# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 08:36:57 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: 4-(3-{4-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]butoxy}phenyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCCOc2cccc(CCCC(O)=O)c2
#
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
 H0I  H0I  "4-(3-{4-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]butoxy}phenyl)butanoic acid"  ligand  55  28  .  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_H0I
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
 H0I  C01   C  CH3    0  -0.666  -2.0152  -1.1101  15.0504
 H0I  C02   C  CH2    0  -0.520  -3.4109  -0.7386  15.5486
 H0I  C03   C  CR6    0   0.232  -4.4428  -1.7498  15.1427
 H0I  N04   N  N      0  -0.499  -4.3643  -2.9416  15.7502
 H0I  C05   C  CR6    0   0.506  -5.2536  -3.8602  15.3943
 H0I  N06   N  NH2    0  -0.825  -5.1399  -5.0888  15.9660
 H0I  N07   N  N      0  -0.501  -6.2345  -3.7081  14.5032
 H0I  C08   C  CR6    0   0.433  -6.3162  -2.5304  13.8974
 H0I  N09   N  NH2    0  -0.822  -7.2764  -2.3563  12.9682
 H0I  C10   C  CR6    0   0.119  -5.4085  -1.4889  14.1955
 H0I  O11   O  O2     0  -0.493  -5.5415  -0.2968  13.5416
 H0I  C12   C  CH2    0  -0.189  -4.7010  -0.1698  12.3942
 H0I  C13   C  CH2    0  -0.464  -5.1544   0.9970  11.5428
 H0I  C14   C  CH2    0  -0.459  -5.2463   2.3526  12.2440
 H0I  C15   C  CH2    0  -0.216  -4.0698   2.7010  13.1325
 H0I  O16   O  O2     0  -0.480  -2.8661   2.5323  12.3993
 H0I  C17   C  CR6    0   0.402  -1.7146   2.3927  13.0907
 H0I  C18   C  CR16   0  -0.386  -1.5325   2.8557  14.3915
 H0I  C19   C  CR16   0  -0.227  -0.3044   2.6588  15.0132
 H0I  C20   C  CR16   0  -0.331   0.7315   2.0091  14.3624
 H0I  C21   C  CR6    0   0.149   0.5545   1.5414  13.0592
 H0I  C22   C  CH2    0  -0.503   1.6330   0.7604  12.3646
 H0I  C23   C  CH2    0  -0.402   1.5730  -0.7277  12.7179
 H0I  C24   C  CH2    0  -0.575   2.6006  -1.5581  11.9644
 H0I  C25   C  C      0   0.404   2.3726  -1.6899  10.4421
 H0I  O26   O  O      0  -0.618   3.3790  -1.9732   9.7604
 H0I  O27   O  OC    -1  -0.608   1.2067  -1.5435  10.0198
 H0I  C28   C  CR16   0  -0.412  -0.6697   1.7418  12.4358
 H0I  H012  H  HCH3   0   0.234  -1.2831  -0.3738  15.3831
 H0I  H011  H  HCH3   0   0.229  -1.7104  -2.0854  15.4285
 H0I  H013  H  HCH3   0   0.227  -1.9766  -1.1441  13.9606
 H0I  H021  H  HCH2   0   0.250  -3.4000  -0.6880  16.6401
 H0I  H022  H  HCH2   0   0.257  -3.6780   0.2553  15.1915
 H0I  H062  H  HNH2   0   0.383  -4.5951  -5.1510  16.8092
 H0I  H061  H  HNH2   0   0.383  -5.9440  -5.6917  15.9256
 H0I  H092  H  HNH2   0   0.390  -8.0107  -3.0418  12.9118
 H0I  H091  H  HNH2   0   0.398  -7.5095  -1.4248  12.6696
 H0I  H121  H  HCH2   0   0.228  -3.6614  -0.0407  12.7145
 H0I  H122  H  HCH2   0   0.233  -4.7392  -1.0876  11.7972
 H0I  H132  H  HCH2   0   0.237  -4.4545   1.0580  10.7065
 H0I  H131  H  HCH2   0   0.237  -6.1276   0.7665  11.1018
 H0I  H142  H  HCH2   0   0.240  -5.3839   3.1274  11.4858
 H0I  H141  H  HCH2   0   0.237  -6.1367   2.3924  12.8757
 H0I  H152  H  HCH2   0   0.238  -4.1652   3.7320  13.4906
 H0I  H151  H  HCH2   0   0.232  -4.0624   2.0536  14.0156
 H0I  H181  H  HCR6   0   0.270  -2.3209   3.3727  14.9220
 H0I  H191  H  HCR6   0   0.251  -0.1619   3.0243  16.0225
 H0I  H201  H  HCR6   0   0.239   1.6810   1.8610  14.8627
 H0I  H221  H  HCH2   0   0.227   2.6154   1.1555  12.6388
 H0I  H222  H  HCH2   0   0.235   1.5334   0.8771  11.2839
 H0I  H231  H  HCH2   0   0.211   1.7257  -0.8373  13.7961
 H0I  H232  H  HCH2   0   0.210   0.5691  -1.1064  12.5112
 H0I  H242  H  HCH2   0   0.203   3.6057  -1.1656  12.1480
 H0I  H241  H  HCH2   0   0.228   2.6073  -2.5739  12.3780
 H0I  H281  H  HCR6   0   0.246  -0.8286   1.3748  11.4274

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
 H0I  C02  C01   single    1.528  0.020  1.528
 H0I  C03  C02   single    1.501  0.020  1.501
 H0I  N04  C03   aromatic  1.340  0.020  1.340
 H0I  C05  N04   aromatic  1.327  0.020  1.327
 H0I  N06  C05   single    1.360  0.020  1.360
 H0I  N07  C05   aromatic  1.334  0.020  1.334
 H0I  C08  N07   aromatic  1.327  0.020  1.327
 H0I  N09  C08   single    1.347  0.020  1.347
 H0I  C10  C08   aromatic  1.413  0.020  1.413
 H0I  O11  C10   single    1.366  0.020  1.366
 H0I  C12  O11   single    1.428  0.020  1.428
 H0I  C13  C12   single    1.514  0.020  1.514
 H0I  C14  C13   single    1.529  0.020  1.529
 H0I  C15  C14   single    1.515  0.020  1.515
 H0I  O16  C15   single    1.419  0.020  1.419
 H0I  C17  O16   single    1.350  0.020  1.350
 H0I  C18  C17   aromatic  1.393  0.020  1.393
 H0I  C19  C18   aromatic  1.391  0.020  1.391
 H0I  C20  C19   aromatic  1.385  0.020  1.385
 H0I  C21  C20   aromatic  1.396  0.020  1.396
 H0I  C23  C22   single    1.531  0.020  1.531
 H0I  C24  C23   single    1.521  0.020  1.521
 H0I  C25  C24   single    1.545  0.020  1.545
 H0I  O26  C25   deloc     1.248  0.020  1.248
 H0I  O27  C25   deloc     1.249  0.020  1.249
 H0I  C22  C21   single    1.502  0.020  1.502
 H0I  C28  C21   aromatic  1.388  0.020  1.388
 H0I  C03  C10   aromatic  1.378  0.020  1.378
 H0I  C17  C28   aromatic  1.394  0.020  1.394
 H0I  C01  H012  single    0.970  0.020  1.090
 H0I  C01  H011  single    0.970  0.020  1.090
 H0I  C01  H013  single    0.970  0.020  1.090
 H0I  C02  H021  single    0.970  0.020  1.090
 H0I  C02  H022  single    0.970  0.020  1.090
 H0I  N06  H062  single    0.890  0.020  1.040
 H0I  N06  H061  single    0.890  0.020  1.040
 H0I  N09  H092  single    0.890  0.020  1.040
 H0I  N09  H091  single    0.890  0.020  1.040
 H0I  C12  H121  single    0.970  0.020  1.090
 H0I  C12  H122  single    0.970  0.020  1.090
 H0I  C13  H132  single    0.970  0.020  1.090
 H0I  C13  H131  single    0.970  0.020  1.090
 H0I  C14  H142  single    0.970  0.020  1.090
 H0I  C14  H141  single    0.970  0.020  1.090
 H0I  C15  H152  single    0.970  0.020  1.090
 H0I  C15  H151  single    0.970  0.020  1.090
 H0I  C18  H181  single    0.930  0.020  1.080
 H0I  C19  H191  single    0.930  0.020  1.080
 H0I  C20  H201  single    0.930  0.020  1.080
 H0I  C22  H221  single    0.970  0.020  1.090
 H0I  C22  H222  single    0.970  0.020  1.090
 H0I  C23  H231  single    0.970  0.020  1.090
 H0I  C23  H232  single    0.970  0.020  1.090
 H0I  C24  H242  single    0.970  0.020  1.090
 H0I  C24  H241  single    0.970  0.020  1.090
 H0I  C28  H281  single    0.930  0.020  1.080

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
 H0I  H013  C01  H011  108.00  3.000
 H0I  H013  C01  H012  107.58  3.000
 H0I  H011  C01  H012  108.10  3.000
 H0I  H013  C01  C02   111.44  3.000
 H0I  H011  C01  C02   111.11  3.000
 H0I  H012  C01  C02   110.46  3.000
 H0I  H022  C02  H021  106.72  3.000
 H0I  H022  C02  C03   110.95  3.000
 H0I  H021  C02  C03   107.95  3.000
 H0I  H022  C02  C01   109.81  3.000
 H0I  H021  C02  C01   109.14  3.000
 H0I  C03   C02  C01   112.09  3.000
 H0I  C10   C03  N04   121.42  3.000
 H0I  C10   C03  C02   122.70  3.000
 H0I  N04   C03  C02   115.88  3.000
 H0I  C05   N04  C03   117.05  3.000
 H0I  N07   C05  N06   116.44  3.000
 H0I  N07   C05  N04   126.37  3.000
 H0I  N06   C05  N04   117.17  3.000
 H0I  H061  N06  H062  115.44  3.000
 H0I  H061  N06  C05   117.25  3.000
 H0I  H062  N06  C05   116.98  3.000
 H0I  C08   N07  C05   116.84  3.000
 H0I  C10   C08  N09   120.52  3.000
 H0I  C10   C08  N07   121.21  3.000
 H0I  N09   C08  N07   118.25  3.000
 H0I  H091  N09  H092  116.44  3.000
 H0I  H091  N09  C08   119.32  3.000
 H0I  H092  N09  C08   118.08  3.000
 H0I  O11   C10  C08   118.66  3.000
 H0I  O11   C10  C03   124.24  3.000
 H0I  C08   C10  C03   117.10  3.000
 H0I  C12   O11  C10   113.89  3.000
 H0I  H122  C12  H121  106.93  3.000
 H0I  H122  C12  C13   109.20  3.000
 H0I  H121  C12  C13   110.97  3.000
 H0I  H122  C12  O11   110.04  3.000
 H0I  H121  C12  O11   109.52  3.000
 H0I  C13   C12  O11   110.13  3.000
 H0I  H131  C13  H132  105.87  3.000
 H0I  H131  C13  C14   108.57  3.000
 H0I  H132  C13  C14   109.89  3.000
 H0I  H131  C13  C12   109.33  3.000
 H0I  H132  C13  C12   106.37  3.000
 H0I  C14   C13  C12   116.32  3.000
 H0I  H141  C14  H142  105.84  3.000
 H0I  H141  C14  C15   106.59  3.000
 H0I  H142  C14  C15   109.98  3.000
 H0I  H141  C14  C13   110.27  3.000
 H0I  H142  C14  C13   108.54  3.000
 H0I  C15   C14  C13   115.22  3.000
 H0I  H151  C15  H152  107.06  3.000
 H0I  H151  C15  O16   109.91  3.000
 H0I  H152  C15  O16   110.76  3.000
 H0I  H151  C15  C14   110.02  3.000
 H0I  H152  C15  C14   109.91  3.000
 H0I  O16   C15  C14   109.17  3.000
 H0I  C17   O16  C15   118.10  3.000
 H0I  C28   C17  C18   119.72  3.000
 H0I  C28   C17  O16   116.54  3.000
 H0I  C18   C17  O16   123.73  3.000
 H0I  H181  C18  C19   119.48  3.000
 H0I  H181  C18  C17   121.44  3.000
 H0I  C19   C18  C17   119.08  3.000
 H0I  H191  C19  C20   119.85  3.000
 H0I  H191  C19  C18   119.03  3.000
 H0I  C20   C19  C18   121.12  3.000
 H0I  H201  C20  C21   119.76  3.000
 H0I  H201  C20  C19   120.17  3.000
 H0I  C21   C20  C19   120.07  3.000
 H0I  C28   C21  C22   120.04  3.000
 H0I  C28   C21  C20   118.86  3.000
 H0I  C22   C21  C20   121.00  3.000
 H0I  H222  C22  H221  106.95  3.000
 H0I  H222  C22  C23   109.20  3.000
 H0I  H221  C22  C23   109.18  3.000
 H0I  H222  C22  C21   109.68  3.000
 H0I  H221  C22  C21   109.95  3.000
 H0I  C23   C22  C21   111.76  3.000
 H0I  H232  C23  H231  106.25  3.000
 H0I  H232  C23  C24   109.74  3.000
 H0I  H231  C23  C24   109.82  3.000
 H0I  H232  C23  C22   109.23  3.000
 H0I  H231  C23  C22   108.62  3.000
 H0I  C24   C23  C22   112.95  3.000
 H0I  H241  C24  H242  105.26  3.000
 H0I  H241  C24  C25   107.06  3.000
 H0I  H242  C24  C25   109.35  3.000
 H0I  H241  C24  C23   108.84  3.000
 H0I  H242  C24  C23   109.97  3.000
 H0I  C25   C24  C23   115.79  3.000
 H0I  O27   C25  O26   126.50  3.000
 H0I  O27   C25  C24   117.45  3.000
 H0I  O26   C25  C24   116.01  3.000
 H0I  H281  C28  C21   119.85  3.000
 H0I  H281  C28  C17   118.99  3.000
 H0I  C21   C28  C17   121.15  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
 H0I  CONST_01  N07   C05  N04  C03     0.00   0.0  0
 H0I  CONST_02  N07   C08  C10  C03     0.00   0.0  0
 H0I  CONST_03  C08   C10  C03  N04     0.00   0.0  0
 H0I  CONST_04  C08   N07  C05  N04     0.00   0.0  0
 H0I  CONST_05  C10   C03  N04  C05     0.00   0.0  0
 H0I  CONST_06  C10   C08  N07  C05     0.00   0.0  0
 H0I  CONST_07  C20   C19  C18  C17     0.00   0.0  0
 H0I  CONST_08  C20   C21  C28  C17     0.00   0.0  0
 H0I  CONST_09  C21   C28  C17  C18     0.00   0.0  0
 H0I  CONST_10  C21   C20  C19  C18     0.00   0.0  0
 H0I  CONST_11  C28   C17  C18  C19     0.00   0.0  0
 H0I  CONST_12  C28   C21  C20  C19     0.00   0.0  0
 H0I  CONST_13  C05   N04  C03  C02   180.00   0.0  0
 H0I  CONST_14  C08   C10  C03  C02   180.00   0.0  0
 H0I  CONST_15  N06   C05  N04  C03   180.00   0.0  0
 H0I  CONST_16  N09   C08  C10  C03   180.00   0.0  0
 H0I  CONST_17  O11   C10  C03  N04   180.00   0.0  0
 H0I  CONST_18  N09   C08  N07  C05   180.00   0.0  0
 H0I  CONST_19  C08   N07  C05  N06   180.00   0.0  0
 H0I  CONST_20  O11   C10  C08  N07   180.00   0.0  0
 H0I  CONST_21  C19   C18  C17  O16   180.00   0.0  0
 H0I  CONST_22  C21   C28  C17  O16   180.00   0.0  0
 H0I  CONST_23  C22   C21  C28  C17   180.00   0.0  0
 H0I  CONST_24  C22   C21  C20  C19   180.00   0.0  0
 H0I  CONST_25  H191  C19  C18  C17   180.00   0.0  0
 H0I  CONST_26  H281  C28  C17  C18   180.00   0.0  0
 H0I  CONST_27  H201  C20  C19  C18   180.00   0.0  0
 H0I  CONST_28  H181  C18  C19  C20   180.00   0.0  0
 H0I  CONST_29  H281  C28  C21  C20   180.00   0.0  0
 H0I  CONST_30  H191  C19  C20  C21   180.00   0.0  0
 H0I  CONST_31  H201  C20  C21  C28   180.00   0.0  0
 H0I  CONST_32  H181  C18  C17  C28   180.00   0.0  0
 H0I  CONST_37  H092  N09  C08  N07     0.00   0.0  0
 H0I  CONST_39  H092  N09  C08  C10   180.00   0.0  0
 H0I  Var_01    N04   C03  C02  C01    69.92  30.0  1
 H0I  Var_02    C10   C03  C02  C01  -109.40  30.0  1
 H0I  Var_03    C12   O11  C10  C03    84.60  30.0  2
 H0I  Var_04    C12   O11  C10  C08   -95.71  30.0  2
 H0I  Var_05    C18   C17  O16  C15   -23.53  30.0  2
 H0I  Var_06    C28   C17  O16  C15   156.38  30.0  2
 H0I  Var_07    C23   C22  C21  C20    84.55  30.0  2
 H0I  Var_08    C28   C21  C22  C23   -91.70  30.0  2
 H0I  Var_09    H021  C02  C03  N04   -50.30  30.0  2
 H0I  Var_10    H022  C02  C03  N04  -166.90  30.0  2
 H0I  Var_11    H021  C02  C03  C10   130.37  30.0  2
 H0I  Var_12    H022  C02  C03  C10    13.77  30.0  2
 H0I  Var_13    H221  C22  C21  C20   -36.86  30.0  2
 H0I  Var_14    H222  C22  C21  C20  -154.20  30.0  2
 H0I  Var_15    H221  C22  C21  C28   146.89  30.0  2
 H0I  Var_16    H222  C22  C21  C28    29.56  30.0  2
 H0I  Var_17    C13   C12  O11  C10   165.60  30.0  2
 H0I  Var_18    C17   O16  C15  C14  -160.23  30.0  1
 H0I  Var_19    C24   C23  C22  C21   176.54  30.0  2
 H0I  Var_20    H012  C01  C02  C03  -178.42  30.0  3
 H0I  Var_21    H011  C01  C02  C03   -58.45  30.0  3
 H0I  Var_22    H013  C01  C02  C03    62.05  30.0  3
 H0I  Var_23    H121  C12  O11  C10   -72.10  30.0  2
 H0I  Var_24    H122  C12  O11  C10    45.16  30.0  2
 H0I  Var_25    H152  C15  O16  C17    78.62  30.0  3
 H0I  Var_26    H151  C15  O16  C17   -39.48  30.0  3
 H0I  Var_27    H231  C23  C22  C21   -61.37  30.0  2
 H0I  Var_28    H232  C23  C22  C21    54.12  30.0  2
 H0I  Var_29    C14   C13  C12  O11    55.42  30.0  1
 H0I  Var_30    C15   C14  C13  C12    44.92  30.0  2
 H0I  Var_31    O16   C15  C14  C13    51.40  30.0  1
 H0I  Var_32    C25   C24  C23  C22   -68.16  30.0  1
 H0I  Var_33    O26   C25  C24  C23   157.66  30.0  2
 H0I  Var_34    O27   C25  C24  C23   -24.36  30.0  2
 H0I  Var_35    H132  C13  C12  O11   178.16  30.0  1
 H0I  Var_36    H131  C13  C12  O11   -67.95  30.0  1
 H0I  Var_37    H142  C14  C13  C12   168.72  30.0  2
 H0I  Var_38    H141  C14  C13  C12   -75.77  30.0  2
 H0I  Var_39    H152  C15  C14  C13   173.07  30.0  1
 H0I  Var_40    H151  C15  C14  C13   -69.29  30.0  1
 H0I  Var_41    H121  C12  C13  C14   -66.02  30.0  3
 H0I  Var_42    H122  C12  C13  C14   176.36  30.0  3
 H0I  Var_43    H132  C13  C14  C15   -75.96  30.0  3
 H0I  Var_44    H131  C13  C14  C15   168.68  30.0  3
 H0I  Var_45    H142  C14  C15  O16   -71.64  30.0  3
 H0I  Var_46    H141  C14  C15  O16   174.07  30.0  3
 H0I  Var_47    H242  C24  C23  C22    56.39  30.0  1
 H0I  Var_48    H241  C24  C23  C22   171.22  30.0  1
 H0I  Var_49    H221  C22  C23  C24   -61.61  30.0  3
 H0I  Var_50    H222  C22  C23  C24    55.00  30.0  3
 H0I  Var_51    H231  C23  C24  C25   170.42  30.0  3
 H0I  Var_52    H232  C23  C24  C25    53.97  30.0  3
 H0I  Var_53    H242  C24  C25  O26    32.79  30.0  3
 H0I  Var_54    H241  C24  C25  O26   -80.76  30.0  3
 H0I  Var_55    H242  C24  C25  O27  -149.22  30.0  3
 H0I  Var_56    H241  C24  C25  O27    97.22  30.0  3

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
 H0I  plan-1  C02   0.020
 H0I  plan-1  C03   0.020
 H0I  plan-1  N04   0.020
 H0I  plan-1  C05   0.020
 H0I  plan-1  N06   0.020
 H0I  plan-1  N07   0.020
 H0I  plan-1  C08   0.020
 H0I  plan-1  N09   0.020
 H0I  plan-1  C10   0.020
 H0I  plan-1  O11   0.020
 H0I  plan-2  O16   0.020
 H0I  plan-2  C17   0.020
 H0I  plan-2  C18   0.020
 H0I  plan-2  C19   0.020
 H0I  plan-2  C20   0.020
 H0I  plan-2  C21   0.020
 H0I  plan-2  C22   0.020
 H0I  plan-2  C28   0.020
 H0I  plan-2  H181  0.020
 H0I  plan-2  H191  0.020
 H0I  plan-2  H201  0.020
 H0I  plan-2  H281  0.020
 H0I  plan-3  C05   0.020
 H0I  plan-3  N06   0.020
 H0I  plan-3  H062  0.020
 H0I  plan-3  H061  0.020
 H0I  plan-4  C08   0.020
 H0I  plan-4  N09   0.020
 H0I  plan-4  H092  0.020
 H0I  plan-4  H091  0.020
 H0I  plan-5  C24   0.020
 H0I  plan-5  C25   0.020
 H0I  plan-5  O26   0.020
 H0I  plan-5  O27   0.020

