# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 20:18:33 2022
#   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  49  26  .  2022-03-23  2022-03-23
;
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  -0.364   -9.2342   7.4757  15.1011
 QKJ  C12  C  CR16   0  -0.224   -9.6931   8.7797  15.0688
 QKJ  C15  C  CH2    0  -0.498   -6.5052  10.7451  15.6805
 QKJ  C16  C  CH2    0  -0.573   -6.2820  10.9877  17.1709
 QKJ  C01  C  CH3    0  -0.665   -9.4246   5.3805  11.8305
 QKJ  C03  C  CR6    0   0.231   -7.2083   4.5946  10.9444
 QKJ  C04  C  CR6    0   0.123   -6.1957   3.9274  11.5997
 QKJ  C06  C  CH2    0  -0.173   -6.4900   3.5921  13.9044
 QKJ  C07  C  CH2    0  -0.500   -5.9849   4.1073  15.2357
 QKJ  C08  C  CH2    0  -0.192   -6.1286   5.6047  15.4190
 QKJ  C10  C  CR6    0   0.408   -7.8746   7.2282  15.3051
 QKJ  C13  C  CR16   0  -0.348   -8.8171   9.8472  15.2355
 QKJ  C14  C  CR6    0   0.156   -7.4630   9.6114  15.4414
 QKJ  C17  C  C      0   0.411   -5.2850  12.1116  17.5211
 QKJ  C20  C  CR16   0  -0.438   -6.9980   8.2951  15.4753
 QKJ  C21  C  CR6    0   0.433   -5.5569   2.8783  10.9021
 QKJ  C24  C  CR6    0   0.506   -6.9289   3.2485   9.1339
 QKJ  N22  N  NH2    0  -0.823   -4.5636   2.1709  11.4765
 QKJ  N23  N  N      0  -0.501   -5.9295   2.5481   9.6722
 QKJ  N25  N  NH2    0  -0.825   -7.3373   2.8670   7.8947
 QKJ  N26  N  N      0  -0.499   -7.5776   4.2576   9.7022
 QKJ  O05  O  O2     0  -0.495   -5.7762   4.2495  12.8586
 QKJ  O09  O  O2     0  -0.480   -7.5033   5.9320  15.3185
 QKJ  O18  O  O      0  -0.621   -5.1206  12.3247  18.7399
 QKJ  O19  O  OC    -1  -0.602   -4.7280  12.7061  16.5772
 QKJ  H1   H  HCR6   0   0.251   -9.9152   6.6445  14.9663
 QKJ  H2   H  HCR6   0   0.249  -10.7474   8.9664  14.9070
 QKJ  H3   H  HCH2   0   0.225   -5.5489  10.5283  15.1994
 QKJ  H4   H  HCH2   0   0.226   -6.8898  11.6538  15.2131
 QKJ  H5   H  HCH2   0   0.223   -7.2408  11.2090  17.6524
 QKJ  H6   H  HCH2   0   0.224   -5.9350  10.0621  17.6436
 QKJ  H7   H  HCH3   0   0.234   -9.9478   6.2284  12.2720
 QKJ  H8   H  HCH3   0   0.228   -9.9340   5.1147  10.9049
 QKJ  H9   H  HCH3   0   0.226   -9.5174   4.5389  12.5183
 QKJ  H10  H  HCH2   0   0.253   -7.4849   6.0352  12.5053
 QKJ  H11  H  HCH2   0   0.248   -7.9093   6.5873  10.8980
 QKJ  H12  H  HCH2   0   0.228   -7.5637   3.7762  13.7977
 QKJ  H13  H  HCH2   0   0.232   -6.3384   2.5087  13.8446
 QKJ  H14  H  HCH2   0   0.247   -6.5206   3.5804  16.0291
 QKJ  H15  H  HCH2   0   0.247   -4.9286   3.8542  15.3561
 QKJ  H16  H  HCH2   0   0.237   -5.7345   5.8972  16.3987
 QKJ  H17  H  HCH2   0   0.226   -5.5482   6.1395  14.6606
 QKJ  H18  H  HCR6   0   0.237   -9.1881  10.8647  15.2056
 QKJ  H19  H  HCR6   0   0.266   -5.9405   8.1286  15.6400
 QKJ  H20  H  HNH2   0   0.391   -4.0195   1.5628  10.8878
 QKJ  H21  H  HNH2   0   0.399   -4.0970   2.5408  12.2870
 QKJ  H22  H  HNH2   0   0.383   -7.8891   3.5265   7.3729
 QKJ  H23  H  HNH2   0   0.383   -6.6996   2.3112   7.3506
 QKJ  C02  C  CH2    0  -0.512   -7.9604   5.7306  11.5748

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    1.359  0.020  1.359
 QKJ  C24  N26  aromatic  1.327  0.020  1.327
 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  1.413  0.020  1.413
 QKJ  C21  N22  single    1.348  0.020  1.348
 QKJ  C02  C01  single    1.527  0.020  1.527
 QKJ  C04  O05  single    1.365  0.020  1.365
 QKJ  O05  C06  single    1.427  0.020  1.427
 QKJ  C06  C07  single    1.514  0.020  1.514
 QKJ  C15  C14  single    1.503  0.020  1.503
 QKJ  C15  C16  single    1.526  0.020  1.526
 QKJ  C14  C13  aromatic  1.390  0.020  1.390
 QKJ  C14  C20  aromatic  1.396  0.020  1.396
 QKJ  C13  C12  aromatic  1.391  0.020  1.391
 QKJ  C07  C08  single    1.515  0.020  1.515
 QKJ  C20  C10  aromatic  1.391  0.020  1.391
 QKJ  C12  C11  aromatic  1.383  0.020  1.383
 QKJ  C16  C17  single    1.543  0.020  1.543
 QKJ  C10  C11  aromatic  1.397  0.020  1.397
 QKJ  C10  O09  single    1.348  0.020  1.348
 QKJ  O09  C08  single    1.417  0.020  1.417
 QKJ  C17  O18  deloc     1.248  0.020  1.248
 QKJ  C17  O19  deloc     1.247  0.020  1.247
 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

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  119.62  3.000
 QKJ  H1   C11  C12  120.81  3.000
 QKJ  C10  C11  C12  119.57  3.000
 QKJ  H2   C12  C13  119.92  3.000
 QKJ  H2   C12  C11  119.29  3.000
 QKJ  C13  C12  C11  120.80  3.000
 QKJ  H4   C15  H3   106.56  3.000
 QKJ  H4   C15  C14  109.58  3.000
 QKJ  H3   C15  C14  109.76  3.000
 QKJ  H4   C15  C16  109.71  3.000
 QKJ  H3   C15  C16  109.49  3.000
 QKJ  C14  C15  C16  111.61  3.000
 QKJ  H6   C16  H5   104.96  3.000
 QKJ  H6   C16  C17  108.23  3.000
 QKJ  H5   C16  C17  108.58  3.000
 QKJ  H6   C16  C15  109.47  3.000
 QKJ  H5   C16  C15  109.47  3.000
 QKJ  C17  C16  C15  115.59  3.000
 QKJ  H9   C01  H8   107.92  3.000
 QKJ  H9   C01  H7   107.69  3.000
 QKJ  H8   C01  H7   108.04  3.000
 QKJ  H9   C01  C02  111.35  3.000
 QKJ  H8   C01  C02  111.23  3.000
 QKJ  H7   C01  C02  110.47  3.000
 QKJ  N26  C03  C04  121.46  3.000
 QKJ  C04  C03  C02  122.32  3.000
 QKJ  N26  C03  C02  116.22  3.000
 QKJ  O05  C04  C21  119.45  3.000
 QKJ  O05  C04  C03  123.36  3.000
 QKJ  C21  C04  C03  117.19  3.000
 QKJ  H13  C06  H12  107.26  3.000
 QKJ  H13  C06  O05  110.26  3.000
 QKJ  H12  C06  O05  109.99  3.000
 QKJ  H13  C06  C07  109.77  3.000
 QKJ  H12  C06  C07  110.84  3.000
 QKJ  O05  C06  C07  108.71  3.000
 QKJ  H15  C07  H14  106.39  3.000
 QKJ  H15  C07  C08  107.89  3.000
 QKJ  H14  C07  C08  110.01  3.000
 QKJ  H15  C07  C06  109.91  3.000
 QKJ  H14  C07  C06  108.11  3.000
 QKJ  C08  C07  C06  114.26  3.000
 QKJ  H17  C08  H16  107.35  3.000
 QKJ  H17  C08  O09  110.64  3.000
 QKJ  H16  C08  O09  110.54  3.000
 QKJ  H17  C08  C07  110.41  3.000
 QKJ  H16  C08  C07  109.74  3.000
 QKJ  O09  C08  C07  108.16  3.000
 QKJ  O09  C10  C20  124.23  3.000
 QKJ  O09  C10  C11  116.09  3.000
 QKJ  C20  C10  C11  119.68  3.000
 QKJ  H18  C13  C14  119.81  3.000
 QKJ  H18  C13  C12  120.12  3.000
 QKJ  C14  C13  C12  120.07  3.000
 QKJ  C20  C14  C13  119.21  3.000
 QKJ  C20  C14  C15  119.66  3.000
 QKJ  C13  C14  C15  121.09  3.000
 QKJ  O19  C17  O18  126.80  3.000
 QKJ  O19  C17  C16  117.66  3.000
 QKJ  O18  C17  C16  115.54  3.000
 QKJ  H19  C20  C14  118.28  3.000
 QKJ  H19  C20  C10  121.05  3.000
 QKJ  C14  C20  C10  120.67  3.000
 QKJ  N23  C21  N22  118.12  3.000
 QKJ  N22  C21  C04  120.83  3.000
 QKJ  N23  C21  C04  121.04  3.000
 QKJ  N26  C24  N25  117.18  3.000
 QKJ  N26  C24  N23  126.34  3.000
 QKJ  N25  C24  N23  116.46  3.000
 QKJ  H21  N22  H20  116.29  3.000
 QKJ  H21  N22  C21  119.50  3.000
 QKJ  H20  N22  C21  117.80  3.000
 QKJ  C24  N23  C21  116.99  3.000
 QKJ  H23  N25  H22  115.44  3.000
 QKJ  H23  N25  C24  117.24  3.000
 QKJ  H22  N25  C24  116.98  3.000
 QKJ  C24  N26  C03  116.98  3.000
 QKJ  C06  O05  C04  114.41  3.000
 QKJ  C10  O09  C08  119.34  3.000
 QKJ  H11  C02  H10  106.83  3.000
 QKJ  H11  C02  C03  108.04  3.000
 QKJ  H10  C02  C03  110.60  3.000
 QKJ  H11  C02  C01  109.16  3.000
 QKJ  H10  C02  C01  109.87  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  Var_01    C13  C14  C15  C16    95.04  30.0  2
 QKJ  Var_02    N26  C03  C02  C01    66.34  30.0  1
 QKJ  Var_03    C21  C04  O05  C06   -93.11  30.0  2
 QKJ  Var_04    C20  C10  O09  C08    -4.56  30.0  2
 QKJ  Var_05    C07  C06  O05  C04  -176.35  30.0  3
 QKJ  Var_06    C17  C16  C15  C14   178.55  30.0  3
 QKJ  Var_07    H7   C01  C02  C03  -179.04  30.0  3
 QKJ  Var_08    H16  C08  O09  C10    66.88  30.0  3
 QKJ  Var_09    O18  C17  C16  C15   178.82  30.0  3
 QKJ  Var_10    O09  C08  C07  C06    59.82  30.0  3
 QKJ  Var_11    O05  C06  C07  C08    58.52  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

