# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 18:11:14 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 7-(2-chlorobenzyl)-1,3-dimethyl-8-piperazin-1-yl-3,7-dihydro-1H-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2nc(N3CCNCC3)n(Cc4ccccc4Cl)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
 RUF  RUF  7-(2-chlorobenzyl)-1,3-dimethyl-8-piperazin-1-yl-3,7-dihydro-1H-purine-2,6-dione  ligand  48  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RUF
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
 RUF  C1    C   CH3   0  -0.533  -3.0979  -2.6885   1.5815
 RUF  N2    N   NR6   0  -0.596  -2.9187  -1.5618   0.6806
 RUF  C3    C   CR56  0   0.468  -1.6875  -1.1905   0.2318
 RUF  N4    N   N     0  -0.497  -0.5290  -1.8101   0.5045
 RUF  C5    C   CR5   0   0.719   0.3814  -1.1288  -0.1749
 RUF  N6    N   NT    0  -0.512   1.7192  -1.4196  -0.1997
 RUF  C7    C   CH2   0  -0.329   2.2085  -1.9667  -1.4735
 RUF  C8    C   CH2   0  -0.322   3.7277  -2.0675  -1.4635
 RUF  N9    N   NH1   0  -0.578   4.2643  -2.7686  -0.3118
 RUF  C10   C   CH2   0  -0.327   3.7217  -2.2238   0.9207
 RUF  C11   C   CH2   0  -0.302   2.2007  -2.1860   0.9453
 RUF  N12   N   NR5   0  -0.530  -0.1478  -0.0946  -0.8709
 RUF  C13   C   CH2   0  -0.430   0.5881   1.0506  -1.3934
 RUF  C14   C   CR6   0   0.210   0.9164   2.0471  -0.3061
 RUF  C15   C   CR16  0  -0.302  -0.1185   2.7716   0.2876
 RUF  C16   C   CR16  0  -0.231   0.1136   3.6731   1.3120
 RUF  C17   C   CR16  0  -0.272   1.4084   3.8803   1.7665
 RUF  C18   C   CR16  0  -0.199   2.4595   3.1979   1.1789
 RUF  C19   C   CR6   0  -0.111   2.2081   2.2969   0.1516
 RUF  CL20  CL  CL    0  -0.118   3.5845   1.5270  -0.5708
 RUF  C21   C   CR56  0   0.106  -1.5130  -0.1317  -0.6185
 RUF  C22   C   CR6   0   0.558  -2.6016   0.6088  -1.1462
 RUF  O23   O   O     0  -0.480  -2.5341   1.5193  -1.9597
 RUF  N24   N   NR6   0  -0.605  -3.8288   0.1874  -0.6156
 RUF  C25   C   CH3   0  -0.528  -5.0420   0.8821  -1.0302
 RUF  C26   C   CR6   0   0.753  -4.0248  -0.8652   0.2672
 RUF  O27   O   O     0  -0.496  -5.1388  -1.1639   0.6540
 RUF  H1    H   HCH3  0   0.259  -3.5311  -2.3621   2.5246
 RUF  H1A   H   HCH3  0   0.259  -3.7432  -3.4409   1.1335
 RUF  H1B   H   HCH3  0   0.269  -2.1258  -3.1293   1.7739
 RUF  H7    H   HCH2  0   0.232   1.7743  -2.9625  -1.6432
 RUF  H7A   H   HCH2  0   0.256   1.8896  -1.3333  -2.3021
 RUF  H8    H   HCH2  0   0.246   4.0495  -2.5727  -2.3756
 RUF  H8A   H   HCH2  0   0.225   4.1532  -1.0626  -1.4879
 RUF  HN9   H   HNH1  0   0.343   4.0199  -3.7509  -0.3751
 RUF  H10   H   HCH2  0   0.244   4.0779  -2.8181   1.7638
 RUF  H10A  H   HCH2  0   0.224   4.1068  -1.2089   1.0539
 RUF  H11   H   HCH2  0   0.251   1.8522  -1.7123   1.8634
 RUF  H11A  H   HCH2  0   0.217   1.8118  -3.2136   0.9320
 RUF  H13   H   HCH2  0   0.289   1.4848   0.6977  -1.8932
 RUF  H13A  H   HCH2  0   0.306  -0.0335   1.5191  -2.1530
 RUF  H15   H   HCR6  0   0.270  -1.1289   2.6429  -0.0757
 RUF  H16   H   HCR6  0   0.265  -0.7129   4.2189   1.7464
 RUF  H17   H   HCR6  0   0.271   1.6049   4.5801   2.5677
 RUF  H18   H   HCR6  0   0.281   3.4742   3.3657   1.5129
 RUF  H25   H   HCH3  0   0.254  -5.7080   0.2089  -1.5662
 RUF  H25A  H   HCH3  0   0.255  -5.5654   1.2839  -0.1657
 RUF  H25B  H   HCH3  0   0.267  -4.7700   1.7003  -1.6855

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
 RUF  C1   N2    single    1.454  0.020  1.454
 RUF  C1   H1    single    0.970  0.020  1.090
 RUF  C1   H1A   single    0.970  0.020  1.090
 RUF  C1   H1B   single    0.970  0.020  1.090
 RUF  C26  N2    single    1.371  0.020  1.371
 RUF  N2   C3    single    1.362  0.020  1.362
 RUF  C3   C21   aromatic  1.369  0.020  1.369
 RUF  C3   N4    aromatic  1.342  0.020  1.342
 RUF  N4   C5    aromatic  1.325  0.020  1.325
 RUF  N12  C5    aromatic  1.354  0.020  1.354
 RUF  C5   N6    single    1.369  0.020  1.369
 RUF  N6   C11   single    1.460  0.020  1.460
 RUF  N6   C7    single    1.470  0.020  1.470
 RUF  C8   C7    single    1.523  0.020  1.523
 RUF  C7   H7    single    0.970  0.020  1.090
 RUF  C7   H7A   single    0.970  0.020  1.090
 RUF  C8   N9    single    1.451  0.020  1.451
 RUF  C8   H8    single    0.970  0.020  1.090
 RUF  C8   H8A   single    0.970  0.020  1.090
 RUF  C10  N9    single    1.453  0.020  1.453
 RUF  N9   HN9   single    0.890  0.020  1.040
 RUF  C10  C11   single    1.522  0.020  1.522
 RUF  C10  H10   single    0.970  0.020  1.090
 RUF  C10  H10A  single    0.970  0.020  1.090
 RUF  C11  H11   single    0.970  0.020  1.090
 RUF  C11  H11A  single    0.970  0.020  1.090
 RUF  C21  N12   aromatic  1.389  0.020  1.389
 RUF  N12  C13   single    1.458  0.020  1.458
 RUF  C14  C13   single    1.511  0.020  1.511
 RUF  C13  H13   single    0.970  0.020  1.090
 RUF  C13  H13A  single    0.970  0.020  1.090
 RUF  C15  C14   aromatic  1.396  0.020  1.396
 RUF  C14  C19   aromatic  1.393  0.020  1.393
 RUF  C16  C15   aromatic  1.384  0.020  1.384
 RUF  C15  H15   single    0.930  0.020  1.080
 RUF  C16  C17   aromatic  1.388  0.020  1.388
 RUF  C16  H16   single    0.930  0.020  1.080
 RUF  C17  C18   aromatic  1.384  0.020  1.384
 RUF  C17  H17   single    0.930  0.020  1.080
 RUF  C18  C19   aromatic  1.389  0.020  1.389
 RUF  C18  H18   single    0.930  0.020  1.080
 RUF  C19  CL20  single    1.735  0.020  1.735
 RUF  C22  C21   single    1.418  0.020  1.418
 RUF  N24  C22   single    1.402  0.020  1.402
 RUF  C22  O23   double    1.223  0.020  1.223
 RUF  C25  N24   single    1.458  0.020  1.458
 RUF  C26  N24   single    1.388  0.020  1.388
 RUF  C25  H25   single    0.970  0.020  1.090
 RUF  C25  H25A  single    0.970  0.020  1.090
 RUF  C25  H25B  single    0.970  0.020  1.090
 RUF  O27  C26   double    1.217  0.020  1.217

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
 RUF  H1B   C1   H1A   108.88  3.000
 RUF  H1B   C1   H1    108.97  3.000
 RUF  H1A   C1   H1    109.17  3.000
 RUF  H1B   C1   N2    108.33  3.000
 RUF  H1A   C1   N2    110.73  3.000
 RUF  H1    C1   N2    110.72  3.000
 RUF  C26   N2   C3    119.44  3.000
 RUF  C3    N2   C1    121.80  3.000
 RUF  C26   N2   C1    118.76  3.000
 RUF  C21   C3   N4    111.92  3.000
 RUF  N4    C3   N2    125.99  3.000
 RUF  C21   C3   N2    122.05  3.000
 RUF  C5    N4   C3    104.57  3.000
 RUF  N12   C5   N6    122.32  3.000
 RUF  N6    C5   N4    124.86  3.000
 RUF  N12   C5   N4    112.82  3.000
 RUF  C11   N6   C7    111.99  3.000
 RUF  C7    N6   C5    114.83  3.000
 RUF  C11   N6   C5    114.81  3.000
 RUF  H7A   C7   H7    107.05  3.000
 RUF  H7A   C7   C8    109.59  3.000
 RUF  H7    C7   C8    109.58  3.000
 RUF  H7A   C7   N6    110.17  3.000
 RUF  H7    C7   N6    109.83  3.000
 RUF  C8    C7   N6    110.55  3.000
 RUF  H8A   C8   H8    107.02  3.000
 RUF  H8A   C8   N9    108.56  3.000
 RUF  H8    C8   N9    109.31  3.000
 RUF  H8A   C8   C7    109.14  3.000
 RUF  H8    C8   C7    108.63  3.000
 RUF  N9    C8   C7    113.96  3.000
 RUF  HN9   N9   C10   109.04  3.000
 RUF  HN9   N9   C8    109.22  3.000
 RUF  C10   N9   C8    110.73  3.000
 RUF  H10A  C10  H10   107.24  3.000
 RUF  H10A  C10  C11   109.08  3.000
 RUF  H10   C10  C11   109.10  3.000
 RUF  H10A  C10  N9    108.65  3.000
 RUF  H10   C10  N9    109.23  3.000
 RUF  C11   C10  N9    113.36  3.000
 RUF  H11A  C11  H11   107.66  3.000
 RUF  H11A  C11  C10   109.29  3.000
 RUF  H11   C11  C10   110.11  3.000
 RUF  H11A  C11  N6    111.40  3.000
 RUF  H11   C11  N6    109.09  3.000
 RUF  C10   C11  N6    109.27  3.000
 RUF  C21   N12  C13   125.60  3.000
 RUF  C13   N12  C5    125.93  3.000
 RUF  C21   N12  C5    105.68  3.000
 RUF  H13A  C13  H13   106.90  3.000
 RUF  H13A  C13  C14   110.04  3.000
 RUF  H13   C13  C14   111.49  3.000
 RUF  H13A  C13  N12   107.47  3.000
 RUF  H13   C13  N12   109.06  3.000
 RUF  C14   C13  N12   111.70  3.000
 RUF  C19   C14  C15   117.04  3.000
 RUF  C19   C14  C13   123.79  3.000
 RUF  C15   C14  C13   119.17  3.000
 RUF  H15   C15  C16   118.87  3.000
 RUF  H15   C15  C14   119.21  3.000
 RUF  C16   C15  C14   121.91  3.000
 RUF  H16   C16  C17   120.40  3.000
 RUF  H16   C16  C15   119.85  3.000
 RUF  C17   C16  C15   119.74  3.000
 RUF  H17   C17  C18   119.70  3.000
 RUF  H17   C17  C16   120.57  3.000
 RUF  C18   C17  C16   119.72  3.000
 RUF  H18   C18  C19   119.92  3.000
 RUF  H18   C18  C17   120.33  3.000
 RUF  C19   C18  C17   119.75  3.000
 RUF  CL20  C19  C18   116.88  3.000
 RUF  CL20  C19  C14   121.29  3.000
 RUF  C18   C19  C14   121.80  3.000
 RUF  C22   C21  N12   132.29  3.000
 RUF  C22   C21  C3    122.48  3.000
 RUF  N12   C21  C3    105.00  3.000
 RUF  N24   C22  O23   121.59  3.000
 RUF  O23   C22  C21   126.43  3.000
 RUF  N24   C22  C21   111.97  3.000
 RUF  C26   N24  C25   115.13  3.000
 RUF  C26   N24  C22   126.33  3.000
 RUF  C25   N24  C22   118.53  3.000
 RUF  H25B  C25  H25A  108.83  3.000
 RUF  H25B  C25  H25   108.85  3.000
 RUF  H25A  C25  H25   109.00  3.000
 RUF  H25B  C25  N24   108.85  3.000
 RUF  H25A  C25  N24   110.51  3.000
 RUF  H25   C25  N24   110.76  3.000
 RUF  O27   C26  N24   121.19  3.000
 RUF  O27   C26  N2    121.21  3.000
 RUF  N24   C26  N2    117.60  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
 RUF  CONST_01  C5    N12  C21  C3      0.00   0.0  0
 RUF  CONST_02  N12   C5   N4   C3      0.00   0.0  0
 RUF  CONST_03  N12   C21  C3   N4      0.00   0.0  0
 RUF  CONST_04  C21   N12  C5   N4      0.00   0.0  0
 RUF  CONST_05  C21   C3   N4   C5      0.00   0.0  0
 RUF  CONST_06  C17   C16  C15  C14     0.00   0.0  0
 RUF  CONST_07  C17   C18  C19  C14     0.00   0.0  0
 RUF  CONST_08  C18   C19  C14  C15     0.00   0.0  0
 RUF  CONST_09  C18   C17  C16  C15     0.00   0.0  0
 RUF  CONST_10  C19   C14  C15  C16     0.00   0.0  0
 RUF  CONST_11  C19   C18  C17  C16     0.00   0.0  0
 RUF  CONST_12  N6    C5   N4   C3    180.00   0.0  0
 RUF  CONST_13  C21   N12  C5   N6    180.00   0.0  0
 RUF  CONST_14  C22   N24  C26  N2      0.00   0.0  0
 RUF  CONST_15  N24   C26  N2   C3      0.00   0.0  0
 RUF  CONST_16  C26   N24  C22  C21     0.00   0.0  0
 RUF  CONST_21  C16   C15  C14  C13   180.00   0.0  0
 RUF  CONST_22  C18   C19  C14  C13   180.00   0.0  0
 RUF  CONST_23  CL20  C19  C14  C15   180.00   0.0  0
 RUF  CONST_24  CL20  C19  C18  C17   180.00   0.0  0
 RUF  CONST_25  N24   C26  N2   C1    180.00   0.0  0
 RUF  CONST_26  C25   N24  C26  N2    180.00   0.0  0
 RUF  CONST_27  O27   C26  N2   C3    180.00   0.0  0
 RUF  CONST_28  C25   N24  C22  C21   180.00   0.0  0
 RUF  CONST_29  O27   C26  N24  C22   180.00   0.0  0
 RUF  CONST_30  C26   N24  C22  O23   180.00   0.0  0
 RUF  CONST_31  H16   C16  C15  C14   180.00   0.0  0
 RUF  CONST_32  H18   C18  C19  C14   180.00   0.0  0
 RUF  CONST_33  H17   C17  C16  C15   180.00   0.0  0
 RUF  CONST_34  H15   C15  C16  C17   180.00   0.0  0
 RUF  CONST_35  O27   C26  N2   C1      0.00   0.0  0
 RUF  CONST_36  C25   N24  C22  O23     0.00   0.0  0
 RUF  CONST_37  O27   C26  N24  C25     0.00   0.0  0
 RUF  Var_01    C11   N6   C5   N4    -23.00  30.0  2
 RUF  Var_02    C10   C11  N6   C5   -169.94  30.0  1
 RUF  Var_03    C8    C7   N6   C5    171.93  30.0  1
 RUF  Var_04    N9    C10  C11  N6    -56.66  30.0  1
 RUF  Var_05    N9    C8   C7   N6     51.95  30.0  1
 RUF  Var_06    C10   N9   C8   C7    -51.18  30.0  1
 RUF  Var_07    C11   C10  N9   C8     53.64  30.0  1
 RUF  Var_08    C14   C13  N12  C5    -77.09  30.0  2
 RUF  Var_09    C15   C14  C13  N12   -68.37  30.0  3
 RUF  Var_10    H1    C1   N2   C3    118.34  30.0  3
 RUF  Var_11    H25   C25  N24  C22   116.46  30.0  3

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
 RUF  plan-1  C13   0.020
 RUF  plan-1  C14   0.020
 RUF  plan-1  C15   0.020
 RUF  plan-1  C16   0.020
 RUF  plan-1  C17   0.020
 RUF  plan-1  C18   0.020
 RUF  plan-1  C19   0.020
 RUF  plan-1  CL20  0.020
 RUF  plan-1  H15   0.020
 RUF  plan-1  H16   0.020
 RUF  plan-1  H17   0.020
 RUF  plan-1  H18   0.020
 RUF  plan-2  C1    0.020
 RUF  plan-2  N2    0.020
 RUF  plan-2  C3    0.020
 RUF  plan-2  N4    0.020
 RUF  plan-2  C5    0.020
 RUF  plan-2  N6    0.020
 RUF  plan-2  N12   0.020
 RUF  plan-2  C13   0.020
 RUF  plan-2  C21   0.020
 RUF  plan-2  C22   0.020
 RUF  plan-2  O23   0.020
 RUF  plan-2  N24   0.020
 RUF  plan-2  C25   0.020
 RUF  plan-2  C26   0.020
 RUF  plan-2  O27   0.020

