# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 19:05:28 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (2R)-2-[(2-{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)c1OCCCOc2ccccc2C[C@@H](C(F)F)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
 HJI  HJI  "(2R)-2-[(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid"  ligand  52  29  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HJI
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
 HJI  C10  C  CR6    0   0.127   8.5824   3.6698  15.0981
 HJI  C13  C  CH2    0  -0.498   8.5082   0.8032  12.8588
 HJI  C17  C  CR16   0  -0.376   6.9462  -2.4618  15.2204
 HJI  C20  C  CR16   0  -0.289   4.2079  -2.7489  14.9458
 HJI  C21  C  CR6    0   0.029   4.8359  -1.6941  14.2988
 HJI  C22  C  CH2    0  -0.512   4.0556  -0.7166  13.4666
 HJI  C24  C  CH1    0   0.563   3.0939   1.5703  13.2915
 HJI  C01  C  CH3    0  -0.678   5.1532   3.4987  16.1760
 HJI  C02  C  CH2    0  -0.504   6.5770   3.0587  16.4984
 HJI  C03  C  CR6    0   0.229   7.6000   4.0329  15.9928
 HJI  C05  C  CR6    0   0.506   8.3974   6.1623  16.0092
 HJI  C08  C  CR6    0   0.434   9.4939   4.6727  14.6979
 HJI  C12  C  CH2    0  -0.176   8.0431   2.1428  13.3912
 HJI  C14  C  CH2    0  -0.188   8.1903  -0.3832  13.7462
 HJI  C16  C  CR6    0   0.352   6.2248  -1.5544  14.4499
 HJI  C18  C  CR16   0  -0.256   6.2869  -3.5089  15.8555
 HJI  C19  C  CR16   0  -0.270   4.9168  -3.6575  15.7246
 HJI  C23  C  CH1    0  -0.499   3.7183   0.5735  14.2327
 HJI  C27  C  C      0   0.430   2.7364   0.2648  15.3918
 HJI  N04  N  N      0  -0.501   7.5076   5.2856  16.4574
 HJI  N06  N  NH2    0  -0.825   8.3207   7.4285  16.4976
 HJI  N07  N  N      0  -0.501   9.3921   5.9138  15.1556
 HJI  N09  N  NH2    0  -0.824  10.4775   4.3976  13.8179
 HJI  O11  O  O2     0  -0.496   8.7319   2.4018  14.6134
 HJI  O15  O  O2     0  -0.473   6.7812  -0.5083  13.8075
 HJI  O28  O  OC    -1  -0.588   3.1635   0.3991  16.5520
 HJI  O29  O  O      0  -0.599   1.6002  -0.1113  15.0416
 HJI  H1   H  HCH2   0   0.247   8.0612   0.6484  11.8735
 HJI  H2   H  HCH2   0   0.246   9.5899   0.8326  12.7044
 HJI  H3   H  HCR6   0   0.273   8.0177  -2.3678  15.3367
 HJI  H4   H  HCR6   0   0.242   3.1359  -2.8614  14.8326
 HJI  H5   H  HCH2   0   0.244   3.1247  -1.1864  13.1428
 HJI  H6   H  HCH2   0   0.247   4.6152  -0.4782  12.5602
 HJI  H7   H  HCH1   0   0.181   2.2278   1.1794  12.7551
 HJI  H8   H  HCH3   0   0.236   4.4392   2.7498  16.5161
 HJI  H9   H  HCH3   0   0.225   4.9135   4.4467  16.6556
 HJI  H10  H  HCH3   0   0.221   5.0163   3.6215  15.1020
 HJI  H11  H  HCH2   0   0.246   6.7600   2.0645  16.0902
 HJI  H12  H  HCH2   0   0.247   6.6935   2.9761  17.5828
 HJI  H13  H  HCH2   0   0.233   8.2659   2.9237  12.6562
 HJI  H14  H  HCH2   0   0.227   6.9599   2.1535  13.5573
 HJI  H15  H  HCH2   0   0.235   8.6342  -1.2904  13.3215
 HJI  H16  H  HCH2   0   0.226   8.6129  -0.2495  14.7476
 HJI  H17  H  HCR6   0   0.252   6.8587  -4.2077  16.4526
 HJI  H18  H  HCR6   0   0.245   4.4017  -4.4723  16.2161
 HJI  H19  H  HCH1   0   0.261   4.6383   1.0125  14.6299
 HJI  H20  H  HNH2   0   0.384   8.7988   8.1507  15.9866
 HJI  H21  H  HNH2   0   0.383   7.4526   7.7022  16.9251
 HJI  H22  H  HNH2   0   0.391  11.2064   5.0809  13.6990
 HJI  H23  H  HNH2   0   0.399  10.7341   3.4399  13.6493
 HJI  F25  F  F      0  -0.351   2.6988   2.6943  13.9662
 HJI  F26  F  F      0  -0.356   4.0033   2.0067  12.3616

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
 HJI  F26  C24  single    1.372  0.020  1.372
 HJI  C13  C12  single    1.515  0.020  1.515
 HJI  C13  C14  single    1.515  0.020  1.515
 HJI  C12  O11  single    1.427  0.020  1.427
 HJI  C24  F25  single    1.369  0.020  1.369
 HJI  C24  C23  single    1.506  0.020  1.506
 HJI  C22  C23  single    1.538  0.020  1.538
 HJI  C22  C21  single    1.502  0.020  1.502
 HJI  N09  C08  single    1.348  0.020  1.348
 HJI  C14  O15  single    1.416  0.020  1.416
 HJI  O15  C16  single    1.348  0.020  1.348
 HJI  C23  C27  single    1.550  0.020  1.550
 HJI  C21  C16  aromatic  1.404  0.020  1.404
 HJI  C21  C20  aromatic  1.388  0.020  1.388
 HJI  C16  C17  aromatic  1.392  0.020  1.392
 HJI  O11  C10  single    1.366  0.020  1.366
 HJI  C08  C10  aromatic  1.413  0.020  1.413
 HJI  C08  N07  aromatic  1.327  0.020  1.327
 HJI  O29  C27  deloc     1.247  0.020  1.247
 HJI  C20  C19  aromatic  1.391  0.020  1.391
 HJI  C10  C03  aromatic  1.377  0.020  1.377
 HJI  N07  C05  aromatic  1.334  0.020  1.334
 HJI  C17  C18  aromatic  1.391  0.020  1.391
 HJI  C27  O28  deloc     1.244  0.020  1.244
 HJI  C19  C18  aromatic  1.384  0.020  1.384
 HJI  C03  N04  aromatic  1.339  0.020  1.339
 HJI  C03  C02  single    1.500  0.020  1.500
 HJI  C05  N04  aromatic  1.327  0.020  1.327
 HJI  C05  N06  single    1.359  0.020  1.359
 HJI  C01  C02  single    1.525  0.020  1.525
 HJI  C13  H1   single    0.970  0.020  1.090
 HJI  C13  H2   single    0.970  0.020  1.090
 HJI  C17  H3   single    0.930  0.020  1.080
 HJI  C20  H4   single    0.930  0.020  1.080
 HJI  C22  H5   single    0.970  0.020  1.090
 HJI  C22  H6   single    0.970  0.020  1.090
 HJI  C24  H7   single    0.970  0.020  1.090
 HJI  C01  H8   single    0.970  0.020  1.090
 HJI  C01  H9   single    0.970  0.020  1.090
 HJI  C01  H10  single    0.970  0.020  1.090
 HJI  C02  H11  single    0.970  0.020  1.090
 HJI  C02  H12  single    0.970  0.020  1.090
 HJI  C12  H13  single    0.970  0.020  1.090
 HJI  C12  H14  single    0.970  0.020  1.090
 HJI  C14  H15  single    0.970  0.020  1.090
 HJI  C14  H16  single    0.970  0.020  1.090
 HJI  C18  H17  single    0.930  0.020  1.080
 HJI  C19  H18  single    0.930  0.020  1.080
 HJI  C23  H19  single    0.970  0.020  1.090
 HJI  N06  H20  single    0.890  0.020  1.040
 HJI  N06  H21  single    0.890  0.020  1.040
 HJI  N09  H22  single    0.890  0.020  1.040
 HJI  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
 HJI  O11  C10  C08  119.20  3.000
 HJI  C08  C10  C03  117.19  3.000
 HJI  O11  C10  C03  123.60  3.000
 HJI  H2   C13  H1   106.34  3.000
 HJI  H2   C13  C14  108.14  3.000
 HJI  H1   C13  C14  109.34  3.000
 HJI  H2   C13  C12  109.25  3.000
 HJI  H1   C13  C12  108.46  3.000
 HJI  C14  C13  C12  114.97  3.000
 HJI  H3   C17  C18  119.06  3.000
 HJI  H3   C17  C16  121.08  3.000
 HJI  C18  C17  C16  119.86  3.000
 HJI  H4   C20  C19  119.66  3.000
 HJI  H4   C20  C21  118.54  3.000
 HJI  C19  C20  C21  121.80  3.000
 HJI  C16  C21  C22  120.57  3.000
 HJI  C16  C21  C20  118.24  3.000
 HJI  C22  C21  C20  121.19  3.000
 HJI  H6   C22  H5   106.54  3.000
 HJI  H6   C22  C23  110.05  3.000
 HJI  H5   C22  C23  108.76  3.000
 HJI  H6   C22  C21  109.62  3.000
 HJI  H5   C22  C21  109.10  3.000
 HJI  C23  C22  C21  112.57  3.000
 HJI  H7   C24  F26  107.88  3.000
 HJI  H7   C24  F25  107.89  3.000
 HJI  F26  C24  F25  105.32  3.000
 HJI  H7   C24  C23  113.52  3.000
 HJI  F25  C24  C23  110.79  3.000
 HJI  F26  C24  C23  111.05  3.000
 HJI  H10  C01  H9   107.95  3.000
 HJI  H10  C01  H8   107.63  3.000
 HJI  H9   C01  H8   108.47  3.000
 HJI  H10  C01  C02  110.99  3.000
 HJI  H9   C01  C02  111.32  3.000
 HJI  H8   C01  C02  110.35  3.000
 HJI  H12  C02  H11  106.53  3.000
 HJI  H12  C02  C03  108.08  3.000
 HJI  H11  C02  C03  110.58  3.000
 HJI  H12  C02  C01  109.32  3.000
 HJI  H11  C02  C01  109.92  3.000
 HJI  C03  C02  C01  112.21  3.000
 HJI  N04  C03  C02  116.32  3.000
 HJI  C02  C03  C10  122.27  3.000
 HJI  N04  C03  C10  121.41  3.000
 HJI  N07  C05  N06  116.45  3.000
 HJI  N06  C05  N04  117.14  3.000
 HJI  N07  C05  N04  126.37  3.000
 HJI  N09  C08  N07  118.17  3.000
 HJI  N07  C08  C10  121.11  3.000
 HJI  N09  C08  C10  120.71  3.000
 HJI  H14  C12  H13  107.20  3.000
 HJI  H14  C12  O11  110.22  3.000
 HJI  H13  C12  O11  110.32  3.000
 HJI  H14  C12  C13  111.43  3.000
 HJI  H13  C12  C13  109.40  3.000
 HJI  O11  C12  C13  108.27  3.000
 HJI  H16  C14  H15  107.41  3.000
 HJI  H16  C14  O15  110.81  3.000
 HJI  H15  C14  O15  110.30  3.000
 HJI  H16  C14  C13  111.04  3.000
 HJI  H15  C14  C13  109.65  3.000
 HJI  O15  C14  C13  107.66  3.000
 HJI  O15  C16  C21  115.74  3.000
 HJI  C21  C16  C17  120.49  3.000
 HJI  O15  C16  C17  123.77  3.000
 HJI  H17  C18  C19  120.38  3.000
 HJI  H17  C18  C17  119.17  3.000
 HJI  C19  C18  C17  120.45  3.000
 HJI  H18  C19  C18  120.60  3.000
 HJI  H18  C19  C20  120.24  3.000
 HJI  C18  C19  C20  119.16  3.000
 HJI  H19  C23  C27  109.94  3.000
 HJI  H19  C23  C24  108.06  3.000
 HJI  C27  C23  C24  109.66  3.000
 HJI  H19  C23  C22  109.45  3.000
 HJI  C27  C23  C22  110.14  3.000
 HJI  C24  C23  C22  109.56  3.000
 HJI  O29  C27  O28  127.41  3.000
 HJI  O28  C27  C23  117.30  3.000
 HJI  O29  C27  C23  115.29  3.000
 HJI  C05  N04  C03  117.03  3.000
 HJI  H21  N06  H20  115.52  3.000
 HJI  H21  N06  C05  117.06  3.000
 HJI  H20  N06  C05  117.36  3.000
 HJI  C08  N07  C05  116.88  3.000
 HJI  H23  N09  H22  116.23  3.000
 HJI  H23  N09  C08  119.34  3.000
 HJI  H22  N09  C08  117.85  3.000
 HJI  C12  O11  C10  114.82  3.000
 HJI  C16  O15  C14  120.00  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
 HJI  CONST_01  C05  N07  C08  C10     0.00   0.0  0
 HJI  CONST_02  C05  N04  C03  C10     0.00   0.0  0
 HJI  CONST_03  C20  C21  C16  C17     0.00   0.0  0
 HJI  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 HJI  CONST_05  C18  C17  C16  C21     0.00   0.0  0
 HJI  CONST_06  C18  C19  C20  C21     0.00   0.0  0
 HJI  CONST_07  N07  C08  C10  C03     0.00   0.0  0
 HJI  CONST_08  N07  C05  N04  C03     0.00   0.0  0
 HJI  CONST_09  N04  C03  C10  C08     0.00   0.0  0
 HJI  CONST_10  N04  C05  N07  C08     0.00   0.0  0
 HJI  CONST_11  C19  C20  C21  C16     0.00   0.0  0
 HJI  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 HJI  CONST_13  C22  C21  C16  C17   180.00   0.0  0
 HJI  CONST_14  O15  C16  C21  C20   180.00   0.0  0
 HJI  CONST_15  C19  C20  C21  C22   180.00   0.0  0
 HJI  CONST_16  C08  C10  C03  C02   180.00   0.0  0
 HJI  CONST_17  C05  N04  C03  C02   180.00   0.0  0
 HJI  CONST_18  N09  C08  C10  C03   180.00   0.0  0
 HJI  CONST_19  N06  C05  N04  C03   180.00   0.0  0
 HJI  CONST_20  N09  C08  N07  C05   180.00   0.0  0
 HJI  CONST_21  N06  C05  N07  C08   180.00   0.0  0
 HJI  CONST_22  O15  C16  C17  C18   180.00   0.0  0
 HJI  CONST_23  O11  C10  C03  N04   180.00   0.0  0
 HJI  CONST_24  O11  C10  C08  N07   180.00   0.0  0
 HJI  CONST_25  H18  C19  C18  C17   180.00   0.0  0
 HJI  CONST_26  H17  C18  C19  C20   180.00   0.0  0
 HJI  CONST_27  H3   C17  C16  C21   180.00   0.0  0
 HJI  CONST_28  H18  C19  C20  C21   180.00   0.0  0
 HJI  CONST_29  H4   C20  C21  C16   180.00   0.0  0
 HJI  CONST_30  H17  C18  C17  C16   180.00   0.0  0
 HJI  CONST_31  H4   C20  C19  C18   180.00   0.0  0
 HJI  CONST_32  H3   C17  C18  C19   180.00   0.0  0
 HJI  CONST_33  H22  N09  C08  C10   180.00   0.0  0
 HJI  CONST_37  H22  N09  C08  N07     0.00   0.0  0
 HJI  Var_01    C01  C02  C03  C10  -120.98  30.0  2
 HJI  Var_02    C14  O15  C16  C17     8.42  30.0  2
 HJI  Var_03    C23  C22  C21  C20    97.81  30.0  2
 HJI  Var_04    C14  O15  C16  C21  -171.43  30.0  2
 HJI  Var_05    N04  C03  C02  C01    58.90  30.0  1
 HJI  Var_06    C12  O11  C10  C03    92.10  30.0  2
 HJI  Var_07    C12  O11  C10  C08   -89.49  30.0  2
 HJI  Var_08    C23  C22  C21  C16   -81.66  30.0  2
 HJI  Var_09    H11  C02  C03  C10     2.15  30.0  2
 HJI  Var_10    H12  C02  C03  C10   118.41  30.0  2
 HJI  Var_11    H5   C22  C21  C20   -23.02  30.0  2
 HJI  Var_12    H6   C22  C21  C20  -139.34  30.0  2
 HJI  Var_13    H5   C22  C21  C16   157.51  30.0  2
 HJI  Var_14    H6   C22  C21  C16    41.19  30.0  2
 HJI  Var_15    H11  C02  C03  N04  -177.97  30.0  2
 HJI  Var_16    H12  C02  C03  N04   -61.72  30.0  2
 HJI  Var_17    C13  C12  O11  C10   169.67  30.0  2
 HJI  Var_18    C16  O15  C14  C13   174.76  30.0  3
 HJI  Var_19    H13  C12  O11  C10    49.99  30.0  2
 HJI  Var_20    H14  C12  O11  C10   -68.21  30.0  2
 HJI  Var_21    H8   C01  C02  C03   177.46  30.0  3
 HJI  Var_22    H9   C01  C02  C03   -62.05  30.0  3
 HJI  Var_23    H10  C01  C02  C03    58.23  30.0  3
 HJI  Var_24    H15  C14  O15  C16    55.16  30.0  1
 HJI  Var_25    H16  C14  O15  C16   -63.64  30.0  1
 HJI  Var_26    O15  C14  C13  C12    64.59  30.0  3
 HJI  Var_27    O11  C12  C13  C14    63.02  30.0  3
 HJI  Var_28    H15  C14  C13  C12  -175.40  30.0  3
 HJI  Var_29    H16  C14  C13  C12   -56.87  30.0  3
 HJI  Var_30    H13  C12  C13  C14  -176.72  30.0  3
 HJI  Var_31    H14  C12  C13  C14   -58.36  30.0  3
 HJI  Var_32    H1   C13  C12  O11  -174.26  30.0  1
 HJI  Var_33    H2   C13  C12  O11   -58.75  30.0  1
 HJI  Var_34    H1   C13  C14  O15   -57.66  30.0  2
 HJI  Var_35    H2   C13  C14  O15  -173.04  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
 HJI  chir_01  C23  C24  C22  C27  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
 HJI  plan-1  C17  0.020
 HJI  plan-1  C20  0.020
 HJI  plan-1  C21  0.020
 HJI  plan-1  C22  0.020
 HJI  plan-1  C16  0.020
 HJI  plan-1  C18  0.020
 HJI  plan-1  C19  0.020
 HJI  plan-1  O15  0.020
 HJI  plan-1  H3   0.020
 HJI  plan-1  H4   0.020
 HJI  plan-1  H17  0.020
 HJI  plan-1  H18  0.020
 HJI  plan-2  C10  0.020
 HJI  plan-2  C02  0.020
 HJI  plan-2  C03  0.020
 HJI  plan-2  C05  0.020
 HJI  plan-2  C08  0.020
 HJI  plan-2  N04  0.020
 HJI  plan-2  N06  0.020
 HJI  plan-2  N07  0.020
 HJI  plan-2  N09  0.020
 HJI  plan-2  O11  0.020
 HJI  plan-3  C05  0.020
 HJI  plan-3  N06  0.020
 HJI  plan-3  H20  0.020
 HJI  plan-3  H21  0.020
 HJI  plan-4  C08  0.020
 HJI  plan-4  N09  0.020
 HJI  plan-4  H22  0.020
 HJI  plan-4  H23  0.020
 HJI  plan-5  C23  0.020
 HJI  plan-5  C27  0.020
 HJI  plan-5  O28  0.020
 HJI  plan-5  O29  0.020

