# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 17:03:35 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 7-[[5-(3,4-dichlorophenyl)-1,3,4-oxadiazol-2-yl]methyl]-1,3-dimethyl-8-piperazin-1-yl-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2nc(N3CCNCC3)n(Cc4oc(nn4)c5ccc(Cl)c(Cl)c5)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
 9CH  9CH  7-[[5-(3,4-dichlorophenyl)-1,3,4-oxadiazol-2-yl]methyl]-1,3-dimethyl-8-piperazin-1-yl-purine-2,6-dione  ligand  53  33  .  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_9CH
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
 9CH  C14  C   CR6   0  -0.027   2.7894   1.1521  -0.0293
 9CH  C10  C   CR5   0   0.487  -0.4081   1.6822   1.2546
 9CH  C13  C   CR5   0   0.498   1.5521   1.7040   0.4915
 9CH  N02  N   NR6   0  -0.592  -2.9770  -2.7972  -0.8618
 9CH  C03  C   CR6   0   0.721  -2.0367  -3.7091  -0.4440
 9CH  N04  N   NR6   0  -0.603  -1.1012  -3.2631   0.4847
 9CH  C05  C   CH3   0  -0.528  -0.0899  -4.2094   0.9436
 9CH  C06  C   CR6   0   0.582  -1.0099  -1.9773   1.0336
 9CH  C07  C   CR56  0   0.141  -1.9986  -1.1044   0.5127
 9CH  N08  N   NR5   0  -0.546  -2.2959   0.2296   0.7409
 9CH  C09  C   CH2   0  -0.455  -1.6901   1.0940   1.7253
 9CH  N11  N   N     0  -0.292  -0.0393   2.9127   1.2276
 9CH  N12  N   N     0  -0.308   1.2377   2.9296   0.7366
 9CH  C15  C   CR16  0  -0.264   3.7901   2.0005  -0.4974
 9CH  C16  C   CR16  0  -0.200   4.9686   1.4723  -0.9872
 9CH  C17  C   CR6   0   0.000   5.1592   0.0971  -1.0159
 9CH  CL1  CL  CL    0  -0.077   6.6279  -0.5410  -1.6335
 9CH  C19  C   CR6   0   0.024   4.1615  -0.7506  -0.5448
 9CH  CL2  CL  CL    0  -0.081   4.3749  -2.4565  -0.5632
 9CH  C21  C   CR16  0  -0.239   2.9797  -0.2264  -0.0515
 9CH  O22  O   O     0  -0.396   0.5506   0.8712   0.7973
 9CH  C23  C   CR5   0   0.720  -3.3767   0.5126  -0.0304
 9CH  N24  N   NT    0  -0.531  -3.9786   1.7382  -0.0165
 9CH  C25  C   CH2   0  -0.306  -5.3948   1.7610  -0.3683
 9CH  C26  C   CH2   0  -0.323  -5.9944   3.0755   0.1165
 9CH  N27  N   NH1   0  -0.579  -5.3022   4.2547  -0.3722
 9CH  C28  C   CH2   0  -0.319  -3.8759   4.1690  -0.1146
 9CH  C29  C   CH2   0  -0.335  -3.2540   2.8697  -0.6024
 9CH  N30  N   N     0  -0.494  -3.7934  -0.5399  -0.7170
 9CH  C31  C   CR56  0   0.461  -2.9451  -1.5245  -0.3785
 9CH  O33  O   O     0  -0.489  -2.0256  -4.8507  -0.8642
 9CH  H1   H   HCH3  0   0.272  -3.7992  -4.1574  -2.2055
 9CH  H2   H   HCH3  0   0.259  -4.9861  -3.1763  -1.3349
 9CH  H3   H   HCH3  0   0.259  -4.0261  -2.4586  -2.6386
 9CH  H4   H   HCH3  0   0.270  -0.2971  -5.1873   0.5295
 9CH  H5   H   HCH3  0   0.248   0.9015  -3.8930   0.6224
 9CH  H6   H   HCH3  0   0.255  -0.1024  -4.2777   2.0286
 9CH  H7   H   HCH2  0   0.330  -1.5183   0.5256   2.6402
 9CH  H8   H   HCH2  0   0.324  -2.3837   1.8994   1.9645
 9CH  H9   H   HCR6  0   0.283   3.6504   3.0726  -0.4837
 9CH  H10  H   HCR6  0   0.300   5.7462   2.1283  -1.3529
 9CH  H11  H   HCR6  0   0.290   2.2222  -0.9014   0.3249
 9CH  H12  H   HCH2  0   0.223  -5.5346   1.6568  -1.4527
 9CH  H13  H   HCH2  0   0.256  -5.8985   0.9228   0.1128
 9CH  H14  H   HCH2  0   0.246  -7.0432   3.1250  -0.1801
 9CH  H15  H   HCH2  0   0.227  -5.9673   3.0888   1.2104
 9CH  H16  H   HNH1  0   0.345  -5.4565   4.3463  -1.3699
 9CH  H18  H   HCH2  0   0.248  -3.3716   5.0110  -0.5910
 9CH  H19  H   HCH2  0   0.228  -3.7097   4.2600   0.9636
 9CH  H20  H   HCH2  0   0.258  -2.2011   2.8337  -0.3292
 9CH  H21  H   HCH2  0   0.240  -3.3065   2.8187  -1.6988
 9CH  O32  O   O     0  -0.476  -0.1559  -1.7104   1.8629
 9CH  C01  C   CH3   0  -0.535  -4.0093  -3.1692  -1.8156

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
 9CH  CL1  C17  single    1.716  0.020  1.716
 9CH  C17  C16  aromatic  1.389  0.020  1.389
 9CH  C17  C19  aromatic  1.391  0.020  1.391
 9CH  CL2  C19  single    1.719  0.020  1.719
 9CH  C16  C15  aromatic  1.381  0.020  1.381
 9CH  C19  C21  aromatic  1.384  0.020  1.384
 9CH  C15  C14  aromatic  1.393  0.020  1.393
 9CH  C21  C14  aromatic  1.392  0.020  1.392
 9CH  C14  C13  single    1.452  0.020  1.452
 9CH  C13  N12  aromatic  1.289  0.020  1.289
 9CH  C13  O22  aromatic  1.338  0.020  1.338
 9CH  N12  N11  aromatic  1.368  0.020  1.368
 9CH  O22  C10  aromatic  1.336  0.020  1.336
 9CH  N11  C10  aromatic  1.285  0.020  1.285
 9CH  C10  C09  single    1.487  0.020  1.487
 9CH  O32  C06  double    1.220  0.020  1.220
 9CH  C09  N08  single    1.443  0.020  1.443
 9CH  C05  N04  single    1.459  0.020  1.459
 9CH  C06  N04  single    1.401  0.020  1.401
 9CH  C06  C07  single    1.418  0.020  1.418
 9CH  N04  C03  single    1.392  0.020  1.392
 9CH  N08  C07  aromatic  1.386  0.020  1.386
 9CH  N08  C23  aromatic  1.358  0.020  1.358
 9CH  C25  C26  single    1.524  0.020  1.524
 9CH  C25  N24  single    1.459  0.020  1.459
 9CH  C07  C31  aromatic  1.366  0.020  1.366
 9CH  C26  N27  single    1.452  0.020  1.452
 9CH  C03  O33  double    1.217  0.020  1.217
 9CH  C03  N02  single    1.375  0.020  1.375
 9CH  C23  N24  single    1.366  0.020  1.366
 9CH  C23  N30  aromatic  1.324  0.020  1.324
 9CH  N24  C29  single    1.466  0.020  1.466
 9CH  C31  N02  single    1.362  0.020  1.362
 9CH  C31  N30  aromatic  1.343  0.020  1.343
 9CH  N27  C28  single    1.452  0.020  1.452
 9CH  N02  C01  single    1.454  0.020  1.454
 9CH  C29  C28  single    1.521  0.020  1.521
 9CH  C01  H1   single    0.970  0.020  1.090
 9CH  C01  H2   single    0.970  0.020  1.090
 9CH  C01  H3   single    0.970  0.020  1.090
 9CH  C05  H4   single    0.970  0.020  1.090
 9CH  C05  H5   single    0.970  0.020  1.090
 9CH  C05  H6   single    0.970  0.020  1.090
 9CH  C09  H7   single    0.970  0.020  1.090
 9CH  C09  H8   single    0.970  0.020  1.090
 9CH  C15  H9   single    0.930  0.020  1.080
 9CH  C16  H10  single    0.930  0.020  1.080
 9CH  C21  H11  single    0.930  0.020  1.080
 9CH  C25  H12  single    0.970  0.020  1.090
 9CH  C25  H13  single    0.970  0.020  1.090
 9CH  C26  H14  single    0.970  0.020  1.090
 9CH  C26  H15  single    0.970  0.020  1.090
 9CH  N27  H16  single    0.890  0.020  1.040
 9CH  C28  H18  single    0.970  0.020  1.090
 9CH  C28  H19  single    0.970  0.020  1.090
 9CH  C29  H20  single    0.970  0.020  1.090
 9CH  C29  H21  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
 9CH  C21  C14  C15  119.98  3.000
 9CH  C21  C14  C13  119.92  3.000
 9CH  C15  C14  C13  120.09  3.000
 9CH  O22  C10  N11  111.60  3.000
 9CH  N11  C10  C09  129.26  3.000
 9CH  O22  C10  C09  119.13  3.000
 9CH  O22  C13  N12  111.46  3.000
 9CH  O22  C13  C14  118.91  3.000
 9CH  N12  C13  C14  129.63  3.000
 9CH  C31  N02  C03  119.74  3.000
 9CH  C31  N02  C01  119.25  3.000
 9CH  C03  N02  C01  121.02  3.000
 9CH  O33  C03  N04  121.68  3.000
 9CH  O33  C03  N02  121.58  3.000
 9CH  N04  C03  N02  116.74  3.000
 9CH  C06  N04  C05  115.26  3.000
 9CH  C06  N04  C03  126.83  3.000
 9CH  C05  N04  C03  117.90  3.000
 9CH  H6   C05  H5   108.85  3.000
 9CH  H6   C05  H4   108.84  3.000
 9CH  H5   C05  H4   108.91  3.000
 9CH  H6   C05  N04  110.28  3.000
 9CH  H5   C05  N04  110.47  3.000
 9CH  H4   C05  N04  109.45  3.000
 9CH  O32  C06  C07  127.09  3.000
 9CH  C07  C06  N04  112.06  3.000
 9CH  O32  C06  N04  120.85  3.000
 9CH  C31  C07  N08  104.76  3.000
 9CH  C31  C07  C06  122.23  3.000
 9CH  N08  C07  C06  132.98  3.000
 9CH  C23  N08  C09  126.64  3.000
 9CH  C23  N08  C07  106.14  3.000
 9CH  C09  N08  C07  126.79  3.000
 9CH  H8   C09  H7   107.55  3.000
 9CH  H8   C09  N08  108.98  3.000
 9CH  H7   C09  N08  109.03  3.000
 9CH  H8   C09  C10  109.03  3.000
 9CH  H7   C09  C10  109.63  3.000
 9CH  N08  C09  C10  112.51  3.000
 9CH  N12  N11  C10  106.69  3.000
 9CH  N11  N12  C13  106.51  3.000
 9CH  H9   C15  C16  119.60  3.000
 9CH  H9   C15  C14  120.46  3.000
 9CH  C16  C15  C14  119.95  3.000
 9CH  H10  C16  C17  119.68  3.000
 9CH  H10  C16  C15  120.11  3.000
 9CH  C17  C16  C15  120.21  3.000
 9CH  C19  C17  CL1  120.59  3.000
 9CH  C19  C17  C16  119.86  3.000
 9CH  CL1  C17  C16  119.55  3.000
 9CH  C21  C19  CL2  119.06  3.000
 9CH  C21  C19  C17  120.15  3.000
 9CH  CL2  C19  C17  120.79  3.000
 9CH  H11  C21  C19  119.05  3.000
 9CH  H11  C21  C14  121.10  3.000
 9CH  C19  C21  C14  119.85  3.000
 9CH  C13  O22  C10  103.74  3.000
 9CH  N30  C23  N24  125.45  3.000
 9CH  N30  C23  N08  112.30  3.000
 9CH  N24  C23  N08  122.16  3.000
 9CH  C29  N24  C25  111.80  3.000
 9CH  C29  N24  C23  118.09  3.000
 9CH  C25  N24  C23  116.06  3.000
 9CH  H13  C25  H12  107.70  3.000
 9CH  H13  C25  C26  109.94  3.000
 9CH  H12  C25  C26  110.24  3.000
 9CH  H13  C25  N24  109.27  3.000
 9CH  H12  C25  N24  111.10  3.000
 9CH  C26  C25  N24  108.58  3.000
 9CH  H15  C26  H14  107.16  3.000
 9CH  H15  C26  N27  108.35  3.000
 9CH  H14  C26  N27  109.26  3.000
 9CH  H15  C26  C25  108.59  3.000
 9CH  H14  C26  C25  109.32  3.000
 9CH  N27  C26  C25  113.94  3.000
 9CH  H16  N27  C28  109.23  3.000
 9CH  H16  N27  C26  109.39  3.000
 9CH  C28  N27  C26  111.14  3.000
 9CH  H19  C28  H18  107.20  3.000
 9CH  H19  C28  C29  108.96  3.000
 9CH  H18  C28  C29  109.28  3.000
 9CH  H19  C28  N27  108.60  3.000
 9CH  H18  C28  N27  109.34  3.000
 9CH  C29  C28  N27  113.28  3.000
 9CH  H21  C29  H20  107.17  3.000
 9CH  H21  C29  C28  109.88  3.000
 9CH  H20  C29  C28  110.08  3.000
 9CH  H21  C29  N24  109.84  3.000
 9CH  H20  C29  N24  110.63  3.000
 9CH  C28  C29  N24  109.21  3.000
 9CH  C31  N30  C23  104.67  3.000
 9CH  N30  C31  C07  112.12  3.000
 9CH  N30  C31  N02  125.52  3.000
 9CH  C07  C31  N02  122.35  3.000
 9CH  H3   C01  H2   108.94  3.000
 9CH  H3   C01  H1   109.08  3.000
 9CH  H2   C01  H1   109.09  3.000
 9CH  H3   C01  N02  109.89  3.000
 9CH  H2   C01  N02  110.43  3.000
 9CH  H1   C01  N02  109.38  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
 9CH  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 9CH  CONST_02  C17  C19  C21  C14     0.00   0.0  0
 9CH  CONST_03  N11  N12  C13  C14   180.00   0.0  0
 9CH  CONST_04  C10  O22  C13  C14   180.00   0.0  0
 9CH  CONST_05  N12  C13  O22  C10     0.00   0.0  0
 9CH  CONST_06  C13  N12  N11  C10     0.00   0.0  0
 9CH  CONST_07  C16  C15  C14  C13   180.00   0.0  0
 9CH  CONST_08  C19  C21  C14  C13   180.00   0.0  0
 9CH  CONST_09  N11  C10  O22  C13     0.00   0.0  0
 9CH  CONST_10  N30  C23  N08  C07     0.00   0.0  0
 9CH  CONST_11  C23  N30  C31  C07     0.00   0.0  0
 9CH  CONST_12  N30  C31  C07  N08     0.00   0.0  0
 9CH  CONST_13  C31  N30  C23  N08     0.00   0.0  0
 9CH  CONST_14  O22  C13  N12  N11     0.00   0.0  0
 9CH  CONST_15  C15  C14  C13  N12     0.00   0.0  0
 9CH  CONST_16  C21  C14  C13  N12   180.00   0.0  0
 9CH  CONST_17  O22  C10  N11  N12     0.00   0.0  0
 9CH  CONST_18  C19  C17  C16  C15     0.00   0.0  0
 9CH  CONST_19  C19  C21  C14  C15     0.00   0.0  0
 9CH  CONST_20  O22  C13  C14  C15   180.00   0.0  0
 9CH  CONST_21  C21  C19  C17  C16     0.00   0.0  0
 9CH  CONST_22  C21  C14  C15  C16     0.00   0.0  0
 9CH  CONST_23  O22  C13  C14  C21     0.00   0.0  0
 9CH  CONST_24  C31  C07  N08  C23     0.00   0.0  0
 9CH  CONST_25  N24  C23  N08  C07   180.00   0.0  0
 9CH  CONST_26  C31  N30  C23  N24   180.00   0.0  0
 9CH  CONST_27  C06  N04  C03  N02     0.00   0.0  0
 9CH  CONST_28  C07  C06  N04  C03     0.00   0.0  0
 9CH  CONST_29  C31  N02  C03  N04     0.00   0.0  0
 9CH  CONST_30  CL2  C19  C21  C14   180.00   0.0  0
 9CH  CONST_31  C09  C10  O22  C13   180.00   0.0  0
 9CH  CONST_32  C09  N08  C07  C06     0.00   0.0  0
 9CH  CONST_33  N12  N11  C10  C09   180.00   0.0  0
 9CH  CONST_34  C31  C07  N08  C09   180.00   0.0  0
 9CH  CONST_35  N24  C23  N08  C09     0.00   0.0  0
 9CH  CONST_36  N30  C23  N08  C09   180.00   0.0  0
 9CH  CONST_37  CL1  C17  C16  C15   180.00   0.0  0
 9CH  CONST_38  CL2  C19  C17  C16   180.00   0.0  0
 9CH  CONST_39  C21  C19  C17  CL1   180.00   0.0  0
 9CH  CONST_40  N04  C03  N02  C01   180.00   0.0  0
 9CH  CONST_41  C05  N04  C03  N02   180.00   0.0  0
 9CH  CONST_42  O32  C06  N04  C03   180.00   0.0  0
 9CH  CONST_43  C07  C06  N04  C05   180.00   0.0  0
 9CH  CONST_44  O33  C03  N04  C06   180.00   0.0  0
 9CH  CONST_45  O33  C03  N02  C31   180.00   0.0  0
 9CH  CONST_46  H10  C16  C15  C14   180.00   0.0  0
 9CH  CONST_47  H9   C15  C14  C13     0.00   0.0  0
 9CH  CONST_48  H11  C21  C14  C13     0.00   0.0  0
 9CH  CONST_49  O33  C03  N02  C01     0.00   0.0  0
 9CH  CONST_50  O32  C06  N04  C05     0.00   0.0  0
 9CH  CONST_51  O33  C03  N04  C05     0.00   0.0  0
 9CH  Var_01    C25  N24  C23  N08  -153.21  30.0  2
 9CH  Var_02    C26  C25  N24  C23   162.22  30.0  1
 9CH  Var_03    C28  C29  N24  C23  -162.70  30.0  1
 9CH  Var_04    N27  C26  C25  N24    54.91  30.0  1
 9CH  Var_05    N27  C28  C29  N24   -54.86  30.0  1
 9CH  Var_06    C28  N27  C26  C25   -51.78  30.0  1
 9CH  Var_07    C29  C28  N27  C26    51.49  30.0  1
 9CH  Var_08    C07  N08  C09  C10    83.35  30.0  2
 9CH  Var_09    O22  C10  C09  N08   -53.31  30.0  1
 9CH  Var_10    H4   C05  N04  C03    -5.33  30.0  3
 9CH  Var_11    H1   C01  N02  C03    -8.50  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
 9CH  plan-1  C14  0.020
 9CH  plan-1  C10  0.020
 9CH  plan-1  C13  0.020
 9CH  plan-1  C09  0.020
 9CH  plan-1  N11  0.020
 9CH  plan-1  N12  0.020
 9CH  plan-1  O22  0.020
 9CH  plan-2  C14  0.020
 9CH  plan-2  C13  0.020
 9CH  plan-2  C15  0.020
 9CH  plan-2  C16  0.020
 9CH  plan-2  C17  0.020
 9CH  plan-2  CL1  0.020
 9CH  plan-2  C19  0.020
 9CH  plan-2  CL2  0.020
 9CH  plan-2  C21  0.020
 9CH  plan-2  H9   0.020
 9CH  plan-2  H10  0.020
 9CH  plan-2  H11  0.020
 9CH  plan-3  N02  0.020
 9CH  plan-3  C03  0.020
 9CH  plan-3  N04  0.020
 9CH  plan-3  C05  0.020
 9CH  plan-3  C06  0.020
 9CH  plan-3  C07  0.020
 9CH  plan-3  N08  0.020
 9CH  plan-3  C09  0.020
 9CH  plan-3  C23  0.020
 9CH  plan-3  N24  0.020
 9CH  plan-3  N30  0.020
 9CH  plan-3  C31  0.020
 9CH  plan-3  O33  0.020
 9CH  plan-3  O32  0.020
 9CH  plan-3  C01  0.020

