# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:58:55 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: 1-[2-({3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propyl}amino)phenyl]piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCNc2ccccc2N3CCC(CC3)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
 WFA  WFA  '1-[2-({3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propyl}amino)phenyl]piperidine-4-carboxylic acid'  ligand  59  30  .  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_WFA
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
 WFA  C16  C  CR6    0   0.320   -7.7243  17.1402  15.9184
 WFA  C17  C  CR16   0  -0.352   -6.5654  17.8674  16.1976
 WFA  C18  C  CR16   0  -0.261   -6.6359  19.2048  16.5721
 WFA  C19  C  CR16   0  -0.287   -7.8609  19.8383  16.6863
 WFA  C20  C  CR16   0  -0.317   -9.0227  19.1236  16.4037
 WFA  C21  C  CR6    0   0.237   -8.9783  17.7918  16.0200
 WFA  C26  C  CH2    0  -0.419  -11.4219  15.7624  14.0790
 WFA  C27  C  CH2    0  -0.312  -10.4095  16.8703  14.3181
 WFA  C28  C  C      0   0.428  -13.7575  14.8717  14.6872
 WFA  C01  C  CH3    0  -0.673   -9.0894  15.6170  11.0594
 WFA  C03  C  CR6    0   0.230   -6.8772  14.4463  10.8818
 WFA  C05  C  CR6    0   0.506   -6.3261  13.0594   9.1655
 WFA  C08  C  CR6    0   0.434   -5.5744  12.4825  11.2254
 WFA  C10  C  CR6    0   0.126   -6.2069  13.6268  11.7630
 WFA  C12  C  CH2    0  -0.167   -7.1611  13.3662  13.8961
 WFA  C13  C  CH2    0  -0.506   -6.8069  13.5520  15.3566
 WFA  C23  C  CH2    0  -0.292  -11.3295  17.3483  16.4909
 WFA  C24  C  CH2    0  -0.415  -12.3632  16.2431  16.3377
 WFA  C25  C  CH1    0  -0.389  -12.7038  15.9905  14.8706
 WFA  N04  N  N      0  -0.501   -6.9342  14.1661   9.5727
 WFA  N07  N  N      0  -0.501   -5.6392  12.2080   9.9288
 WFA  N15  N  NH1    0  -0.678   -7.7051  15.8158  15.5454
 WFA  N22  N  NT     0  -0.504  -10.1294  17.0224  15.7425
 WFA  O11  O  O2     0  -0.495   -6.0947  13.8799  13.0999
 WFA  H1   H  HCR6   0   0.254   -5.5965  17.3893  16.1372
 WFA  H2   H  HCR6   0   0.241   -5.7206  19.7420  16.7866
 WFA  H3   H  HCR6   0   0.238   -7.9215  20.8764  16.9859
 WFA  H4   H  HCR6   0   0.248   -9.9816  19.6202  16.4904
 WFA  H5   H  HCH2   0   0.220  -11.6339  15.7041  13.0104
 WFA  H6   H  HCH2   0   0.202  -10.9720  14.8053  14.3643
 WFA  H7   H  HCH2   0   0.253   -9.4780  16.6418  13.7980
 WFA  H8   H  HCH2   0   0.200  -10.7855  17.8176  13.8963
 WFA  H9   H  HCH3   0   0.235   -9.5765  16.5524  11.3341
 WFA  H10  H  HCH3   0   0.233   -9.2977  15.4276  10.0072
 WFA  H11  H  HCH3   0   0.229   -9.5489  14.8186  11.6439
 WFA  H12  H  HCH2   0   0.245   -7.4023  15.8991  12.3737
 WFA  H13  H  HCH2   0   0.249   -7.1677  16.5347  10.7576
 WFA  H14  H  HCH2   0   0.224   -8.0955  13.8824  13.6467
 WFA  H15  H  HCH2   0   0.231   -7.3125  12.3014  13.6865
 WFA  H16  H  HCH2   0   0.242   -7.6267  13.1415  15.9536
 WFA  H17  H  HCH2   0   0.248   -5.9245  12.9544  15.5978
 WFA  H18  H  HCH2   0   0.222   -6.2336  15.0024  16.8287
 WFA  H19  H  HCH2   0   0.230   -5.6979  15.3857  15.2047
 WFA  H20  H  HCH2   0   0.235  -11.0636  17.4728  17.5429
 WFA  H21  H  HCH2   0   0.190  -11.7770  18.2999  16.1578
 WFA  H22  H  HCH2   0   0.221  -13.2596  16.5185  16.8942
 WFA  H23  H  HCH2   0   0.203  -11.9729  15.3267  16.7936
 WFA  H24  H  HCH1   0   0.211  -13.1643  16.9145  14.4860
 WFA  H25  H  HNH2   0   0.383   -6.7105  13.4771   7.2216
 WFA  H26  H  HNH2   0   0.383   -5.7721  12.0827   7.4759
 WFA  H27  H  HNH2   0   0.391   -4.3259  10.9293  11.5909
 WFA  H28  H  HNH2   0   0.399   -4.6392  11.9204  12.9493
 WFA  H29  H  HNH1   0   0.369   -8.5909  15.3626  15.7341
 WFA  O29  O  OC    -1  -0.608  -14.6575  14.8105  15.5497
 WFA  C14  C  CH2    0  -0.278   -6.5421  14.9917  15.7740
 WFA  N06  N  NH2    0  -0.825   -6.4367  12.7395   7.8482
 WFA  C02  C  CH2    0  -0.507   -7.5868  15.6953  11.3189
 WFA  O30  O  O      0  -0.601  -13.6442  14.1386  13.6839
 WFA  N09  N  NH2    0  -0.823   -4.9039  11.6296  12.0240

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
 WFA  N06  C05  single    1.360  0.020  1.360
 WFA  C05  N04  aromatic  1.327  0.020  1.327
 WFA  C05  N07  aromatic  1.334  0.020  1.334
 WFA  N04  C03  aromatic  1.340  0.020  1.340
 WFA  N07  C08  aromatic  1.327  0.020  1.327
 WFA  C03  C02  single    1.502  0.020  1.502
 WFA  C03  C10  aromatic  1.377  0.020  1.377
 WFA  C08  C10  aromatic  1.414  0.020  1.414
 WFA  C08  N09  single    1.347  0.020  1.347
 WFA  C01  C02  single    1.527  0.020  1.527
 WFA  C10  O11  single    1.365  0.020  1.365
 WFA  O11  C12  single    1.427  0.020  1.427
 WFA  C26  C27  single    1.520  0.020  1.520
 WFA  C26  C25  single    1.524  0.020  1.524
 WFA  C12  C13  single    1.514  0.020  1.514
 WFA  O30  C28  deloc     1.248  0.020  1.248
 WFA  C27  N22  single    1.460  0.020  1.460
 WFA  C25  C28  single    1.548  0.020  1.548
 WFA  C25  C24  single    1.527  0.020  1.527
 WFA  C28  O29  deloc     1.248  0.020  1.248
 WFA  C13  C14  single    1.522  0.020  1.522
 WFA  N22  C21  single    1.412  0.020  1.412
 WFA  N22  C23  single    1.451  0.020  1.451
 WFA  N15  C14  single    1.444  0.020  1.444
 WFA  N15  C16  single    1.376  0.020  1.376
 WFA  C21  C16  aromatic  1.417  0.020  1.417
 WFA  C21  C20  aromatic  1.387  0.020  1.387
 WFA  C16  C17  aromatic  1.396  0.020  1.396
 WFA  C20  C19  aromatic  1.393  0.020  1.393
 WFA  C17  C18  aromatic  1.391  0.020  1.391
 WFA  C19  C18  aromatic  1.384  0.020  1.384
 WFA  C24  C23  single    1.521  0.020  1.521
 WFA  C17  H1   single    0.930  0.020  1.080
 WFA  C18  H2   single    0.930  0.020  1.080
 WFA  C19  H3   single    0.930  0.020  1.080
 WFA  C20  H4   single    0.930  0.020  1.080
 WFA  C26  H5   single    0.970  0.020  1.090
 WFA  C26  H6   single    0.970  0.020  1.090
 WFA  C27  H7   single    0.970  0.020  1.090
 WFA  C27  H8   single    0.970  0.020  1.090
 WFA  C01  H9   single    0.970  0.020  1.090
 WFA  C01  H10  single    0.970  0.020  1.090
 WFA  C01  H11  single    0.970  0.020  1.090
 WFA  C02  H12  single    0.970  0.020  1.090
 WFA  C02  H13  single    0.970  0.020  1.090
 WFA  C12  H14  single    0.970  0.020  1.090
 WFA  C12  H15  single    0.970  0.020  1.090
 WFA  C13  H16  single    0.970  0.020  1.090
 WFA  C13  H17  single    0.970  0.020  1.090
 WFA  C14  H18  single    0.970  0.020  1.090
 WFA  C14  H19  single    0.970  0.020  1.090
 WFA  C23  H20  single    0.970  0.020  1.090
 WFA  C23  H21  single    0.970  0.020  1.090
 WFA  C24  H22  single    0.970  0.020  1.090
 WFA  C24  H23  single    0.970  0.020  1.090
 WFA  C25  H24  single    0.970  0.020  1.090
 WFA  N06  H25  single    0.890  0.020  1.040
 WFA  N06  H26  single    0.890  0.020  1.040
 WFA  N09  H27  single    0.890  0.020  1.040
 WFA  N09  H28  single    0.890  0.020  1.040
 WFA  N15  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
 WFA  N15  C16  C21  118.33  3.000
 WFA  C21  C16  C17  118.73  3.000
 WFA  N15  C16  C17  122.94  3.000
 WFA  H1   C17  C18  119.04  3.000
 WFA  H1   C17  C16  120.12  3.000
 WFA  C18  C17  C16  120.83  3.000
 WFA  H2   C18  C19  120.32  3.000
 WFA  H2   C18  C17  119.18  3.000
 WFA  C19  C18  C17  120.49  3.000
 WFA  H3   C19  C20  120.11  3.000
 WFA  H3   C19  C18  120.77  3.000
 WFA  C20  C19  C18  119.12  3.000
 WFA  H4   C20  C21  119.39  3.000
 WFA  H4   C20  C19  119.13  3.000
 WFA  C21  C20  C19  121.48  3.000
 WFA  N22  C21  C20  123.47  3.000
 WFA  C20  C21  C16  119.34  3.000
 WFA  N22  C21  C16  117.18  3.000
 WFA  H6   C26  H5   106.76  3.000
 WFA  H6   C26  C25  109.94  3.000
 WFA  H5   C26  C25  110.69  3.000
 WFA  H6   C26  C27  108.81  3.000
 WFA  H5   C26  C27  108.81  3.000
 WFA  C25  C26  C27  111.69  3.000
 WFA  H8   C27  H7   106.77  3.000
 WFA  H8   C27  N22  110.44  3.000
 WFA  H7   C27  N22  108.85  3.000
 WFA  H8   C27  C26  109.80  3.000
 WFA  H7   C27  C26  109.94  3.000
 WFA  N22  C27  C26  110.94  3.000
 WFA  O30  C28  O29  126.33  3.000
 WFA  O29  C28  C25  116.39  3.000
 WFA  O30  C28  C25  117.27  3.000
 WFA  H11  C01  H10  108.05  3.000
 WFA  H11  C01  H9   107.74  3.000
 WFA  H10  C01  H9   107.89  3.000
 WFA  H11  C01  C02  111.16  3.000
 WFA  H10  C01  C02  111.18  3.000
 WFA  H9   C01  C02  110.67  3.000
 WFA  N04  C03  C10  121.42  3.000
 WFA  C10  C03  C02  122.59  3.000
 WFA  N04  C03  C02  115.99  3.000
 WFA  N07  C05  N06  116.49  3.000
 WFA  N07  C05  N04  126.35  3.000
 WFA  N06  C05  N04  117.14  3.000
 WFA  N09  C08  N07  118.20  3.000
 WFA  N09  C08  C10  120.65  3.000
 WFA  N07  C08  C10  121.14  3.000
 WFA  O11  C10  C08  119.06  3.000
 WFA  O11  C10  C03  123.79  3.000
 WFA  C08  C10  C03  117.13  3.000
 WFA  H15  C12  H14  107.23  3.000
 WFA  H15  C12  O11  110.27  3.000
 WFA  H14  C12  O11  109.92  3.000
 WFA  H15  C12  C13  109.64  3.000
 WFA  H14  C12  C13  111.17  3.000
 WFA  O11  C12  C13  108.62  3.000
 WFA  H17  C13  H16  106.23  3.000
 WFA  H17  C13  C14  108.44  3.000
 WFA  H16  C13  C14  109.61  3.000
 WFA  H17  C13  C12  109.56  3.000
 WFA  H16  C13  C12  107.76  3.000
 WFA  C14  C13  C12  114.91  3.000
 WFA  H21  C23  H20  106.94  3.000
 WFA  H21  C23  N22  111.93  3.000
 WFA  H20  C23  N22  108.72  3.000
 WFA  H21  C23  C24  108.71  3.000
 WFA  H20  C23  C24  110.20  3.000
 WFA  N22  C23  C24  110.29  3.000
 WFA  H23  C24  H22  106.96  3.000
 WFA  H23  C24  C25  109.93  3.000
 WFA  H22  C24  C25  110.41  3.000
 WFA  H23  C24  C23  108.90  3.000
 WFA  H22  C24  C23  108.89  3.000
 WFA  C25  C24  C23  111.63  3.000
 WFA  H24  C25  C24  106.85  3.000
 WFA  H24  C25  C28  106.28  3.000
 WFA  C24  C25  C28  112.66  3.000
 WFA  H24  C25  C26  107.21  3.000
 WFA  C24  C25  C26  109.65  3.000
 WFA  C28  C25  C26  113.76  3.000
 WFA  C05  N04  C03  117.05  3.000
 WFA  C08  N07  C05  116.89  3.000
 WFA  H29  N15  C14  114.81  3.000
 WFA  H29  N15  C16  111.59  3.000
 WFA  C14  N15  C16  121.19  3.000
 WFA  C23  N22  C27  111.59  3.000
 WFA  C23  N22  C21  116.77  3.000
 WFA  C27  N22  C21  113.89  3.000
 WFA  C12  O11  C10  114.73  3.000
 WFA  H19  C14  H18  106.26  3.000
 WFA  H19  C14  N15  109.53  3.000
 WFA  H18  C14  N15  111.87  3.000
 WFA  H19  C14  C13  109.44  3.000
 WFA  H18  C14  C13  108.74  3.000
 WFA  N15  C14  C13  110.88  3.000
 WFA  H26  N06  H25  115.35  3.000
 WFA  H26  N06  C05  117.28  3.000
 WFA  H25  N06  C05  116.94  3.000
 WFA  H13  C02  H12  106.76  3.000
 WFA  H13  C02  C03  107.94  3.000
 WFA  H12  C02  C03  110.93  3.000
 WFA  H13  C02  C01  109.23  3.000
 WFA  H12  C02  C01  109.92  3.000
 WFA  C03  C02  C01  111.89  3.000
 WFA  H28  N09  H27  116.51  3.000
 WFA  H28  N09  C08  119.57  3.000
 WFA  H27  N09  C08  118.13  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
 WFA  CONST_01  C19  C20  C21  C16     0.00   0.0  0
 WFA  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 WFA  CONST_03  C20  C21  C16  C17     0.00   0.0  0
 WFA  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 WFA  CONST_05  C21  C16  C17  C18     0.00   0.0  0
 WFA  CONST_06  C21  C20  C19  C18     0.00   0.0  0
 WFA  CONST_07  N07  C05  N04  C03     0.00   0.0  0
 WFA  CONST_08  N07  C08  C10  C03     0.00   0.0  0
 WFA  CONST_09  C10  C03  N04  C05     0.00   0.0  0
 WFA  CONST_10  C10  C08  N07  C05     0.00   0.0  0
 WFA  CONST_11  N04  C05  N07  C08     0.00   0.0  0
 WFA  CONST_12  N04  C03  C10  C08     0.00   0.0  0
 WFA  CONST_13  N22  C21  C16  C17   180.00   0.0  0
 WFA  CONST_14  N22  C21  C20  C19   180.00   0.0  0
 WFA  CONST_15  N15  C16  C17  C18   180.00   0.0  0
 WFA  CONST_16  N15  C16  C21  C20   180.00   0.0  0
 WFA  CONST_17  C05  N04  C03  C02   180.00   0.0  0
 WFA  CONST_18  C08  C10  C03  C02   180.00   0.0  0
 WFA  CONST_19  N06  C05  N04  C03   180.00   0.0  0
 WFA  CONST_20  N09  C08  C10  C03   180.00   0.0  0
 WFA  CONST_21  N09  C08  N07  C05   180.00   0.0  0
 WFA  CONST_22  N06  C05  N07  C08   180.00   0.0  0
 WFA  CONST_23  O11  C10  C03  N04   180.00   0.0  0
 WFA  CONST_24  O11  C10  C08  N07   180.00   0.0  0
 WFA  CONST_25  N22  C21  C16  N15     0.00   0.0  0
 WFA  CONST_26  H4   C20  C21  C16   180.00   0.0  0
 WFA  CONST_27  H2   C18  C17  C16   180.00   0.0  0
 WFA  CONST_28  H3   C19  C18  C17   180.00   0.0  0
 WFA  CONST_29  H1   C17  C18  C19   180.00   0.0  0
 WFA  CONST_33  H27  N09  C08  C10   180.00   0.0  0
 WFA  Var_01    C27  N22  C21  C16   -80.59  30.0  3
 WFA  Var_02    C26  C27  N22  C21   165.42  30.0  1
 WFA  Var_03    C24  C23  N22  C21  -166.27  30.0  1
 WFA  Var_04    N22  C27  C26  C25    55.37  30.0  1
 WFA  Var_05    N22  C23  C24  C25   -56.92  30.0  1
 WFA  Var_06    N04  C03  C02  C01    62.74  30.0  2
 WFA  Var_07    C13  C14  N15  C16   176.30  30.0  3
 WFA  Var_08    C13  C12  O11  C10   172.22  30.0  3
 WFA  Var_09    H9   C01  C02  C03  -176.97  30.0  3
 WFA  Var_10    N15  C14  C13  C12    60.19  30.0  3
 WFA  Var_11    O11  C12  C13  C14    58.27  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
 WFA  chir_01  C25  C26  C28  C24  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
 WFA  plan-1  C16  0.020
 WFA  plan-1  C17  0.020
 WFA  plan-1  C18  0.020
 WFA  plan-1  C19  0.020
 WFA  plan-1  C20  0.020
 WFA  plan-1  C21  0.020
 WFA  plan-1  N15  0.020
 WFA  plan-1  N22  0.020
 WFA  plan-1  H1   0.020
 WFA  plan-1  H2   0.020
 WFA  plan-1  H3   0.020
 WFA  plan-1  H4   0.020
 WFA  plan-2  C03  0.020
 WFA  plan-2  C05  0.020
 WFA  plan-2  C08  0.020
 WFA  plan-2  C10  0.020
 WFA  plan-2  N04  0.020
 WFA  plan-2  N07  0.020
 WFA  plan-2  O11  0.020
 WFA  plan-2  N06  0.020
 WFA  plan-2  C02  0.020
 WFA  plan-2  N09  0.020
 WFA  plan-3  C16  0.020
 WFA  plan-3  N15  0.020
 WFA  plan-3  H29  0.020
 WFA  plan-3  C14  0.020
 WFA  plan-4  C05  0.020
 WFA  plan-4  H25  0.020
 WFA  plan-4  H26  0.020
 WFA  plan-4  N06  0.020
 WFA  plan-5  C08  0.020
 WFA  plan-5  H27  0.020
 WFA  plan-5  H28  0.020
 WFA  plan-5  N09  0.020
 WFA  plan-6  C28  0.020
 WFA  plan-6  C25  0.020
 WFA  plan-6  O29  0.020
 WFA  plan-6  O30  0.020

