# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:50:15 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 8-(dimethylamino)-1,3-dimethyl-7-[[5-(3-methylphenyl)-1,3,4-oxadiazol-2-yl]methyl]purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1nc2N(C)C(=O)N(C)C(=O)c2n1Cc3oc(nn3)c4cccc(C)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
 958  958  8-(dimethylamino)-1,3-dimethyl-7-[[5-(3-methylphenyl)-1,3,4-oxadiazol-2-yl]methyl]purine-2,6-dione  ligand  50  29  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_958
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
 958  C4   C  CR56  0   0.474   2.5027  -0.5694   0.3566
 958  C5   C  CR56  0   0.098   2.1839  -0.4415  -0.9665
 958  C6   C  CR6   0   0.555   2.3771  -1.4763  -1.9087
 958  C8   C  CR5   0   0.740   1.8657   1.4308   0.1336
 958  N1   N  NR6   0  -0.604   2.8440  -2.6540  -1.3016
 958  N3   N  NR6   0  -0.597   2.9919  -1.7315   0.8666
 958  CAT  C  CR6   0   0.120  -5.3319   0.2867   1.3807
 958  CAU  C  CR16  0  -0.327  -4.4368   0.9426   0.5478
 958  CAS  C  CR16  0  -0.286  -4.9249  -0.9050   1.9832
 958  CAR  C  CR16  0  -0.226  -3.6608  -1.4251   1.7548
 958  CAQ  C  CR16  0  -0.301  -2.7708  -0.7674   0.9193
 958  CAP  C  CR6   0  -0.008  -3.1622   0.4234   0.3126
 958  CAN  C  CR5   0   0.486  -2.2597   1.1477  -0.5652
 958  OAO  O  O     0  -0.410  -1.0399   0.6485  -0.8283
 958  NAM  N  N     0  -0.316  -2.4453   2.2701  -1.1714
 958  NAL  N  N     0  -0.290  -1.2952   2.5420  -1.8618
 958  CAK  C  CR5   0   0.477  -0.4937   1.5665  -1.6377
 958  N7   N  NR5   0  -0.555   1.7711   0.8843  -1.1124
 958  O6   O  O     0  -0.484   2.1704  -1.4133  -3.1132
 958  CAY  C  CH3   0  -0.528   3.0568  -3.8298  -2.1362
 958  C2   C  CR6   0   0.754   3.1697  -2.8113   0.0362
 958  O2   O  O     0  -0.496   3.6020  -3.8657   0.4626
 958  CAW  C  CH3   0  -0.533   3.3343  -1.8683   2.2725
 958  N9   N  N     0  -0.513   2.3184   0.5731   1.0385
 958  NBA  N  NT    0  -0.499   1.4741   2.6874   0.4108
 958  CBC  C  CH3   0  -0.534   1.2711   3.0502   1.7995
 958  CBB  C  CH3   0  -0.552   1.7650   3.7907  -0.4918
 958  H1   H  HCH3  0   0.253  -7.4538   0.2619   1.0571
 958  H2   H  HCH3  0   0.249  -6.9842   0.7704   2.6707
 958  H3   H  HCH3  0   0.247  -6.7903   1.8713   1.3065
 958  H4   H  HCR6  0   0.259  -4.7281   1.8719   0.0739
 958  H5   H  HCR6  0   0.260  -5.6065  -1.4291   2.6421
 958  H6   H  HCR6  0   0.266  -3.3630  -2.3490   2.2321
 958  H7   H  HCR6  0   0.261  -1.7860  -1.1827   0.7525
 958  H8   H  HCH2  0   0.337   0.8685   0.5921  -2.9422
 958  H9   H  HCH2  0   0.317   1.2299   2.2694  -2.6208
 958  H10  H  HCH3  0   0.253   4.1152  -4.0782  -2.1951
 958  H11  H  HCH3  0   0.254   2.5156  -4.6839  -1.7363
 958  H12  H  HCH3  0   0.266   2.6915  -3.6206  -3.1341
 958  H13  H  HCH3  0   0.259   2.7487  -2.6606   2.7336
 958  H14  H  HCH3  0   0.259   4.3926  -2.0901   2.3929
 958  H15  H  HCH3  0   0.269   3.1108  -0.9317   2.7714
 958  H16  H  HCH3  0   0.238   2.2039   3.3374   2.2919
 958  H17  H  HCH3  0   0.254   0.5862   3.8955   1.8402
 958  H18  H  HCH3  0   0.256   0.8259   2.2254   2.3493
 958  H19  H  HCH3  0   0.269   2.2801   4.5773   0.0603
 958  H20  H  HCH3  0   0.256   2.4321   3.4822  -1.2933
 958  H21  H  HCH3  0   0.251   0.8577   4.2119  -0.9258
 958  CAJ  C  CH2   0  -0.455   0.8817   1.3484  -2.1576
 958  CAV  C  CH3   0  -0.723  -6.7096   0.8307   1.6175

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
 958  CAS  CAR  aromatic  1.386  0.020  1.386
 958  CAS  CAT  aromatic  1.396  0.020  1.396
 958  CAR  CAQ  aromatic  1.387  0.020  1.387
 958  CAV  CAT  single    1.500  0.020  1.500
 958  CAT  CAU  aromatic  1.387  0.020  1.387
 958  CAQ  CAP  aromatic  1.393  0.020  1.393
 958  CAU  CAP  aromatic  1.396  0.020  1.396
 958  CAP  CAN  single    1.452  0.020  1.452
 958  CAN  NAM  aromatic  1.289  0.020  1.289
 958  CAN  OAO  aromatic  1.344  0.020  1.344
 958  NAM  NAL  aromatic  1.369  0.020  1.369
 958  OAO  CAK  aromatic  1.340  0.020  1.340
 958  CBB  NBA  single    1.455  0.020  1.455
 958  NAL  CAK  aromatic  1.282  0.020  1.282
 958  CAK  CAJ  single    1.486  0.020  1.486
 958  CAJ  N7   single    1.449  0.020  1.449
 958  NBA  CBC  single    1.450  0.020  1.450
 958  NBA  C8   single    1.345  0.020  1.345
 958  N7   C8   aromatic  1.364  0.020  1.364
 958  N7   C5   aromatic  1.396  0.020  1.396
 958  C8   N9   aromatic  1.326  0.020  1.326
 958  O6   C6   double    1.224  0.020  1.224
 958  C5   C6   single    1.413  0.020  1.413
 958  C5   C4   aromatic  1.367  0.020  1.367
 958  N9   C4   aromatic  1.343  0.020  1.343
 958  C6   N1   single    1.405  0.020  1.405
 958  C4   N3   single    1.360  0.020  1.360
 958  N1   CAY  single    1.458  0.020  1.458
 958  N1   C2   single    1.386  0.020  1.386
 958  N3   C2   single    1.374  0.020  1.374
 958  N3   CAW  single    1.454  0.020  1.454
 958  C2   O2   double    1.217  0.020  1.217
 958  CAV  H1   single    0.970  0.020  1.090
 958  CAV  H2   single    0.970  0.020  1.090
 958  CAV  H3   single    0.970  0.020  1.090
 958  CAU  H4   single    0.930  0.020  1.080
 958  CAS  H5   single    0.930  0.020  1.080
 958  CAR  H6   single    0.930  0.020  1.080
 958  CAQ  H7   single    0.930  0.020  1.080
 958  CAJ  H8   single    0.970  0.020  1.090
 958  CAJ  H9   single    0.970  0.020  1.090
 958  CAY  H10  single    0.970  0.020  1.090
 958  CAY  H11  single    0.970  0.020  1.090
 958  CAY  H12  single    0.970  0.020  1.090
 958  CAW  H13  single    0.970  0.020  1.090
 958  CAW  H14  single    0.970  0.020  1.090
 958  CAW  H15  single    0.970  0.020  1.090
 958  CBC  H16  single    0.970  0.020  1.090
 958  CBC  H17  single    0.970  0.020  1.090
 958  CBC  H18  single    0.970  0.020  1.090
 958  CBB  H19  single    0.970  0.020  1.090
 958  CBB  H20  single    0.970  0.020  1.090
 958  CBB  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
 958  N9   C4   N3   125.86  3.000
 958  N3   C4   C5   121.78  3.000
 958  N9   C4   C5   112.32  3.000
 958  N7   C5   C6   131.79  3.000
 958  C6   C5   C4   123.03  3.000
 958  N7   C5   C4   105.00  3.000
 958  O6   C6   N1   121.64  3.000
 958  N1   C6   C5   111.80  3.000
 958  O6   C6   C5   126.55  3.000
 958  NBA  C8   N9   124.25  3.000
 958  N9   C8   N7   112.82  3.000
 958  NBA  C8   N7   122.85  3.000
 958  C2   N1   CAY  115.27  3.000
 958  C2   N1   C6   126.19  3.000
 958  CAY  N1   C6   118.52  3.000
 958  CAW  N3   C2   118.70  3.000
 958  CAW  N3   C4   121.86  3.000
 958  C2   N3   C4   119.44  3.000
 958  CAS  CAT  CAU  118.33  3.000
 958  CAU  CAT  CAV  121.06  3.000
 958  CAS  CAT  CAV  120.61  3.000
 958  H4   CAU  CAP  119.39  3.000
 958  H4   CAU  CAT  119.65  3.000
 958  CAP  CAU  CAT  120.95  3.000
 958  H5   CAS  CAR  119.51  3.000
 958  H5   CAS  CAT  119.48  3.000
 958  CAR  CAS  CAT  121.01  3.000
 958  H6   CAR  CAQ  119.62  3.000
 958  H6   CAR  CAS  119.93  3.000
 958  CAQ  CAR  CAS  120.45  3.000
 958  H7   CAQ  CAP  121.13  3.000
 958  H7   CAQ  CAR  119.68  3.000
 958  CAP  CAQ  CAR  119.19  3.000
 958  CAN  CAP  CAQ  121.00  3.000
 958  CAN  CAP  CAU  118.92  3.000
 958  CAQ  CAP  CAU  120.07  3.000
 958  NAM  CAN  OAO  111.22  3.000
 958  OAO  CAN  CAP  119.80  3.000
 958  NAM  CAN  CAP  128.97  3.000
 958  CAK  OAO  CAN  103.51  3.000
 958  NAL  NAM  CAN  106.81  3.000
 958  CAK  NAL  NAM  106.61  3.000
 958  CAJ  CAK  NAL  128.96  3.000
 958  CAJ  CAK  OAO  119.20  3.000
 958  NAL  CAK  OAO  111.83  3.000
 958  CAJ  N7   C8   124.98  3.000
 958  C8   N7   C5   105.34  3.000
 958  CAJ  N7   C5   124.13  3.000
 958  H12  CAY  H11  108.83  3.000
 958  H12  CAY  H10  108.79  3.000
 958  H11  CAY  H10  108.94  3.000
 958  H12  CAY  N1   108.81  3.000
 958  H11  CAY  N1   110.51  3.000
 958  H10  CAY  N1   110.91  3.000
 958  O2   C2   N3   121.02  3.000
 958  O2   C2   N1   121.34  3.000
 958  N3   C2   N1   117.64  3.000
 958  H15  CAW  H14  109.01  3.000
 958  H15  CAW  H13  108.85  3.000
 958  H14  CAW  H13  109.16  3.000
 958  H15  CAW  N3   108.37  3.000
 958  H14  CAW  N3   110.82  3.000
 958  H13  CAW  N3   110.59  3.000
 958  C8   N9   C4   104.51  3.000
 958  CBB  NBA  CBC  115.63  3.000
 958  CBC  NBA  C8   118.16  3.000
 958  CBB  NBA  C8   121.49  3.000
 958  H18  CBC  H17  108.23  3.000
 958  H18  CBC  H16  108.73  3.000
 958  H17  CBC  H16  108.42  3.000
 958  H18  CBC  NBA  110.62  3.000
 958  H17  CBC  NBA  108.55  3.000
 958  H16  CBC  NBA  112.20  3.000
 958  H21  CBB  H20  109.07  3.000
 958  H21  CBB  H19  108.42  3.000
 958  H20  CBB  H19  106.74  3.000
 958  H21  CBB  NBA  111.92  3.000
 958  H20  CBB  NBA  111.40  3.000
 958  H19  CBB  NBA  109.11  3.000
 958  H9   CAJ  H8   106.54  3.000
 958  H9   CAJ  N7   112.44  3.000
 958  H8   CAJ  N7   107.72  3.000
 958  H9   CAJ  CAK  108.72  3.000
 958  H8   CAJ  CAK  110.02  3.000
 958  N7   CAJ  CAK  111.27  3.000
 958  H3   CAV  H2   108.06  3.000
 958  H3   CAV  H1   107.51  3.000
 958  H2   CAV  H1   107.19  3.000
 958  H3   CAV  CAT  111.68  3.000
 958  H2   CAV  CAT  111.34  3.000
 958  H1   CAV  CAT  110.87  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
 958  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 958  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 958  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 958  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 958  CONST_05  CAQ  CAR  CAS  CAT     0.00   0.0  0
 958  CONST_06  CAQ  CAP  CAU  CAT     0.00   0.0  0
 958  CONST_07  CAN  CAP  CAU  CAT   180.00   0.0  0
 958  CONST_08  CAR  CAS  CAT  CAU     0.00   0.0  0
 958  CONST_09  CAR  CAQ  CAP  CAU     0.00   0.0  0
 958  CONST_10  NAM  CAN  CAP  CAU     0.00   0.0  0
 958  CONST_11  OAO  CAN  CAP  CAU   180.00   0.0  0
 958  CONST_12  CAP  CAQ  CAR  CAS     0.00   0.0  0
 958  CONST_13  CAP  CAU  CAT  CAS     0.00   0.0  0
 958  CONST_14  CAN  CAP  CAQ  CAR   180.00   0.0  0
 958  CONST_15  NAM  CAN  CAP  CAQ   180.00   0.0  0
 958  CONST_16  OAO  CAN  CAP  CAQ     0.00   0.0  0
 958  CONST_17  NAL  NAM  CAN  CAP   180.00   0.0  0
 958  CONST_18  CAK  OAO  CAN  CAP   180.00   0.0  0
 958  CONST_19  CAK  NAL  NAM  CAN     0.00   0.0  0
 958  CONST_20  NAL  CAK  OAO  CAN     0.00   0.0  0
 958  CONST_21  NAL  NAM  CAN  OAO     0.00   0.0  0
 958  CONST_22  NAM  NAL  CAK  OAO     0.00   0.0  0
 958  CONST_23  CAK  OAO  CAN  NAM     0.00   0.0  0
 958  CONST_24  N9   C4   C5   N7      0.00   0.0  0
 958  CONST_25  N1   C2   N3   C4      0.00   0.0  0
 958  CONST_26  C2   N1   C6   C5      0.00   0.0  0
 958  CONST_27  N3   C2   N1   C6      0.00   0.0  0
 958  CONST_29  NBA  C8   N9   C4    180.00   0.0  0
 958  CONST_30  NBA  C8   N7   C5    180.00   0.0  0
 958  CONST_32  CAR  CAS  CAT  CAV   180.00   0.0  0
 958  CONST_33  CAP  CAU  CAT  CAV   180.00   0.0  0
 958  CONST_34  CAJ  CAK  OAO  CAN   180.00   0.0  0
 958  CONST_35  CAJ  CAK  NAL  NAM   180.00   0.0  0
 958  CONST_37  O2   C2   N3   C4    180.00   0.0  0
 958  CONST_38  CAY  N1   C6   C5    180.00   0.0  0
 958  CONST_39  O2   C2   N1   C6    180.00   0.0  0
 958  CONST_40  CAW  N3   C2   N1    180.00   0.0  0
 958  CONST_41  CAY  N1   C2   N3    180.00   0.0  0
 958  CONST_42  C2   N1   C6   O6    180.00   0.0  0
 958  CONST_43  H6   CAR  CAS  CAT   180.00   0.0  0
 958  CONST_44  H5   CAS  CAT  CAU   180.00   0.0  0
 958  CONST_45  H7   CAQ  CAP  CAU   180.00   0.0  0
 958  CONST_46  H4   CAU  CAT  CAS   180.00   0.0  0
 958  CONST_50  CBC  NBA  C8   N9      0.00   0.0  0
 958  CONST_51  CAY  N1   C6   O6      0.00   0.0  0
 958  CONST_52  O2   C2   N1   CAY     0.00   0.0  0
 958  CONST_53  CAW  N3   C2   O2      0.00   0.0  0
 958  Var_01    CAK  CAJ  N7   C5    102.94  30.0  2
 958  Var_02    N7   CAJ  CAK  OAO   -44.33  30.0  2
 958  Var_03    H13  CAW  N3   C4    120.37  30.0  3
 958  Var_04    H10  CAY  N1   C6    112.99  30.0  3
 958  Var_05    H1   CAV  CAT  CAU   104.05  30.0  2
 958  Var_06    H19  CBB  NBA  C8   -125.67  30.0  3
 958  Var_07    H16  CBC  NBA  C8     83.78  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
 958  plan-1  CAP  0.020
 958  plan-1  CAN  0.020
 958  plan-1  OAO  0.020
 958  plan-1  NAM  0.020
 958  plan-1  NAL  0.020
 958  plan-1  CAK  0.020
 958  plan-1  CAJ  0.020
 958  plan-2  CAT  0.020
 958  plan-2  CAU  0.020
 958  plan-2  CAS  0.020
 958  plan-2  CAR  0.020
 958  plan-2  CAQ  0.020
 958  plan-2  CAP  0.020
 958  plan-2  CAN  0.020
 958  plan-2  H4   0.020
 958  plan-2  H5   0.020
 958  plan-2  H6   0.020
 958  plan-2  H7   0.020
 958  plan-2  CAV  0.020
 958  plan-3  C4   0.020
 958  plan-3  C5   0.020
 958  plan-3  C6   0.020
 958  plan-3  C8   0.020
 958  plan-3  N1   0.020
 958  plan-3  N3   0.020
 958  plan-3  N7   0.020
 958  plan-3  O6   0.020
 958  plan-3  CAY  0.020
 958  plan-3  C2   0.020
 958  plan-3  O2   0.020
 958  plan-3  CAW  0.020
 958  plan-3  N9   0.020
 958  plan-3  NBA  0.020
 958  plan-3  CAJ  0.020
 958  plan-4  C8   0.020
 958  plan-4  NBA  0.020
 958  plan-4  CBC  0.020
 958  plan-4  CBB  0.020

