# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 17:53:40 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 5-(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-6-ethylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2cccc(c2)c3c(N)nc(N)nc3CC
#
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
 9QO  9QO  5-(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-6-ethylpyrimidine-2,4-diamine  ligand  59  31  .  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_9QO
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
 9QO  C2   C  CR6   0   0.524  -7.6064   0.3293  -1.0771
 9QO  C4   C  CR6   0   0.478  -5.7222   1.4168  -0.4355
 9QO  C5   C  CR6   0  -0.147  -5.2712   0.2541   0.2316
 9QO  C6   C  CR6   0   0.271  -6.1107  -0.8455   0.1600
 9QO  C9   C  CH2   0  -0.510  -5.7268  -2.1673   0.7599
 9QO  C10  C  CH3   0  -0.664  -4.9432  -3.0206  -0.2367
 9QO  C12  C  CR16  0  -0.303  -3.9237   0.3514   2.3384
 9QO  C14  C  CR16  0  -0.391  -1.5082   0.2615   2.2701
 9QO  C16  C  CR16  0  -0.384  -2.7875   0.1591   0.2301
 9QO  C18  C  CH2   0  -0.178   0.8173   0.0912   0.6898
 9QO  C20  C  CH2   0  -0.157   3.2495   0.0340   0.1681
 9QO  C11  C  CR6   0   0.022  -3.9745   0.2460   0.9466
 9QO  C13  C  CR16  0  -0.231  -2.6991   0.3511   2.9829
 9QO  C15  C  CR6   0   0.403  -1.5523   0.1685   0.8817
 9QO  N1   N  N     0  -0.506  -7.2766  -0.8190  -0.4893
 9QO  C19  C  CH2   0  -0.503   1.8512   0.0300  -0.4156
 9QO  C25  C  CR6   0   0.511   8.0325   0.3726   0.2020
 9QO  C23  C  CR6   0   0.211   6.2830  -1.0067  -0.2457
 9QO  C27  C  CR6   0   0.437   6.0877   1.3597  -0.4243
 9QO  C22  C  CR6   0   0.127   5.4889   0.0851  -0.5201
 9QO  N3   N  N     0  -0.509  -6.8824   1.4464  -1.0845
 9QO  N29  N  NH2   0  -0.825   9.3121   0.5231   0.6319
 9QO  N24  N  N     0  -0.497   7.5640  -0.8680   0.1154
 9QO  C31  C  CH3   0  -0.663   6.1343  -2.9643  -1.7848
 9QO  N26  N  N     0  -0.502   7.3578   1.4923  -0.0623
 9QO  N28  N  NH2   0  -0.823   5.3785   2.4782  -0.6793
 9QO  O21  O  O2    0  -0.499   4.1823  -0.0235  -0.9077
 9QO  O17  O  O2    0  -0.477  -0.4660   0.0803   0.0893
 9QO  N8   N  NH2   0  -0.827  -5.0075   2.5581  -0.4117
 9QO  N7   N  NH2   0  -0.825  -8.8084   0.3782  -1.6991
 9QO  H1   H  HCH2  0   0.245  -5.1296  -2.0222   1.6601
 9QO  H2   H  HCH2  0   0.244  -6.6369  -2.6914   1.0559
 9QO  H3   H  HCH3  0   0.228  -5.5184  -3.1928  -1.1467
 9QO  H4   H  HCH3  0   0.230  -4.0065  -2.5382  -0.5173
 9QO  H5   H  HCH3  0   0.236  -4.7017  -3.9908   0.1974
 9QO  H6   H  HCR6  0   0.248  -4.8402   0.4299   2.9090
 9QO  H7   H  HCR6  0   0.280  -0.5717   0.2671   2.8107
 9QO  H8   H  HCR6  0   0.258  -2.8141   0.0774  -0.8505
 9QO  H9   H  HCH2  0   0.227   0.9277  -0.7635   1.3670
 9QO  H10  H  HCH2  0   0.226   0.9511   1.0017   1.2853
 9QO  H11  H  HCH2  0   0.224   3.4106   0.9374   0.7682
 9QO  H12  H  HCH2  0   0.223   3.3889  -0.8259   0.8341
 9QO  H13  H  HCR6  0   0.260  -2.6584   0.4254   4.0619
 9QO  H14  H  HCH2  0   0.247   1.7054  -0.8754  -1.0103
 9QO  H15  H  HCH2  0   0.246   1.7292   0.8888  -1.0808
 9QO  H16  H  HCH2  0   0.244   6.2507  -3.0301   0.3655
 9QO  H17  H  HCH2  0   0.244   4.7060  -2.4701  -0.2494
 9QO  H18  H  HNH2  0   0.385   9.7597   1.4053   0.4515
 9QO  H19  H  HNH2  0   0.385   9.9096  -0.2845   0.5887
 9QO  H20  H  HCH3  0   0.229   5.6414  -2.3957  -2.5737
 9QO  H21  H  HCH3  0   0.229   7.2095  -2.9232  -1.9603
 9QO  H22  H  HCH3  0   0.236   5.8199  -4.0040  -1.8755
 9QO  H23  H  HNH2  0   0.398   4.5228   2.4071  -1.2031
 9QO  H24  H  HNH2  0   0.393   5.8863   3.3410  -0.7808
 9QO  H25  H  HNH2  0   0.402  -4.0532   2.5540  -0.0972
 9QO  H26  H  HNH2  0   0.392  -5.2805   3.3087  -1.0229
 9QO  H27  H  HNH2  0   0.388  -9.2638  -0.4934  -1.9076
 9QO  H28  H  HNH2  0   0.388  -8.9796   1.1343  -2.3391
 9QO  C30  C  CH2   0  -0.495   5.7836  -2.4124  -0.4032

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
 9QO  N7   C2   single    1.354  0.020  1.354
 9QO  C2   N1   aromatic  1.332  0.020  1.332
 9QO  C2   N3   aromatic  1.331  0.020  1.331
 9QO  N1   C6   aromatic  1.335  0.020  1.335
 9QO  N3   C4   aromatic  1.330  0.020  1.330
 9QO  C10  C9   single    1.528  0.020  1.528
 9QO  C6   C9   single    1.501  0.020  1.501
 9QO  C6   C5   aromatic  1.385  0.020  1.385
 9QO  C4   C5   aromatic  1.414  0.020  1.414
 9QO  C4   N8   single    1.347  0.020  1.347
 9QO  C5   C11  single    1.481  0.020  1.481
 9QO  C11  C12  aromatic  1.397  0.020  1.397
 9QO  C11  C16  aromatic  1.389  0.020  1.389
 9QO  C12  C13  aromatic  1.384  0.020  1.384
 9QO  N29  C25  single    1.358  0.020  1.358
 9QO  C16  C15  aromatic  1.397  0.020  1.397
 9QO  C31  C30  single    1.529  0.020  1.529
 9QO  N24  C25  aromatic  1.329  0.020  1.329
 9QO  N24  C23  aromatic  1.338  0.020  1.338
 9QO  C25  N26  aromatic  1.334  0.020  1.334
 9QO  C30  C23  single    1.500  0.020  1.500
 9QO  C23  C22  aromatic  1.378  0.020  1.378
 9QO  N26  C27  aromatic  1.327  0.020  1.327
 9QO  C13  C14  aromatic  1.391  0.020  1.391
 9QO  C15  C14  aromatic  1.392  0.020  1.392
 9QO  C15  O17  single    1.347  0.020  1.347
 9QO  C27  C22  aromatic  1.412  0.020  1.412
 9QO  C27  N28  single    1.349  0.020  1.349
 9QO  C22  O21  single    1.367  0.020  1.367
 9QO  O21  C20  single    1.425  0.020  1.425
 9QO  O17  C18  single    1.417  0.020  1.417
 9QO  C19  C20  single    1.515  0.020  1.515
 9QO  C19  C18  single    1.515  0.020  1.515
 9QO  C9   H1   single    0.970  0.020  1.090
 9QO  C9   H2   single    0.970  0.020  1.090
 9QO  C10  H3   single    0.970  0.020  1.090
 9QO  C10  H4   single    0.970  0.020  1.090
 9QO  C10  H5   single    0.970  0.020  1.090
 9QO  C12  H6   single    0.930  0.020  1.080
 9QO  C14  H7   single    0.930  0.020  1.080
 9QO  C16  H8   single    0.930  0.020  1.080
 9QO  C18  H9   single    0.970  0.020  1.090
 9QO  C18  H10  single    0.970  0.020  1.090
 9QO  C20  H11  single    0.970  0.020  1.090
 9QO  C20  H12  single    0.970  0.020  1.090
 9QO  C13  H13  single    0.930  0.020  1.080
 9QO  C19  H14  single    0.970  0.020  1.090
 9QO  C19  H15  single    0.970  0.020  1.090
 9QO  C30  H16  single    0.970  0.020  1.090
 9QO  C30  H17  single    0.970  0.020  1.090
 9QO  N29  H18  single    0.890  0.020  1.040
 9QO  N29  H19  single    0.890  0.020  1.040
 9QO  C31  H20  single    0.970  0.020  1.090
 9QO  C31  H21  single    0.970  0.020  1.090
 9QO  C31  H22  single    0.970  0.020  1.090
 9QO  N28  H23  single    0.890  0.020  1.040
 9QO  N28  H24  single    0.890  0.020  1.040
 9QO  N8   H25  single    0.890  0.020  1.040
 9QO  N8   H26  single    0.890  0.020  1.040
 9QO  N7   H27  single    0.890  0.020  1.040
 9QO  N7   H28  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
 9QO  N7   C2   N3   116.74  3.000
 9QO  N3   C2   N1   126.26  3.000
 9QO  N7   C2   N1   116.98  3.000
 9QO  N8   C4   N3   116.92  3.000
 9QO  N8   C4   C5   121.27  3.000
 9QO  N3   C4   C5   121.78  3.000
 9QO  C11  C5   C6   123.46  3.000
 9QO  C11  C5   C4   120.76  3.000
 9QO  C6   C5   C4   115.78  3.000
 9QO  N1   C6   C9   115.79  3.000
 9QO  C9   C6   C5   121.55  3.000
 9QO  N1   C6   C5   122.60  3.000
 9QO  H2   C9   H1   107.27  3.000
 9QO  H2   C9   C10  109.66  3.000
 9QO  H1   C9   C10  109.39  3.000
 9QO  H2   C9   C6   108.55  3.000
 9QO  H1   C9   C6   110.66  3.000
 9QO  C10  C9   C6   111.23  3.000
 9QO  H5   C10  H4   107.82  3.000
 9QO  H5   C10  H3   107.98  3.000
 9QO  H4   C10  H3   107.95  3.000
 9QO  H5   C10  C9   110.55  3.000
 9QO  H4   C10  C9   111.18  3.000
 9QO  H3   C10  C9   111.22  3.000
 9QO  H6   C12  C13  120.26  3.000
 9QO  H6   C12  C11  120.00  3.000
 9QO  C13  C12  C11  119.75  3.000
 9QO  H7   C14  C15  121.75  3.000
 9QO  H7   C14  C13  119.02  3.000
 9QO  C15  C14  C13  119.23  3.000
 9QO  H8   C16  C15  119.16  3.000
 9QO  H8   C16  C11  119.86  3.000
 9QO  C15  C16  C11  120.98  3.000
 9QO  H10  C18  H9   107.44  3.000
 9QO  H10  C18  O17  110.32  3.000
 9QO  H9   C18  O17  110.30  3.000
 9QO  H10  C18  C19  110.28  3.000
 9QO  H9   C18  C19  110.53  3.000
 9QO  O17  C18  C19  107.98  3.000
 9QO  H12  C20  H11  107.16  3.000
 9QO  H12  C20  O21  110.10  3.000
 9QO  H11  C20  O21  110.50  3.000
 9QO  H12  C20  C19  110.44  3.000
 9QO  H11  C20  C19  110.40  3.000
 9QO  O21  C20  C19  108.25  3.000
 9QO  C16  C11  C12  119.18  3.000
 9QO  C16  C11  C5   119.97  3.000
 9QO  C12  C11  C5   120.83  3.000
 9QO  H13  C13  C14  118.89  3.000
 9QO  H13  C13  C12  119.83  3.000
 9QO  C14  C13  C12  121.27  3.000
 9QO  O17  C15  C16  115.99  3.000
 9QO  O17  C15  C14  124.43  3.000
 9QO  C16  C15  C14  119.58  3.000
 9QO  C6   N1   C2   116.63  3.000
 9QO  H15  C19  H14  107.74  3.000
 9QO  H15  C19  C20  109.59  3.000
 9QO  H14  C19  C20  109.56  3.000
 9QO  H15  C19  C18  109.64  3.000
 9QO  H14  C19  C18  109.85  3.000
 9QO  C20  C19  C18  110.41  3.000
 9QO  N26  C25  N24  126.33  3.000
 9QO  N26  C25  N29  116.51  3.000
 9QO  N24  C25  N29  117.14  3.000
 9QO  N24  C23  C30  116.37  3.000
 9QO  C30  C23  C22  121.99  3.000
 9QO  N24  C23  C22  121.56  3.000
 9QO  N28  C27  N26  118.16  3.000
 9QO  N28  C27  C22  120.86  3.000
 9QO  N26  C27  C22  120.97  3.000
 9QO  O21  C22  C27  119.76  3.000
 9QO  O21  C22  C23  122.99  3.000
 9QO  C27  C22  C23  117.23  3.000
 9QO  C4   N3   C2   116.95  3.000
 9QO  H19  N29  H18  115.61  3.000
 9QO  H19  N29  C25  117.21  3.000
 9QO  H18  N29  C25  117.37  3.000
 9QO  C23  N24  C25  116.86  3.000
 9QO  H22  C31  H21  107.88  3.000
 9QO  H22  C31  H20  107.87  3.000
 9QO  H21  C31  H20  108.04  3.000
 9QO  H22  C31  C30  110.70  3.000
 9QO  H21  C31  C30  110.99  3.000
 9QO  H20  C31  C30  111.22  3.000
 9QO  C27  N26  C25  117.02  3.000
 9QO  H24  N28  H23  115.93  3.000
 9QO  H24  N28  C27  117.70  3.000
 9QO  H23  N28  C27  119.16  3.000
 9QO  C22  O21  C20  114.10  3.000
 9QO  C15  O17  C18  118.71  3.000
 9QO  H26  N8   H25  116.81  3.000
 9QO  H26  N8   C4   118.53  3.000
 9QO  H25  N8   C4   120.40  3.000
 9QO  H28  N7   H27  116.29  3.000
 9QO  H28  N7   C2   118.08  3.000
 9QO  H27  N7   C2   117.78  3.000
 9QO  H17  C30  H16  107.09  3.000
 9QO  H17  C30  C31  109.59  3.000
 9QO  H16  C30  C31  109.52  3.000
 9QO  H17  C30  C23  111.34  3.000
 9QO  H16  C30  C23  108.30  3.000
 9QO  C31  C30  C23  110.91  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
 9QO  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 9QO  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 9QO  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 9QO  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 9QO  CONST_07  C13  C12  C11  C5    180.00   0.0  0
 9QO  CONST_08  C15  C16  C11  C5    180.00   0.0  0
 9QO  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 9QO  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 9QO  CONST_13  C15  C16  C11  C12     0.00   0.0  0
 9QO  CONST_14  C15  C14  C13  C12     0.00   0.0  0
 9QO  CONST_15  C11  C12  C13  C14     0.00   0.0  0
 9QO  CONST_16  C11  C16  C15  C14     0.00   0.0  0
 9QO  CONST_17  C13  C12  C11  C16     0.00   0.0  0
 9QO  CONST_18  C13  C14  C15  C16     0.00   0.0  0
 9QO  CONST_19  N1   C6   C5   C11   180.00   0.0  0
 9QO  CONST_20  N3   C4   C5   C11   180.00   0.0  0
 9QO  CONST_21  C22  C23  N24  C25     0.00   0.0  0
 9QO  CONST_22  C22  C27  N26  C25     0.00   0.0  0
 9QO  CONST_23  N26  C25  N24  C23     0.00   0.0  0
 9QO  CONST_24  N26  C27  C22  C23     0.00   0.0  0
 9QO  CONST_25  N24  C25  N26  C27     0.00   0.0  0
 9QO  CONST_26  N24  C23  C22  C27     0.00   0.0  0
 9QO  CONST_27  C9   C6   N1   C2    180.00   0.0  0
 9QO  CONST_28  N8   C4   N3   C2    180.00   0.0  0
 9QO  CONST_29  N7   C2   N3   C4    180.00   0.0  0
 9QO  CONST_30  C9   C6   C5   C4    180.00   0.0  0
 9QO  CONST_31  N7   C2   N1   C6    180.00   0.0  0
 9QO  CONST_32  N8   C4   C5   C6    180.00   0.0  0
 9QO  CONST_33  C11  C5   C6   C9      0.00   0.0  0
 9QO  CONST_34  N8   C4   C5   C11     0.00   0.0  0
 9QO  CONST_35  O17  C15  C16  C11   180.00   0.0  0
 9QO  CONST_36  O17  C15  C14  C13   180.00   0.0  0
 9QO  CONST_37  C30  C23  N24  C25   180.00   0.0  0
 9QO  CONST_38  N28  C27  N26  C25   180.00   0.0  0
 9QO  CONST_39  N29  C25  N24  C23   180.00   0.0  0
 9QO  CONST_40  N28  C27  C22  C23   180.00   0.0  0
 9QO  CONST_41  N29  C25  N26  C27   180.00   0.0  0
 9QO  CONST_42  C30  C23  C22  C27   180.00   0.0  0
 9QO  CONST_43  O21  C22  C23  N24   180.00   0.0  0
 9QO  CONST_44  O21  C22  C27  N26   180.00   0.0  0
 9QO  CONST_45  H6   C12  C11  C5      0.00   0.0  0
 9QO  CONST_46  H8   C16  C11  C5      0.00   0.0  0
 9QO  CONST_47  H7   C14  C13  C12   180.00   0.0  0
 9QO  CONST_48  H13  C13  C12  C11   180.00   0.0  0
 9QO  CONST_49  H25  N8   C4   C5      0.00   0.0  0
 9QO  CONST_50  H26  N8   C4   C5    180.00   0.0  0
 9QO  CONST_54  H24  N28  C27  C22   180.00   0.0  0
 9QO  Var_01    C10  C9   C6   C5    -88.32  30.0  2
 9QO  Var_02    C23  C22  O21  C20    92.75  30.0  3
 9QO  Var_03    C31  C30  C23  C22    93.57  30.0  1
 9QO  Var_04    C19  C18  O17  C15  -178.05  30.0  3
 9QO  Var_05    H3   C10  C9   C6    -58.00  30.0  3
 9QO  Var_06    H20  C31  C30  C23   -63.29  30.0  3
 9QO  Var_07    H11  C20  O21  C22    53.88  30.0  3
 9QO  Var_08    O21  C20  C19  C18  -179.96  30.0  3
 9QO  Var_09    O17  C18  C19  C20  -179.81  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
 9QO  plan-1  C2   0.020
 9QO  plan-1  C4   0.020
 9QO  plan-1  C5   0.020
 9QO  plan-1  C6   0.020
 9QO  plan-1  C9   0.020
 9QO  plan-1  C11  0.020
 9QO  plan-1  N1   0.020
 9QO  plan-1  N3   0.020
 9QO  plan-1  N8   0.020
 9QO  plan-1  N7   0.020
 9QO  plan-2  C2   0.020
 9QO  plan-2  N7   0.020
 9QO  plan-2  H27  0.020
 9QO  plan-2  H28  0.020
 9QO  plan-3  C5   0.020
 9QO  plan-3  C12  0.020
 9QO  plan-3  C14  0.020
 9QO  plan-3  C16  0.020
 9QO  plan-3  C11  0.020
 9QO  plan-3  C13  0.020
 9QO  plan-3  C15  0.020
 9QO  plan-3  O17  0.020
 9QO  plan-3  H6   0.020
 9QO  plan-3  H7   0.020
 9QO  plan-3  H8   0.020
 9QO  plan-3  H13  0.020
 9QO  plan-4  C25  0.020
 9QO  plan-4  C23  0.020
 9QO  plan-4  C27  0.020
 9QO  plan-4  C22  0.020
 9QO  plan-4  N29  0.020
 9QO  plan-4  N24  0.020
 9QO  plan-4  N26  0.020
 9QO  plan-4  N28  0.020
 9QO  plan-4  O21  0.020
 9QO  plan-4  C30  0.020
 9QO  plan-5  C25  0.020
 9QO  plan-5  N29  0.020
 9QO  plan-5  H18  0.020
 9QO  plan-5  H19  0.020
 9QO  plan-6  C27  0.020
 9QO  plan-6  N28  0.020
 9QO  plan-6  H23  0.020
 9QO  plan-6  H24  0.020
 9QO  plan-7  C4   0.020
 9QO  plan-7  N8   0.020
 9QO  plan-7  H25  0.020
 9QO  plan-7  H26  0.020

