# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 17:23:01 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 5-(4-{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)c1OCCCOc2ccc(cc2)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
 9QR  9QR  5-(4-{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_9QR
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
 9QR  N1   N  N     0  -0.501   7.2979   1.7382  -0.6703
 9QR  C2   C  CR6   0   0.514   7.9348   0.6966  -1.2060
 9QR  N3   N  N     0  -0.498   7.6096  -0.5849  -1.0625
 9QR  C4   C  CR6   0   0.209   6.5200  -0.8536  -0.3345
 9QR  C5   C  CR6   0   0.129   5.7763   0.1504   0.2474
 9QR  C6   C  CR6   0   0.437   6.2201   1.4759   0.0589
 9QR  N7   N  NH2   0  -0.823   5.5463   2.5153   0.5953
 9QR  C12  C  CH2   0  -0.158   3.4446  -0.0746   0.2781
 9QR  C21  C  CR16  0  -0.336  -2.3222  -0.2102   2.0762
 9QR  C22  C  CR6   0  -0.144  -5.5068  -0.1986   0.0331
 9QR  C31  C  CH3   0  -0.663  -5.1468   2.9912  -0.7847
 9QR  N8   N  NH2   0  -0.826   8.9980   0.9796  -2.0012
 9QR  C9   C  CH2   0  -0.498   6.1876  -2.3027  -0.1283
 9QR  C10  C  CH3   0  -0.663   6.8253  -2.8392   1.1530
 9QR  O11  O  O2    0  -0.499   4.6677  -0.0914   1.0102
 9QR  C13  C  CH2   0  -0.502   2.2973  -0.1304   1.2663
 9QR  C14  C  CH2   0  -0.178   0.9723  -0.1688   0.5319
 9QR  O15  O  O2    0  -0.475  -0.0628  -0.1964   1.4998
 9QR  C16  C  CR6   0   0.377  -1.3432  -0.2073   1.0803
 9QR  C20  C  CR16  0  -0.264  -3.6619  -0.2143   1.7345
 9QR  C17  C  CR16  0  -0.373  -1.7327  -0.2153  -0.2564
 9QR  C18  C  CR16  0  -0.263  -3.0845  -0.2147  -0.5792
 9QR  C19  C  CR6   0  -0.017  -4.0725  -0.2060   0.3994
 9QR  C23  C  CR6   0   0.269  -6.2943   0.9404   0.0634
 9QR  C30  C  CH2   0  -0.511  -5.7246   2.2785   0.4383
 9QR  C27  C  CR6   0   0.477  -6.1552  -1.3805  -0.3944
 9QR  N28  N  NH2   0  -0.826  -5.4875  -2.5459  -0.4894
 9QR  N26  N  N     0  -0.509  -7.4389  -1.3909  -0.7426
 9QR  C25  C  CR6   0   0.520  -8.0910  -0.2330  -0.6730
 9QR  N24  N  N     0  -0.507  -7.5834   0.9352  -0.2863
 9QR  N29  N  NH2   0  -0.825  -9.4093  -0.2565  -0.9902
 9QR  H1   H  HNH2  0   0.392   6.0023   3.4124   0.5944
 9QR  H2   H  HNH2  0   0.397   4.9214   2.3447   1.3647
 9QR  H3   H  HCH2  0   0.224   3.3779   0.8324  -0.3334
 9QR  H4   H  HCH2  0   0.224   3.4055  -0.9304  -0.4057
 9QR  H5   H  HCR6  0   0.261  -2.0242  -0.2101   3.1176
 9QR  H6   H  HCH3  0   0.235  -4.7939   3.9877  -0.5190
 9QR  H7   H  HCH3  0   0.230  -4.3038   2.4376  -1.1988
 9QR  H8   H  HCH3  0   0.228  -5.8981   3.0980  -1.5678
 9QR  H9   H  HNH2  0   0.386   9.6389   0.2311  -2.2024
 9QR  H10  H  HNH2  0   0.386   9.4063   1.8951  -1.9245
 9QR  H11  H  HCH2  0   0.244   5.1087  -2.4558  -0.0893
 9QR  H12  H  HCH2  0   0.244   6.5603  -2.8636  -0.9864
 9QR  H13  H  HCH3  0   0.229   7.9065  -2.6991   1.1412
 9QR  H14  H  HCH3  0   0.230   6.4283  -2.3320   2.0322
 9QR  H15  H  HCH3  0   0.236   6.6274  -3.9055   1.2626
 9QR  H16  H  HCH2  0   0.247   2.3955  -1.0196   1.8944
 9QR  H17  H  HCH2  0   0.246   2.3333   0.7461   1.9185
 9QR  H18  H  HCH2  0   0.226   0.8689   0.7115  -0.1135
 9QR  H19  H  HCH2  0   0.227   0.9200  -1.0558  -0.1101
 9QR  H20  H  HCR6  0   0.252  -4.4070  -0.2174   2.5205
 9QR  H21  H  HCR6  0   0.280  -1.0089  -0.2170  -1.0592
 9QR  H22  H  HCR6  0   0.253  -3.3684  -0.2124  -1.6247
 9QR  H23  H  HCH2  0   0.244  -4.9467   2.1659   1.1940
 9QR  H24  H  HCH2  0   0.243  -6.5197   2.8841   0.8758
 9QR  H25  H  HNH2  0   0.400  -4.5781  -2.6456  -0.0741
 9QR  H26  H  HNH2  0   0.391  -6.0118  -3.3898  -0.6444
 9QR  H27  H  HNH2  0   0.386  -9.7487  -1.0446  -1.5145
 9QR  H28  H  HNH2  0   0.386  -9.8554   0.6234  -1.1850

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
 9QR  N8   C2   single    1.358  0.020  1.358
 9QR  C2   N3   aromatic  1.330  0.020  1.330
 9QR  C2   N1   aromatic  1.333  0.020  1.333
 9QR  N3   C4   aromatic  1.338  0.020  1.338
 9QR  N1   C6   aromatic  1.328  0.020  1.328
 9QR  C4   C9   single    1.501  0.020  1.501
 9QR  C4   C5   aromatic  1.378  0.020  1.378
 9QR  C10  C9   single    1.528  0.020  1.528
 9QR  C6   C5   aromatic  1.410  0.020  1.410
 9QR  C6   N7   single    1.350  0.020  1.350
 9QR  C5   O11  single    1.367  0.020  1.367
 9QR  C30  C31  single    1.529  0.020  1.529
 9QR  C30  C23  single    1.502  0.020  1.502
 9QR  O11  C12  single    1.426  0.020  1.426
 9QR  N24  C23  aromatic  1.336  0.020  1.336
 9QR  N24  C25  aromatic  1.331  0.020  1.331
 9QR  C23  C22  aromatic  1.385  0.020  1.385
 9QR  N29  C25  single    1.356  0.020  1.356
 9QR  C12  C13  single    1.515  0.020  1.515
 9QR  C25  N26  aromatic  1.331  0.020  1.331
 9QR  C22  C19  single    1.480  0.020  1.480
 9QR  C22  C27  aromatic  1.414  0.020  1.414
 9QR  C18  C17  aromatic  1.390  0.020  1.390
 9QR  C18  C19  aromatic  1.391  0.020  1.391
 9QR  C17  C16  aromatic  1.392  0.020  1.392
 9QR  N26  C27  aromatic  1.330  0.020  1.330
 9QR  C19  C20  aromatic  1.397  0.020  1.397
 9QR  C27  N28  single    1.346  0.020  1.346
 9QR  C13  C14  single    1.515  0.020  1.515
 9QR  C16  C21  aromatic  1.397  0.020  1.397
 9QR  C16  O15  single    1.347  0.020  1.347
 9QR  C20  C21  aromatic  1.383  0.020  1.383
 9QR  O15  C14  single    1.417  0.020  1.417
 9QR  N7   H1   single    0.890  0.020  1.040
 9QR  N7   H2   single    0.890  0.020  1.040
 9QR  C12  H3   single    0.970  0.020  1.090
 9QR  C12  H4   single    0.970  0.020  1.090
 9QR  C21  H5   single    0.930  0.020  1.080
 9QR  C31  H6   single    0.970  0.020  1.090
 9QR  C31  H7   single    0.970  0.020  1.090
 9QR  C31  H8   single    0.970  0.020  1.090
 9QR  N8   H9   single    0.890  0.020  1.040
 9QR  N8   H10  single    0.890  0.020  1.040
 9QR  C9   H11  single    0.970  0.020  1.090
 9QR  C9   H12  single    0.970  0.020  1.090
 9QR  C10  H13  single    0.970  0.020  1.090
 9QR  C10  H14  single    0.970  0.020  1.090
 9QR  C10  H15  single    0.970  0.020  1.090
 9QR  C13  H16  single    0.970  0.020  1.090
 9QR  C13  H17  single    0.970  0.020  1.090
 9QR  C14  H18  single    0.970  0.020  1.090
 9QR  C14  H19  single    0.970  0.020  1.090
 9QR  C20  H20  single    0.930  0.020  1.080
 9QR  C17  H21  single    0.930  0.020  1.080
 9QR  C18  H22  single    0.930  0.020  1.080
 9QR  C30  H23  single    0.970  0.020  1.090
 9QR  C30  H24  single    0.970  0.020  1.090
 9QR  N28  H25  single    0.890  0.020  1.040
 9QR  N28  H26  single    0.890  0.020  1.040
 9QR  N29  H27  single    0.890  0.020  1.040
 9QR  N29  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
 9QR  C6   N1   C2   117.02  3.000
 9QR  N8   C2   N3   117.10  3.000
 9QR  N3   C2   N1   126.35  3.000
 9QR  N8   C2   N1   116.53  3.000
 9QR  C4   N3   C2   116.84  3.000
 9QR  C9   C4   C5   121.72  3.000
 9QR  C5   C4   N3   121.53  3.000
 9QR  C9   C4   N3   116.69  3.000
 9QR  O11  C5   C6   119.72  3.000
 9QR  O11  C5   C4   122.97  3.000
 9QR  C6   C5   C4   117.29  3.000
 9QR  N7   C6   C5   120.90  3.000
 9QR  N7   C6   N1   118.13  3.000
 9QR  C5   C6   N1   120.96  3.000
 9QR  H2   N7   H1   115.68  3.000
 9QR  H2   N7   C6   118.91  3.000
 9QR  H1   N7   C6   117.38  3.000
 9QR  H4   C12  H3   107.21  3.000
 9QR  H4   C12  C13  110.55  3.000
 9QR  H3   C12  C13  110.38  3.000
 9QR  H4   C12  O11  109.99  3.000
 9QR  H3   C12  O11  110.40  3.000
 9QR  C13  C12  O11  108.32  3.000
 9QR  H5   C21  C20  120.28  3.000
 9QR  H5   C21  C16  119.52  3.000
 9QR  C20  C21  C16  120.20  3.000
 9QR  C27  C22  C23  115.67  3.000
 9QR  C27  C22  C19  120.98  3.000
 9QR  C23  C22  C19  123.34  3.000
 9QR  H8   C31  H7   108.04  3.000
 9QR  H8   C31  H6   107.98  3.000
 9QR  H7   C31  H6   107.85  3.000
 9QR  H8   C31  C30  111.09  3.000
 9QR  H7   C31  C30  111.06  3.000
 9QR  H6   C31  C30  110.70  3.000
 9QR  H10  N8   H9   115.73  3.000
 9QR  H10  N8   C2   117.60  3.000
 9QR  H9   N8   C2   117.46  3.000
 9QR  H12  C9   H11  107.10  3.000
 9QR  H12  C9   C10  109.66  3.000
 9QR  H11  C9   C10  109.49  3.000
 9QR  H12  C9   C4   108.22  3.000
 9QR  H11  C9   C4   111.07  3.000
 9QR  C10  C9   C4   111.20  3.000
 9QR  H15  C10  H14  107.94  3.000
 9QR  H15  C10  H13  107.87  3.000
 9QR  H14  C10  H13  108.07  3.000
 9QR  H15  C10  C9   110.60  3.000
 9QR  H14  C10  C9   111.16  3.000
 9QR  H13  C10  C9   111.07  3.000
 9QR  C12  O11  C5   114.02  3.000
 9QR  H17  C13  H16  107.85  3.000
 9QR  H17  C13  C14  109.77  3.000
 9QR  H16  C13  C14  109.66  3.000
 9QR  H17  C13  C12  109.55  3.000
 9QR  H16  C13  C12  109.67  3.000
 9QR  C14  C13  C12  110.30  3.000
 9QR  H19  C14  H18  107.48  3.000
 9QR  H19  C14  O15  110.44  3.000
 9QR  H18  C14  O15  110.41  3.000
 9QR  H19  C14  C13  110.25  3.000
 9QR  H18  C14  C13  110.33  3.000
 9QR  O15  C14  C13  107.95  3.000
 9QR  C16  O15  C14  118.78  3.000
 9QR  C17  C16  O15  124.39  3.000
 9QR  O15  C16  C21  116.37  3.000
 9QR  C17  C16  C21  119.25  3.000
 9QR  H20  C20  C19  119.43  3.000
 9QR  H20  C20  C21  119.16  3.000
 9QR  C19  C20  C21  121.41  3.000
 9QR  H21  C17  C18  118.61  3.000
 9QR  H21  C17  C16  121.72  3.000
 9QR  C18  C17  C16  119.67  3.000
 9QR  H22  C18  C19  119.53  3.000
 9QR  H22  C18  C17  118.62  3.000
 9QR  C19  C18  C17  121.85  3.000
 9QR  C18  C19  C20  117.62  3.000
 9QR  C20  C19  C22  121.43  3.000
 9QR  C18  C19  C22  120.95  3.000
 9QR  N24  C23  C30  115.78  3.000
 9QR  N24  C23  C22  122.67  3.000
 9QR  C30  C23  C22  121.50  3.000
 9QR  H24  C30  H23  107.41  3.000
 9QR  H24  C30  C23  108.55  3.000
 9QR  H23  C30  C23  110.58  3.000
 9QR  H24  C30  C31  109.72  3.000
 9QR  H23  C30  C31  109.45  3.000
 9QR  C23  C30  C31  111.04  3.000
 9QR  N26  C27  N28  116.96  3.000
 9QR  N28  C27  C22  121.15  3.000
 9QR  N26  C27  C22  121.88  3.000
 9QR  H26  N28  H25  116.89  3.000
 9QR  H26  N28  C27  118.60  3.000
 9QR  H25  N28  C27  120.37  3.000
 9QR  C25  N26  C27  116.91  3.000
 9QR  N29  C25  N24  117.00  3.000
 9QR  N29  C25  N26  116.68  3.000
 9QR  N24  C25  N26  126.29  3.000
 9QR  C25  N24  C23  116.58  3.000
 9QR  H28  N29  H27  115.79  3.000
 9QR  H28  N29  C25  117.47  3.000
 9QR  H27  N29  C25  117.63  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
 9QR  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 9QR  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 9QR  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 9QR  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 9QR  CONST_05  C6   N1   C2   N3      0.00   0.0  0
 9QR  CONST_06  C6   C5   C4   N3      0.00   0.0  0
 9QR  CONST_07  C18  C17  C16  C21     0.00   0.0  0
 9QR  CONST_08  C22  C19  C20  C21   180.00   0.0  0
 9QR  CONST_09  C18  C19  C20  C21     0.00   0.0  0
 9QR  CONST_10  C25  N24  C23  C22     0.00   0.0  0
 9QR  CONST_11  C17  C18  C19  C22   180.00   0.0  0
 9QR  CONST_12  C25  N26  C27  C22     0.00   0.0  0
 9QR  CONST_13  C19  C18  C17  C16     0.00   0.0  0
 9QR  CONST_14  C19  C20  C21  C16     0.00   0.0  0
 9QR  CONST_17  C17  C18  C19  C20     0.00   0.0  0
 9QR  CONST_18  C17  C16  C21  C20     0.00   0.0  0
 9QR  CONST_21  N24  C23  C22  C19   180.00   0.0  0
 9QR  CONST_22  N26  C27  C22  C19   180.00   0.0  0
 9QR  CONST_23  N26  C25  N24  C23     0.00   0.0  0
 9QR  CONST_24  N26  C27  C22  C23     0.00   0.0  0
 9QR  CONST_25  N24  C23  C22  C27     0.00   0.0  0
 9QR  CONST_26  N24  C25  N26  C27     0.00   0.0  0
 9QR  CONST_27  O11  C5   C6   N1    180.00   0.0  0
 9QR  CONST_28  C9   C4   N3   C2    180.00   0.0  0
 9QR  CONST_29  N7   C6   N1   C2    180.00   0.0  0
 9QR  CONST_30  O11  C5   C4   N3    180.00   0.0  0
 9QR  CONST_31  N8   C2   N3   C4    180.00   0.0  0
 9QR  CONST_32  N7   C6   C5   C4    180.00   0.0  0
 9QR  CONST_33  N8   C2   N1   C6    180.00   0.0  0
 9QR  CONST_34  C9   C4   C5   C6    180.00   0.0  0
 9QR  CONST_35  C18  C17  C16  O15   180.00   0.0  0
 9QR  CONST_36  C20  C21  C16  O15   180.00   0.0  0
 9QR  CONST_37  C30  C23  C22  C19     0.00   0.0  0
 9QR  CONST_38  N28  C27  C22  C19     0.00   0.0  0
 9QR  CONST_39  N29  C25  N24  C23   180.00   0.0  0
 9QR  CONST_40  N28  C27  C22  C23   180.00   0.0  0
 9QR  CONST_41  C25  N24  C23  C30   180.00   0.0  0
 9QR  CONST_42  C27  C22  C23  C30   180.00   0.0  0
 9QR  CONST_43  N29  C25  N26  C27   180.00   0.0  0
 9QR  CONST_44  C25  N26  C27  N28   180.00   0.0  0
 9QR  CONST_45  H21  C17  C16  C21   180.00   0.0  0
 9QR  CONST_46  H22  C18  C19  C22     0.00   0.0  0
 9QR  CONST_47  H20  C20  C19  C22     0.00   0.0  0
 9QR  CONST_48  H5   C21  C16  C17   180.00   0.0  0
 9QR  CONST_51  H1   N7   C6   N1      0.00   0.0  0
 9QR  CONST_53  H25  N28  C27  C22     0.00   0.0  0
 9QR  CONST_54  H26  N28  C27  C22   180.00   0.0  0
 9QR  Var_01    C10  C9   C4   N3     91.68  30.0  2
 9QR  Var_02    C31  C30  C23  C22    87.36  30.0  1
 9QR  Var_03    C17  C16  O15  C14     1.11  30.0  2
 9QR  Var_04    C13  C12  O11  C5   -170.98  30.0  3
 9QR  Var_05    H13  C10  C9   C4    -56.89  30.0  3
 9QR  Var_06    H18  C14  O15  C16    58.07  30.0  3
 9QR  Var_07    H6   C31  C30  C23   176.31  30.0  3
 9QR  Var_08    O15  C14  C13  C12  -178.99  30.0  3
 9QR  Var_09    C14  C13  C12  O11  -177.82  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
 9QR  plan-1  N1   0.020
 9QR  plan-1  C2   0.020
 9QR  plan-1  N3   0.020
 9QR  plan-1  C4   0.020
 9QR  plan-1  C5   0.020
 9QR  plan-1  C6   0.020
 9QR  plan-1  N7   0.020
 9QR  plan-1  N8   0.020
 9QR  plan-1  C9   0.020
 9QR  plan-1  O11  0.020
 9QR  plan-2  C25  0.020
 9QR  plan-2  N29  0.020
 9QR  plan-2  H27  0.020
 9QR  plan-2  H28  0.020
 9QR  plan-3  C21  0.020
 9QR  plan-3  C22  0.020
 9QR  plan-3  O15  0.020
 9QR  plan-3  C16  0.020
 9QR  plan-3  C20  0.020
 9QR  plan-3  C17  0.020
 9QR  plan-3  C18  0.020
 9QR  plan-3  C19  0.020
 9QR  plan-3  H5   0.020
 9QR  plan-3  H20  0.020
 9QR  plan-3  H21  0.020
 9QR  plan-3  H22  0.020
 9QR  plan-4  C22  0.020
 9QR  plan-4  C19  0.020
 9QR  plan-4  C23  0.020
 9QR  plan-4  C30  0.020
 9QR  plan-4  C27  0.020
 9QR  plan-4  N28  0.020
 9QR  plan-4  N26  0.020
 9QR  plan-4  C25  0.020
 9QR  plan-4  N24  0.020
 9QR  plan-4  N29  0.020
 9QR  plan-5  C6   0.020
 9QR  plan-5  N7   0.020
 9QR  plan-5  H1   0.020
 9QR  plan-5  H2   0.020
 9QR  plan-6  C2   0.020
 9QR  plan-6  N8   0.020
 9QR  plan-6  H9   0.020
 9QR  plan-6  H10  0.020
 9QR  plan-7  C27  0.020
 9QR  plan-7  N28  0.020
 9QR  plan-7  H25  0.020
 9QR  plan-7  H26  0.020

