# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 14:41:34 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (2S)-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
 WPD  WPD  '(2S)-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_WPD
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
 WPD  C10  C  CR6    0   0.126  -20.9569  18.7730  -5.5447
 WPD  O11  O  O2     0  -0.497  -21.7021  17.6445  -5.7325
 WPD  C01  C  CH3    0  -0.679  -22.7138  20.7942  -7.8193
 WPD  C02  C  CH2    0  -0.516  -22.7811  20.3094  -6.3720
 WPD  C03  C  CR6    0   0.230  -21.4155  20.0457  -5.8071
 WPD  C05  C  CR6    0   0.507  -19.4349  20.9080  -5.0958
 WPD  C08  C  CR6    0   0.434  -19.6496  18.6516  -5.0230
 WPD  C12  C  CH2    0  -0.173  -21.6643  17.1131  -7.0543
 WPD  C13  C  CH2    0  -0.502  -22.5187  15.8626  -7.0996
 WPD  C14  C  CH2    0  -0.189  -23.9346  16.0551  -6.5941
 WPD  C16  C  CR6    0   0.413  -25.7377  17.5730  -6.9442
 WPD  C17  C  CR16   0  -0.399  -26.5118  17.0029  -5.9352
 WPD  C18  C  CR16   0  -0.224  -27.7246  17.5934  -5.6025
 WPD  C19  C  CR16   0  -0.344  -28.1689  18.7332  -6.2521
 WPD  C20  C  CR6    0   0.173  -27.3998  19.3069  -7.2634
 WPD  C21  C  CH2    0  -0.531  -27.8767  20.5344  -7.9926
 WPD  C22  C  CH1    0  -0.503  -27.0015  21.7877  -7.8316
 WPD  C23  C  CH1    0   0.571  -27.0545  22.3242  -6.4273
 WPD  C26  C  C      0   0.414  -27.5165  22.8754  -8.8144
 WPD  C29  C  CR16   0  -0.415  -26.1901  18.7163  -7.6021
 WPD  F24  F  F      0  -0.349  -26.5043  21.4555  -5.5227
 WPD  F25  F  F      0  -0.356  -26.3037  23.4677  -6.3371
 WPD  N04  N  N      0  -0.499  -20.6518  21.1230  -5.5810
 WPD  N06  N  NH2    0  -0.825  -18.6704  22.0001  -4.8285
 WPD  N07  N  N      0  -0.501  -18.8988  19.7227  -4.8004
 WPD  N09  N  NH2    0  -0.824  -19.1259  17.4391  -4.7575
 WPD  O15  O  O2     0  -0.481  -24.5469  17.0867  -7.3487
 WPD  O27  O  O      0  -0.601  -28.6035  23.4021  -8.5046
 WPD  O28  O  OC    -1  -0.588  -26.8278  23.0946  -9.8245
 WPD  H1   H  HCH3   0   0.246  -23.7141  21.0056  -8.1978
 WPD  H2   H  HCH3   0   0.229  -22.1225  21.7058  -7.9009
 WPD  H3   H  HCH3   0   0.228  -22.2653  20.0437  -8.4710
 WPD  H4   H  HCH2   0   0.248  -23.2611  21.0765  -5.7596
 WPD  H5   H  HCH2   0   0.254  -23.4033  19.4178  -6.3100
 WPD  H6   H  HCH2   0   0.233  -20.6347  16.8679  -7.3376
 WPD  H7   H  HCH2   0   0.228  -22.0290  17.8572  -7.7682
 WPD  H8   H  HCH2   0   0.248  -22.5317  15.4979  -8.1296
 WPD  H9   H  HCH2   0   0.246  -22.0588  15.0741  -6.4985
 WPD  H10  H  HCH2   0   0.226  -23.9267  16.3129  -5.5308
 WPD  H11  H  HCH2   0   0.235  -24.4941  15.1189  -6.6989
 WPD  H12  H  HCR6   0   0.273  -26.1942  16.1109  -5.4127
 WPD  H13  H  HCR6   0   0.251  -28.3268  17.1508  -4.8191
 WPD  H14  H  HCR6   0   0.241  -29.1147  19.1820  -5.9746
 WPD  H15  H  HCH2   0   0.249  -28.8984  20.7686  -7.6847
 WPD  H16  H  HCH2   0   0.258  -27.9248  20.3064  -9.0613
 WPD  H17  H  HCH1   0   0.256  -25.9626  21.5374  -8.0696
 WPD  H18  H  HCH1   0   0.174  -28.0669  22.5561  -6.0946
 WPD  H19  H  HCR6   0   0.249  -25.5745  19.1439  -8.3866
 WPD  H20  H  HNH2   0   0.383  -17.6810  21.8554  -4.7206
 WPD  H21  H  HNH2   0   0.383  -18.9357  22.8644  -5.2691
 WPD  H22  H  HNH2   0   0.391  -18.2724  17.3971  -4.2267
 WPD  H23  H  HNH2   0   0.399  -19.7334  16.6404  -4.6951

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
 WPD  O27  C26  deloc     1.247  0.020  1.247
 WPD  O28  C26  deloc     1.242  0.020  1.242
 WPD  C26  C22  single    1.554  0.020  1.554
 WPD  C22  C21  single    1.537  0.020  1.537
 WPD  C22  C23  single    1.504  0.020  1.504
 WPD  C21  C20  single    1.505  0.020  1.505
 WPD  F25  C23  single    1.371  0.020  1.371
 WPD  C23  F24  single    1.370  0.020  1.370
 WPD  C29  C20  aromatic  1.388  0.020  1.388
 WPD  C29  C16  aromatic  1.395  0.020  1.395
 WPD  C20  C19  aromatic  1.394  0.020  1.394
 WPD  C12  C13  single    1.515  0.020  1.515
 WPD  C12  O11  single    1.425  0.020  1.425
 WPD  O15  C16  single    1.348  0.020  1.348
 WPD  O15  C14  single    1.417  0.020  1.417
 WPD  C13  C14  single    1.516  0.020  1.516
 WPD  N09  C08  single    1.347  0.020  1.347
 WPD  C16  C17  aromatic  1.394  0.020  1.394
 WPD  C19  C18  aromatic  1.385  0.020  1.385
 WPD  C08  N07  aromatic  1.327  0.020  1.327
 WPD  C08  C10  aromatic  1.413  0.020  1.413
 WPD  O11  C10  single    1.365  0.020  1.365
 WPD  N07  C05  aromatic  1.334  0.020  1.334
 WPD  C17  C18  aromatic  1.389  0.020  1.389
 WPD  C10  C03  aromatic  1.378  0.020  1.378
 WPD  C05  N06  single    1.360  0.020  1.360
 WPD  C05  N04  aromatic  1.328  0.020  1.328
 WPD  C01  C02  single    1.528  0.020  1.528
 WPD  C03  N04  aromatic  1.340  0.020  1.340
 WPD  C03  C02  single    1.501  0.020  1.501
 WPD  C01  H1   single    0.970  0.020  1.090
 WPD  C01  H2   single    0.970  0.020  1.090
 WPD  C01  H3   single    0.970  0.020  1.090
 WPD  C02  H4   single    0.970  0.020  1.090
 WPD  C02  H5   single    0.970  0.020  1.090
 WPD  C12  H6   single    0.970  0.020  1.090
 WPD  C12  H7   single    0.970  0.020  1.090
 WPD  C13  H8   single    0.970  0.020  1.090
 WPD  C13  H9   single    0.970  0.020  1.090
 WPD  C14  H10  single    0.970  0.020  1.090
 WPD  C14  H11  single    0.970  0.020  1.090
 WPD  C17  H12  single    0.930  0.020  1.080
 WPD  C18  H13  single    0.930  0.020  1.080
 WPD  C19  H14  single    0.930  0.020  1.080
 WPD  C21  H15  single    0.970  0.020  1.090
 WPD  C21  H16  single    0.970  0.020  1.090
 WPD  C22  H17  single    0.970  0.020  1.090
 WPD  C23  H18  single    0.970  0.020  1.090
 WPD  C29  H19  single    0.930  0.020  1.080
 WPD  N06  H20  single    0.890  0.020  1.040
 WPD  N06  H21  single    0.890  0.020  1.040
 WPD  N09  H22  single    0.890  0.020  1.040
 WPD  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
 WPD  C08  C10  C03  117.23  3.000
 WPD  C03  C10  O11  123.75  3.000
 WPD  C08  C10  O11  119.00  3.000
 WPD  C12  O11  C10  114.91  3.000
 WPD  H3   C01  H2   107.93  3.000
 WPD  H3   C01  H1   107.66  3.000
 WPD  H2   C01  H1   108.04  3.000
 WPD  H3   C01  C02  111.46  3.000
 WPD  H2   C01  C02  111.12  3.000
 WPD  H1   C01  C02  110.49  3.000
 WPD  H5   C02  H4   106.97  3.000
 WPD  H5   C02  C03  110.76  3.000
 WPD  H4   C02  C03  108.19  3.000
 WPD  H5   C02  C01  109.81  3.000
 WPD  H4   C02  C01  109.12  3.000
 WPD  C03  C02  C01  111.85  3.000
 WPD  N04  C03  C02  116.15  3.000
 WPD  C02  C03  C10  122.46  3.000
 WPD  N04  C03  C10  121.39  3.000
 WPD  N07  C05  N06  116.37  3.000
 WPD  N06  C05  N04  117.20  3.000
 WPD  N07  C05  N04  126.39  3.000
 WPD  N09  C08  N07  118.26  3.000
 WPD  N07  C08  C10  121.08  3.000
 WPD  N09  C08  C10  120.65  3.000
 WPD  H7   C12  H6   107.27  3.000
 WPD  H7   C12  C13  110.73  3.000
 WPD  H6   C12  C13  109.72  3.000
 WPD  H7   C12  O11  110.05  3.000
 WPD  H6   C12  O11  110.37  3.000
 WPD  C13  C12  O11  108.69  3.000
 WPD  H9   C13  H8   106.42  3.000
 WPD  H9   C13  C14  107.54  3.000
 WPD  H8   C13  C14  110.22  3.000
 WPD  H9   C13  C12  109.98  3.000
 WPD  H8   C13  C12  108.07  3.000
 WPD  C14  C13  C12  114.33  3.000
 WPD  H11  C14  H10  107.34  3.000
 WPD  H11  C14  O15  110.52  3.000
 WPD  H10  C14  O15  110.43  3.000
 WPD  H11  C14  C13  109.67  3.000
 WPD  H10  C14  C13  110.32  3.000
 WPD  O15  C14  C13  108.57  3.000
 WPD  O15  C16  C29  116.14  3.000
 WPD  O15  C16  C17  124.07  3.000
 WPD  C29  C16  C17  119.79  3.000
 WPD  H12  C17  C18  119.42  3.000
 WPD  H12  C17  C16  121.61  3.000
 WPD  C18  C17  C16  118.97  3.000
 WPD  H13  C18  C19  119.82  3.000
 WPD  H13  C18  C17  119.02  3.000
 WPD  C19  C18  C17  121.16  3.000
 WPD  H14  C19  C20  119.81  3.000
 WPD  H14  C19  C18  120.06  3.000
 WPD  C20  C19  C18  120.12  3.000
 WPD  C29  C20  C21  120.32  3.000
 WPD  C29  C20  C19  118.86  3.000
 WPD  C21  C20  C19  120.81  3.000
 WPD  H16  C21  H15  106.20  3.000
 WPD  H16  C21  C22  107.30  3.000
 WPD  H15  C21  C22  109.16  3.000
 WPD  H16  C21  C20  108.50  3.000
 WPD  H15  C21  C20  109.55  3.000
 WPD  C22  C21  C20  115.71  3.000
 WPD  H17  C22  C26  109.70  3.000
 WPD  H17  C22  C23  108.54  3.000
 WPD  C26  C22  C23  109.22  3.000
 WPD  H17  C22  C21  109.33  3.000
 WPD  C23  C22  C21  111.63  3.000
 WPD  C26  C22  C21  108.41  3.000
 WPD  H18  C23  F25  108.12  3.000
 WPD  H18  C23  F24  107.84  3.000
 WPD  F25  C23  F24  105.40  3.000
 WPD  H18  C23  C22  113.17  3.000
 WPD  F24  C23  C22  112.10  3.000
 WPD  F25  C23  C22  109.85  3.000
 WPD  O28  C26  O27  127.65  3.000
 WPD  O28  C26  C22  117.01  3.000
 WPD  O27  C26  C22  115.31  3.000
 WPD  H19  C29  C20  120.21  3.000
 WPD  H19  C29  C16  118.70  3.000
 WPD  C20  C29  C16  121.09  3.000
 WPD  C05  N04  C03  117.00  3.000
 WPD  H21  N06  H20  115.48  3.000
 WPD  H21  N06  C05  117.12  3.000
 WPD  H20  N06  C05  117.30  3.000
 WPD  C08  N07  C05  116.92  3.000
 WPD  H23  N09  H22  116.54  3.000
 WPD  H23  N09  C08  119.49  3.000
 WPD  H22  N09  C08  118.12  3.000
 WPD  C16  O15  C14  118.96  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
 WPD  CONST_01  C05  N07  C08  C10     0.00   0.0  0
 WPD  CONST_02  C05  N04  C03  C10     0.00   0.0  0
 WPD  CONST_03  N07  C08  C10  C03     0.00   0.0  0
 WPD  CONST_04  N07  C05  N04  C03     0.00   0.0  0
 WPD  CONST_05  N04  C05  N07  C08     0.00   0.0  0
 WPD  CONST_06  N04  C03  C10  C08     0.00   0.0  0
 WPD  CONST_07  C19  C20  C29  C16     0.00   0.0  0
 WPD  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 WPD  CONST_09  C20  C29  C16  C17     0.00   0.0  0
 WPD  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 WPD  CONST_11  C29  C20  C19  C18     0.00   0.0  0
 WPD  CONST_12  C29  C16  C17  C18     0.00   0.0  0
 WPD  CONST_13  N07  C08  C10  O11   180.00   0.0  0
 WPD  CONST_14  N04  C03  C10  O11   180.00   0.0  0
 WPD  CONST_15  C08  C10  C03  C02   180.00   0.0  0
 WPD  CONST_16  C05  N04  C03  C02   180.00   0.0  0
 WPD  CONST_17  N09  C08  C10  C03   180.00   0.0  0
 WPD  CONST_18  N06  C05  N04  C03   180.00   0.0  0
 WPD  CONST_19  N09  C08  N07  C05   180.00   0.0  0
 WPD  CONST_20  N06  C05  N07  C08   180.00   0.0  0
 WPD  CONST_21  C21  C20  C29  C16   180.00   0.0  0
 WPD  CONST_22  C21  C20  C19  C18   180.00   0.0  0
 WPD  CONST_23  O15  C16  C17  C18   180.00   0.0  0
 WPD  CONST_24  O15  C16  C29  C20   180.00   0.0  0
 WPD  CONST_25  H13  C18  C17  C16   180.00   0.0  0
 WPD  CONST_26  H19  C29  C16  C17   180.00   0.0  0
 WPD  CONST_27  H14  C19  C18  C17   180.00   0.0  0
 WPD  CONST_28  H12  C17  C18  C19   180.00   0.0  0
 WPD  CONST_29  H22  N09  C08  C10   180.00   0.0  0
 WPD  Var_01    C01  C02  C03  C10  -109.32  30.0  2
 WPD  Var_02    C29  C16  O15  C14   170.56  30.0  2
 WPD  Var_03    C22  C21  C20  C19   117.01  30.0  1
 WPD  Var_04    C13  C12  O11  C10   179.29  30.0  2
 WPD  Var_05    H1   C01  C02  C03  -178.40  30.0  3
 WPD  Var_06    H10  C14  O15  C16   -48.88  30.0  3
 WPD  Var_07    C14  C13  C12  O11    53.50  30.0  3
 WPD  Var_08    O15  C14  C13  C12    56.84  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
 WPD  chir_01  C22  C26  C21  C23  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
 WPD  plan-1  C10  0.020
 WPD  plan-1  O11  0.020
 WPD  plan-1  C02  0.020
 WPD  plan-1  C03  0.020
 WPD  plan-1  C05  0.020
 WPD  plan-1  C08  0.020
 WPD  plan-1  N04  0.020
 WPD  plan-1  N06  0.020
 WPD  plan-1  N07  0.020
 WPD  plan-1  N09  0.020
 WPD  plan-2  C16  0.020
 WPD  plan-2  C17  0.020
 WPD  plan-2  C18  0.020
 WPD  plan-2  C19  0.020
 WPD  plan-2  C20  0.020
 WPD  plan-2  C21  0.020
 WPD  plan-2  C29  0.020
 WPD  plan-2  O15  0.020
 WPD  plan-2  H12  0.020
 WPD  plan-2  H13  0.020
 WPD  plan-2  H14  0.020
 WPD  plan-2  H19  0.020
 WPD  plan-3  C05  0.020
 WPD  plan-3  N06  0.020
 WPD  plan-3  H20  0.020
 WPD  plan-3  H21  0.020
 WPD  plan-4  C08  0.020
 WPD  plan-4  N09  0.020
 WPD  plan-4  H22  0.020
 WPD  plan-4  H23  0.020
 WPD  plan-5  C22  0.020
 WPD  plan-5  C26  0.020
 WPD  plan-5  O27  0.020
 WPD  plan-5  O28  0.020

