# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 06:45:38 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (2R)-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
 GXJ  GXJ  "(2R)-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 OK
;

data_comp_GXJ
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
 GXJ  C10   C  C      0   0.348  -2.3440   2.8761  15.1712
 GXJ  C13   C  C1     0  -0.269  -1.1596   4.5484  17.0624
 GXJ  C15   C  C      0   0.028  -1.0726   2.5527  15.6710
 GXJ  C17   C  CH1    0  -0.353   0.7952   1.6711  14.1981
 GXJ  C22   C  C      0   0.434  -6.5102  -2.3562  14.8188
 GXJ  C01   C  CH3    0  -0.669  -1.9272  -2.2363  15.6610
 GXJ  C03   C  C      0   0.228  -4.4171  -2.2160  15.9463
 GXJ  C04   C  C      0   0.127  -5.3439  -1.6168  15.1215
 GXJ  O05   O  O2     0  -0.497  -5.2074  -0.3590  14.6065
 GXJ  C06   C  CH2    0  -0.174  -4.4308  -0.2824  13.4131
 GXJ  C07   C  CH2    0  -0.499  -4.5441   1.1146  12.8390
 GXJ  C08   C  CH2    0  -0.188  -4.1847   2.2342  13.7950
 GXJ  O09   O  O2     0  -0.472  -2.8628   2.0298  14.2556
 GXJ  C11   C  C1     0  -0.377  -3.0069   4.0193  15.6154
 GXJ  C12   C  C1     0  -0.259  -2.4125   4.8512  16.5565
 GXJ  C14   C  C1     0  -0.293  -0.5103   3.4046  16.6142
 GXJ  C16   C  CH2    0  -0.491  -0.3064   1.3409  15.2122
 GXJ  C18   C  CH3    0  -0.650   0.2298   2.2823  12.9163
 GXJ  C19   C  C      0   0.419   1.6809   0.4493  13.8475
 GXJ  O20   O  O      0  -0.616   2.7120   0.7003  13.1897
 GXJ  O21   O  OC    -1  -0.596   1.3041  -0.6786  14.2261
 GXJ  N24   N  N      0  -0.501  -6.7004  -3.5717  15.3160
 GXJ  C25   C  C      0   0.508  -5.7418  -4.0577  16.1064
 GXJ  N26   N  NH2    0  -0.825  -5.9680  -5.2834  16.6482
 GXJ  N27   N  N      0  -0.500  -4.6147  -3.4437  16.4453
 GXJ  H131  H  H      0   0.243  -0.6925   5.1884  17.7994
 GXJ  H171  H  HCH1   0   0.209   1.4529   2.4227  14.6537
 GXJ  H012  H  HCH3   0   0.235  -0.9960  -1.7569  15.9601
 GXJ  H011  H  HCH3   0   0.229  -1.8711  -3.2873  15.9427
 GXJ  H013  H  HCH3   0   0.226  -1.9914  -2.1829  14.5734
 GXJ  H021  H  HCH2   0   0.249  -3.0158  -1.6148  17.4081
 GXJ  H022  H  HCH2   0   0.247  -3.1381  -0.4948  16.0655
 GXJ  H061  H  HCH2   0   0.229  -3.3864  -0.5294  13.6283
 GXJ  H062  H  HCH2   0   0.232  -4.7907  -1.0097  12.6772
 GXJ  H072  H  HCH2   0   0.247  -3.9066   1.1631  11.9526
 GXJ  H071  H  HCH2   0   0.245  -5.5662   1.2928  12.4952
 GXJ  H082  H  HCH2   0   0.232  -4.2671   3.1935  13.2718
 GXJ  H081  H  HCH2   0   0.224  -4.8827   2.2629  14.6381
 GXJ  H111  H  H      0   0.272  -3.9863   4.2773  15.2362
 GXJ  H121  H  H      0   0.249  -2.9411   5.7351  16.8900
 GXJ  H141  H  H      0   0.241   0.4672   3.1562  17.0136
 GXJ  H161  H  HCH2   0   0.226   0.1532   0.8782  16.0888
 GXJ  H162  H  HCH2   0   0.235  -0.9761   0.5921  14.7894
 GXJ  H181  H  HCH3   0   0.220   1.0314   2.5417  12.2258
 GXJ  H182  H  HCH3   0   0.207  -0.4385   1.5833  12.4082
 GXJ  H183  H  HCH3   0   0.217  -0.3369   3.1922  13.1189
 GXJ  H231  H  HNH2   0   0.391  -8.3375  -2.3201  13.9442
 GXJ  H232  H  HNH2   0   0.398  -7.4463  -0.8678  13.7848
 GXJ  H261  H  HNH2   0   0.384  -6.6667  -5.8616  16.2137
 GXJ  H262  H  HNH2   0   0.384  -5.1764  -5.7712  17.0311
 GXJ  C02   C  CH2    0  -0.510  -3.1234  -1.5541  16.3223
 GXJ  N23   N  NH2    0  -0.823  -7.4492  -1.8507  13.9959

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
 GXJ  C02  C01   single    1.528  0.020  1.528
 GXJ  C03  C02   single    1.501  0.020  1.501
 GXJ  C04  C03   aromatic  1.378  0.020  1.378
 GXJ  C06  O05   single    1.426  0.020  1.426
 GXJ  C07  C06   single    1.515  0.020  1.515
 GXJ  C08  C07   single    1.515  0.020  1.515
 GXJ  O09  C08   single    1.415  0.020  1.415
 GXJ  C10  O09   single    1.350  0.020  1.350
 GXJ  C11  C10   aromatic  1.394  0.020  1.394
 GXJ  C12  C11   aromatic  1.390  0.020  1.390
 GXJ  C13  C12   aromatic  1.385  0.020  1.385
 GXJ  C14  C13   aromatic  1.390  0.020  1.390
 GXJ  C15  C14   aromatic  1.390  0.020  1.390
 GXJ  C16  C15   single    1.505  0.020  1.505
 GXJ  C17  C16   single    1.533  0.020  1.533
 GXJ  C18  C17   single    1.528  0.020  1.528
 GXJ  C19  C17   single    1.549  0.020  1.549
 GXJ  O20  C19   deloc     1.248  0.020  1.248
 GXJ  O21  C19   deloc     1.248  0.020  1.248
 GXJ  O05  C04   single    1.366  0.020  1.366
 GXJ  C22  C04   aromatic  1.414  0.020  1.414
 GXJ  N23  C22   single    1.347  0.020  1.347
 GXJ  N24  C22   aromatic  1.327  0.020  1.327
 GXJ  C25  N24   aromatic  1.334  0.020  1.334
 GXJ  N26  C25   single    1.359  0.020  1.359
 GXJ  N27  C25   aromatic  1.328  0.020  1.328
 GXJ  C03  N27   aromatic  1.340  0.020  1.340
 GXJ  C10  C15   aromatic  1.404  0.020  1.404
 GXJ  C13  H131  single    0.930  0.020  1.080
 GXJ  C17  H171  single    0.970  0.020  1.090
 GXJ  C01  H012  single    0.970  0.020  1.090
 GXJ  C01  H011  single    0.970  0.020  1.090
 GXJ  C01  H013  single    0.970  0.020  1.090
 GXJ  C02  H021  single    0.970  0.020  1.090
 GXJ  C02  H022  single    0.970  0.020  1.090
 GXJ  C06  H061  single    0.970  0.020  1.090
 GXJ  C06  H062  single    0.970  0.020  1.090
 GXJ  C07  H072  single    0.970  0.020  1.090
 GXJ  C07  H071  single    0.970  0.020  1.090
 GXJ  C08  H082  single    0.970  0.020  1.090
 GXJ  C08  H081  single    0.970  0.020  1.090
 GXJ  C11  H111  single    0.930  0.020  1.080
 GXJ  C12  H121  single    0.930  0.020  1.080
 GXJ  C14  H141  single    0.930  0.020  1.080
 GXJ  C16  H161  single    0.970  0.020  1.090
 GXJ  C16  H162  single    0.970  0.020  1.090
 GXJ  C18  H181  single    0.970  0.020  1.090
 GXJ  C18  H182  single    0.970  0.020  1.090
 GXJ  C18  H183  single    0.970  0.020  1.090
 GXJ  N23  H231  single    0.890  0.020  1.040
 GXJ  N23  H232  single    0.890  0.020  1.040
 GXJ  N26  H261  single    0.890  0.020  1.040
 GXJ  N26  H262  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
 GXJ  C11   C10  O09   123.17  3.000
 GXJ  C11   C10  C15   120.41  3.000
 GXJ  O09   C10  C15   116.42  3.000
 GXJ  H131  C13  C14   120.32  3.000
 GXJ  H131  C13  C12   120.67  3.000
 GXJ  C14   C13  C12   119.01  3.000
 GXJ  C16   C15  C14   119.62  3.000
 GXJ  C16   C15  C10   122.55  3.000
 GXJ  C14   C15  C10   117.83  3.000
 GXJ  H171  C17  C19   106.94  3.000
 GXJ  H171  C17  C18   107.21  3.000
 GXJ  C19   C17  C18   109.70  3.000
 GXJ  H171  C17  C16   107.66  3.000
 GXJ  C19   C17  C16   112.99  3.000
 GXJ  C18   C17  C16   112.02  3.000
 GXJ  N24   C22  N23   118.21  3.000
 GXJ  N24   C22  C04   121.14  3.000
 GXJ  N23   C22  C04   120.65  3.000
 GXJ  H013  C01  H011  107.95  3.000
 GXJ  H013  C01  H012  107.62  3.000
 GXJ  H011  C01  H012  108.03  3.000
 GXJ  H013  C01  C02   111.32  3.000
 GXJ  H011  C01  C02   111.05  3.000
 GXJ  H012  C01  C02   110.73  3.000
 GXJ  N27   C03  C04   121.48  3.000
 GXJ  N27   C03  C02   115.96  3.000
 GXJ  C04   C03  C02   122.55  3.000
 GXJ  O05   C04  C03   123.98  3.000
 GXJ  O05   C04  C22   118.90  3.000
 GXJ  C03   C04  C22   117.11  3.000
 GXJ  C06   O05  C04   114.80  3.000
 GXJ  H062  C06  H061  107.20  3.000
 GXJ  H062  C06  C07   109.46  3.000
 GXJ  H061  C06  C07   110.73  3.000
 GXJ  H062  C06  O05   110.34  3.000
 GXJ  H061  C06  O05   110.06  3.000
 GXJ  C07   C06  O05   109.03  3.000
 GXJ  H071  C07  H072  106.44  3.000
 GXJ  H071  C07  C08   107.44  3.000
 GXJ  H072  C07  C08   109.91  3.000
 GXJ  H071  C07  C06   109.85  3.000
 GXJ  H072  C07  C06   107.74  3.000
 GXJ  C08   C07  C06   115.13  3.000
 GXJ  H081  C08  H082  107.27  3.000
 GXJ  H081  C08  O09   110.41  3.000
 GXJ  H082  C08  O09   110.62  3.000
 GXJ  H081  C08  C07   110.73  3.000
 GXJ  H082  C08  C07   109.14  3.000
 GXJ  O09   C08  C07   108.68  3.000
 GXJ  C08   O09  C10   119.29  3.000
 GXJ  H111  C11  C12   118.82  3.000
 GXJ  H111  C11  C10   120.96  3.000
 GXJ  C12   C11  C10   120.21  3.000
 GXJ  H121  C12  C11   119.25  3.000
 GXJ  H121  C12  C13   120.51  3.000
 GXJ  C11   C12  C13   120.24  3.000
 GXJ  H141  C14  C15   118.30  3.000
 GXJ  H141  C14  C13   119.40  3.000
 GXJ  C15   C14  C13   122.30  3.000
 GXJ  H162  C16  H161  106.19  3.000
 GXJ  H162  C16  C17   109.44  3.000
 GXJ  H161  C16  C17   108.64  3.000
 GXJ  H162  C16  C15   111.01  3.000
 GXJ  H161  C16  C15   108.09  3.000
 GXJ  C17   C16  C15   113.20  3.000
 GXJ  H183  C18  H182  107.60  3.000
 GXJ  H183  C18  H181  107.54  3.000
 GXJ  H182  C18  H181  107.92  3.000
 GXJ  H183  C18  C17   111.71  3.000
 GXJ  H182  C18  C17   111.13  3.000
 GXJ  H181  C18  C17   110.77  3.000
 GXJ  O21   C19  O20   126.22  3.000
 GXJ  O21   C19  C17   118.13  3.000
 GXJ  O20   C19  C17   115.64  3.000
 GXJ  C25   N24  C22   116.92  3.000
 GXJ  N27   C25  N26   117.17  3.000
 GXJ  N27   C25  N24   126.36  3.000
 GXJ  N26   C25  N24   116.43  3.000
 GXJ  H262  N26  H261  115.63  3.000
 GXJ  H262  N26  C25   117.27  3.000
 GXJ  H261  N26  C25   117.51  3.000
 GXJ  C25   N27  C03   116.99  3.000
 GXJ  H022  C02  H021  106.82  3.000
 GXJ  H022  C02  C03   110.97  3.000
 GXJ  H021  C02  C03   108.02  3.000
 GXJ  H022  C02  C01   110.03  3.000
 GXJ  H021  C02  C01   109.16  3.000
 GXJ  C03   C02  C01   111.69  3.000
 GXJ  H232  N23  H231  116.62  3.000
 GXJ  H232  N23  C22   119.54  3.000
 GXJ  H231  N23  C22   118.16  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
 GXJ  CONST_01  C13   C12  C11  C10     0.00   0.0  0
 GXJ  CONST_02  C13   C14  C15  C10     0.00   0.0  0
 GXJ  CONST_03  C12   C13  C14  C15     0.00   0.0  0
 GXJ  CONST_04  C12   C11  C10  C15     0.00   0.0  0
 GXJ  CONST_05  N27   C03  C04  C22     0.00   0.0  0
 GXJ  CONST_06  N27   C25  N24  C22     0.00   0.0  0
 GXJ  CONST_07  N24   C22  C04  C03     0.00   0.0  0
 GXJ  CONST_08  N24   C25  N27  C03     0.00   0.0  0
 GXJ  CONST_09  C25   N27  C03  C04     0.00   0.0  0
 GXJ  CONST_10  C25   N24  C22  C04     0.00   0.0  0
 GXJ  CONST_11  C14   C15  C10  C11     0.00   0.0  0
 GXJ  CONST_12  C14   C13  C12  C11     0.00   0.0  0
 GXJ  CONST_13  C16   C15  C14  C13   180.00   0.0  0
 GXJ  CONST_14  C02   C03  C04  C22   180.00   0.0  0
 GXJ  CONST_15  N26   C25  N24  C22   180.00   0.0  0
 GXJ  CONST_16  C25   N27  C03  C02   180.00   0.0  0
 GXJ  CONST_17  N23   C22  C04  C03   180.00   0.0  0
 GXJ  CONST_18  N26   C25  N27  C03   180.00   0.0  0
 GXJ  CONST_19  N27   C03  C04  O05   180.00   0.0  0
 GXJ  CONST_20  N24   C22  C04  O05   180.00   0.0  0
 GXJ  CONST_21  C12   C11  C10  O09   180.00   0.0  0
 GXJ  CONST_22  C14   C15  C10  O09   180.00   0.0  0
 GXJ  CONST_23  C16   C15  C10  C11   180.00   0.0  0
 GXJ  CONST_24  C25   N24  C22  N23   180.00   0.0  0
 GXJ  CONST_25  H121  C12  C11  C10   180.00   0.0  0
 GXJ  CONST_26  H141  C14  C15  C10   180.00   0.0  0
 GXJ  CONST_27  H111  C11  C12  C13   180.00   0.0  0
 GXJ  CONST_28  H131  C13  C14  C15   180.00   0.0  0
 GXJ  CONST_29  H111  C11  C10  C15   180.00   0.0  0
 GXJ  CONST_30  H131  C13  C12  C11   180.00   0.0  0
 GXJ  CONST_31  H141  C14  C13  C12   180.00   0.0  0
 GXJ  CONST_32  H121  C12  C13  C14   180.00   0.0  0
 GXJ  CONST_33  H231  N23  C22  C04   180.00   0.0  0
 GXJ  CONST_35  H231  N23  C22  N24     0.00   0.0  0
 GXJ  CONST_36  H232  N23  C22  N24   180.00   0.0  0
 GXJ  Var_01    C17   C16  C15  C10   101.44  30.0  2
 GXJ  Var_02    C08   O09  C10  C15   174.72  30.0  2
 GXJ  Var_03    C14   C15  C16  C17   -77.82  30.0  2
 GXJ  Var_04    C06   O05  C04  C22   -96.90  30.0  1
 GXJ  Var_05    C04   C03  C02  C01  -109.62  30.0  1
 GXJ  Var_06    N27   C03  C02  C01    69.38  30.0  1
 GXJ  Var_07    C06   O05  C04  C03    84.17  30.0  1
 GXJ  Var_08    C11   C10  O09  C08    -5.42  30.0  2
 GXJ  Var_09    H161  C16  C15  C10  -138.17  30.0  2
 GXJ  Var_10    H162  C16  C15  C10   -22.10  30.0  2
 GXJ  Var_11    H021  C02  C03  C04   130.33  30.0  2
 GXJ  Var_12    H022  C02  C03  C04    13.55  30.0  2
 GXJ  Var_13    H161  C16  C15  C14    42.56  30.0  2
 GXJ  Var_14    H162  C16  C15  C14   158.64  30.0  2
 GXJ  Var_15    H021  C02  C03  N27   -50.67  30.0  2
 GXJ  Var_16    H022  C02  C03  N27  -167.45  30.0  2
 GXJ  Var_17    C07   C08  O09  C10  -177.03  30.0  3
 GXJ  Var_18    C07   C06  O05  C04   171.16  30.0  1
 GXJ  Var_19    H082  C08  O09  C10    63.18  30.0  3
 GXJ  Var_20    H081  C08  O09  C10   -55.40  30.0  3
 GXJ  Var_21    H012  C01  C02  C03  -178.85  30.0  3
 GXJ  Var_22    H011  C01  C02  C03   -58.83  30.0  3
 GXJ  Var_23    H013  C01  C02  C03    61.48  30.0  3
 GXJ  Var_24    H061  C06  O05  C04   -67.20  30.0  1
 GXJ  Var_25    H062  C06  O05  C04    50.91  30.0  1
 GXJ  Var_26    C08   C07  C06  O05    54.46  30.0  1
 GXJ  Var_27    O09   C08  C07  C06    57.36  30.0  1
 GXJ  Var_28    H072  C07  C06  O05   177.48  30.0  1
 GXJ  Var_29    H071  C07  C06  O05   -66.96  30.0  1
 GXJ  Var_30    H082  C08  C07  C06   178.08  30.0  1
 GXJ  Var_31    H081  C08  C07  C06   -64.07  30.0  1
 GXJ  Var_32    H061  C06  C07  C08   -66.77  30.0  3
 GXJ  Var_33    H062  C06  C07  C08   175.24  30.0  3
 GXJ  Var_34    H072  C07  C08  O09   -64.49  30.0  3
 GXJ  Var_35    H071  C07  C08  O09  -179.92  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
 GXJ  chir_01  C17  C16  C18  C19  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
 GXJ  plan-1  C22   0.020
 GXJ  plan-1  C03   0.020
 GXJ  plan-1  C04   0.020
 GXJ  plan-1  O05   0.020
 GXJ  plan-1  N24   0.020
 GXJ  plan-1  C25   0.020
 GXJ  plan-1  N26   0.020
 GXJ  plan-1  N27   0.020
 GXJ  plan-1  C02   0.020
 GXJ  plan-1  N23   0.020
 GXJ  plan-2  C10   0.020
 GXJ  plan-2  C13   0.020
 GXJ  plan-2  C15   0.020
 GXJ  plan-2  O09   0.020
 GXJ  plan-2  C11   0.020
 GXJ  plan-2  C12   0.020
 GXJ  plan-2  C14   0.020
 GXJ  plan-2  C16   0.020
 GXJ  plan-2  H131  0.020
 GXJ  plan-2  H111  0.020
 GXJ  plan-2  H121  0.020
 GXJ  plan-2  H141  0.020
 GXJ  plan-3  C25   0.020
 GXJ  plan-3  N26   0.020
 GXJ  plan-3  H261  0.020
 GXJ  plan-3  H262  0.020
 GXJ  plan-4  C22   0.020
 GXJ  plan-4  H231  0.020
 GXJ  plan-4  H232  0.020
 GXJ  plan-4  N23   0.020
 GXJ  plan-5  C17   0.020
 GXJ  plan-5  C19   0.020
 GXJ  plan-5  O20   0.020
 GXJ  plan-5  O21   0.020

