# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 01:09:19 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (2S)-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
 I6J  I6J  "(2S)-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 GRAND
;

data_comp_I6J
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
 I6J  C10   C  CR6    0   0.127  -28.0935  11.2238  -24.8063
 I6J  C13   C  CH2    0  -0.501  -29.1304   7.7512  -24.4163
 I6J  C17   C  CR16   0  -0.376  -33.3733   8.2476  -25.0399
 I6J  C20   C  CR16   0  -0.289  -34.0454   8.5107  -27.7105
 I6J  C21   C  CR6    0   0.032  -32.7140   8.3115  -27.3757
 I6J  C22   C  CH2    0  -0.520  -31.6498   8.2291  -28.4338
 I6J  C24   C  CH1    0   0.565  -30.1395   6.7777  -29.7845
 I6J  C01   C  CH3    0  -0.673  -29.2902  11.3306  -28.1343
 I6J  C02   C  CH2    0  -0.507  -29.6816  11.7079  -26.7075
 I6J  C03   C  CR6    0   0.226  -28.4806  12.0193  -25.8622
 I6J  C05   C  CR6    0   0.507  -26.7195  13.4029  -25.4683
 I6J  C08   C  CR6    0   0.434  -26.9444  11.6198  -24.0856
 I6J  C12   C  CH2    0  -0.174  -28.3990   8.9058  -25.0684
 I6J  C14   C  CH2    0  -0.188  -30.6399   7.8851  -24.4070
 I6J  C16   C  CR6    0   0.352  -32.3849   8.1786  -26.0171
 I6J  C18   C  CR16   0  -0.257  -34.6993   8.4484  -25.4093
 I6J  C19   C  CR16   0  -0.270  -35.0428   8.5812  -26.7432
 I6J  C23   C  CH1    0  -0.487  -31.1811   6.7893  -28.6996
 I6J  C27   C  C      0   0.422  -32.3874   5.9128  -29.1265
 I6J  F25   F  F      0  -0.354  -29.6934   5.4993  -29.9953
 I6J  F26   F  F      0  -0.356  -29.0289   7.4988  -29.4242
 I6J  N04   N  N      0  -0.500  -27.7927  13.1194  -26.1961
 I6J  N06   N  NH2    0  -0.825  -25.9886  14.4880  -25.8382
 I6J  N07   N  N      0  -0.501  -26.2661  12.7094  -24.4223
 I6J  N09   N  NH2    0  -0.823  -26.4971  10.8858  -23.0477
 I6J  O11   O  O2     0  -0.496  -28.7757  10.1110  -24.4068
 I6J  O15   O  O2     0  -0.474  -31.0781   7.9869  -25.7490
 I6J  O28   O  O      0  -0.603  -32.8618   6.1665  -30.2524
 I6J  O29   O  OC    -1  -0.591  -32.7846   5.0642  -28.3111
 I6J  H131  H  HCH2   0   0.248  -28.8428   6.8316  -24.9321
 I6J  H132  H  HCH2   0   0.246  -28.7992   7.6417  -23.3804
 I6J  H171  H  HCR6   0   0.274  -33.1301   8.1451  -23.9908
 I6J  H201  H  HCR6   0   0.242  -34.3069   8.6139  -28.7570
 I6J  H221  H  HCH2   0   0.240  -32.0413   8.6528  -29.3616
 I6J  H222  H  HCH2   0   0.264  -30.7984   8.8483  -28.1435
 I6J  H241  H  HCH1   0   0.175  -30.4975   7.1732  -30.7355
 I6J  H013  H  HCH3   0   0.235  -30.1788  11.1616  -28.7419
 I6J  H011  H  HCH3   0   0.233  -28.7073  12.1227  -28.6031
 I6J  H012  H  HCH3   0   0.226  -28.6952  10.4165  -28.1539
 I6J  H021  H  HCH2   0   0.249  -30.3153  12.5979  -26.7316
 I6J  H022  H  HCH2   0   0.249  -30.2743  10.9104  -26.2597
 I6J  H121  H  HCH2   0   0.229  -28.6389   8.9721  -26.1349
 I6J  H122  H  HCH2   0   0.233  -27.3179   8.7486  -24.9871
 I6J  H142  H  HCH2   0   0.235  -31.0834   7.0077  -23.9231
 I6J  H141  H  HCH2   0   0.226  -30.9489   8.7652  -23.8343
 I6J  H181  H  HCR6   0   0.251  -35.4592   8.4999  -24.6399
 I6J  H191  H  HCR6   0   0.245  -36.0731   8.7386  -27.0337
 I6J  H231  H  HCH1   0   0.243  -30.7270   6.3852  -27.7909
 I6J  H062  H  HNH2   0   0.383  -26.4382  15.1598  -26.4365
 I6J  H061  H  HNH2   0   0.383  -25.3540  14.8713  -25.1587
 I6J  H091  H  HNH2   0   0.391  -25.7929  11.2890  -22.4529
 I6J  H092  H  HNH2   0   0.399  -27.1072  10.2095  -22.6216

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
 I6J  C02  C01   single    1.527  0.020  1.527
 I6J  C03  C02   single    1.501  0.020  1.501
 I6J  N04  C03   aromatic  1.340  0.020  1.340
 I6J  C05  N04   aromatic  1.327  0.020  1.327
 I6J  N06  C05   single    1.360  0.020  1.360
 I6J  N07  C05   aromatic  1.334  0.020  1.334
 I6J  C08  N07   aromatic  1.327  0.020  1.327
 I6J  N09  C08   single    1.348  0.020  1.348
 I6J  C10  C08   aromatic  1.413  0.020  1.413
 I6J  O11  C10   single    1.365  0.020  1.365
 I6J  C12  O11   single    1.426  0.020  1.426
 I6J  C13  C12   single    1.514  0.020  1.514
 I6J  C14  C13   single    1.516  0.020  1.516
 I6J  O15  C14   single    1.415  0.020  1.415
 I6J  C16  O15   single    1.348  0.020  1.348
 I6J  C17  C16   aromatic  1.392  0.020  1.392
 I6J  C18  C17   aromatic  1.391  0.020  1.391
 I6J  C19  C18   aromatic  1.384  0.020  1.384
 I6J  C20  C19   aromatic  1.391  0.020  1.391
 I6J  C21  C20   aromatic  1.387  0.020  1.387
 I6J  C22  C21   single    1.503  0.020  1.503
 I6J  C23  C22   single    1.537  0.020  1.537
 I6J  F25  C24   single    1.370  0.020  1.370
 I6J  F26  C24   single    1.372  0.020  1.372
 I6J  C24  C23   single    1.504  0.020  1.504
 I6J  C27  C23   single    1.551  0.020  1.551
 I6J  O28  C27   deloc     1.248  0.020  1.248
 I6J  O29  C27   deloc     1.242  0.020  1.242
 I6J  C03  C10   aromatic  1.378  0.020  1.378
 I6J  C16  C21   aromatic  1.404  0.020  1.404
 I6J  C13  H131  single    0.970  0.020  1.090
 I6J  C13  H132  single    0.970  0.020  1.090
 I6J  C17  H171  single    0.930  0.020  1.080
 I6J  C20  H201  single    0.930  0.020  1.080
 I6J  C22  H221  single    0.970  0.020  1.090
 I6J  C22  H222  single    0.970  0.020  1.090
 I6J  C24  H241  single    0.970  0.020  1.090
 I6J  C01  H013  single    0.970  0.020  1.090
 I6J  C01  H011  single    0.970  0.020  1.090
 I6J  C01  H012  single    0.970  0.020  1.090
 I6J  C02  H021  single    0.970  0.020  1.090
 I6J  C02  H022  single    0.970  0.020  1.090
 I6J  C12  H121  single    0.970  0.020  1.090
 I6J  C12  H122  single    0.970  0.020  1.090
 I6J  C14  H142  single    0.970  0.020  1.090
 I6J  C14  H141  single    0.970  0.020  1.090
 I6J  C18  H181  single    0.930  0.020  1.080
 I6J  C19  H191  single    0.930  0.020  1.080
 I6J  C23  H231  single    0.970  0.020  1.090
 I6J  N06  H062  single    0.890  0.020  1.040
 I6J  N06  H061  single    0.890  0.020  1.040
 I6J  N09  H091  single    0.890  0.020  1.040
 I6J  N09  H092  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
 I6J  O11   C10  C08   119.06  3.000
 I6J  O11   C10  C03   123.69  3.000
 I6J  C08   C10  C03   117.23  3.000
 I6J  H132  C13  H131  106.45  3.000
 I6J  H132  C13  C14   107.75  3.000
 I6J  H131  C13  C14   109.84  3.000
 I6J  H132  C13  C12   109.76  3.000
 I6J  H131  C13  C12   108.14  3.000
 I6J  C14   C13  C12   114.60  3.000
 I6J  H171  C17  C18   119.04  3.000
 I6J  H171  C17  C16   121.11  3.000
 I6J  C18   C17  C16   119.85  3.000
 I6J  H201  C20  C19   119.58  3.000
 I6J  H201  C20  C21   118.58  3.000
 I6J  C19   C20  C21   121.84  3.000
 I6J  C16   C21  C22   120.67  3.000
 I6J  C16   C21  C20   118.17  3.000
 I6J  C22   C21  C20   121.16  3.000
 I6J  H222  C22  H221  106.57  3.000
 I6J  H222  C22  C23   109.83  3.000
 I6J  H221  C22  C23   109.01  3.000
 I6J  H222  C22  C21   109.50  3.000
 I6J  H221  C22  C21   108.84  3.000
 I6J  C23   C22  C21   112.89  3.000
 I6J  H241  C24  F26   107.71  3.000
 I6J  H241  C24  F25   108.13  3.000
 I6J  F26   C24  F25   105.50  3.000
 I6J  H241  C24  C23   113.51  3.000
 I6J  F26   C24  C23   111.53  3.000
 I6J  F25   C24  C23   110.10  3.000
 I6J  H012  C01  H011  108.04  3.000
 I6J  H012  C01  H013  107.74  3.000
 I6J  H011  C01  H013  108.01  3.000
 I6J  H012  C01  C02   111.33  3.000
 I6J  H011  C01  C02   111.08  3.000
 I6J  H013  C01  C02   110.51  3.000
 I6J  H022  C02  H021  106.84  3.000
 I6J  H022  C02  C03   110.82  3.000
 I6J  H021  C02  C03   107.90  3.000
 I6J  H022  C02  C01   110.03  3.000
 I6J  H021  C02  C01   109.22  3.000
 I6J  C03   C02  C01   111.86  3.000
 I6J  N04   C03  C02   116.15  3.000
 I6J  N04   C03  C10   121.39  3.000
 I6J  C02   C03  C10   122.45  3.000
 I6J  N07   C05  N06   116.45  3.000
 I6J  N07   C05  N04   126.41  3.000
 I6J  N06   C05  N04   117.13  3.000
 I6J  N09   C08  N07   118.23  3.000
 I6J  N09   C08  C10   120.67  3.000
 I6J  N07   C08  C10   121.09  3.000
 I6J  H122  C12  H121  107.28  3.000
 I6J  H122  C12  O11   110.34  3.000
 I6J  H121  C12  O11   110.05  3.000
 I6J  H122  C12  C13   109.59  3.000
 I6J  H121  C12  C13   111.08  3.000
 I6J  O11   C12  C13   108.49  3.000
 I6J  H141  C14  H142  107.37  3.000
 I6J  H141  C14  O15   110.54  3.000
 I6J  H142  C14  O15   110.55  3.000
 I6J  H141  C14  C13   110.82  3.000
 I6J  H142  C14  C13   109.58  3.000
 I6J  O15   C14  C13   107.99  3.000
 I6J  O15   C16  C21   115.67  3.000
 I6J  C21   C16  C17   120.55  3.000
 I6J  O15   C16  C17   123.78  3.000
 I6J  H181  C18  C19   120.41  3.000
 I6J  H181  C18  C17   119.16  3.000
 I6J  C19   C18  C17   120.43  3.000
 I6J  H191  C19  C18   120.61  3.000
 I6J  H191  C19  C20   120.23  3.000
 I6J  C18   C19  C20   119.17  3.000
 I6J  H231  C23  C27   110.05  3.000
 I6J  H231  C23  C24   108.00  3.000
 I6J  C27   C23  C24   109.62  3.000
 I6J  H231  C23  C22   109.22  3.000
 I6J  C27   C23  C22   109.86  3.000
 I6J  C24   C23  C22   110.07  3.000
 I6J  O29   C27  O28   127.56  3.000
 I6J  O29   C27  C23   117.01  3.000
 I6J  O28   C27  C23   115.41  3.000
 I6J  C05   N04  C03   117.00  3.000
 I6J  H061  N06  H062  115.43  3.000
 I6J  H061  N06  C05   117.36  3.000
 I6J  H062  N06  C05   117.04  3.000
 I6J  C08   N07  C05   116.87  3.000
 I6J  H092  N09  H091  116.33  3.000
 I6J  H092  N09  C08   119.43  3.000
 I6J  H091  N09  C08   118.00  3.000
 I6J  C12   O11  C10   114.92  3.000
 I6J  C16   O15  C14   119.94  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
 I6J  CONST_01  C05   N07  C08  C10     0.00   0.0  0
 I6J  CONST_02  C05   N04  C03  C10     0.00   0.0  0
 I6J  CONST_03  C20   C21  C16  C17     0.00   0.0  0
 I6J  CONST_04  C20   C19  C18  C17     0.00   0.0  0
 I6J  CONST_05  C18   C19  C20  C21     0.00   0.0  0
 I6J  CONST_06  C18   C17  C16  C21     0.00   0.0  0
 I6J  CONST_07  N07   C05  N04  C03     0.00   0.0  0
 I6J  CONST_08  N07   C08  C10  C03     0.00   0.0  0
 I6J  CONST_09  N04   C05  N07  C08     0.00   0.0  0
 I6J  CONST_10  N04   C03  C10  C08     0.00   0.0  0
 I6J  CONST_11  C19   C18  C17  C16     0.00   0.0  0
 I6J  CONST_12  C19   C20  C21  C16     0.00   0.0  0
 I6J  CONST_13  C22   C21  C16  C17   180.00   0.0  0
 I6J  CONST_14  O15   C16  C21  C20   180.00   0.0  0
 I6J  CONST_15  C19   C20  C21  C22   180.00   0.0  0
 I6J  CONST_16  C05   N04  C03  C02   180.00   0.0  0
 I6J  CONST_17  C08   C10  C03  C02   180.00   0.0  0
 I6J  CONST_18  N06   C05  N04  C03   180.00   0.0  0
 I6J  CONST_19  N09   C08  C10  C03   180.00   0.0  0
 I6J  CONST_20  N09   C08  N07  C05   180.00   0.0  0
 I6J  CONST_21  N06   C05  N07  C08   180.00   0.0  0
 I6J  CONST_22  O15   C16  C17  C18   180.00   0.0  0
 I6J  CONST_23  O11   C10  C03  N04   180.00   0.0  0
 I6J  CONST_24  O11   C10  C08  N07   180.00   0.0  0
 I6J  CONST_25  H191  C19  C18  C17   180.00   0.0  0
 I6J  CONST_26  H181  C18  C19  C20   180.00   0.0  0
 I6J  CONST_27  H191  C19  C20  C21   180.00   0.0  0
 I6J  CONST_28  H171  C17  C16  C21   180.00   0.0  0
 I6J  CONST_29  H181  C18  C17  C16   180.00   0.0  0
 I6J  CONST_30  H201  C20  C21  C16   180.00   0.0  0
 I6J  CONST_31  H201  C20  C19  C18   180.00   0.0  0
 I6J  CONST_32  H171  C17  C18  C19   180.00   0.0  0
 I6J  CONST_33  H091  N09  C08  C10   180.00   0.0  0
 I6J  CONST_39  H091  N09  C08  N07     0.00   0.0  0
 I6J  Var_01    C01   C02  C03  C10  -112.66  30.0  2
 I6J  Var_02    C14   O15  C16  C17    -1.99  30.0  2
 I6J  Var_03    C23   C22  C21  C20  -103.50  30.0  1
 I6J  Var_04    C14   O15  C16  C21   177.94  30.0  2
 I6J  Var_05    N04   C03  C02  C01    66.98  30.0  1
 I6J  Var_06    C12   O11  C10  C03    87.95  30.0  1
 I6J  Var_07    C12   O11  C10  C08   -93.91  30.0  1
 I6J  Var_08    C23   C22  C21  C16    76.03  30.0  1
 I6J  Var_09    H021  C02  C03  C10   127.18  30.0  2
 I6J  Var_10    H022  C02  C03  C10    10.53  30.0  2
 I6J  Var_11    H221  C22  C21  C20    17.67  30.0  1
 I6J  Var_12    H222  C22  C21  C20   133.80  30.0  1
 I6J  Var_13    H221  C22  C21  C16  -162.80  30.0  1
 I6J  Var_14    H222  C22  C21  C16   -46.66  30.0  1
 I6J  Var_15    H021  C02  C03  N04   -53.17  30.0  2
 I6J  Var_16    H022  C02  C03  N04  -169.83  30.0  2
 I6J  Var_17    C13   C12  O11  C10   173.97  30.0  2
 I6J  Var_18    C16   O15  C14  C13  -176.93  30.0  1
 I6J  Var_19    H121  C12  O11  C10   -64.31  30.0  2
 I6J  Var_20    H122  C12  O11  C10    53.90  30.0  2
 I6J  Var_21    H013  C01  C02  C03  -176.96  30.0  3
 I6J  Var_22    H011  C01  C02  C03   -57.10  30.0  3
 I6J  Var_23    H012  C01  C02  C03    63.35  30.0  3
 I6J  Var_24    H142  C14  O15  C16    63.20  30.0  3
 I6J  Var_25    H141  C14  O15  C16   -55.54  30.0  3
 I6J  Var_26    O15   C14  C13  C12    59.24  30.0  2
 I6J  Var_27    O11   C12  C13  C14    56.75  30.0  3
 I6J  Var_28    H142  C14  C13  C12   179.72  30.0  2
 I6J  Var_29    H141  C14  C13  C12   -61.97  30.0  2
 I6J  Var_30    H121  C12  C13  C14   -64.34  30.0  3
 I6J  Var_31    H122  C12  C13  C14   177.29  30.0  3
 I6J  Var_32    H131  C13  C12  O11   179.62  30.0  1
 I6J  Var_33    H132  C13  C12  O11   -64.64  30.0  1
 I6J  Var_34    H131  C13  C14  O15   -62.70  30.0  3
 I6J  Var_35    H132  C13  C14  O15  -178.27  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
 I6J  chir_01  C23  C22  C24  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
 I6J  plan-1  C17   0.020
 I6J  plan-1  C20   0.020
 I6J  plan-1  C21   0.020
 I6J  plan-1  C22   0.020
 I6J  plan-1  C16   0.020
 I6J  plan-1  C18   0.020
 I6J  plan-1  C19   0.020
 I6J  plan-1  O15   0.020
 I6J  plan-1  H171  0.020
 I6J  plan-1  H201  0.020
 I6J  plan-1  H181  0.020
 I6J  plan-1  H191  0.020
 I6J  plan-2  C10   0.020
 I6J  plan-2  C02   0.020
 I6J  plan-2  C03   0.020
 I6J  plan-2  C05   0.020
 I6J  plan-2  C08   0.020
 I6J  plan-2  N04   0.020
 I6J  plan-2  N06   0.020
 I6J  plan-2  N07   0.020
 I6J  plan-2  N09   0.020
 I6J  plan-2  O11   0.020
 I6J  plan-3  C05   0.020
 I6J  plan-3  N06   0.020
 I6J  plan-3  H062  0.020
 I6J  plan-3  H061  0.020
 I6J  plan-4  C08   0.020
 I6J  plan-4  N09   0.020
 I6J  plan-4  H091  0.020
 I6J  plan-4  H092  0.020
 I6J  plan-5  C23   0.020
 I6J  plan-5  C27   0.020
 I6J  plan-5  O28   0.020
 I6J  plan-5  O29   0.020

