# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:17:19 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (2S)-3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-2-methylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2ccccc2C[C@H](C)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
 I0E  I0E  "(2S)-3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-2-methylpropanoic acid"  ligand  52  27  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I0E
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
 I0E  C10  C  CH2    0  -0.198  -28.6508   6.0339  -26.5469
 I0E  C13  C  CR16   0  -0.379  -29.4242   4.2533  -28.6015
 I0E  C15  C  CR16   0  -0.269  -31.1193   3.5468  -30.1564
 I0E  C17  C  CR6    0   0.021  -31.4741   5.5403  -28.8078
 I0E  C20  C  CH3    0  -0.670  -30.9061   8.3781  -29.7106
 I0E  C21  C  C      0   0.409  -33.2501   8.9998  -29.0622
 I0E  C24  C  C      0   0.230  -28.6739  11.7065  -25.8648
 I0E  C26  C  CH3    0  -0.666  -30.2556  11.8067  -27.8147
 I0E  C02  C  C      0   0.505  -26.8506  13.0561  -25.6901
 I0E  C04  C  C      0   0.438  -26.6351  10.9451  -24.8949
 I0E  C06  C  C      0   0.119  -27.9709  10.6795  -25.2748
 I0E  C08  C  CH2    0  -0.161  -28.3836   8.5024  -26.0707
 I0E  C09  C  CH2    0  -0.495  -28.5844   7.1160  -25.4891
 I0E  C12  C  CR6    0   0.352  -30.2139   5.3367  -28.2229
 I0E  C14  C  CR16   0  -0.257  -29.8799   3.3634  -29.5669
 I0E  C16  C  CR16   0  -0.292  -31.8982   4.6308  -29.7687
 I0E  C19  C  CH1    0  -0.318  -32.3171   7.8415  -29.4823
 I0E  N03  N  N      0  -0.501  -26.0838  12.1330  -25.1072
 I0E  N05  N  NH2    0  -0.824  -25.8834   9.9846  -24.3239
 I0E  N27  N  N      0  -0.503  -28.1134  12.9066  -26.0684
 I0E  O07  O  O2     0  -0.497  -28.4963   9.4472  -25.0081
 I0E  O11  O  O2     0  -0.470  -29.8349   6.2383  -27.2940
 I0E  O23  O  OC    -1  -0.612  -33.0749   9.4661  -27.9141
 I0E  H1   H  HCH2   0   0.238  -28.6634   5.0498  -26.0660
 I0E  H2   H  HCH2   0   0.223  -27.7684   6.0719  -27.1971
 I0E  H3   H  HCR6   0   0.272  -28.4516   4.0891  -28.1570
 I0E  H4   H  HCR6   0   0.243  -31.4810   2.8555  -30.9062
 I0E  H5   H  HCH3   0   0.221  -30.9095   9.1815  -30.4499
 I0E  H6   H  HCH3   0   0.225  -30.4832   8.7793  -28.7889
 I0E  H7   H  HCH3   0   0.219  -30.2326   7.6021  -30.0781
 I0E  H8   H  HCH3   0   0.234  -31.2935  11.6651  -28.1126
 I0E  H9   H  HCH3   0   0.224  -29.9570  12.8190  -28.0819
 I0E  H10  H  HCH3   0   0.223  -29.6475  11.1107  -28.3940
 I0E  H11  H  HCH2   0   0.219  -27.3976   8.5700  -26.5441
 I0E  H12  H  HCH2   0   0.235  -29.1320   8.7223  -26.8391
 I0E  H13  H  HCH2   0   0.243  -29.4983   7.0871  -24.8897
 I0E  H14  H  HCH2   0   0.246  -27.7550   6.8821  -24.8168
 I0E  H15  H  HCR6   0   0.250  -29.2555   2.5263  -29.8516
 I0E  H16  H  HCR6   0   0.241  -32.8726   4.7771  -30.2219
 I0E  H19  H  HCH1   0   0.195  -32.6785   7.4321  -30.4317
 I0E  H24  H  HNH2   0   0.391  -25.0020  10.2477  -23.9168
 I0E  H25  H  HNH2   0   0.400  -26.3275   9.1648  -23.9477
 I0E  C25  C  CH2    0  -0.502  -30.0980  11.5591  -26.3164
 I0E  C18  C  CH2    0  -0.490  -32.3452   6.7118  -28.4412
 I0E  N01  N  NH2    0  -0.825  -26.2630  14.2552  -25.9496
 I0E  O22  O  O      0  -0.603  -34.0835   9.3964  -29.9008
 I0E  H17  H  HCH2   0   0.232  -33.3755   6.3559  -28.3440
 I0E  H18  H  HCH2   0   0.230  -32.0649   7.1164  -27.4698
 I0E  H20  H  HCH2   0   0.249  -30.7045  12.2839  -25.7661
 I0E  H21  H  HCH2   0   0.243  -30.4872  10.5731  -26.0639
 I0E  H22  H  HNH2   0   0.383  -26.8756  15.0315  -26.1338
 I0E  H23  H  HNH2   0   0.383  -25.4288  14.4797  -25.4341

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
 I0E  C15  C16  aromatic  1.390  0.020  1.390
 I0E  C15  C14  aromatic  1.385  0.020  1.385
 I0E  C16  C17  aromatic  1.389  0.020  1.389
 I0E  C14  C13  aromatic  1.390  0.020  1.390
 I0E  C17  C12  aromatic  1.404  0.020  1.404
 I0E  C17  C18  single    1.505  0.020  1.505
 I0E  O22  C21  deloc     1.247  0.020  1.247
 I0E  C13  C12  aromatic  1.393  0.020  1.393
 I0E  C19  C20  single    1.527  0.020  1.527
 I0E  C19  C18  single    1.537  0.020  1.537
 I0E  C19  C21  single    1.546  0.020  1.546
 I0E  C26  C25  single    1.527  0.020  1.527
 I0E  C12  O11  single    1.349  0.020  1.349
 I0E  C21  O23  deloc     1.251  0.020  1.251
 I0E  C25  C24  single    1.501  0.020  1.501
 I0E  O11  C10  single    1.415  0.020  1.415
 I0E  N27  C24  aromatic  1.340  0.020  1.340
 I0E  N27  C02  aromatic  1.327  0.020  1.327
 I0E  C24  C06  aromatic  1.377  0.020  1.377
 I0E  C10  C09  single    1.515  0.020  1.515
 I0E  N01  C02  single    1.360  0.020  1.360
 I0E  C02  N03  aromatic  1.334  0.020  1.334
 I0E  C08  C09  single    1.517  0.020  1.517
 I0E  C08  O07  single    1.426  0.020  1.426
 I0E  C06  O07  single    1.366  0.020  1.366
 I0E  C06  C04  aromatic  1.414  0.020  1.414
 I0E  N03  C04  aromatic  1.327  0.020  1.327
 I0E  C04  N05  single    1.347  0.020  1.347
 I0E  C10  H1   single    0.970  0.020  1.090
 I0E  C10  H2   single    0.970  0.020  1.090
 I0E  C13  H3   single    0.930  0.020  1.080
 I0E  C15  H4   single    0.930  0.020  1.080
 I0E  C20  H5   single    0.970  0.020  1.090
 I0E  C20  H6   single    0.970  0.020  1.090
 I0E  C20  H7   single    0.970  0.020  1.090
 I0E  C26  H8   single    0.970  0.020  1.090
 I0E  C26  H9   single    0.970  0.020  1.090
 I0E  C26  H10  single    0.970  0.020  1.090
 I0E  C08  H11  single    0.970  0.020  1.090
 I0E  C08  H12  single    0.970  0.020  1.090
 I0E  C09  H13  single    0.970  0.020  1.090
 I0E  C09  H14  single    0.970  0.020  1.090
 I0E  C14  H15  single    0.930  0.020  1.080
 I0E  C16  H16  single    0.930  0.020  1.080
 I0E  C18  H17  single    0.970  0.020  1.090
 I0E  C18  H18  single    0.970  0.020  1.090
 I0E  C19  H19  single    0.970  0.020  1.090
 I0E  C25  H20  single    0.970  0.020  1.090
 I0E  C25  H21  single    0.970  0.020  1.090
 I0E  N01  H22  single    0.890  0.020  1.040
 I0E  N01  H23  single    0.890  0.020  1.040
 I0E  N05  H24  single    0.890  0.020  1.040
 I0E  N05  H25  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
 I0E  H2   C10  H1   107.50  3.000
 I0E  H2   C10  O11  110.81  3.000
 I0E  H1   C10  O11  110.61  3.000
 I0E  H2   C10  C09  110.73  3.000
 I0E  H1   C10  C09  109.62  3.000
 I0E  O11  C10  C09  107.59  3.000
 I0E  H3   C13  C14  118.88  3.000
 I0E  H3   C13  C12  121.06  3.000
 I0E  C14  C13  C12  120.06  3.000
 I0E  H4   C15  C16  120.27  3.000
 I0E  H4   C15  C14  120.64  3.000
 I0E  C16  C15  C14  119.09  3.000
 I0E  C18  C17  C16  120.09  3.000
 I0E  C18  C17  C12  122.06  3.000
 I0E  C16  C17  C12  117.85  3.000
 I0E  H7   C20  H6   107.87  3.000
 I0E  H7   C20  H5   107.29  3.000
 I0E  H6   C20  H5   107.63  3.000
 I0E  H7   C20  C19  111.76  3.000
 I0E  H6   C20  C19  111.18  3.000
 I0E  H5   C20  C19  110.91  3.000
 I0E  O23  C21  O22  126.29  3.000
 I0E  O23  C21  C19  116.37  3.000
 I0E  O22  C21  C19  117.32  3.000
 I0E  N27  C24  C25  116.04  3.000
 I0E  N27  C24  C06  121.29  3.000
 I0E  C25  C24  C06  122.67  3.000
 I0E  H10  C26  H9   108.06  3.000
 I0E  H10  C26  H8   107.64  3.000
 I0E  H9   C26  H8   108.37  3.000
 I0E  H10  C26  C25  111.11  3.000
 I0E  H9   C26  C25  111.31  3.000
 I0E  H8   C26  C25  110.23  3.000
 I0E  N27  C02  N03  126.42  3.000
 I0E  N03  C02  N01  116.43  3.000
 I0E  N27  C02  N01  117.13  3.000
 I0E  N05  C04  N03  118.33  3.000
 I0E  N05  C04  C06  120.48  3.000
 I0E  N03  C04  C06  121.18  3.000
 I0E  O07  C06  C04  118.71  3.000
 I0E  C04  C06  C24  117.21  3.000
 I0E  O07  C06  C24  124.06  3.000
 I0E  H12  C08  H11  107.43  3.000
 I0E  H12  C08  O07  109.62  3.000
 I0E  H11  C08  O07  110.61  3.000
 I0E  H12  C08  C09  111.24  3.000
 I0E  H11  C08  C09  109.95  3.000
 I0E  O07  C08  C09  108.02  3.000
 I0E  H14  C09  H13  106.95  3.000
 I0E  H14  C09  C08  109.33  3.000
 I0E  H13  C09  C08  110.18  3.000
 I0E  H14  C09  C10  108.06  3.000
 I0E  H13  C09  C10  109.10  3.000
 I0E  C08  C09  C10  113.01  3.000
 I0E  O11  C12  C17  116.24  3.000
 I0E  O11  C12  C13  123.21  3.000
 I0E  C17  C12  C13  120.55  3.000
 I0E  H15  C14  C15  120.45  3.000
 I0E  H15  C14  C13  119.25  3.000
 I0E  C15  C14  C13  120.30  3.000
 I0E  H16  C16  C17  118.35  3.000
 I0E  H16  C16  C15  119.48  3.000
 I0E  C17  C16  C15  122.17  3.000
 I0E  H19  C19  C18  107.85  3.000
 I0E  H19  C19  C21  108.46  3.000
 I0E  C18  C19  C21  110.84  3.000
 I0E  H19  C19  C20  107.86  3.000
 I0E  C21  C19  C20  109.58  3.000
 I0E  C18  C19  C20  112.12  3.000
 I0E  C04  N03  C02  116.79  3.000
 I0E  H25  N05  H24  116.67  3.000
 I0E  H25  N05  C04  119.58  3.000
 I0E  H24  N05  C04  118.30  3.000
 I0E  C02  N27  C24  117.11  3.000
 I0E  C08  O07  C06  114.95  3.000
 I0E  C12  O11  C10  120.15  3.000
 I0E  H21  C25  H20  106.56  3.000
 I0E  H21  C25  C26  109.71  3.000
 I0E  H20  C25  C26  109.21  3.000
 I0E  H21  C25  C24  110.97  3.000
 I0E  H20  C25  C24  108.04  3.000
 I0E  C26  C25  C24  112.16  3.000
 I0E  H18  C18  H17  106.49  3.000
 I0E  H18  C18  C19  109.06  3.000
 I0E  H17  C18  C19  108.45  3.000
 I0E  H18  C18  C17  110.95  3.000
 I0E  H17  C18  C17  108.26  3.000
 I0E  C19  C18  C17  113.37  3.000
 I0E  H23  N01  H22  115.26  3.000
 I0E  H23  N01  C02  117.20  3.000
 I0E  H22  N01  C02  116.88  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
 I0E  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 I0E  CONST_02  C16  C17  C12  C13     0.00   0.0  0
 I0E  CONST_03  C12  C17  C16  C15     0.00   0.0  0
 I0E  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 I0E  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 I0E  CONST_06  C14  C13  C12  C17     0.00   0.0  0
 I0E  CONST_07  N03  C02  N27  C24     0.00   0.0  0
 I0E  CONST_08  N03  C04  C06  C24     0.00   0.0  0
 I0E  CONST_09  C06  C24  N27  C02     0.00   0.0  0
 I0E  CONST_10  C06  C04  N03  C02     0.00   0.0  0
 I0E  CONST_11  N27  C24  C06  C04     0.00   0.0  0
 I0E  CONST_12  N27  C02  N03  C04     0.00   0.0  0
 I0E  CONST_13  C18  C17  C12  C13   180.00   0.0  0
 I0E  CONST_14  C18  C17  C16  C15   180.00   0.0  0
 I0E  CONST_15  N01  C02  N27  C24   180.00   0.0  0
 I0E  CONST_16  N05  C04  C06  C24   180.00   0.0  0
 I0E  CONST_17  C25  C24  N27  C02   180.00   0.0  0
 I0E  CONST_18  N05  C04  N03  C02   180.00   0.0  0
 I0E  CONST_19  C25  C24  C06  C04   180.00   0.0  0
 I0E  CONST_20  N01  C02  N03  C04   180.00   0.0  0
 I0E  CONST_21  O11  C12  C13  C14   180.00   0.0  0
 I0E  CONST_22  O11  C12  C17  C16   180.00   0.0  0
 I0E  CONST_23  O07  C06  C04  N03   180.00   0.0  0
 I0E  CONST_24  O07  C06  C24  N27   180.00   0.0  0
 I0E  CONST_25  H4   C15  C14  C13   180.00   0.0  0
 I0E  CONST_26  H3   C13  C14  C15   180.00   0.0  0
 I0E  CONST_27  H4   C15  C16  C17   180.00   0.0  0
 I0E  CONST_28  H3   C13  C12  C17   180.00   0.0  0
 I0E  CONST_29  H16  C16  C17  C12   180.00   0.0  0
 I0E  CONST_30  H15  C14  C13  C12   180.00   0.0  0
 I0E  CONST_31  H16  C16  C15  C14   180.00   0.0  0
 I0E  CONST_32  H15  C14  C15  C16   180.00   0.0  0
 I0E  CONST_33  H24  N05  C04  C06   180.00   0.0  0
 I0E  CONST_37  H24  N05  C04  N03     0.00   0.0  0
 I0E  Var_01    C17  C12  O11  C10   173.03  30.0  1
 I0E  Var_02    C13  C12  O11  C10    -6.89  30.0  1
 I0E  Var_03    C08  O07  C06  C24    88.39  30.0  2
 I0E  Var_04    N27  C24  C25  C26    59.95  30.0  2
 I0E  Var_05    C06  C24  C25  C26  -120.05  30.0  2
 I0E  Var_06    C08  O07  C06  C04   -93.41  30.0  2
 I0E  Var_07    C19  C18  C17  C12   102.01  30.0  2
 I0E  Var_08    C19  C18  C17  C16   -76.86  30.0  2
 I0E  Var_09    H20  C25  C24  C06   119.53  30.0  2
 I0E  Var_10    H21  C25  C24  C06     3.05  30.0  2
 I0E  Var_11    H17  C18  C17  C12  -137.61  30.0  2
 I0E  Var_12    H18  C18  C17  C12   -21.10  30.0  2
 I0E  Var_13    H17  C18  C17  C16    43.52  30.0  2
 I0E  Var_14    H18  C18  C17  C16   160.03  30.0  2
 I0E  Var_15    H20  C25  C24  N27   -60.47  30.0  2
 I0E  Var_16    H21  C25  C24  N27  -176.95  30.0  2
 I0E  Var_17    C09  C08  O07  C06   161.98  30.0  2
 I0E  Var_18    C12  O11  C10  C09  -173.49  30.0  3
 I0E  Var_19    H8   C26  C25  C24   178.45  30.0  3
 I0E  Var_20    H9   C26  C25  C24   -61.27  30.0  3
 I0E  Var_21    H10  C26  C25  C24    59.21  30.0  3
 I0E  Var_22    H11  C08  O07  C06    41.60  30.0  2
 I0E  Var_23    H12  C08  O07  C06   -76.67  30.0  2
 I0E  Var_24    H1   C10  O11  C12   -53.79  30.0  3
 I0E  Var_25    H2   C10  O11  C12    65.33  30.0  3
 I0E  Var_26    O07  C08  C09  C10   173.19  30.0  2
 I0E  Var_27    O11  C10  C09  C08   -67.06  30.0  2
 I0E  Var_28    H11  C08  C09  C10   -66.03  30.0  2
 I0E  Var_29    H12  C08  C09  C10    52.84  30.0  2
 I0E  Var_30    H1   C10  C09  C08   172.61  30.0  2
 I0E  Var_31    H2   C10  C09  C08    54.17  30.0  2
 I0E  Var_32    H13  C09  C08  O07    50.84  30.0  3
 I0E  Var_33    H14  C09  C08  O07   -66.42  30.0  3
 I0E  Var_34    H13  C09  C10  O11    55.88  30.0  3
 I0E  Var_35    H14  C09  C10  O11   171.82  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
 I0E  chir_01  C19  C20  C18  C21  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
 I0E  plan-1  C13  0.020
 I0E  plan-1  C15  0.020
 I0E  plan-1  C17  0.020
 I0E  plan-1  C12  0.020
 I0E  plan-1  C14  0.020
 I0E  plan-1  C16  0.020
 I0E  plan-1  O11  0.020
 I0E  plan-1  H3   0.020
 I0E  plan-1  H4   0.020
 I0E  plan-1  H15  0.020
 I0E  plan-1  H16  0.020
 I0E  plan-1  C18  0.020
 I0E  plan-2  C24  0.020
 I0E  plan-2  C02  0.020
 I0E  plan-2  C04  0.020
 I0E  plan-2  C06  0.020
 I0E  plan-2  N03  0.020
 I0E  plan-2  N05  0.020
 I0E  plan-2  N27  0.020
 I0E  plan-2  O07  0.020
 I0E  plan-2  C25  0.020
 I0E  plan-2  N01  0.020
 I0E  plan-3  C04  0.020
 I0E  plan-3  N05  0.020
 I0E  plan-3  H24  0.020
 I0E  plan-3  H25  0.020
 I0E  plan-4  C02  0.020
 I0E  plan-4  N01  0.020
 I0E  plan-4  H22  0.020
 I0E  plan-4  H23  0.020
 I0E  plan-5  C21  0.020
 I0E  plan-5  C19  0.020
 I0E  plan-5  O23  0.020
 I0E  plan-5  O22  0.020

