# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 08:29:49 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 8-[(3~{R})-3-azanylpiperidin-1-yl]-7-[(2-bromophenyl)methyl]-1,3-dimethyl-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2nc(N3CCC[C@@H](N)C3)n(Cc4ccccc4Br)c2C1=O
#
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
 6Z8  6Z8  8-[(3~{R})-3-azanylpiperidin-1-yl]-7-[(2-bromophenyl)methyl]-1,3-dimethyl-purine-2,6-dione  ligand  51  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6Z8
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
 6Z8  N1   N   NR5   0  -0.548  -0.8758   0.1796   0.8039
 6Z8  C4   C   CH2   0  -0.391   0.0400  -0.8375   1.2795
 6Z8  C5   C   CR56  0   0.469  -2.6293   1.0902  -0.1313
 6Z8  C6   C   CR6   0   0.569  -3.1691  -0.9354   1.1143
 6Z8  C13  C   CH2   0  -0.300   1.0420   2.6630  -1.0648
 6Z8  C15  C   CR6   0  -0.180   2.1177  -2.0046   0.3808
 6Z8  C17  C   CR6   0   0.726  -4.8989   0.4235  -0.0594
 6Z8  C20  C   CH1   0  -0.111   2.5166   2.5200  -1.4286
 6Z8  C21  C   CH2   0  -0.442   2.9773   1.9485   0.9887
 6Z8  C22  C   CR16  0  -0.221   2.8600  -2.5609  -0.6535
 6Z8  C24  C   CR16  0  -0.235   1.0695  -2.0691  -2.1698
 6Z8  C26  C   CH2   0  -0.454   3.3852   2.8112  -0.1997
 6Z8  C28  C   CR16  0  -0.262   2.3345  -2.5868  -1.9351
 6Z8  C2   C   CR56  0   0.104  -2.2443   0.0236   0.6326
 6Z8  C3   C   CR5   0   0.724  -0.5476   1.3205   0.1454
 6Z8  N7   N   N     0  -0.500  -1.5972   1.8948  -0.4289
 6Z8  N8   N   NT    0  -0.526   0.7327   1.7669   0.0428
 6Z8  C9   C   CR6   0   0.146   0.8583  -1.4481   0.1663
 6Z8  N10  N   NR6   0  -0.593  -3.9263   1.2884  -0.4988
 6Z8  N11  N   NR6   0  -0.602  -4.4773  -0.6690   0.6898
 6Z8  O12  O   O     0  -0.480  -2.9288  -1.9045   1.8192
 6Z8  C14  C   CH2   0  -0.322   1.4893   2.0910   1.2541
 6Z8  C16  C   CR16  0  -0.280   0.3468  -1.5108  -1.1292
 6Z8  C18  C   CH3   0  -0.531  -4.2978   2.4643  -1.2685
 6Z8  C19  C   CH3   0  -0.530  -5.4873  -1.6248   1.1316
 6Z8  O25  O   O     0  -0.493  -6.0724   0.6108  -0.3215
 6Z8  N27  N   NH2   0  -0.795   2.7295   1.2116  -2.0322
 6Z8  H1   H   HCH2  0   0.282   0.6727  -0.4189   2.0580
 6Z8  H2   H   HCH2  0   0.318  -0.5576  -1.6080   1.7647
 6Z8  H3   H   HCH2  0   0.232   0.8218   3.7041  -0.7973
 6Z8  H4   H   HCH2  0   0.259   0.4257   2.4003  -1.9230
 6Z8  H5   H   HCH1  0   0.238   2.7304   3.2779  -2.1889
 6Z8  H6   H   HCH2  0   0.221   3.2152   0.8974   0.8039
 6Z8  H7   H   HCH2  0   0.246   3.5284   2.2432   1.8837
 6Z8  H8   H   HCR6  0   0.282   3.8417  -2.9736  -0.4635
 6Z8  H9   H   HCR6  0   0.268   0.6445  -2.0952  -3.1640
 6Z8  H10  H   HCH2  0   0.239   4.4393   2.6573  -0.4452
 6Z8  H11  H   HCH2  0   0.219   3.2784   3.8675   0.0700
 6Z8  H12  H   HCR6  0   0.271   2.9136  -3.0159  -2.7415
 6Z8  H13  H   HCH2  0   0.261   1.1796   1.4546   2.0802
 6Z8  H14  H   HCH2  0   0.241   1.2628   3.1239   1.5534
 6Z8  H15  H   HCR6  0   0.268  -0.6371  -1.1088  -1.3362
 6Z8  H16  H   HCH3  0   0.265  -5.1607   2.2447  -1.8877
 6Z8  H17  H   HCH3  0   0.257  -4.5307   3.3038  -0.6141
 6Z8  H18  H   HCH3  0   0.263  -3.4662   2.7394  -1.9098
 6Z8  H19  H   HCH3  0   0.268  -6.4411  -1.3700   0.6885
 6Z8  H20  H   HCH3  0   0.255  -5.2121  -2.6301   0.8219
 6Z8  H21  H   HCH3  0   0.253  -5.5875  -1.6055   2.2154
 6Z8  H22  H   HNH2  0   0.342   3.7220   1.0319  -2.1238
 6Z8  H23  H   HNH2  0   0.349   2.3680   0.4879  -1.4222
 6Z8  BR   BR  BR    0  -0.039   2.8758  -2.0534   2.1171

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
 6Z8  C19  N11  single    1.459  0.020  1.459
 6Z8  O25  C17  double    1.217  0.020  1.217
 6Z8  N11  C17  single    1.390  0.020  1.390
 6Z8  N11  C6   single    1.401  0.020  1.401
 6Z8  C17  N10  single    1.374  0.020  1.374
 6Z8  O12  C6   double    1.222  0.020  1.222
 6Z8  C6   C2   single    1.417  0.020  1.417
 6Z8  N10  C18  single    1.454  0.020  1.454
 6Z8  N10  C5   single    1.363  0.020  1.363
 6Z8  C2   C5   aromatic  1.367  0.020  1.367
 6Z8  C2   N1   aromatic  1.388  0.020  1.388
 6Z8  C5   N7   aromatic  1.342  0.020  1.342
 6Z8  N1   C4   single    1.449  0.020  1.449
 6Z8  N1   C3   aromatic  1.358  0.020  1.358
 6Z8  N7   C3   aromatic  1.327  0.020  1.327
 6Z8  C4   C9   single    1.511  0.020  1.511
 6Z8  C16  C9   aromatic  1.394  0.020  1.394
 6Z8  C16  C24  aromatic  1.385  0.020  1.385
 6Z8  C9   C15  aromatic  1.393  0.020  1.393
 6Z8  C24  C28  aromatic  1.387  0.020  1.387
 6Z8  C15  C22  aromatic  1.389  0.020  1.389
 6Z8  C15  BR   single    1.895  0.020  1.895
 6Z8  C28  C22  aromatic  1.385  0.020  1.385
 6Z8  C3   N8   single    1.360  0.020  1.360
 6Z8  N8   C13  single    1.458  0.020  1.458
 6Z8  N8   C14  single    1.464  0.020  1.464
 6Z8  C13  C20  single    1.526  0.020  1.526
 6Z8  C14  C21  single    1.518  0.020  1.518
 6Z8  C20  N27  single    1.457  0.020  1.457
 6Z8  C20  C26  single    1.533  0.020  1.533
 6Z8  C21  C26  single    1.524  0.020  1.524
 6Z8  C4   H1   single    0.970  0.020  1.090
 6Z8  C4   H2   single    0.970  0.020  1.090
 6Z8  C13  H3   single    0.970  0.020  1.090
 6Z8  C13  H4   single    0.970  0.020  1.090
 6Z8  C20  H5   single    0.970  0.020  1.090
 6Z8  C21  H6   single    0.970  0.020  1.090
 6Z8  C21  H7   single    0.970  0.020  1.090
 6Z8  C22  H8   single    0.930  0.020  1.080
 6Z8  C24  H9   single    0.930  0.020  1.080
 6Z8  C26  H10  single    0.970  0.020  1.090
 6Z8  C26  H11  single    0.970  0.020  1.090
 6Z8  C28  H12  single    0.930  0.020  1.080
 6Z8  C14  H13  single    0.970  0.020  1.090
 6Z8  C14  H14  single    0.970  0.020  1.090
 6Z8  C16  H15  single    0.930  0.020  1.080
 6Z8  C18  H16  single    0.970  0.020  1.090
 6Z8  C18  H17  single    0.970  0.020  1.090
 6Z8  C18  H18  single    0.970  0.020  1.090
 6Z8  C19  H19  single    0.970  0.020  1.090
 6Z8  C19  H20  single    0.970  0.020  1.090
 6Z8  C19  H21  single    0.970  0.020  1.090
 6Z8  N27  H22  single    0.890  0.020  1.040
 6Z8  N27  H23  single    0.890  0.020  1.040

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
 6Z8  C3   N1   C2   105.84  3.000
 6Z8  C3   N1   C4   126.61  3.000
 6Z8  C2   N1   C4   125.79  3.000
 6Z8  H2   C4   H1   105.83  3.000
 6Z8  H2   C4   C9   109.85  3.000
 6Z8  H1   C4   C9   111.60  3.000
 6Z8  H2   C4   N1   107.21  3.000
 6Z8  H1   C4   N1   109.43  3.000
 6Z8  C9   C4   N1   112.60  3.000
 6Z8  N10  C5   N7   125.80  3.000
 6Z8  N7   C5   C2   112.03  3.000
 6Z8  N10  C5   C2   122.16  3.000
 6Z8  O12  C6   N11  120.60  3.000
 6Z8  O12  C6   C2   127.20  3.000
 6Z8  N11  C6   C2   112.20  3.000
 6Z8  H4   C13  H3   107.91  3.000
 6Z8  H4   C13  N8   109.30  3.000
 6Z8  H3   C13  N8   110.82  3.000
 6Z8  H4   C13  C20  109.66  3.000
 6Z8  H3   C13  C20  109.94  3.000
 6Z8  N8   C13  C20  109.19  3.000
 6Z8  BR   C15  C9   120.85  3.000
 6Z8  BR   C15  C22  117.26  3.000
 6Z8  C9   C15  C22  121.88  3.000
 6Z8  O25  C17  N11  121.97  3.000
 6Z8  N11  C17  N10  116.90  3.000
 6Z8  O25  C17  N10  121.13  3.000
 6Z8  H5   C20  N27  107.80  3.000
 6Z8  H5   C20  C26  108.34  3.000
 6Z8  N27  C20  C26  114.83  3.000
 6Z8  H5   C20  C13  106.83  3.000
 6Z8  C26  C20  C13  109.80  3.000
 6Z8  N27  C20  C13  108.93  3.000
 6Z8  H7   C21  H6   106.76  3.000
 6Z8  H7   C21  C14  109.03  3.000
 6Z8  H6   C21  C14  109.45  3.000
 6Z8  H7   C21  C26  110.57  3.000
 6Z8  H6   C21  C26  110.74  3.000
 6Z8  C14  C21  C26  110.21  3.000
 6Z8  H8   C22  C28  119.97  3.000
 6Z8  H8   C22  C15  120.45  3.000
 6Z8  C28  C22  C15  119.57  3.000
 6Z8  H9   C24  C16  119.70  3.000
 6Z8  H9   C24  C28  120.34  3.000
 6Z8  C16  C24  C28  119.96  3.000
 6Z8  H11  C26  H10  106.56  3.000
 6Z8  H11  C26  C21  109.13  3.000
 6Z8  H10  C26  C21  110.70  3.000
 6Z8  H11  C26  C20  108.98  3.000
 6Z8  H10  C26  C20  109.85  3.000
 6Z8  C21  C26  C20  111.47  3.000
 6Z8  H12  C28  C24  120.68  3.000
 6Z8  H12  C28  C22  119.61  3.000
 6Z8  C24  C28  C22  119.71  3.000
 6Z8  C6   C2   C5   122.29  3.000
 6Z8  C5   C2   N1   105.01  3.000
 6Z8  C6   C2   N1   132.67  3.000
 6Z8  N8   C3   N7   124.74  3.000
 6Z8  N8   C3   N1   122.69  3.000
 6Z8  N7   C3   N1   112.48  3.000
 6Z8  C3   N7   C5   104.64  3.000
 6Z8  C14  N8   C3   119.77  3.000
 6Z8  C14  N8   C13  112.51  3.000
 6Z8  C3   N8   C13  117.31  3.000
 6Z8  C16  C9   C15  117.17  3.000
 6Z8  C15  C9   C4   122.52  3.000
 6Z8  C16  C9   C4   120.28  3.000
 6Z8  C18  N10  C17  119.85  3.000
 6Z8  C18  N10  C5   120.25  3.000
 6Z8  C17  N10  C5   119.74  3.000
 6Z8  C19  N11  C17  117.91  3.000
 6Z8  C17  N11  C6   126.58  3.000
 6Z8  C19  N11  C6   115.48  3.000
 6Z8  H14  C14  H13  106.52  3.000
 6Z8  H14  C14  N8   109.07  3.000
 6Z8  H13  C14  N8   110.59  3.000
 6Z8  H14  C14  C21  109.74  3.000
 6Z8  H13  C14  C21  110.91  3.000
 6Z8  N8   C14  C21  109.94  3.000
 6Z8  H15  C16  C9   119.63  3.000
 6Z8  H15  C16  C24  118.70  3.000
 6Z8  C9   C16  C24  121.67  3.000
 6Z8  H18  C18  H17  108.86  3.000
 6Z8  H18  C18  H16  108.88  3.000
 6Z8  H17  C18  H16  109.20  3.000
 6Z8  H18  C18  N10  108.78  3.000
 6Z8  H17  C18  N10  111.09  3.000
 6Z8  H16  C18  N10  109.99  3.000
 6Z8  H21  C19  H20  108.86  3.000
 6Z8  H21  C19  H19  108.80  3.000
 6Z8  H20  C19  H19  108.92  3.000
 6Z8  H21  C19  N11  110.70  3.000
 6Z8  H20  C19  N11  110.13  3.000
 6Z8  H19  C19  N11  109.39  3.000
 6Z8  H23  N27  H22  106.11  3.000
 6Z8  H23  N27  C20  109.88  3.000
 6Z8  H22  N27  C20  109.89  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
 6Z8  CONST_01  N7   C5   C2   N1      0.00   0.0  0
 6Z8  CONST_02  C5   N7   C3   N1      0.00   0.0  0
 6Z8  CONST_03  C3   N1   C2   C5      0.00   0.0  0
 6Z8  CONST_04  C24  C16  C9   C15     0.00   0.0  0
 6Z8  CONST_05  C24  C28  C22  C15     0.00   0.0  0
 6Z8  CONST_06  C16  C9   C15  C22     0.00   0.0  0
 6Z8  CONST_07  C16  C24  C28  C22     0.00   0.0  0
 6Z8  CONST_08  C9   C16  C24  C28     0.00   0.0  0
 6Z8  CONST_09  C9   C15  C22  C28     0.00   0.0  0
 6Z8  CONST_10  C3   N7   C5   C2      0.00   0.0  0
 6Z8  CONST_11  N7   C3   N1   C2      0.00   0.0  0
 6Z8  CONST_12  N8   C3   N7   C5    180.00   0.0  0
 6Z8  CONST_13  N8   C3   N1   C2    180.00   0.0  0
 6Z8  CONST_14  N11  C17  N10  C5      0.00   0.0  0
 6Z8  CONST_15  N10  C17  N11  C6      0.00   0.0  0
 6Z8  CONST_16  C2   C6   N11  C17     0.00   0.0  0
 6Z8  CONST_18  C5   C2   N1   C4    180.00   0.0  0
 6Z8  CONST_19  N7   C3   N1   C4    180.00   0.0  0
 6Z8  CONST_20  N8   C3   N1   C4      0.00   0.0  0
 6Z8  CONST_21  C24  C16  C9   C4    180.00   0.0  0
 6Z8  CONST_22  C22  C15  C9   C4    180.00   0.0  0
 6Z8  CONST_23  BR   C15  C22  C28   180.00   0.0  0
 6Z8  CONST_24  BR   C15  C9   C16   180.00   0.0  0
 6Z8  CONST_25  O25  C17  N10  C5    180.00   0.0  0
 6Z8  CONST_26  O25  C17  N11  C6    180.00   0.0  0
 6Z8  CONST_27  O12  C6   N11  C17   180.00   0.0  0
 6Z8  CONST_28  C19  N11  C6   C2    180.00   0.0  0
 6Z8  CONST_29  C19  N11  C17  N10   180.00   0.0  0
 6Z8  CONST_30  C18  N10  C17  N11   180.00   0.0  0
 6Z8  CONST_31  H15  C16  C9   C15   180.00   0.0  0
 6Z8  CONST_32  H12  C28  C22  C15   180.00   0.0  0
 6Z8  CONST_33  H9   C24  C28  C22   180.00   0.0  0
 6Z8  CONST_34  H8   C22  C28  C24   180.00   0.0  0
 6Z8  CONST_35  C19  N11  C6   O12     0.00   0.0  0
 6Z8  CONST_36  O25  C17  N10  C18     0.00   0.0  0
 6Z8  CONST_37  O25  C17  N11  C19     0.00   0.0  0
 6Z8  Var_01    C13  N8   C3   N1    157.04  30.0  2
 6Z8  Var_02    C21  C14  N8   C13   -61.57  30.0  1
 6Z8  Var_03    C3   N8   C13  C20  -152.83  30.0  1
 6Z8  Var_04    C14  C21  C26  C20   -53.14  30.0  1
 6Z8  Var_05    N8   C14  C21  C26    55.54  30.0  1
 6Z8  Var_06    C16  C9   C4   N1    -28.74  30.0  2
 6Z8  Var_07    C9   C4   N1   C2    103.35  30.0  2
 6Z8  Var_08    H16  C18  N10  C5    150.95  30.0  3
 6Z8  Var_09    H19  C19  N11  C6   -175.68  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
 6Z8  chir_01  C20  C13  N27  C26  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
 6Z8  plan-1  C4   0.020
 6Z8  plan-1  C15  0.020
 6Z8  plan-1  C22  0.020
 6Z8  plan-1  C24  0.020
 6Z8  plan-1  C28  0.020
 6Z8  plan-1  C9   0.020
 6Z8  plan-1  C16  0.020
 6Z8  plan-1  H8   0.020
 6Z8  plan-1  H9   0.020
 6Z8  plan-1  H12  0.020
 6Z8  plan-1  H15  0.020
 6Z8  plan-1  BR   0.020
 6Z8  plan-2  N1   0.020
 6Z8  plan-2  C4   0.020
 6Z8  plan-2  C5   0.020
 6Z8  plan-2  C6   0.020
 6Z8  plan-2  C17  0.020
 6Z8  plan-2  C2   0.020
 6Z8  plan-2  C3   0.020
 6Z8  plan-2  N7   0.020
 6Z8  plan-2  N8   0.020
 6Z8  plan-2  N10  0.020
 6Z8  plan-2  N11  0.020
 6Z8  plan-2  O12  0.020
 6Z8  plan-2  C18  0.020
 6Z8  plan-2  C19  0.020
 6Z8  plan-2  O25  0.020

