# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:50:31 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 3-(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2cccc(CCC(O)=O)c2
#
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
 QKJ  QKJ  '3-(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid'  ligand  50  26  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QKJ
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
 QKJ  C11  C  CR16  0  -0.354   -9.1800   7.4832  14.9911
 QKJ  C12  C  CR16  0  -0.227   -9.6733   8.7751  14.9845
 QKJ  C15  C  CH2   0  -0.524   -6.5765  10.7930  15.8241
 QKJ  C16  C  CH2   0  -0.549   -6.5990  11.0715  17.3321
 QKJ  C01  C  CH3   0  -0.664   -9.3749   5.4774  11.7588
 QKJ  C03  C  CR6   0   0.230   -7.2044   4.5703  10.8765
 QKJ  C04  C  CR6   0   0.120   -6.1827   3.9136  11.5285
 QKJ  C06  C  CH2   0  -0.172   -6.3911   3.6400  13.8464
 QKJ  C07  C  CH2   0  -0.501   -5.8539   4.1908  15.1495
 QKJ  C08  C  CH2   0  -0.194   -6.0352   5.6857  15.3206
 QKJ  C10  C  CR6   0   0.409   -7.8255   7.2609  15.2474
 QKJ  C13  C  CR16  0  -0.338   -8.8364   9.8580  15.2316
 QKJ  C14  C  CR6   0   0.147   -7.4887   9.6442  15.4906
 QKJ  C17  C  C     0   0.534   -5.7491  12.2331  17.7702
 QKJ  C20  C  CR16  0  -0.437   -6.9859   8.3431  15.4958
 QKJ  C21  C  CR6   0   0.432   -5.5844   2.8241  10.8577
 QKJ  C24  C  CR6   0   0.508   -7.0278   3.1208   9.1333
 QKJ  N22  N  NH2   0  -0.822   -4.5733   2.1347  11.4255
 QKJ  N23  N  N     0  -0.503   -6.0141   2.4349   9.6644
 QKJ  N25  N  NH2   0  -0.826   -7.5044   2.6727   7.9432
 QKJ  N26  N  N     0  -0.500   -7.6289   4.1763   9.6691
 QKJ  O05  O  O2    0  -0.496   -5.7214   4.2804  12.7611
 QKJ  O09  O  O2    0  -0.478   -7.4205   5.9765  15.2384
 QKJ  O18  O  O     0  -0.446   -6.1043  13.0888  18.5432
 QKJ  O19  O  OH1   0  -0.591   -4.5352  12.2071  17.2308
 QKJ  H1   H  HCR6  0   0.256   -9.8312   6.6406  14.7954
 QKJ  H2   H  HCR6  0   0.255  -10.7236   8.9405  14.7805
 QKJ  H3   H  HCH2  0   0.259   -5.5603  10.5638  15.5012
 QKJ  H4   H  HCH2  0   0.259   -6.8925  11.6876  15.2829
 QKJ  H5   H  HCH2  0   0.271   -7.6197  11.2575  17.6656
 QKJ  H6   H  HCH2  0   0.283   -6.2473  10.1844  17.8694
 QKJ  H7   H  HCH3  0   0.233   -9.8642   6.3698  12.1481
 QKJ  H8   H  HCH3  0   0.229   -9.9010   5.1689  10.8559
 QKJ  H9   H  HCH3  0   0.225   -9.4899   4.6872  12.5022
 QKJ  H10  H  HCH2  0   0.252   -7.4009   6.0877  12.3770
 QKJ  H11  H  HCH2  0   0.249   -7.8301   6.5819  10.7513
 QKJ  H12  H  HCH2  0   0.227   -7.4699   3.8060  13.7709
 QKJ  H13  H  HCH2  0   0.233   -6.2273   2.5575  13.8075
 QKJ  H14  H  HCH2  0   0.250   -6.3452   3.6599  15.9686
 QKJ  H15  H  HCH2  0   0.248   -4.7867   3.9716  15.2366
 QKJ  H16  H  HCH2  0   0.238   -5.6321   5.9949  16.2912
 QKJ  H17  H  HCH2  0   0.227   -5.4849   6.2318  14.5475
 QKJ  H18  H  HCR6  0   0.244   -9.2330  10.8660  15.2216
 QKJ  H19  H  HCR6  0   0.270   -5.9326   8.1992  15.7018
 QKJ  H20  H  HNH2  0   0.392   -4.0605   1.4967  10.8402
 QKJ  H21  H  HNH2  0   0.398   -4.0523   2.5580  12.1745
 QKJ  H22  H  HNH2  0   0.385   -8.0835   3.2997   7.4120
 QKJ  H23  H  HNH2  0   0.386   -6.9149   2.0614   7.4053
 QKJ  H24  H  HOH1  0   0.482   -4.0137  12.9565  17.5553
 QKJ  C02  C  CH2   0  -0.507   -7.9033   5.7600  11.4683

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
 QKJ  N25  C24  single    1.358  0.020  1.358
 QKJ  C24  N26  aromatic  1.328  0.020  1.328
 QKJ  C24  N23  aromatic  1.334  0.020  1.334
 QKJ  N26  C03  aromatic  1.339  0.020  1.339
 QKJ  N23  C21  aromatic  1.327  0.020  1.327
 QKJ  C03  C02  single    1.501  0.020  1.501
 QKJ  C03  C04  aromatic  1.378  0.020  1.378
 QKJ  C21  C04  aromatic  1.412  0.020  1.412
 QKJ  C21  N22  single    1.349  0.020  1.349
 QKJ  C02  C01  single    1.526  0.020  1.526
 QKJ  C04  O05  single    1.366  0.020  1.366
 QKJ  O05  C06  single    1.427  0.020  1.427
 QKJ  C06  C07  single    1.513  0.020  1.513
 QKJ  C15  C14  single    1.504  0.020  1.504
 QKJ  C15  C16  single    1.534  0.020  1.534
 QKJ  C14  C13  aromatic  1.389  0.020  1.389
 QKJ  C14  C20  aromatic  1.395  0.020  1.395
 QKJ  C13  C12  aromatic  1.391  0.020  1.391
 QKJ  C07  C08  single    1.516  0.020  1.516
 QKJ  C20  C10  aromatic  1.392  0.020  1.392
 QKJ  C12  C11  aromatic  1.383  0.020  1.383
 QKJ  C16  C17  single    1.504  0.020  1.504
 QKJ  C10  C11  aromatic  1.396  0.020  1.396
 QKJ  C10  O09  single    1.347  0.020  1.347
 QKJ  O09  C08  single    1.418  0.020  1.418
 QKJ  C17  O18  double    1.207  0.020  1.207
 QKJ  C17  O19  single    1.329  0.020  1.329
 QKJ  C11  H1   single    0.930  0.020  1.080
 QKJ  C12  H2   single    0.930  0.020  1.080
 QKJ  C15  H3   single    0.970  0.020  1.090
 QKJ  C15  H4   single    0.970  0.020  1.090
 QKJ  C16  H5   single    0.970  0.020  1.090
 QKJ  C16  H6   single    0.970  0.020  1.090
 QKJ  C01  H7   single    0.970  0.020  1.090
 QKJ  C01  H8   single    0.970  0.020  1.090
 QKJ  C01  H9   single    0.970  0.020  1.090
 QKJ  C02  H10  single    0.970  0.020  1.090
 QKJ  C02  H11  single    0.970  0.020  1.090
 QKJ  C06  H12  single    0.970  0.020  1.090
 QKJ  C06  H13  single    0.970  0.020  1.090
 QKJ  C07  H14  single    0.970  0.020  1.090
 QKJ  C07  H15  single    0.970  0.020  1.090
 QKJ  C08  H16  single    0.970  0.020  1.090
 QKJ  C08  H17  single    0.970  0.020  1.090
 QKJ  C13  H18  single    0.930  0.020  1.080
 QKJ  C20  H19  single    0.930  0.020  1.080
 QKJ  N22  H20  single    0.890  0.020  1.040
 QKJ  N22  H21  single    0.890  0.020  1.040
 QKJ  N25  H22  single    0.890  0.020  1.040
 QKJ  N25  H23  single    0.890  0.020  1.040
 QKJ  O19  H24  single    0.850  0.020  0.980

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
 QKJ  H1   C11  C10  119.52  3.000
 QKJ  H1   C11  C12  120.77  3.000
 QKJ  C10  C11  C12  119.71  3.000
 QKJ  H2   C12  C13  119.89  3.000
 QKJ  H2   C12  C11  119.32  3.000
 QKJ  C13  C12  C11  120.79  3.000
 QKJ  H4   C15  H3   107.16  3.000
 QKJ  H4   C15  C14  109.88  3.000
 QKJ  H3   C15  C14  109.81  3.000
 QKJ  H4   C15  C16  109.52  3.000
 QKJ  H3   C15  C16  110.06  3.000
 QKJ  C14  C15  C16  110.35  3.000
 QKJ  H6   C16  H5   106.79  3.000
 QKJ  H6   C16  C17  107.53  3.000
 QKJ  H5   C16  C17  107.95  3.000
 QKJ  H6   C16  C15  109.30  3.000
 QKJ  H5   C16  C15  110.23  3.000
 QKJ  C17  C16  C15  114.72  3.000
 QKJ  H9   C01  H8   107.98  3.000
 QKJ  H9   C01  H7   107.60  3.000
 QKJ  H8   C01  H7   108.13  3.000
 QKJ  H9   C01  C02  111.43  3.000
 QKJ  H8   C01  C02  111.11  3.000
 QKJ  H7   C01  C02  110.44  3.000
 QKJ  N26  C03  C04  121.42  3.000
 QKJ  C04  C03  C02  122.41  3.000
 QKJ  N26  C03  C02  116.17  3.000
 QKJ  O05  C04  C21  119.51  3.000
 QKJ  O05  C04  C03  123.30  3.000
 QKJ  C21  C04  C03  117.18  3.000
 QKJ  H13  C06  H12  107.16  3.000
 QKJ  H13  C06  O05  110.26  3.000
 QKJ  H12  C06  O05  110.01  3.000
 QKJ  H13  C06  C07  109.71  3.000
 QKJ  H12  C06  C07  110.75  3.000
 QKJ  O05  C06  C07  108.96  3.000
 QKJ  H15  C07  H14  106.36  3.000
 QKJ  H15  C07  C08  107.79  3.000
 QKJ  H14  C07  C08  109.92  3.000
 QKJ  H15  C07  C06  110.02  3.000
 QKJ  H14  C07  C06  108.00  3.000
 QKJ  C08  C07  C06  114.44  3.000
 QKJ  H17  C08  H16  107.46  3.000
 QKJ  H17  C08  O09  110.36  3.000
 QKJ  H16  C08  O09  110.67  3.000
 QKJ  H17  C08  C07  110.62  3.000
 QKJ  H16  C08  C07  109.53  3.000
 QKJ  O09  C08  C07  108.21  3.000
 QKJ  O09  C10  C20  124.14  3.000
 QKJ  O09  C10  C11  116.25  3.000
 QKJ  C20  C10  C11  119.61  3.000
 QKJ  H18  C13  C14  120.01  3.000
 QKJ  H18  C13  C12  120.17  3.000
 QKJ  C14  C13  C12  119.81  3.000
 QKJ  C20  C14  C13  119.61  3.000
 QKJ  C20  C14  C15  119.53  3.000
 QKJ  C13  C14  C15  120.81  3.000
 QKJ  O19  C17  O18  122.88  3.000
 QKJ  O19  C17  C16  112.51  3.000
 QKJ  O18  C17  C16  124.60  3.000
 QKJ  H19  C20  C14  118.38  3.000
 QKJ  H19  C20  C10  121.15  3.000
 QKJ  C14  C20  C10  120.46  3.000
 QKJ  N23  C21  N22  118.13  3.000
 QKJ  N22  C21  C04  120.78  3.000
 QKJ  N23  C21  C04  121.08  3.000
 QKJ  N26  C24  N25  117.20  3.000
 QKJ  N26  C24  N23  126.30  3.000
 QKJ  N25  C24  N23  116.48  3.000
 QKJ  H21  N22  H20  115.85  3.000
 QKJ  H21  N22  C21  119.11  3.000
 QKJ  H20  N22  C21  117.46  3.000
 QKJ  C24  N23  C21  116.96  3.000
 QKJ  H23  N25  H22  115.74  3.000
 QKJ  H23  N25  C24  117.63  3.000
 QKJ  H22  N25  C24  117.35  3.000
 QKJ  C24  N26  C03  117.02  3.000
 QKJ  C06  O05  C04  114.02  3.000
 QKJ  C10  O09  C08  119.28  3.000
 QKJ  H24  O19  C17  109.92  3.000
 QKJ  H11  C02  H10  106.87  3.000
 QKJ  H11  C02  C03  107.82  3.000
 QKJ  H10  C02  C03  110.65  3.000
 QKJ  H11  C02  C01  109.18  3.000
 QKJ  H10  C02  C01  109.99  3.000
 QKJ  C03  C02  C01  112.16  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
 QKJ  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 QKJ  CONST_02  C14  C20  C10  C11     0.00   0.0  0
 QKJ  CONST_03  C20  C14  C13  C12     0.00   0.0  0
 QKJ  CONST_04  C20  C10  C11  C12     0.00   0.0  0
 QKJ  CONST_05  N23  C24  N26  C03     0.00   0.0  0
 QKJ  CONST_06  N23  C21  C04  C03     0.00   0.0  0
 QKJ  CONST_07  C24  N26  C03  C04     0.00   0.0  0
 QKJ  CONST_08  C24  N23  C21  C04     0.00   0.0  0
 QKJ  CONST_09  C13  C14  C20  C10     0.00   0.0  0
 QKJ  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 QKJ  CONST_11  N26  C24  N23  C21     0.00   0.0  0
 QKJ  CONST_12  N26  C03  C04  C21     0.00   0.0  0
 QKJ  CONST_13  C15  C14  C13  C12   180.00   0.0  0
 QKJ  CONST_14  O09  C10  C11  C12   180.00   0.0  0
 QKJ  CONST_15  C10  C20  C14  C15   180.00   0.0  0
 QKJ  CONST_16  C24  N26  C03  C02   180.00   0.0  0
 QKJ  CONST_17  C21  C04  C03  C02   180.00   0.0  0
 QKJ  CONST_18  N25  C24  N26  C03   180.00   0.0  0
 QKJ  CONST_19  N22  C21  C04  C03   180.00   0.0  0
 QKJ  CONST_20  O09  C10  C20  C14   180.00   0.0  0
 QKJ  CONST_21  N25  C24  N23  C21   180.00   0.0  0
 QKJ  CONST_22  N22  C21  N23  C24   180.00   0.0  0
 QKJ  CONST_23  O05  C04  C21  N23   180.00   0.0  0
 QKJ  CONST_24  O05  C04  C03  N26   180.00   0.0  0
 QKJ  CONST_25  H18  C13  C12  C11   180.00   0.0  0
 QKJ  CONST_26  H19  C20  C10  C11   180.00   0.0  0
 QKJ  CONST_27  H2   C12  C11  C10   180.00   0.0  0
 QKJ  CONST_28  H1   C11  C12  C13   180.00   0.0  0
 QKJ  CONST_29  H20  N22  C21  C04   180.00   0.0  0
 QKJ  CONST_33  H24  O19  C17  C16   180.00   0.0  0
 QKJ  Var_01    C13  C14  C15  C16    87.37  30.0  2
 QKJ  Var_02    N26  C03  C02  C01    64.73  30.0  1
 QKJ  Var_03    C21  C04  O05  C06   -90.95  30.0  2
 QKJ  Var_04    C20  C10  O09  C08    -8.16  30.0  1
 QKJ  Var_05    C07  C06  O05  C04  -176.46  30.0  3
 QKJ  Var_06    C17  C16  C15  C14  -178.24  30.0  3
 QKJ  Var_07    H7   C01  C02  C03  -177.66  30.0  3
 QKJ  Var_08    H16  C08  O09  C10    65.61  30.0  3
 QKJ  Var_09    O18  C17  C16  C15   134.66  30.0  3
 QKJ  Var_10    O09  C08  C07  C06    58.53  30.0  3
 QKJ  Var_11    O05  C06  C07  C08    59.64  30.0  1

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
 QKJ  plan-1  C11  0.020
 QKJ  plan-1  C12  0.020
 QKJ  plan-1  C15  0.020
 QKJ  plan-1  C10  0.020
 QKJ  plan-1  C13  0.020
 QKJ  plan-1  C14  0.020
 QKJ  plan-1  C20  0.020
 QKJ  plan-1  O09  0.020
 QKJ  plan-1  H1   0.020
 QKJ  plan-1  H2   0.020
 QKJ  plan-1  H18  0.020
 QKJ  plan-1  H19  0.020
 QKJ  plan-2  C03  0.020
 QKJ  plan-2  C04  0.020
 QKJ  plan-2  C21  0.020
 QKJ  plan-2  C24  0.020
 QKJ  plan-2  N22  0.020
 QKJ  plan-2  N23  0.020
 QKJ  plan-2  N25  0.020
 QKJ  plan-2  N26  0.020
 QKJ  plan-2  O05  0.020
 QKJ  plan-2  C02  0.020
 QKJ  plan-3  C21  0.020
 QKJ  plan-3  N22  0.020
 QKJ  plan-3  H20  0.020
 QKJ  plan-3  H21  0.020
 QKJ  plan-4  C24  0.020
 QKJ  plan-4  N25  0.020
 QKJ  plan-4  H22  0.020
 QKJ  plan-4  H23  0.020
 QKJ  plan-5  C16  0.020
 QKJ  plan-5  C17  0.020
 QKJ  plan-5  O18  0.020
 QKJ  plan-5  O19  0.020
 QKJ  plan-5  H24  0.020

