# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 11:48:59 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (2R)-2-[(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2cccc(C[C@@H](C(F)F)C(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
 WPJ  WPJ  '(2R)-2-[(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid'  ligand  52  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WPJ
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
 WPJ  C01  C  CH3    0  -0.663  -22.7604  21.0735   -5.8271
 WPJ  C02  C  CH2    0  -0.505  -22.3641  19.9044   -4.9288
 WPJ  C03  C  CR6    0   0.226  -20.8885  19.6321   -4.9749
 WPJ  C05  C  CR6    0   0.507  -18.7912  20.3734   -4.5026
 WPJ  C08  C  CR6    0   0.430  -18.9567  18.3413   -5.4962
 WPJ  C10  C  CR6    0   0.125  -20.3630  18.4768   -5.5136
 WPJ  C12  C  CH2    0  -0.172  -21.3658  17.5502   -7.4314
 WPJ  C13  C  CH2    0  -0.499  -22.4067  16.5176   -7.8109
 WPJ  C14  C  CH2    0  -0.191  -23.7666  16.7373   -7.1779
 WPJ  C16  C  CR6    0   0.409  -25.3801  18.4960   -7.0708
 WPJ  C17  C  CR16   0  -0.401  -26.1904  17.8105   -6.1714
 WPJ  C18  C  CR16   0  -0.227  -27.3238  18.4446   -5.6697
 WPJ  C19  C  CR16   0  -0.330  -27.6501  19.7343   -6.0492
 WPJ  C20  C  CR6    0   0.145  -26.8436  20.4242   -6.9591
 WPJ  C21  C  CH2    0  -0.502  -27.1965  21.8308   -7.3626
 WPJ  C22  C  CH1    0  -0.492  -28.3592  21.8775   -8.3558
 WPJ  C23  C  CH1    0   0.539  -28.9994  23.2407   -8.4486
 WPJ  C26  C  C      0   0.421  -28.0105  21.4340   -9.8089
 WPJ  C29  C  CR16   0  -0.401  -25.7202  19.7914   -7.4653
 WPJ  F24  F  F      0  -0.355  -29.3661  23.7163   -7.2175
 WPJ  F25  F  F      0  -0.358  -28.1143  24.1598   -8.9494
 WPJ  N04  N  N      0  -0.498  -20.1005  20.5865   -4.4634
 WPJ  N06  N  NH2    0  -0.825  -17.9899  21.3229   -3.9506
 WPJ  N07  N  N      0  -0.500  -18.1816  19.2928   -4.9923
 WPJ  N09  N  NH2    0  -0.823  -18.3600  17.2497   -6.0197
 WPJ  O11  O  O2     0  -0.495  -21.1353  17.4727   -6.0240
 WPJ  O15  O  O2     0  -0.481  -24.2509  17.9953   -7.6133
 WPJ  O27  O  O      0  -0.606  -29.0004  21.2683  -10.5479
 WPJ  O28  O  OC    -1  -0.571  -26.8125  21.3073  -10.1076
 WPJ  H1   H  HCH3   0   0.236  -23.8287  21.2714   -5.7457
 WPJ  H2   H  HCH3   0   0.227  -22.2242  21.9811   -5.5517
 WPJ  H3   H  HCH3   0   0.225  -22.5456  20.8571   -6.8743
 WPJ  H4   H  HCH2   0   0.246  -22.6296  20.1379   -3.8946
 WPJ  H5   H  HCH2   0   0.252  -22.9294  19.0160   -5.2059
 WPJ  H6   H  HCH2   0   0.230  -20.4371  17.3540   -7.9782
 WPJ  H7   H  HCH2   0   0.227  -21.6968  18.5573   -7.7033
 WPJ  H8   H  HCH2   0   0.247  -22.5015  16.5127   -8.8996
 WPJ  H9   H  HCH2   0   0.247  -22.0567  15.5211   -7.5294
 WPJ  H10  H  HCH2   0   0.224  -23.6910  16.7081   -6.0859
 WPJ  H11  H  HCH2   0   0.237  -24.4516  15.9375   -7.4805
 WPJ  H12  H  HCR6   0   0.271  -25.9601  16.8030   -5.8524
 WPJ  H13  H  HCR6   0   0.249  -27.9512  17.9155   -4.9635
 WPJ  H14  H  HCR6   0   0.237  -28.5297  20.2152   -5.6375
 WPJ  H15  H  HCH2   0   0.242  -26.3215  22.3252   -7.7840
 WPJ  H16  H  HCH2   0   0.242  -27.4648  22.3800   -6.4569
 WPJ  H17  H  HCH1   0   0.257  -29.1535  21.2075   -8.0066
 WPJ  H18  H  HCH1   0   0.198  -29.8879  23.2445   -9.0803
 WPJ  H19  H  HCR6   0   0.243  -25.0832  20.3066   -8.1726
 WPJ  H20  H  HNH2   0   0.384  -17.0156  21.3056   -4.1993
 WPJ  H21  H  HNH2   0   0.384  -18.3866  22.2378   -3.8198
 WPJ  H22  H  HNH2   0   0.390  -17.3861  17.1080   -5.8089
 WPJ  H23  H  HNH2   0   0.399  -18.9039  16.4150   -6.1589

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
 WPJ  O27  C26  deloc     1.246  0.020  1.246
 WPJ  C26  O28  deloc     1.241  0.020  1.241
 WPJ  C26  C22  single    1.559  0.020  1.559
 WPJ  C22  C23  single    1.509  0.020  1.509
 WPJ  C22  C21  single    1.530  0.020  1.530
 WPJ  C23  F25  single    1.371  0.020  1.371
 WPJ  C23  F24  single    1.370  0.020  1.370
 WPJ  C21  C20  single    1.505  0.020  1.505
 WPJ  C29  C20  aromatic  1.385  0.020  1.385
 WPJ  C29  C16  aromatic  1.396  0.020  1.396
 WPJ  O15  C16  single    1.349  0.020  1.349
 WPJ  O15  C14  single    1.417  0.020  1.417
 WPJ  C12  C13  single    1.515  0.020  1.515
 WPJ  C12  O11  single    1.428  0.020  1.428
 WPJ  C20  C19  aromatic  1.398  0.020  1.398
 WPJ  C13  C14  single    1.516  0.020  1.516
 WPJ  C16  C17  aromatic  1.391  0.020  1.391
 WPJ  N09  C08  single    1.350  0.020  1.350
 WPJ  C19  C18  aromatic  1.383  0.020  1.383
 WPJ  C17  C18  aromatic  1.392  0.020  1.392
 WPJ  C08  N07  aromatic  1.327  0.020  1.327
 WPJ  C08  C10  aromatic  1.413  0.020  1.413
 WPJ  O11  C10  single    1.366  0.020  1.366
 WPJ  N07  C05  aromatic  1.334  0.020  1.334
 WPJ  C10  C03  aromatic  1.379  0.020  1.379
 WPJ  C01  C02  single    1.527  0.020  1.527
 WPJ  C05  N06  single    1.359  0.020  1.359
 WPJ  C05  N04  aromatic  1.327  0.020  1.327
 WPJ  C03  N04  aromatic  1.339  0.020  1.339
 WPJ  C03  C02  single    1.501  0.020  1.501
 WPJ  C01  H1   single    0.970  0.020  1.090
 WPJ  C01  H2   single    0.970  0.020  1.090
 WPJ  C01  H3   single    0.970  0.020  1.090
 WPJ  C02  H4   single    0.970  0.020  1.090
 WPJ  C02  H5   single    0.970  0.020  1.090
 WPJ  C12  H6   single    0.970  0.020  1.090
 WPJ  C12  H7   single    0.970  0.020  1.090
 WPJ  C13  H8   single    0.970  0.020  1.090
 WPJ  C13  H9   single    0.970  0.020  1.090
 WPJ  C14  H10  single    0.970  0.020  1.090
 WPJ  C14  H11  single    0.970  0.020  1.090
 WPJ  C17  H12  single    0.930  0.020  1.080
 WPJ  C18  H13  single    0.930  0.020  1.080
 WPJ  C19  H14  single    0.930  0.020  1.080
 WPJ  C21  H15  single    0.970  0.020  1.090
 WPJ  C21  H16  single    0.970  0.020  1.090
 WPJ  C22  H17  single    0.970  0.020  1.090
 WPJ  C23  H18  single    0.970  0.020  1.090
 WPJ  C29  H19  single    0.930  0.020  1.080
 WPJ  N06  H20  single    0.890  0.020  1.040
 WPJ  N06  H21  single    0.890  0.020  1.040
 WPJ  N09  H22  single    0.890  0.020  1.040
 WPJ  N09  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
 WPJ  H3   C01  H2   108.12  3.000
 WPJ  H3   C01  H1   107.51  3.000
 WPJ  H2   C01  H1   108.20  3.000
 WPJ  H3   C01  C02  111.22  3.000
 WPJ  H2   C01  C02  111.18  3.000
 WPJ  H1   C01  C02  110.47  3.000
 WPJ  H5   C02  H4   106.80  3.000
 WPJ  H5   C02  C03  110.77  3.000
 WPJ  H4   C02  C03  107.86  3.000
 WPJ  H5   C02  C01  109.89  3.000
 WPJ  H4   C02  C01  109.27  3.000
 WPJ  C03  C02  C01  112.08  3.000
 WPJ  N04  C03  C10  121.47  3.000
 WPJ  N04  C03  C02  115.94  3.000
 WPJ  C10  C03  C02  122.59  3.000
 WPJ  N07  C05  N06  116.46  3.000
 WPJ  N06  C05  N04  117.22  3.000
 WPJ  N07  C05  N04  126.29  3.000
 WPJ  N09  C08  N07  117.98  3.000
 WPJ  N07  C08  C10  121.16  3.000
 WPJ  N09  C08  C10  120.85  3.000
 WPJ  O11  C10  C08  119.79  3.000
 WPJ  O11  C10  C03  123.13  3.000
 WPJ  C08  C10  C03  117.06  3.000
 WPJ  H7   C12  H6   107.30  3.000
 WPJ  H7   C12  O11  110.09  3.000
 WPJ  H6   C12  O11  110.20  3.000
 WPJ  H7   C12  C13  110.94  3.000
 WPJ  H6   C12  C13  109.60  3.000
 WPJ  O11  C12  C13  108.71  3.000
 WPJ  H9   C13  H8   106.28  3.000
 WPJ  H9   C13  C14  108.17  3.000
 WPJ  H8   C13  C14  109.80  3.000
 WPJ  H9   C13  C12  109.69  3.000
 WPJ  H8   C13  C12  108.20  3.000
 WPJ  C14  C13  C12  114.39  3.000
 WPJ  H11  C14  H10  107.40  3.000
 WPJ  H11  C14  O15  110.47  3.000
 WPJ  H10  C14  O15  110.72  3.000
 WPJ  H11  C14  C13  109.86  3.000
 WPJ  H10  C14  C13  110.53  3.000
 WPJ  O15  C14  C13  107.88  3.000
 WPJ  O15  C16  C29  115.76  3.000
 WPJ  O15  C16  C17  124.38  3.000
 WPJ  C29  C16  C17  119.86  3.000
 WPJ  H12  C17  C18  119.43  3.000
 WPJ  H12  C17  C16  121.71  3.000
 WPJ  C18  C17  C16  118.87  3.000
 WPJ  H13  C18  C19  119.86  3.000
 WPJ  H13  C18  C17  118.96  3.000
 WPJ  C19  C18  C17  121.18  3.000
 WPJ  H14  C19  C20  119.77  3.000
 WPJ  H14  C19  C18  120.06  3.000
 WPJ  C20  C19  C18  120.17  3.000
 WPJ  C29  C20  C21  121.27  3.000
 WPJ  C29  C20  C19  118.70  3.000
 WPJ  C21  C20  C19  120.03  3.000
 WPJ  H16  C21  H15  106.84  3.000
 WPJ  H16  C21  C22  109.64  3.000
 WPJ  H15  C21  C22  110.20  3.000
 WPJ  H16  C21  C20  107.76  3.000
 WPJ  H15  C21  C20  109.84  3.000
 WPJ  C22  C21  C20  112.38  3.000
 WPJ  H17  C22  C26  106.56  3.000
 WPJ  H17  C22  C23  105.33  3.000
 WPJ  C26  C22  C23  107.14  3.000
 WPJ  H17  C22  C21  108.98  3.000
 WPJ  C23  C22  C21  112.95  3.000
 WPJ  C26  C22  C21  115.24  3.000
 WPJ  H18  C23  F25  108.19  3.000
 WPJ  H18  C23  F24  107.54  3.000
 WPJ  F25  C23  F24  105.58  3.000
 WPJ  H18  C23  C22  112.62  3.000
 WPJ  F24  C23  C22  111.84  3.000
 WPJ  F25  C23  C22  110.75  3.000
 WPJ  O28  C26  O27  127.61  3.000
 WPJ  O28  C26  C22  117.99  3.000
 WPJ  O27  C26  C22  114.39  3.000
 WPJ  H19  C29  C20  119.91  3.000
 WPJ  H19  C29  C16  118.88  3.000
 WPJ  C20  C29  C16  121.21  3.000
 WPJ  C05  N04  C03  117.05  3.000
 WPJ  H21  N06  H20  115.46  3.000
 WPJ  H21  N06  C05  117.11  3.000
 WPJ  H20  N06  C05  117.30  3.000
 WPJ  C08  N07  C05  116.97  3.000
 WPJ  H23  N09  H22  115.80  3.000
 WPJ  H23  N09  C08  119.06  3.000
 WPJ  H22  N09  C08  117.41  3.000
 WPJ  C12  O11  C10  114.81  3.000
 WPJ  C16  O15  C14  119.48  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
 WPJ  CONST_01  N07  C08  C10  C03     0.00   0.0  0
 WPJ  CONST_02  N07  C05  N04  C03     0.00   0.0  0
 WPJ  CONST_03  C10  C08  N07  C05     0.00   0.0  0
 WPJ  CONST_04  C10  C03  N04  C05     0.00   0.0  0
 WPJ  CONST_05  N04  C05  N07  C08     0.00   0.0  0
 WPJ  CONST_06  N04  C03  C10  C08     0.00   0.0  0
 WPJ  CONST_07  C19  C20  C29  C16     0.00   0.0  0
 WPJ  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 WPJ  CONST_09  C20  C29  C16  C17     0.00   0.0  0
 WPJ  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 WPJ  CONST_11  C29  C20  C19  C18     0.00   0.0  0
 WPJ  CONST_12  C29  C16  C17  C18     0.00   0.0  0
 WPJ  CONST_13  C08  C10  C03  C02   180.00   0.0  0
 WPJ  CONST_14  C05  N04  C03  C02   180.00   0.0  0
 WPJ  CONST_15  N09  C08  C10  C03   180.00   0.0  0
 WPJ  CONST_16  N06  C05  N04  C03   180.00   0.0  0
 WPJ  CONST_17  N09  C08  N07  C05   180.00   0.0  0
 WPJ  CONST_18  N06  C05  N07  C08   180.00   0.0  0
 WPJ  CONST_19  C21  C20  C29  C16   180.00   0.0  0
 WPJ  CONST_20  C21  C20  C19  C18   180.00   0.0  0
 WPJ  CONST_21  O15  C16  C17  C18   180.00   0.0  0
 WPJ  CONST_22  O15  C16  C29  C20   180.00   0.0  0
 WPJ  CONST_23  O11  C10  C03  N04   180.00   0.0  0
 WPJ  CONST_24  O11  C10  C08  N07   180.00   0.0  0
 WPJ  CONST_25  H13  C18  C17  C16   180.00   0.0  0
 WPJ  CONST_26  H19  C29  C16  C17   180.00   0.0  0
 WPJ  CONST_27  H14  C19  C18  C17   180.00   0.0  0
 WPJ  CONST_28  H12  C17  C18  C19   180.00   0.0  0
 WPJ  CONST_29  H22  N09  C08  C10   180.00   0.0  0
 WPJ  Var_01    C10  C03  C02  C01  -113.25  30.0  2
 WPJ  Var_02    C29  C16  O15  C14   174.34  30.0  2
 WPJ  Var_03    C22  C21  C20  C19   -76.17  30.0  1
 WPJ  Var_04    C13  C12  O11  C10  -170.92  30.0  2
 WPJ  Var_05    H1   C01  C02  C03  -177.91  30.0  3
 WPJ  Var_06    H10  C14  O15  C16   -51.44  30.0  3
 WPJ  Var_07    O15  C14  C13  C12    60.99  30.0  3
 WPJ  Var_08    O11  C12  C13  C14    63.02  30.0  2

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
 WPJ  chir_01  C22  C26  C23  C21  positiv

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
 WPJ  plan-1  C02  0.020
 WPJ  plan-1  C03  0.020
 WPJ  plan-1  C05  0.020
 WPJ  plan-1  C08  0.020
 WPJ  plan-1  C10  0.020
 WPJ  plan-1  N04  0.020
 WPJ  plan-1  N06  0.020
 WPJ  plan-1  N07  0.020
 WPJ  plan-1  N09  0.020
 WPJ  plan-1  O11  0.020
 WPJ  plan-2  C16  0.020
 WPJ  plan-2  C17  0.020
 WPJ  plan-2  C18  0.020
 WPJ  plan-2  C19  0.020
 WPJ  plan-2  C20  0.020
 WPJ  plan-2  C21  0.020
 WPJ  plan-2  C29  0.020
 WPJ  plan-2  O15  0.020
 WPJ  plan-2  H12  0.020
 WPJ  plan-2  H13  0.020
 WPJ  plan-2  H14  0.020
 WPJ  plan-2  H19  0.020
 WPJ  plan-3  C05  0.020
 WPJ  plan-3  N06  0.020
 WPJ  plan-3  H20  0.020
 WPJ  plan-3  H21  0.020
 WPJ  plan-4  C08  0.020
 WPJ  plan-4  N09  0.020
 WPJ  plan-4  H22  0.020
 WPJ  plan-4  H23  0.020
 WPJ  plan-5  C22  0.020
 WPJ  plan-5  C26  0.020
 WPJ  plan-5  O27  0.020
 WPJ  plan-5  O28  0.020

