# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 03:53:15 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: 1-[2-(3-{[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]methyl}azetidin-1-yl)phenyl]piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OC[C@H]2CN(C2)c3ccccc3N4CC[C@@H](CC4)C(O)=O
#
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
 WFJ  WFJ  '1-[2-(3-{[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]methyl}azetidin-1-yl)phenyl]piperidine-4-carboxylic acid'  ligand  60  31  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WFJ
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
 WFJ  C01  C  CH3    0  -0.665   -7.6403  16.4560  10.6292
 WFJ  C02  C  CH2    0  -0.509   -6.2961  15.7562  10.8198
 WFJ  C03  C  CR6    0   0.224   -6.3787  14.2828  10.5451
 WFJ  C05  C  CR6    0   0.507   -6.6064  12.6299   9.0011
 WFJ  C08  C  CR6    0   0.437   -6.3746  11.9826  11.1633
 WFJ  C10  C  CR6    0   0.119   -6.3080  13.3403  11.5481
 WFJ  C12  C  CH2    0  -0.152   -7.3760  13.8201  13.5802
 WFJ  C13  C  CH1    0  -0.338   -7.0597  14.2635  14.9861
 WFJ  C14  C  CH2    0  -0.286   -6.5520  15.7100  15.0958
 WFJ  C16  C  CH2    0  -0.285   -8.3145  14.7478  15.7324
 WFJ  C17  C  CR6    0   0.297   -8.2062  17.2442  16.1845
 WFJ  C18  C  CR16   0  -0.356   -7.2126  18.1875  16.4559
 WFJ  C19  C  CR16   0  -0.262   -7.4734  19.3157  17.2219
 WFJ  C20  C  CR16   0  -0.278   -8.7409  19.5176  17.7393
 WFJ  C21  C  CR16   0  -0.335   -9.7490  18.6061  17.4452
 WFJ  C22  C  CR6    0   0.267   -9.5204  17.4777  16.6613
 WFJ  C24  C  CH2    0  -0.299  -11.6971  16.5398  17.2106
 WFJ  C25  C  CH2    0  -0.421  -12.5693  15.3312  16.9138
 WFJ  C26  C  CH1    0  -0.373  -13.0353  15.3161  15.4581
 WFJ  C27  C  CH2    0  -0.424  -11.8245  15.4428  14.5448
 WFJ  C28  C  CH2    0  -0.311  -10.9468  16.6261  14.9227
 WFJ  C29  C  C      0   0.421  -13.9239  14.0834  15.1759
 WFJ  N04  N  N      0  -0.498   -6.5277  13.9294   9.2618
 WFJ  N06  N  NH2    0  -0.824   -6.8202  12.2669   7.7084
 WFJ  N07  N  N      0  -0.501   -6.5235  11.6391   9.8901
 WFJ  N09  N  NH2    0  -0.823   -6.3086  11.0002  12.0835
 WFJ  N15  N  NT     0  -0.480   -7.9087  16.1248  15.4333
 WFJ  N23  N  NT     0  -0.487  -10.5460  16.5721  16.3273
 WFJ  O11  O  O2     0  -0.496   -6.1523  13.6619  12.8671
 WFJ  O30  O  OC    -1  -0.617  -14.9497  13.9783  15.8811
 WFJ  O31  O  O      0  -0.596  -13.5540  13.2917  14.2861
 WFJ  H1   H  HCH3   0   0.235   -7.5399  17.5274  10.8012
 WFJ  H2   H  HCH3   0   0.227   -8.0198  16.3109   9.6181
 WFJ  H3   H  HCH3   0   0.230   -8.3878  16.0763  11.3266
 WFJ  H4   H  HCH2   0   0.252   -5.9233  15.9402  11.8269
 WFJ  H5   H  HCH2   0   0.248   -5.5667  16.1854  10.1289
 WFJ  H6   H  HCH2   0   0.224   -8.0115  14.5645  13.0844
 WFJ  H7   H  HCH2   0   0.231   -7.9335  12.8757  13.5992
 WFJ  H8   H  HCH1   0   0.261   -6.4610  13.5160  15.5068
 WFJ  H9   H  HCH2   0   0.226   -5.8362  15.8358  15.9174
 WFJ  H10  H  HCH2   0   0.245   -6.1350  16.1758  14.1992
 WFJ  H11  H  HCH2   0   0.246   -9.2757  14.4404  15.3220
 WFJ  H12  H  HCH2   0   0.231   -8.2971  14.5094  16.8005
 WFJ  H13  H  HCR6   0   0.255   -6.2101  18.0326  16.0772
 WFJ  H14  H  HCR6   0   0.242   -6.6767  20.0205  17.4231
 WFJ  H15  H  HCR6   0   0.240   -8.9586  20.3835  18.3509
 WFJ  H16  H  HCR6   0   0.253  -10.7440  18.7935  17.8275
 WFJ  H17  H  HCH2   0   0.238  -11.3459  16.5020  18.2441
 WFJ  H18  H  HCH2   0   0.190  -12.3151  17.4487  17.1148
 WFJ  H19  H  HCH2   0   0.223  -13.4303  15.3431  17.5841
 WFJ  H20  H  HCH2   0   0.207  -12.0028  14.4194  17.1332
 WFJ  H21  H  HCH1   0   0.203  -13.6619  16.2091  15.3167
 WFJ  H22  H  HCH2   0   0.218  -12.1350  15.5611  13.5041
 WFJ  H23  H  HCH2   0   0.211  -11.2342  14.5241  14.5880
 WFJ  H24  H  HCH2   0   0.247  -10.0524  16.6339  14.2982
 WFJ  H25  H  HCH2   0   0.203  -11.4859  17.5662  14.7180
 WFJ  H26  H  HNH2   0   0.383   -6.6245  12.9553   7.0017
 WFJ  H27  H  HNH2   0   0.384   -6.6071  11.3168   7.4561
 WFJ  H28  H  HNH2   0   0.391   -6.1811  10.0567  11.7582
 WFJ  H29  H  HNH2   0   0.400   -5.9587  11.2056  13.0037

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
 WFJ  N06  C05  single    1.360  0.020  1.360
 WFJ  C05  N04  aromatic  1.328  0.020  1.328
 WFJ  C05  N07  aromatic  1.334  0.020  1.334
 WFJ  N04  C03  aromatic  1.339  0.020  1.339
 WFJ  N07  C08  aromatic  1.327  0.020  1.327
 WFJ  C03  C02  single    1.501  0.020  1.501
 WFJ  C03  C10  aromatic  1.378  0.020  1.378
 WFJ  C08  C10  aromatic  1.413  0.020  1.413
 WFJ  C08  N09  single    1.348  0.020  1.348
 WFJ  C01  C02  single    1.527  0.020  1.527
 WFJ  C10  O11  single    1.367  0.020  1.367
 WFJ  O11  C12  single    1.425  0.020  1.425
 WFJ  C12  C13  single    1.508  0.020  1.508
 WFJ  C27  C28  single    1.521  0.020  1.521
 WFJ  C27  C26  single    1.522  0.020  1.522
 WFJ  O31  C29  deloc     1.247  0.020  1.247
 WFJ  C28  N23  single    1.462  0.020  1.462
 WFJ  C29  C26  single    1.546  0.020  1.546
 WFJ  C29  O30  deloc     1.249  0.020  1.249
 WFJ  C26  C25  single    1.529  0.020  1.529
 WFJ  C13  C14  single    1.537  0.020  1.537
 WFJ  C13  C16  single    1.538  0.020  1.538
 WFJ  C14  N15  single    1.458  0.020  1.458
 WFJ  N15  C17  single    1.381  0.020  1.381
 WFJ  N15  C16  single    1.466  0.020  1.466
 WFJ  N23  C22  single    1.408  0.020  1.408
 WFJ  N23  C24  single    1.451  0.020  1.451
 WFJ  C17  C22  aromatic  1.417  0.020  1.417
 WFJ  C17  C18  aromatic  1.397  0.020  1.397
 WFJ  C22  C21  aromatic  1.393  0.020  1.393
 WFJ  C18  C19  aromatic  1.388  0.020  1.388
 WFJ  C21  C20  aromatic  1.391  0.020  1.391
 WFJ  C19  C20  aromatic  1.384  0.020  1.384
 WFJ  C25  C24  single    1.520  0.020  1.520
 WFJ  C01  H1   single    0.970  0.020  1.090
 WFJ  C01  H2   single    0.970  0.020  1.090
 WFJ  C01  H3   single    0.970  0.020  1.090
 WFJ  C02  H4   single    0.970  0.020  1.090
 WFJ  C02  H5   single    0.970  0.020  1.090
 WFJ  C12  H6   single    0.970  0.020  1.090
 WFJ  C12  H7   single    0.970  0.020  1.090
 WFJ  C13  H8   single    0.970  0.020  1.090
 WFJ  C14  H9   single    0.970  0.020  1.090
 WFJ  C14  H10  single    0.970  0.020  1.090
 WFJ  C16  H11  single    0.970  0.020  1.090
 WFJ  C16  H12  single    0.970  0.020  1.090
 WFJ  C18  H13  single    0.930  0.020  1.080
 WFJ  C19  H14  single    0.930  0.020  1.080
 WFJ  C20  H15  single    0.930  0.020  1.080
 WFJ  C21  H16  single    0.930  0.020  1.080
 WFJ  C24  H17  single    0.970  0.020  1.090
 WFJ  C24  H18  single    0.970  0.020  1.090
 WFJ  C25  H19  single    0.970  0.020  1.090
 WFJ  C25  H20  single    0.970  0.020  1.090
 WFJ  C26  H21  single    0.970  0.020  1.090
 WFJ  C27  H22  single    0.970  0.020  1.090
 WFJ  C27  H23  single    0.970  0.020  1.090
 WFJ  C28  H24  single    0.970  0.020  1.090
 WFJ  C28  H25  single    0.970  0.020  1.090
 WFJ  N06  H26  single    0.890  0.020  1.040
 WFJ  N06  H27  single    0.890  0.020  1.040
 WFJ  N09  H28  single    0.890  0.020  1.040
 WFJ  N09  H29  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
 WFJ  H3   C01  H2   107.96  3.000
 WFJ  H3   C01  H1   107.73  3.000
 WFJ  H2   C01  H1   108.03  3.000
 WFJ  H3   C01  C02  111.34  3.000
 WFJ  H2   C01  C02  111.18  3.000
 WFJ  H1   C01  C02  110.47  3.000
 WFJ  H5   C02  H4   106.85  3.000
 WFJ  H5   C02  C03  107.86  3.000
 WFJ  H4   C02  C03  110.72  3.000
 WFJ  H5   C02  C01  109.19  3.000
 WFJ  H4   C02  C01  109.82  3.000
 WFJ  C03  C02  C01  112.24  3.000
 WFJ  N04  C03  C10  121.50  3.000
 WFJ  C10  C03  C02  122.37  3.000
 WFJ  N04  C03  C02  116.13  3.000
 WFJ  N07  C05  N06  116.43  3.000
 WFJ  N07  C05  N04  126.33  3.000
 WFJ  N06  C05  N04  117.22  3.000
 WFJ  N09  C08  N07  118.16  3.000
 WFJ  N09  C08  C10  120.81  3.000
 WFJ  N07  C08  C10  121.03  3.000
 WFJ  O11  C10  C08  119.64  3.000
 WFJ  O11  C10  C03  123.18  3.000
 WFJ  C08  C10  C03  117.17  3.000
 WFJ  H7   C12  H6   107.31  3.000
 WFJ  H7   C12  O11  110.46  3.000
 WFJ  H6   C12  O11  110.28  3.000
 WFJ  H7   C12  C13  110.10  3.000
 WFJ  H6   C12  C13  110.08  3.000
 WFJ  O11  C12  C13  108.61  3.000
 WFJ  H8   C13  C16  115.61  3.000
 WFJ  H8   C13  C14  115.46  3.000
 WFJ  C16  C13  C14   86.47  3.000
 WFJ  H8   C13  C12  111.04  3.000
 WFJ  C16  C13  C12  111.95  3.000
 WFJ  C14  C13  C12  114.37  3.000
 WFJ  H10  C14  H9   108.45  3.000
 WFJ  H10  C14  N15  115.06  3.000
 WFJ  H9   C14  N15  113.65  3.000
 WFJ  H10  C14  C13  117.94  3.000
 WFJ  H9   C14  C13  112.15  3.000
 WFJ  N15  C14  C13   88.68  3.000
 WFJ  H12  C16  H11  108.67  3.000
 WFJ  H12  C16  N15  113.53  3.000
 WFJ  H11  C16  N15  115.61  3.000
 WFJ  H12  C16  C13  113.07  3.000
 WFJ  H11  C16  C13  116.63  3.000
 WFJ  N15  C16  C13   88.34  3.000
 WFJ  N15  C17  C22  121.09  3.000
 WFJ  C22  C17  C18  118.88  3.000
 WFJ  N15  C17  C18  120.01  3.000
 WFJ  H13  C18  C19  118.89  3.000
 WFJ  H13  C18  C17  119.61  3.000
 WFJ  C19  C18  C17  121.49  3.000
 WFJ  H14  C19  C20  120.64  3.000
 WFJ  H14  C19  C18  119.56  3.000
 WFJ  C20  C19  C18  119.80  3.000
 WFJ  H15  C20  C21  119.88  3.000
 WFJ  H15  C20  C19  120.81  3.000
 WFJ  C21  C20  C19  119.30  3.000
 WFJ  H16  C21  C22  119.34  3.000
 WFJ  H16  C21  C20  118.58  3.000
 WFJ  C22  C21  C20  122.08  3.000
 WFJ  N23  C22  C21  122.34  3.000
 WFJ  C21  C22  C17  118.36  3.000
 WFJ  N23  C22  C17  119.30  3.000
 WFJ  H18  C24  H17  106.90  3.000
 WFJ  H18  C24  N23  111.91  3.000
 WFJ  H17  C24  N23  108.76  3.000
 WFJ  H18  C24  C25  108.46  3.000
 WFJ  H17  C24  C25  109.99  3.000
 WFJ  N23  C24  C25  110.74  3.000
 WFJ  H20  C25  H19  107.11  3.000
 WFJ  H20  C25  C26  109.88  3.000
 WFJ  H19  C25  C26  110.15  3.000
 WFJ  H20  C25  C24  109.02  3.000
 WFJ  H19  C25  C24  108.92  3.000
 WFJ  C26  C25  C24  111.64  3.000
 WFJ  H21  C26  C29  107.25  3.000
 WFJ  H21  C26  C27  107.97  3.000
 WFJ  C29  C26  C27  114.47  3.000
 WFJ  H21  C26  C25  106.74  3.000
 WFJ  C29  C26  C25  110.91  3.000
 WFJ  C27  C26  C25  109.16  3.000
 WFJ  H23  C27  H22  106.39  3.000
 WFJ  H23  C27  C28  109.42  3.000
 WFJ  H22  C27  C28  108.45  3.000
 WFJ  H23  C27  C26  109.64  3.000
 WFJ  H22  C27  C26  110.77  3.000
 WFJ  C28  C27  C26  112.01  3.000
 WFJ  H25  C28  H24  106.76  3.000
 WFJ  H25  C28  N23  110.11  3.000
 WFJ  H24  C28  N23  109.00  3.000
 WFJ  H25  C28  C27  109.57  3.000
 WFJ  H24  C28  C27  109.66  3.000
 WFJ  N23  C28  C27  111.61  3.000
 WFJ  O31  C29  O30  126.36  3.000
 WFJ  O30  C29  C26  115.86  3.000
 WFJ  O31  C29  C26  117.78  3.000
 WFJ  C05  N04  C03  116.93  3.000
 WFJ  H27  N06  H26  115.41  3.000
 WFJ  H27  N06  C05  117.22  3.000
 WFJ  H26  N06  C05  117.05  3.000
 WFJ  C08  N07  C05  117.01  3.000
 WFJ  H29  N09  H28  116.31  3.000
 WFJ  H29  N09  C08  119.54  3.000
 WFJ  H28  N09  C08  117.97  3.000
 WFJ  C17  N15  C16  126.21  3.000
 WFJ  C16  N15  C14   92.15  3.000
 WFJ  C17  N15  C14  123.85  3.000
 WFJ  C28  N23  C24  111.60  3.000
 WFJ  C24  N23  C22  116.59  3.000
 WFJ  C28  N23  C22  113.82  3.000
 WFJ  C12  O11  C10  114.29  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
 WFJ  CONST_01  N07  C05  N04  C03     0.00   0.0  0
 WFJ  CONST_02  N07  C08  C10  C03     0.00   0.0  0
 WFJ  CONST_03  C10  C03  N04  C05     0.00   0.0  0
 WFJ  CONST_04  C10  C08  N07  C05     0.00   0.0  0
 WFJ  CONST_05  N04  C05  N07  C08     0.00   0.0  0
 WFJ  CONST_06  N04  C03  C10  C08     0.00   0.0  0
 WFJ  CONST_07  C20  C21  C22  C17     0.00   0.0  0
 WFJ  CONST_08  C20  C19  C18  C17     0.00   0.0  0
 WFJ  CONST_09  C21  C22  C17  C18     0.00   0.0  0
 WFJ  CONST_10  C21  C20  C19  C18     0.00   0.0  0
 WFJ  CONST_11  C22  C17  C18  C19     0.00   0.0  0
 WFJ  CONST_12  C22  C21  C20  C19     0.00   0.0  0
 WFJ  CONST_13  N23  C22  C17  C18   180.00   0.0  0
 WFJ  CONST_14  N15  C17  C18  C19   180.00   0.0  0
 WFJ  CONST_15  N23  C22  C21  C20   180.00   0.0  0
 WFJ  CONST_16  N15  C17  C22  C21   180.00   0.0  0
 WFJ  CONST_17  N23  C22  C17  N15     0.00   0.0  0
 WFJ  CONST_18  C05  N04  C03  C02   180.00   0.0  0
 WFJ  CONST_19  C08  C10  C03  C02   180.00   0.0  0
 WFJ  CONST_20  N06  C05  N04  C03   180.00   0.0  0
 WFJ  CONST_21  N09  C08  C10  C03   180.00   0.0  0
 WFJ  CONST_22  N09  C08  N07  C05   180.00   0.0  0
 WFJ  CONST_23  N06  C05  N07  C08   180.00   0.0  0
 WFJ  CONST_24  O11  C10  C03  N04   180.00   0.0  0
 WFJ  CONST_25  O11  C10  C08  N07   180.00   0.0  0
 WFJ  CONST_26  H16  C21  C22  C17   180.00   0.0  0
 WFJ  CONST_27  H14  C19  C18  C17   180.00   0.0  0
 WFJ  CONST_28  H15  C20  C19  C18   180.00   0.0  0
 WFJ  CONST_29  H13  C18  C19  C20   180.00   0.0  0
 WFJ  CONST_30  H28  N09  C08  C10   180.00   0.0  0
 WFJ  Var_01    C17  N15  C14  C13   153.60  30.0  1
 WFJ  Var_02    C22  C17  N15  C14  -169.68  30.0  2
 WFJ  Var_03    C28  N23  C22  C17   -70.93  30.0  2
 WFJ  Var_04    C27  C28  N23  C22   167.60  30.0  1
 WFJ  Var_05    C25  C24  N23  C22  -167.71  30.0  1
 WFJ  Var_06    N23  C28  C27  C26    54.58  30.0  1
 WFJ  Var_07    N23  C24  C25  C26   -57.41  30.0  1
 WFJ  Var_08    N04  C03  C02  C01    71.53  30.0  2
 WFJ  Var_09    C13  C12  O11  C10  -176.15  30.0  3
 WFJ  Var_10    H1   C01  C02  C03  -178.00  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 WFJ  chir_01  C13  C12  C14  C16  negativ
 WFJ  chir_02  C26  C27  C29  C25  negativ

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
 WFJ  plan-1  C02  0.020
 WFJ  plan-1  C03  0.020
 WFJ  plan-1  C05  0.020
 WFJ  plan-1  C08  0.020
 WFJ  plan-1  C10  0.020
 WFJ  plan-1  N04  0.020
 WFJ  plan-1  N06  0.020
 WFJ  plan-1  N07  0.020
 WFJ  plan-1  N09  0.020
 WFJ  plan-1  O11  0.020
 WFJ  plan-2  C17  0.020
 WFJ  plan-2  C18  0.020
 WFJ  plan-2  C19  0.020
 WFJ  plan-2  C20  0.020
 WFJ  plan-2  C21  0.020
 WFJ  plan-2  C22  0.020
 WFJ  plan-2  N15  0.020
 WFJ  plan-2  N23  0.020
 WFJ  plan-2  H13  0.020
 WFJ  plan-2  H14  0.020
 WFJ  plan-2  H15  0.020
 WFJ  plan-2  H16  0.020
 WFJ  plan-3  C05  0.020
 WFJ  plan-3  N06  0.020
 WFJ  plan-3  H26  0.020
 WFJ  plan-3  H27  0.020
 WFJ  plan-4  C08  0.020
 WFJ  plan-4  N09  0.020
 WFJ  plan-4  H28  0.020
 WFJ  plan-4  H29  0.020
 WFJ  plan-5  C26  0.020
 WFJ  plan-5  C29  0.020
 WFJ  plan-5  O30  0.020
 WFJ  plan-5  O31  0.020

