# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 11:51:12 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: (2E)-3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}pyridin-3-yl)prop-2-en-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2ncccc2/C=C/CO
#
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
 HI9  HI9  "(2E)-3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}pyridin-3-yl)prop-2-en-1-ol"
  ligand  48  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HI9
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
 HI9  C10   C  CR6   0   0.128   8.6993   3.5165  14.8633
 HI9  C12   C  CH2   0  -0.174   8.1903   1.9675  13.1640
 HI9  C13   C  CH2   0  -0.506   8.6282   0.6012  12.6764
 HI9  C14   C  CH2   0  -0.170   8.4547  -0.5210  13.6802
 HI9  C01   C  CH3   0  -0.665   5.1830   3.4862  15.3929
 HI9  C02   C  CH2   0  -0.504   6.5012   3.0159  16.0049
 HI9  C03   C  CR6   0   0.229   7.6378   3.9262  15.6395
 HI9  C05   C  CR6   0   0.506   8.5399   6.0098  15.7786
 HI9  C08   C  CR6   0   0.434   9.6980   4.4752  14.5770
 HI9  C16   C  CR6   0   0.493   6.6796  -1.4270  14.9839
 HI9  C18   C  CR16  0  -0.065   7.1627  -3.1257  16.4282
 HI9  C19   C  CR16  0  -0.341   5.8757  -3.1566  16.9202
 HI9  C20   C  CR16  0  -0.202   4.9608  -2.2556  16.3879
 HI9  C21   C  CR6   0  -0.018   5.3245  -1.3644  15.3860
 HI9  C22   C  C1    0  -0.277   4.3126  -0.4455  14.8635
 HI9  C23   C  C1    0  -0.296   4.3240   0.2613  13.7302
 HI9  C24   C  CH2   0  -0.181   3.2202   1.1532  13.2773
 HI9  N04   N  N     0  -0.500   7.5579   5.1797  16.1059
 HI9  N06   N  NH2   0  -0.825   8.4343   7.2960  16.2074
 HI9  N07   N  N     0  -0.501   9.6108   5.7159  15.0394
 HI9  N09   N  NH2   0  -0.823  10.7563   4.1542  13.8088
 HI9  N17   N  N     0  -0.458   7.5541  -2.2715  15.4838
 HI9  O11   O  O2    0  -0.497   8.8543   2.2437  14.3939
 HI9  O15   O  O2    0  -0.474   7.0814  -0.5634  14.0523
 HI9  O25   O  OH1   0  -0.661   2.2143   1.2583  14.2489
 HI9  H121  H  HCH2  0   0.229   7.1050   2.0060  13.3065
 HI9  H122  H  HCH2  0   0.233   8.4451   2.7233  12.4128
 HI9  H132  H  HCH2  0   0.246   8.0755   0.3752  11.7609
 HI9  H131  H  HCH2  0   0.247   9.6851   0.6295  12.3987
 HI9  H142  H  HCH2  0   0.237   8.7562  -1.4712  13.2319
 HI9  H141  H  HCH2  0   0.228   9.0813  -0.3626  14.5600
 HI9  H012  H  HCH3  0   0.233   4.3675   2.8219  15.6768
 HI9  H011  H  HCH3  0   0.228   4.9333   4.4927  15.7257
 HI9  H013  H  HCH3  0   0.225   5.2371   3.4950  14.3031
 HI9  H021  H  HCH2  0   0.249   6.4096   3.0078  17.0942
 HI9  H022  H  HCH2  0   0.243   6.7070   1.9906  15.6992
 HI9  H181  H  HCR6  0   0.261   7.9193  -3.8057  16.8028
 HI9  H191  H  HCR6  0   0.263   5.5925  -3.8563  17.6936
 HI9  H201  H  HCR6  0   0.268   3.9402  -2.2445  16.7522
 HI9  H221  H  H     0   0.247   3.4316  -0.3791  15.4939
 HI9  H231  H  H     0   0.264   5.1580   0.2126  13.0436
 HI9  H241  H  HCH2  0   0.214   3.6560   2.1330  13.0329
 HI9  H242  H  HCH2  0   0.219   2.8311   0.7591  12.3261
 HI9  H062  H  HNH2  0   0.383   7.7953   7.4724  16.9639
 HI9  H061  H  HNH2  0   0.383   9.2739   7.8499  16.2136
 HI9  H092  H  HNH2  0   0.391  11.5264   4.7999  13.7644
 HI9  H091  H  HNH2  0   0.399  10.9689   3.1871  13.6349
 HI9  H251  H  HOH1  0   0.459   1.5174   1.8222  13.9022

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
 HI9  C02  C01   single    1.528  0.020  1.528
 HI9  C03  C02   single    1.501  0.020  1.501
 HI9  N04  C03   aromatic  1.340  0.020  1.340
 HI9  C05  N04   aromatic  1.327  0.020  1.327
 HI9  N06  C05   single    1.360  0.020  1.360
 HI9  N07  C05   aromatic  1.334  0.020  1.334
 HI9  C08  N07   aromatic  1.327  0.020  1.327
 HI9  N09  C08   single    1.347  0.020  1.347
 HI9  C10  C08   aromatic  1.414  0.020  1.414
 HI9  O11  C10   single    1.365  0.020  1.365
 HI9  C12  O11   single    1.425  0.020  1.425
 HI9  C13  C12   single    1.515  0.020  1.515
 HI9  C14  C13   single    1.516  0.020  1.516
 HI9  O15  C14   single    1.423  0.020  1.423
 HI9  C16  O15   single    1.332  0.020  1.332
 HI9  N17  C16   aromatic  1.314  0.020  1.314
 HI9  C18  N17   aromatic  1.332  0.020  1.332
 HI9  C19  C18   aromatic  1.378  0.020  1.378
 HI9  C20  C19   aromatic  1.390  0.020  1.390
 HI9  C21  C20   aromatic  1.389  0.020  1.389
 HI9  C22  C21   single    1.463  0.020  1.463
 HI9  C23  C22   double    1.336  0.020  1.336
 HI9  C24  C23   single    1.490  0.020  1.490
 HI9  O25  C24   single    1.403  0.020  1.403
 HI9  C03  C10   aromatic  1.377  0.020  1.377
 HI9  C16  C21   aromatic  1.415  0.020  1.415
 HI9  C12  H121  single    0.970  0.020  1.090
 HI9  C12  H122  single    0.970  0.020  1.090
 HI9  C13  H132  single    0.970  0.020  1.090
 HI9  C13  H131  single    0.970  0.020  1.090
 HI9  C14  H142  single    0.970  0.020  1.090
 HI9  C14  H141  single    0.970  0.020  1.090
 HI9  C01  H012  single    0.970  0.020  1.090
 HI9  C01  H011  single    0.970  0.020  1.090
 HI9  C01  H013  single    0.970  0.020  1.090
 HI9  C02  H021  single    0.970  0.020  1.090
 HI9  C02  H022  single    0.970  0.020  1.090
 HI9  C18  H181  single    0.930  0.020  1.080
 HI9  C19  H191  single    0.930  0.020  1.080
 HI9  C20  H201  single    0.930  0.020  1.080
 HI9  C22  H221  single    0.930  0.020  1.080
 HI9  C23  H231  single    0.930  0.020  1.080
 HI9  C24  H241  single    0.970  0.020  1.090
 HI9  C24  H242  single    0.970  0.020  1.090
 HI9  N06  H062  single    0.890  0.020  1.040
 HI9  N06  H061  single    0.890  0.020  1.040
 HI9  N09  H092  single    0.890  0.020  1.040
 HI9  N09  H091  single    0.890  0.020  1.040
 HI9  O25  H251  single    0.850  0.020  0.980

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
 HI9  O11   C10  C08   118.84  3.000
 HI9  O11   C10  C03   123.95  3.000
 HI9  C08   C10  C03   117.18  3.000
 HI9  H122  C12  H121  107.18  3.000
 HI9  H122  C12  O11   110.48  3.000
 HI9  H121  C12  O11   110.04  3.000
 HI9  H122  C12  C13   109.52  3.000
 HI9  H121  C12  C13   111.09  3.000
 HI9  O11   C12  C13   108.54  3.000
 HI9  H131  C13  H132  106.35  3.000
 HI9  H131  C13  C14   107.34  3.000
 HI9  H132  C13  C14   110.10  3.000
 HI9  H131  C13  C12   109.74  3.000
 HI9  H132  C13  C12   108.05  3.000
 HI9  C14   C13  C12   114.92  3.000
 HI9  H141  C14  H142  107.36  3.000
 HI9  H141  C14  O15   110.33  3.000
 HI9  H142  C14  O15   110.33  3.000
 HI9  H141  C14  C13   111.14  3.000
 HI9  H142  C14  C13   109.90  3.000
 HI9  O15   C14  C13   107.80  3.000
 HI9  H013  C01  H011  108.00  3.000
 HI9  H013  C01  H012  107.59  3.000
 HI9  H011  C01  H012  108.20  3.000
 HI9  H013  C01  C02   111.09  3.000
 HI9  H011  C01  C02   111.09  3.000
 HI9  H012  C01  C02   110.72  3.000
 HI9  H022  C02  H021  106.77  3.000
 HI9  H022  C02  C03   111.05  3.000
 HI9  H021  C02  C03   108.09  3.000
 HI9  H022  C02  C01   109.89  3.000
 HI9  H021  C02  C01   109.23  3.000
 HI9  C03   C02  C01   111.66  3.000
 HI9  N04   C03  C02   115.93  3.000
 HI9  N04   C03  C10   121.36  3.000
 HI9  C02   C03  C10   122.70  3.000
 HI9  N07   C05  N06   116.45  3.000
 HI9  N07   C05  N04   126.37  3.000
 HI9  N06   C05  N04   117.15  3.000
 HI9  N09   C08  N07   118.25  3.000
 HI9  N09   C08  C10   120.60  3.000
 HI9  N07   C08  C10   121.14  3.000
 HI9  O15   C16  N17   118.80  3.000
 HI9  N17   C16  C21   123.88  3.000
 HI9  O15   C16  C21   117.31  3.000
 HI9  H181  C18  N17   116.24  3.000
 HI9  H181  C18  C19   120.96  3.000
 HI9  N17   C18  C19   122.80  3.000
 HI9  H191  C19  C20   121.41  3.000
 HI9  H191  C19  C18   120.98  3.000
 HI9  C20   C19  C18   117.61  3.000
 HI9  H201  C20  C21   118.84  3.000
 HI9  H201  C20  C19   119.86  3.000
 HI9  C21   C20  C19   121.30  3.000
 HI9  C22   C21  C20   118.64  3.000
 HI9  C22   C21  C16   126.06  3.000
 HI9  C20   C21  C16   115.30  3.000
 HI9  H221  C22  C23   117.86  3.000
 HI9  H221  C22  C21   113.10  3.000
 HI9  C23   C22  C21   129.00  3.000
 HI9  H231  C23  C24   113.91  3.000
 HI9  H231  C23  C22   121.43  3.000
 HI9  C24   C23  C22   124.65  3.000
 HI9  H242  C24  H241  105.49  3.000
 HI9  H242  C24  O25   111.84  3.000
 HI9  H241  C24  O25   111.80  3.000
 HI9  H242  C24  C23   108.08  3.000
 HI9  H241  C24  C23   107.90  3.000
 HI9  O25   C24  C23   111.45  3.000
 HI9  C05   N04  C03   117.08  3.000
 HI9  H061  N06  H062  115.41  3.000
 HI9  H061  N06  C05   117.25  3.000
 HI9  H062  N06  C05   116.90  3.000
 HI9  C08   N07  C05   116.86  3.000
 HI9  H091  N09  H092  116.61  3.000
 HI9  H091  N09  C08   119.62  3.000
 HI9  H092  N09  C08   118.28  3.000
 HI9  C18   N17  C16   119.09  3.000
 HI9  C12   O11  C10   115.12  3.000
 HI9  C16   O15  C14   119.53  3.000
 HI9  H251  O25  C24   108.30  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
 HI9  CONST_01  C05   N07  C08  C10      0.00   0.0  0
 HI9  CONST_02  C05   N04  C03  C10      0.00   0.0  0
 HI9  CONST_03  N07   C05  N04  C03      0.00   0.0  0
 HI9  CONST_04  N07   C08  C10  C03      0.00   0.0  0
 HI9  CONST_05  N04   C05  N07  C08      0.00   0.0  0
 HI9  CONST_06  N04   C03  C10  C08      0.00   0.0  0
 HI9  CONST_07  C19   C18  N17  C16      0.00   0.0  0
 HI9  CONST_08  C19   C20  C21  C16      0.00   0.0  0
 HI9  CONST_09  C21   C16  N17  C18      0.00   0.0  0
 HI9  CONST_10  C21   C20  C19  C18      0.00   0.0  0
 HI9  CONST_11  N17   C18  C19  C20      0.00   0.0  0
 HI9  CONST_12  N17   C16  C21  C20      0.00   0.0  0
 HI9  CONST_13  C05   N04  C03  C02    180.00   0.0  0
 HI9  CONST_14  C08   C10  C03  C02    180.00   0.0  0
 HI9  CONST_15  N06   C05  N04  C03    180.00   0.0  0
 HI9  CONST_16  N09   C08  C10  C03    180.00   0.0  0
 HI9  CONST_17  N09   C08  N07  C05    180.00   0.0  0
 HI9  CONST_18  N06   C05  N07  C08    180.00   0.0  0
 HI9  CONST_19  O15   C16  N17  C18    180.00   0.0  0
 HI9  CONST_20  C22   C21  C20  C19    180.00   0.0  0
 HI9  CONST_21  O15   C16  C21  C20    180.00   0.0  0
 HI9  CONST_22  N17   C16  C21  C22    180.00   0.0  0
 HI9  CONST_23  O11   C10  C03  N04    180.00   0.0  0
 HI9  CONST_24  O11   C10  C08  N07    180.00   0.0  0
 HI9  CONST_25  H181  C18  N17  C16    180.00   0.0  0
 HI9  CONST_26  H201  C20  C21  C16    180.00   0.0  0
 HI9  CONST_27  H201  C20  C19  C18    180.00   0.0  0
 HI9  CONST_28  H181  C18  C19  C20    180.00   0.0  0
 HI9  CONST_29  H191  C19  C20  C21    180.00   0.0  0
 HI9  CONST_30  H191  C19  C18  N17    180.00   0.0  0
 HI9  CONST_31  H092  N09  C08  C10    180.00   0.0  0
 HI9  CONST_37  H092  N09  C08  N07      0.00   0.0  0
 HI9  Var_01    C01   C02  C03  C10   -115.07  30.0  2
 HI9  Var_02    C08   C10  O11  C12    -95.87  30.0  2
 HI9  Var_03    C03   C10  O11  C12     86.02  30.0  2
 HI9  Var_04    N17   C16  O15  C14     -3.72  30.0  2
 HI9  Var_05    C21   C16  O15  C14    175.61  30.0  2
 HI9  Var_06    N04   C03  C02  C01     64.38  30.0  2
 HI9  Var_07    C23   C22  C21  C16     18.33  30.0  2
 HI9  Var_08    C23   C22  C21  C20   -162.90  30.0  2
 HI9  Var_09    H021  C02  C03  C10    124.77  30.0  2
 HI9  Var_10    H022  C02  C03  C10      7.96  30.0  2
 HI9  Var_11    H221  C22  C21  C16   -163.85  30.0  2
 HI9  Var_12    H221  C22  C21  C20     14.91  30.0  2
 HI9  Var_13    H021  C02  C03  N04    -55.78  30.0  2
 HI9  Var_14    H022  C02  C03  N04   -172.58  30.0  2
 HI9  Var_15    C24   C23  C22  C21    178.70   0.0  2
 HI9  Var_16    C13   C12  O11  C10    171.47  30.0  2
 HI9  Var_17    C16   O15  C14  C13   -176.55  30.0  1
 HI9  Var_18    H231  C23  C22  C21     -0.24   0.0  2
 HI9  Var_19    H121  C12  O11  C10    -66.77  30.0  2
 HI9  Var_20    H122  C12  O11  C10     51.38  30.0  2
 HI9  Var_21    H012  C01  C02  C03   -179.35  30.0  3
 HI9  Var_22    H011  C01  C02  C03    -59.11  30.0  3
 HI9  Var_23    H013  C01  C02  C03     61.15  30.0  3
 HI9  Var_24    H142  C14  O15  C16     63.44  30.0  3
 HI9  Var_25    H141  C14  O15  C16    -55.03  30.0  3
 HI9  Var_26    O15   C14  C13  C12     57.43  30.0  2
 HI9  Var_27    O11   C12  C13  C14     53.72  30.0  3
 HI9  Var_28    O25   C24  C23  C22      5.51  30.0  1
 HI9  Var_29    H221  C22  C23  C24      0.97   0.0  2
 HI9  Var_30    H142  C14  C13  C12    177.72  30.0  2
 HI9  Var_31    H141  C14  C13  C12    -63.59  30.0  2
 HI9  Var_32    H121  C12  C13  C14    -67.39  30.0  3
 HI9  Var_33    H122  C12  C13  C14    174.40  30.0  3
 HI9  Var_34    H241  C24  C23  C22    128.62  30.0  1
 HI9  Var_35    H242  C24  C23  C22   -117.76  30.0  1
 HI9  Var_36    H132  C13  C12  O11    177.09  30.0  1
 HI9  Var_37    H131  C13  C12  O11    -67.35  30.0  1
 HI9  Var_38    H132  C13  C14  O15    -64.84  30.0  3
 HI9  Var_39    H131  C13  C14  O15    179.80  30.0  3
 HI9  Var_40    H231  C23  C24  O25   -175.48  30.0  3
 HI9  Var_41    H231  C23  C22  H221  -177.97   0.0  2

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
 HI9  plan-1  C10   0.020
 HI9  plan-1  C02   0.020
 HI9  plan-1  C03   0.020
 HI9  plan-1  C05   0.020
 HI9  plan-1  C08   0.020
 HI9  plan-1  N04   0.020
 HI9  plan-1  N06   0.020
 HI9  plan-1  N07   0.020
 HI9  plan-1  N09   0.020
 HI9  plan-1  O11   0.020
 HI9  plan-2  C16   0.020
 HI9  plan-2  C18   0.020
 HI9  plan-2  C19   0.020
 HI9  plan-2  C20   0.020
 HI9  plan-2  C21   0.020
 HI9  plan-2  C22   0.020
 HI9  plan-2  N17   0.020
 HI9  plan-2  O15   0.020
 HI9  plan-2  H181  0.020
 HI9  plan-2  H191  0.020
 HI9  plan-2  H201  0.020
 HI9  plan-3  C05   0.020
 HI9  plan-3  N06   0.020
 HI9  plan-3  H062  0.020
 HI9  plan-3  H061  0.020
 HI9  plan-4  C08   0.020
 HI9  plan-4  N09   0.020
 HI9  plan-4  H092  0.020
 HI9  plan-4  H091  0.020
 HI9  plan-5  C21   0.020
 HI9  plan-5  C22   0.020
 HI9  plan-5  C23   0.020
 HI9  plan-5  C24   0.020
 HI9  plan-5  H221  0.020
 HI9  plan-5  H231  0.020

