# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 10:17:05 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-butyl-3-(3-oxidanylpropyl)-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(CCCO)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
 8K8  8K8  1-butyl-3-(3-oxidanylpropyl)-8-[(1~{R},5~{S})-3-tricyclo[3.3.1.0^{3,7}]nonanyl]-7~{H}-purine-2,6-dione  ligand  58  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 PERFECT
;

data_comp_8K8
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
 8K8  C10  C  CH2   0  -0.468   0.9298  -3.3933   0.5794
 8K8  C13  C  CR56  0   0.445   0.3367  -0.2589  -0.0232
 8K8  C14  C  CR56  0   0.110   0.5148   1.0342   0.3867
 8K8  C16  C  CR5   0   0.556  -1.6022   0.5819   0.0724
 8K8  C18  C  CT    0  -0.201  -3.0754   0.7370   0.0379
 8K8  C21  C  C     0  -0.416  -4.7545  -0.9142  -0.6782
 8K8  C22  C  CR16  0  -0.245  -3.7585   0.1041  -1.2455
 8K8  C23  C  C     0  -0.416  -4.5688   1.2628  -1.8390
 8K8  C24  C  CR16  0  -0.254  -4.9638   2.0161  -0.5695
 8K8  C25  C  CH2   0  -0.438  -3.5812   2.1911   0.0572
 8K8  C26  C  C     0  -0.419  -5.8412   1.1179   0.3210
 8K8  C27  C  CR6   0   0.544   1.7917   1.5981   0.6368
 8K8  C01  C  CH3   0  -0.661   6.9007   2.7460  -1.5750
 8K8  C02  C  CH2   0  -0.428   6.2528   2.1605  -0.3283
 8K8  C03  C  CH2   0  -0.423   4.8271   1.6865  -0.5830
 8K8  N05  N  NR6   0  -0.616   2.8170   0.6594   0.4579
 8K8  C06  C  CR6   0   0.747   2.6678  -0.6587   0.0331
 8K8  O07  O  O     0  -0.493   3.6310  -1.3886  -0.1103
 8K8  N08  N  NR6   0  -0.606   1.3925  -1.1010  -0.2204
 8K8  C09  C  CH2   0  -0.319   1.1591  -2.4827  -0.6193
 8K8  C11  C  CH2   0  -0.143   0.6446  -4.8145   0.1336
 8K8  O12  O  OH1   0  -0.672   0.4239  -5.6109   1.2767
 8K8  N15  N  NR15  0  -0.688  -0.7548   1.5559   0.4356
 8K8  N17  N  N     0  -0.476  -0.9608  -0.5451  -0.2144
 8K8  C19  C  CH2   0  -0.408  -3.7717   0.0190   1.2184
 8K8  C20  C  CR16  0  -0.259  -5.1565  -0.2277   0.6256
 8K8  H1   H  HCH2  0   0.239   1.8102  -3.3767   1.2267
 8K8  H2   H  H     0   0.231  -5.5878  -1.0967  -1.3609
 8K8  H3   H  H     0   0.234  -4.2803  -1.8771  -0.4718
 8K8  H4   H  HCR6  0   0.240  -3.0429  -0.3334  -1.9407
 8K8  H5   H  H     0   0.235  -3.9591   1.8998  -2.4851
 8K8  H6   H  H     0   0.232  -5.4190   0.9101  -2.4264
 8K8  H7   H  HCR6  0   0.230  -5.4634   2.9673  -0.7649
 8K8  H8   H  HCH2  0   0.247  -3.5978   2.6121   1.0646
 8K8  H9   H  HCH2  0   0.242  -2.9741   2.8474  -0.5736
 8K8  H10  H  H     0   0.230  -6.0685   1.6346   1.2583
 8K8  H11  H  H     0   0.231  -6.7989   0.9360  -0.1759
 8K8  H12  H  HCH3  0   0.229   7.9196   3.0797  -1.3765
 8K8  H13  H  HCH3  0   0.218   6.9444   2.0117  -2.3814
 8K8  H14  H  HCH3  0   0.219   6.3370   3.6057  -1.9414
 8K8  H15  H  HCH2  0   0.218   6.8537   1.3245   0.0426
 8K8  H16  H  HCH2  0   0.218   6.2500   2.9110   0.4676
 8K8  H17  H  HCH2  0   0.226   4.2263   2.5208  -0.9563
 8K8  H18  H  HCH2  0   0.226   4.8305   0.9226  -1.3659
 8K8  H19  H  HCH2  0   0.260   4.7731   0.2892   1.0609
 8K8  H20  H  HCH2  0   0.258   4.1602   1.8794   1.4596
 8K8  H21  H  HCH2  0   0.269   2.0100  -2.8175  -1.2084
 8K8  H22  H  HCH2  0   0.194  -0.2298  -4.8170  -0.5312
 8K8  H23  H  HCH2  0   0.195   1.4917  -5.1880  -0.4569
 8K8  H24  H  HOH1  0   0.454   0.2666  -6.5134   0.9855
 8K8  H25  H  HNR5  0   0.433  -1.0030   2.4942   0.7100
 8K8  H27  H  HCH2  0   0.243  -3.2843  -0.9291   1.4576
 8K8  H28  H  HCH2  0   0.242  -3.7701   0.6330   2.1221
 8K8  H29  H  HCR6  0   0.230  -5.7902  -0.8450   1.2665
 8K8  H30  H  HCH2  0   0.237   0.0847  -3.0166   1.1614
 8K8  H31  H  HCH2  0   0.264   0.2883  -2.4872  -1.2739
 8K8  O28  O  O     0  -0.473   2.0190   2.7484   0.9718
 8K8  C04  C  CH2   0  -0.302   4.1887   1.1227   0.6784

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
 8K8  C01  C02  single    1.522  0.020  1.522
 8K8  C02  C03  single    1.524  0.020  1.524
 8K8  C03  C04  single    1.522  0.020  1.522
 8K8  C04  N05  single    1.464  0.020  1.464
 8K8  O07  C06  double    1.217  0.020  1.217
 8K8  N05  C06  single    1.393  0.020  1.393
 8K8  N05  C27  single    1.402  0.020  1.402
 8K8  O28  C27  double    1.219  0.020  1.219
 8K8  C06  N08  single    1.374  0.020  1.374
 8K8  C27  C14  single    1.418  0.020  1.418
 8K8  N08  C09  single    1.457  0.020  1.457
 8K8  N08  C13  single    1.365  0.020  1.365
 8K8  C14  C13  aromatic  1.368  0.020  1.368
 8K8  C14  N15  aromatic  1.373  0.020  1.373
 8K8  C09  C10  single    1.523  0.020  1.523
 8K8  C13  N17  aromatic  1.342  0.020  1.342
 8K8  C10  C11  single    1.517  0.020  1.517
 8K8  N15  C16  aromatic  1.341  0.020  1.341
 8K8  C11  O12  single    1.411  0.020  1.411
 8K8  N17  C16  aromatic  1.328  0.020  1.328
 8K8  C16  C18  single    1.482  0.020  1.482
 8K8  C19  C18  single    1.547  0.020  1.547
 8K8  C19  C20  single    1.526  0.020  1.526
 8K8  C18  C25  single    1.540  0.020  1.540
 8K8  C18  C22  single    1.586  0.020  1.586
 8K8  C25  C24  single    1.528  0.020  1.528
 8K8  C20  C26  single    1.540  0.020  1.540
 8K8  C20  C21  single    1.527  0.020  1.527
 8K8  C22  C21  single    1.533  0.020  1.533
 8K8  C22  C23  single    1.533  0.020  1.533
 8K8  C24  C26  single    1.539  0.020  1.539
 8K8  C24  C23  single    1.528  0.020  1.528
 8K8  C10  H1   single    0.970  0.020  1.090
 8K8  C21  H2   single    0.970  0.020  1.090
 8K8  C21  H3   single    0.970  0.020  1.090
 8K8  C22  H4   single    0.970  0.020  1.090
 8K8  C23  H5   single    0.970  0.020  1.090
 8K8  C23  H6   single    0.970  0.020  1.090
 8K8  C24  H7   single    0.970  0.020  1.090
 8K8  C25  H8   single    0.970  0.020  1.090
 8K8  C25  H9   single    0.970  0.020  1.090
 8K8  C26  H10  single    0.970  0.020  1.090
 8K8  C26  H11  single    0.970  0.020  1.090
 8K8  C01  H12  single    0.970  0.020  1.090
 8K8  C01  H13  single    0.970  0.020  1.090
 8K8  C01  H14  single    0.970  0.020  1.090
 8K8  C02  H15  single    0.970  0.020  1.090
 8K8  C02  H16  single    0.970  0.020  1.090
 8K8  C03  H17  single    0.970  0.020  1.090
 8K8  C03  H18  single    0.970  0.020  1.090
 8K8  C04  H19  single    0.970  0.020  1.090
 8K8  C04  H20  single    0.970  0.020  1.090
 8K8  C09  H21  single    0.970  0.020  1.090
 8K8  C11  H22  single    0.970  0.020  1.090
 8K8  C11  H23  single    0.970  0.020  1.090
 8K8  O12  H24  single    0.850  0.020  0.980
 8K8  N15  H25  single    0.860  0.020  1.020
 8K8  C19  H27  single    0.970  0.020  1.090
 8K8  C19  H28  single    0.970  0.020  1.090
 8K8  C20  H29  single    0.970  0.020  1.090
 8K8  C10  H30  single    0.970  0.020  1.090
 8K8  C09  H31  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
 8K8  H30  C10  H1   107.59  3.000
 8K8  H30  C10  C11  109.52  3.000
 8K8  H1   C10  C11  109.86  3.000
 8K8  H30  C10  C09  109.24  3.000
 8K8  H1   C10  C09  109.62  3.000
 8K8  C11  C10  C09  110.93  3.000
 8K8  N17  C13  N08  126.55  3.000
 8K8  N17  C13  C14  111.71  3.000
 8K8  N08  C13  C14  121.72  3.000
 8K8  N15  C14  C27  132.46  3.000
 8K8  N15  C14  C13  104.44  3.000
 8K8  C27  C14  C13  123.08  3.000
 8K8  N17  C16  N15  111.70  3.000
 8K8  N17  C16  C18  124.33  3.000
 8K8  N15  C16  C18  123.95  3.000
 8K8  C19  C18  C25  106.31  3.000
 8K8  C25  C18  C22  104.21  3.000
 8K8  C19  C18  C22  103.79  3.000
 8K8  C22  C18  C16  113.91  3.000
 8K8  C25  C18  C16  115.16  3.000
 8K8  C19  C18  C16  112.41  3.000
 8K8  H3   C21  H2   107.56  3.000
 8K8  H3   C21  C20  110.42  3.000
 8K8  H2   C21  C20  114.06  3.000
 8K8  H3   C21  C22  111.91  3.000
 8K8  H2   C21  C22  112.04  3.000
 8K8  C20  C21  C22  100.85  3.000
 8K8  H4   C22  C23  113.80  3.000
 8K8  H4   C22  C21  113.33  3.000
 8K8  C23  C22  C21  107.56  3.000
 8K8  H4   C22  C18  113.19  3.000
 8K8  C23  C22  C18  103.85  3.000
 8K8  C21  C22  C18  104.21  3.000
 8K8  H6   C23  H5   107.73  3.000
 8K8  H6   C23  C24  113.88  3.000
 8K8  H5   C23  C24  110.37  3.000
 8K8  H6   C23  C22  112.06  3.000
 8K8  H5   C23  C22  111.98  3.000
 8K8  C24  C23  C22  100.81  3.000
 8K8  H7   C24  C26  110.55  3.000
 8K8  H7   C24  C25  112.80  3.000
 8K8  C26  C24  C25  110.20  3.000
 8K8  H7   C24  C23  113.52  3.000
 8K8  C26  C24  C23  109.89  3.000
 8K8  C25  C24  C23   99.40  3.000
 8K8  H9   C25  H8   108.00  3.000
 8K8  H9   C25  C24  109.52  3.000
 8K8  H8   C25  C24  114.13  3.000
 8K8  H9   C25  C18  112.15  3.000
 8K8  H8   C25  C18  112.38  3.000
 8K8  C24  C25  C18  100.60  3.000
 8K8  H11  C26  H10  106.60  3.000
 8K8  H11  C26  C20  109.49  3.000
 8K8  H10  C26  C20  109.60  3.000
 8K8  H11  C26  C24  109.47  3.000
 8K8  H10  C26  C24  109.78  3.000
 8K8  C20  C26  C24  111.77  3.000
 8K8  O28  C27  N05  122.04  3.000
 8K8  O28  C27  C14  126.25  3.000
 8K8  N05  C27  C14  111.71  3.000
 8K8  H14  C01  H13  107.61  3.000
 8K8  H14  C01  H12  107.63  3.000
 8K8  H13  C01  H12  107.64  3.000
 8K8  H14  C01  C02  110.99  3.000
 8K8  H13  C01  C02  111.30  3.000
 8K8  H12  C01  C02  111.49  3.000
 8K8  H16  C02  H15  106.20  3.000
 8K8  H16  C02  C03  109.42  3.000
 8K8  H15  C02  C03  109.44  3.000
 8K8  H16  C02  C01  109.46  3.000
 8K8  H15  C02  C01  109.74  3.000
 8K8  C03  C02  C01  112.40  3.000
 8K8  H18  C03  H17  106.86  3.000
 8K8  H18  C03  C04  109.63  3.000
 8K8  H17  C03  C04  109.57  3.000
 8K8  H18  C03  C02  109.51  3.000
 8K8  H17  C03  C02  109.49  3.000
 8K8  C04  C03  C02  111.66  3.000
 8K8  C06  N05  C04  116.47  3.000
 8K8  C06  N05  C27  126.47  3.000
 8K8  C04  N05  C27  117.00  3.000
 8K8  N08  C06  O07  121.33  3.000
 8K8  N08  C06  N05  117.42  3.000
 8K8  O07  C06  N05  121.25  3.000
 8K8  C09  N08  C06  120.31  3.000
 8K8  C09  N08  C13  120.06  3.000
 8K8  C06  N08  C13  119.53  3.000
 8K8  H31  C09  H21  107.38  3.000
 8K8  H31  C09  N08  107.25  3.000
 8K8  H21  C09  N08  108.35  3.000
 8K8  H31  C09  C10  110.49  3.000
 8K8  H21  C09  C10  111.11  3.000
 8K8  N08  C09  C10  112.06  3.000
 8K8  H23  C11  H22  106.73  3.000
 8K8  H23  C11  O12  111.38  3.000
 8K8  H22  C11  O12  111.38  3.000
 8K8  H23  C11  C10  109.38  3.000
 8K8  H22  C11  C10  109.25  3.000
 8K8  O12  C11  C10  108.68  3.000
 8K8  H24  O12  C11  108.07  3.000
 8K8  H25  N15  C16  126.43  3.000
 8K8  H25  N15  C14  126.19  3.000
 8K8  C16  N15  C14  107.37  3.000
 8K8  C16  N17  C13  104.78  3.000
 8K8  H28  C19  H27  107.81  3.000
 8K8  H28  C19  C20  114.42  3.000
 8K8  H27  C19  C20  110.46  3.000
 8K8  H28  C19  C18  111.69  3.000
 8K8  H27  C19  C18  111.65  3.000
 8K8  C20  C19  C18  100.78  3.000
 8K8  H29  C20  C19  112.94  3.000
 8K8  H29  C20  C26  110.60  3.000
 8K8  C19  C20  C26  109.81  3.000
 8K8  H29  C20  C21  113.55  3.000
 8K8  C26  C20  C21  109.93  3.000
 8K8  C19  C20  C21   99.52  3.000
 8K8  H20  C04  H19  107.13  3.000
 8K8  H20  C04  N05  107.68  3.000
 8K8  H19  C04  N05  108.29  3.000
 8K8  H20  C04  C03  110.40  3.000
 8K8  H19  C04  C03  110.49  3.000
 8K8  N05  C04  C03  112.66  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
 8K8  CONST_01  C16  N15  C14  C13     0.00   0.0  0
 8K8  CONST_02  N15  C16  N17  C13     0.00   0.0  0
 8K8  CONST_03  C16  N17  C13  C14     0.00   0.0  0
 8K8  CONST_04  N17  C16  N15  C14     0.00   0.0  0
 8K8  CONST_05  N17  C13  C14  N15     0.00   0.0  0
 8K8  CONST_06  C18  C16  N17  C13   180.00   0.0  0
 8K8  CONST_07  C18  C16  N15  C14   180.00   0.0  0
 8K8  CONST_08  N05  C06  N08  C13     0.00   0.0  0
 8K8  CONST_09  C06  N05  C27  C14     0.00   0.0  0
 8K8  CONST_10  N08  C06  N05  C27     0.00   0.0  0
 8K8  CONST_11  O07  C06  N08  C13   180.00   0.0  0
 8K8  CONST_12  C04  N05  C27  C14   180.00   0.0  0
 8K8  CONST_13  O07  C06  N05  C27   180.00   0.0  0
 8K8  CONST_14  N08  C06  N05  C04   180.00   0.0  0
 8K8  CONST_15  C09  N08  C06  N05   180.00   0.0  0
 8K8  CONST_16  O28  C27  N05  C06   180.00   0.0  0
 8K8  CONST_17  H25  N15  C14  C13   180.00   0.0  0
 8K8  CONST_18  O07  C06  N05  C04     0.00   0.0  0
 8K8  CONST_19  O28  C27  N05  C04     0.00   0.0  0
 8K8  CONST_20  C09  N08  C06  O07     0.00   0.0  0
 8K8  Var_01    C20  C19  C18  C16  -154.96  30.0  3
 8K8  Var_02    C24  C25  C18  C16   157.00  30.0  1
 8K8  Var_03    N15  C16  C18  C22   137.03  30.0  2
 8K8  Var_04    C06  N08  C09  C10    89.83  30.0  3
 8K8  Var_05    C03  C04  N05  C27   -89.28  30.0  2
 8K8  Var_06    N05  C04  C03  C02  -179.96  30.0  3
 8K8  Var_07    C11  C10  C09  N08   178.13  30.0  3
 8K8  Var_08    C04  C03  C02  C01  -179.18  30.0  3
 8K8  Var_09    O12  C11  C10  C09  -179.28  30.0  3
 8K8  Var_10    H12  C01  C02  C03  -179.97  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
 8K8  chir_01  C22  C18  C21  C23  negativ
 8K8  chir_02  C24  C23  C26  C25  negativ
 8K8  chir_03  C20  C21  C26  C19  positiv

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
 8K8  plan-1  C13  0.020
 8K8  plan-1  C14  0.020
 8K8  plan-1  C16  0.020
 8K8  plan-1  C18  0.020
 8K8  plan-1  C27  0.020
 8K8  plan-1  N05  0.020
 8K8  plan-1  C06  0.020
 8K8  plan-1  O07  0.020
 8K8  plan-1  N08  0.020
 8K8  plan-1  C09  0.020
 8K8  plan-1  N15  0.020
 8K8  plan-1  N17  0.020
 8K8  plan-1  H25  0.020
 8K8  plan-1  O28  0.020
 8K8  plan-1  C04  0.020

