    0.970  0.020  1.090
 8JN  C01  H12  single    0.970  0.020  1.090
 8JN  C01  H13  single    0.970  0.020  1.090
 8JN  C01  H14  single    0.970  0.020  1.090
 8JN  C02  H15  single    0.970  0.020  1.090
 8JN  C02  H16  single    0.970  0.020  1.090
 8JN  C03  H17  single    0.970  0.020  1.090
 8JN  C03  H18  single    0.970  0.020  1.090
 8JN  C04  H19  single    0.970  0.020  1.090
 8JN  C04  H20  single    0.970  0.020  1.090
 8JN  C09  H21  single    0.930  0.020  1.080
 8JN  C11  H22  single    0.970  0.020  1.090
 8JN  C11  H23  single    0.970  0.020  1.090
 8JN  O12  H24  single    0.850  0.020  0.980
 8JN  N15  H25  single    0.860  0.020  1.020
 8JN  C19  H27  single    0.970  0.020  1.090
 8JN  C19  H28  single    0.970  0.020  1.090
 8JN  C20  H29  single    0.970  0.020  1.090

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
 8JN  H1   C10  C11  117.52  3.000
 8JN  H1   C10  C09  122.04  3.000
 8JN  C11  C10  C09  120.44  3.000
 8JN  N17  C13  N08  127.56  3.000
 8JN  N17  C13  C14  111.25  3.000
 8JN  N08  C13  C14  121.19  3.000
 8JN  N15  C14  C27  131.23  3.000
 8JN  C27  C14  C13  124.08  3.000
 8JN  N15  C14  C13  104.69  3.000
 8JN  N17  C16  N15  111.49  3.000
 8JN  N15  C16  C18  124.59  3.000
 8JN  N17  C16  C18  123.91  3.000
 8JN  C19  C18  C25  106.66  3.000
 8JN  C19  C18  C22  103.72  3.000
 8JN  C25  C18  C22  104.12  3.000
 8JN  C22  C18  C16  113.75  3.000
 8JN  C19  C18  C16  112.07  3.000
 8JN  C25  C18  C16  115.49  3.000
 8JN  H3   C21  H2   107.66  3.000
 8JN  H3   C21  C20  110.43  3.000
 8JN  H2   C21  C20  113.98  3.000
 8JN  H3   C21  C22  111.83  3.000
 8JN  H2   C21  C22  112.11  3.000
 8JN  C20  C21  C22  100.82  3.000
 8JN  H4   C22  C23  113.69  3.000
 8JN  H4   C22  C21  113.48  3.000
 8JN  C23  C22  C21  107.59  3.000
 8JN  H4   C22  C18  113.19  3.000
 8JN  C21  C22  C18  104.13  3.000
 8JN  C23  C22  C18  103.86  3.000
 8JN  H6   C23  H5   107.58  3.000
 8JN  H6   C23  C24  114.00  3.000
 8JN  H5   C23  C24  110.42  3.000
 8JN  H6   C23  C22  112.11  3.000
 8JN  H5   C23  C22  111.95  3.000
 8JN  C24  C23  C22  100.78  3.000
 8JN  H7   C24  C26  110.46  3.000
 8JN  H7   C24  C25  112.77  3.000
 8JN  C26  C24  C25  110.13  3.000
 8JN  H7   C24  C23  113.66  3.000
 8JN  C26  C24  C23  109.91  3.000
 8JN  C25  C24  C23   99.44  3.000
 8JN  H9   C25  H8   107.81  3.000
 8JN  H9   C25  C24  109.46  3.000
 8JN  H8   C25  C24  114.13  3.000
 8JN  H9   C25  C18  112.25  3.000
 8JN  H8   C25  C18  112.54  3.000
 8JN  C24  C25  C18  100.60  3.000
 8JN  H11  C26  H10  106.64  3.000
 8JN  H11  C26  C20  109.70  3.000
 8JN  H10  C26  C20  109.53  3.000
 8JN  H11  C26  C24  109.47  3.000
 8JN  H10  C26  C24  109.56  3.000
 8JN  C20  C26  C24  111.80  3.000
 8JN  O28  C27  N05  122.26  3.000
 8JN  O28  C27  C14  126.17  3.000
 8JN  N05  C27  C14  111.57  3.000
 8JN  H14  C01  H13  107.56  3.000
 8JN  H14  C01  H12  107.69  3.000
 8JN  H13  C01  H12  107.65  3.000
 8JN  H14  C01  C02  111.07  3.000
 8JN  H13  C01  C02  111.23  3.000
 8JN  H12  C01  C02  111.45  3.000
 8JN  H16  C02  H15  106.19  3.000
 8JN  H16  C02  C03  109.41  3.000
 8JN  H15  C02  C03  109.50  3.000
 8JN  H16  C02  C01  109.52  3.000
 8JN  H15  C02  C01  109.61  3.000
 8JN  C03  C02  C01  112.42  3.000
 8JN  H18  C03  H17  106.83  3.000
 8JN  H18  C03  C04  109.52  3.000
 8JN  H17  C03  C04  109.73  3.000
 8JN  H18  C03  C02  109.56  3.000
 8JN  H17  C03  C02  109.55  3.000
 8JN  C04  C03  C02  111.54  3.000
 8JN  C06  N05  C04  116.35  3.000
 8JN  C04  N05  C27  117.13  3.000
 8JN  C06  N05  C27  126.46  3.000
 8JN  N08  C06  O07  120.99  3.000
 8JN  O07  C06  N05  120.95  3.000
 8JN  N08  C06  N05  118.07  3.000
 8JN  C09  N08  C06  117.30  3.000
 8JN  C06  N08  C13  118.58  3.000
 8JN  C09  N08  C13  124.10  3.000
 8JN  H21  C09  N08  112.19  3.000
 8JN  H21  C09  C10  120.03  3.000
 8JN  N08  C09  C10  127.78  3.000
 8JN  H23  C11  H22  106.76  3.000
 8JN  H23  C11  O12  111.76  3.000
 8JN  H22  C11  O12  110.75  3.000
 8JN  H23  C11  C10  110.11  3.000
 8JN  H22  C11  C10  108.84  3.000
 8JN  O12  C11  C10  108.58  3.000
 8JN  H24  O12  C11  107.89  3.000
 8JN  H25  N15  C16  126.59  3.000
 8JN  H25  N15  C14  125.98  3.000
 8JN  C16  N15  C14  107.43  3.000
 8JN  C16  N17  C13  105.14  3.000
 8JN  H28  C19  H27  107.84  3.000
 8JN  H28  C19  C20  114.38  3.000
 8JN  H27  C19  C20  110.48  3.000
 8JN  H28  C19  C18  111.89  3.000
 8JN  H27  C19  C18  111.38  3.000
 8JN  C20  C19  C18  100.83  3.000
 8JN  H29  C20  C19  112.90  3.000
 8JN  H29  C20  C26  110.55  3.000
 8JN  C19  C20  C26  109.70  3.000
 8JN  H29  C20  C21  113.61  3.000
 8JN  C19  C20  C21   99.45  3.000
 8JN  C26  C20  C21  110.13  3.000
 8JN  H20  C04  H19  107.08  3.000
 8JN  H20  C04  N05  108.31  3.000
 8JN  H19  C04  N05  107.46  3.000
 8JN  H20  C04  C03  110.76  3.000
 8JN  H19  C04  C03  110.23  3.000
 8JN  N05  C04  C03  112.79  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
 8JN  CONST_01  N15  C16  N17  C13     0.00   0.0  0
 8JN  CONST_02  C16  N15  C14  C13     0.00   0.0  0
 8JN  CONST_03  C16  N17  C13  C14     0.00   0.0  0
 8JN  CONST_04  N17  C16  N15  C14     0.00   0.0  0
 8JN  CONST_05  N17  C13  C14  N15     0.00   0.0  0
 8JN  CONST_06  C18  C16  N17  C13   180.00   0.0  0
 8JN  CONST_07  C18  C16  N15  C14   180.00   0.0  0
 8JN  CONST_08  N05  C06  N08  C13     0.00   0.0  0
 8JN  CONST_09  C06  N05  C27  C14     0.00   0.0  0
 8JN  CONST_10  N08  C06  N05  C27     0.00   0.0  0
 8JN  CONST_11  O07  C06  N08  C13   180.00   0.0  0
 8JN  CONST_12  C04  N05  C27  C14   180.00   0.0  0
 8JN  CONST_13  O07  C06  N05  C27   180.00   0.0  0
 8JN  CONST_14  N08  C06  N05  C04   180.00   0.0  0
 8JN  CONST_15  C09  N08  C06  N05   180.00   0.0  0
 8JN  CONST_16  O28  C27  N05  C06   180.00   0.0  0
 8JN  CONST_17  H25  N15  C14  C13   180.00   0.0  0
 8JN  CONST_18  O07  C06  N05  C04     0.00   0.0  0
 8JN  CONST_19  O28  C27  N05  C04     0.00   0.0  0
 8JN  CONST_20  C09  N08  C06  O07     0.00   0.0  0
 8JN  CONST_21  C11  C10  C09  N08   180.00   0.0  0
 8JN  CONST_22  H1   C10  C09  N08     0.00   0.0  0
 8JN  CONST_23  H21  C09  C10  C11     0.00   0.0  0
 8JN  Var_01    C24  C25  C18  C16   157.18  30.0  1
 8JN  Var_02    C20  C19  C18  C16  -154.65  30.0  3
 8JN  Var_03    N17  C16  C18  C22   -53.09  30.0  2
 8JN  Var_04    C13  N08  C09  C10     6.17  30.0  2
 8JN  Var_05    C03  C04  N05  C27    90.85  30.0  3
 8JN  Var_06    N05  C04  C03  C02   179.45  30.0  3
 8JN  Var_07    C04  C03  C02  C01  -179.98  30.0  3
 8JN  Var_08    O12  C11  C10  C09   120.71  30.0  2
 8JN  Var_09    H12  C01  C02  C03   179.01  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
 8JN  chir_01  C22  C18  C23  C21  positiv
 8JN  chir_02  C24  C23  C26  C25  negativ
 8JN  chir_03  C20  C21  C19  C26  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
 8JN  plan-1  C13  0.020
 8JN  plan-1  C14  0.020
 8JN  plan-1  C16  0.020
 8JN  plan-1  C18  0.020
 8JN  plan-1  C27  0.020
 8JN  plan-1  N05  0.020
 8JN  plan-1  C06  0.020
 8JN  plan-1  O07  0.020
 8JN  plan-1  N08  0.020
 8JN  plan-1  C09  0.020
 8JN  plan-1  N15  0.020
 8JN  plan-1  N17  0.020
 8JN  plan-1  H25  0.020
 8JN  plan-1  O28  0.020
 8JN  plan-1  C04  0.020
 8JN  plan-2  C10  0.020
 8JN  plan-2  N08  0.020
 8JN  plan-2  C09  0.020
 8JN  plan-2  C11  0.020
 8JN  plan-2  H1   0.020
 8JN  plan-2  H21  0.020

