# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:54:49 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}pyridin-3-yl)propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCCCOc2ncccc2CCCO
#
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
 HIK  HIK  "3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}pyridin-3-yl)propan-1-ol"
  ligand  50  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_HIK
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
 HIK  C14   C  CH2   0  -0.176   8.3528  -0.2866  13.6869
 HIK  C13   C  CH2   0  -0.503   8.8136   0.7378  12.6705
 HIK  C12   C  CH2   0  -0.174   8.5543   2.1738  13.0767
 HIK  C16   C  CR6   0   0.509   6.3016  -0.8203  14.7790
 HIK  C17   C  CR6   0  -0.049   4.9006  -0.6764  14.8279
 HIK  C10   C  CR6   0   0.126   9.0355   3.6573  14.8404
 HIK  C01   C  CH3   0  -0.670   5.8333   2.7667  15.9378
 HIK  C03   C  CR6   0   0.224   8.1088   3.8159  15.8482
 HIK  C05   C  CR6   0   0.508   8.5824   6.0372  15.9427
 HIK  C08   C  CR6   0   0.431   9.7529   4.8064  14.4392
 HIK  C19   C  CH2   0  -0.457   3.9026  -0.7106  12.5015
 HIK  C20   C  CH2   0  -0.155   3.0837  -1.9713  12.6943
 HIK  C22   C  CR16  0  -0.182   4.2641  -1.3184  15.8725
 HIK  C23   C  CR16  0  -0.345   4.9904  -2.0608  16.8031
 HIK  C24   C  CR16  0  -0.071   6.3560  -2.1317  16.6396
 HIK  N04   N  N     0  -0.498   7.8795   5.0112  16.4068
 HIK  N06   N  NH2   0  -0.825   8.3069   7.2640  16.4596
 HIK  N07   N  N     0  -0.500   9.5187   5.9886  14.9940
 HIK  N09   N  NH2   0  -0.823  10.6822   4.7342  13.4637
 HIK  N25   N  N     0  -0.466   7.0006  -1.5217  15.6438
 HIK  O11   O  O2    0  -0.495   9.3052   2.4523  14.2583
 HIK  O15   O  O2    0  -0.477   6.9345  -0.1924  13.7827
 HIK  O21   O  OH1   0  -0.668   1.8147  -1.6287  13.2112
 HIK  H142  H  HCH2  0   0.237   8.6377  -1.2937  13.3693
 HIK  H141  H  HCH2  0   0.230   8.8170  -0.1090  14.6584
 HIK  H132  H  HCH2  0   0.246   8.3257   0.5579  11.7092
 HIK  H131  H  HCH2  0   0.246   9.8835   0.5901  12.5025
 HIK  H122  H  HCH2  0   0.227   7.4878   2.3400  13.2590
 HIK  H121  H  HCH2  0   0.231   8.8545   2.8486  12.2678
 HIK  H182  H  HCH2  0   0.250   4.6744   1.0097  13.5303
 HIK  H181  H  HCH2  0   0.244   3.1842   0.4028  14.2057
 HIK  H012  H  HCH3  0   0.235   5.2543   1.9407  16.3507
 HIK  H011  H  HCH3  0   0.230   5.3803   3.6991  16.2742
 HIK  H013  H  HCH3  0   0.232   5.7436   2.7227  14.8520
 HIK  H021  H  HCH2  0   0.247   7.3405   2.7027  17.4691
 HIK  H022  H  HCH2  0   0.251   7.7153   1.7181  16.0698
 HIK  H192  H  HCH2  0   0.232   3.4069  -0.0651  11.7708
 HIK  H191  H  HCH2  0   0.230   4.8593  -0.9954  12.0575
 HIK  H202  H  HCH2  0   0.203   2.9955  -2.4835  11.7272
 HIK  H201  H  HCH2  0   0.193   3.6155  -2.6582  13.3652
 HIK  H221  H  HCR6  0   0.260   3.1869  -1.2408  15.9610
 HIK  H231  H  HCR6  0   0.259   4.5032  -2.5672  17.6245
 HIK  H241  H  HCR6  0   0.257   6.9699  -2.6988  17.3301
 HIK  H062  H  HNH2  0   0.384   7.8166   7.2915  17.3374
 HIK  H061  H  HNH2  0   0.384   8.9940   7.9861  16.3249
 HIK  H092  H  HNH2  0   0.391  11.2988   5.5210  13.3473
 HIK  H091  H  HNH2  0   0.399  11.0634   3.8364  13.2178
 HIK  H211  H  HOH1  0   0.450   1.3319  -2.4414  13.3854
 HIK  C02   C  CH2   0  -0.507   7.2924   2.6737  16.3781
 HIK  C18   C  CH2   0  -0.505   4.1422   0.0920  13.7863

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
 HIK  C02  C01   single    1.527  0.020  1.527
 HIK  C03  C02   single    1.501  0.020  1.501
 HIK  N04  C03   aromatic  1.339  0.020  1.339
 HIK  C05  N04   aromatic  1.327  0.020  1.327
 HIK  N06  C05   single    1.359  0.020  1.359
 HIK  N07  C05   aromatic  1.334  0.020  1.334
 HIK  C08  N07   aromatic  1.327  0.020  1.327
 HIK  N09  C08   single    1.349  0.020  1.349
 HIK  C10  C08   aromatic  1.413  0.020  1.413
 HIK  O11  C10   single    1.365  0.020  1.365
 HIK  C12  O11   single    1.427  0.020  1.427
 HIK  C13  C12   single    1.515  0.020  1.515
 HIK  C14  C13   single    1.515  0.020  1.515
 HIK  O15  C14   single    1.425  0.020  1.425
 HIK  C16  O15   single    1.337  0.020  1.337
 HIK  C17  C16   aromatic  1.409  0.020  1.409
 HIK  C19  C18   single    1.534  0.020  1.534
 HIK  C20  C19   single    1.516  0.020  1.516
 HIK  O21  C20   single    1.412  0.020  1.412
 HIK  C18  C17   single    1.500  0.020  1.500
 HIK  C22  C17   aromatic  1.381  0.020  1.381
 HIK  C23  C22   aromatic  1.394  0.020  1.394
 HIK  C24  C23   aromatic  1.377  0.020  1.377
 HIK  N25  C24   aromatic  1.334  0.020  1.334
 HIK  C03  C10   aromatic  1.378  0.020  1.378
 HIK  C16  N25   aromatic  1.315  0.020  1.315
 HIK  C14  H142  single    0.970  0.020  1.090
 HIK  C14  H141  single    0.970  0.020  1.090
 HIK  C13  H132  single    0.970  0.020  1.090
 HIK  C13  H131  single    0.970  0.020  1.090
 HIK  C12  H122  single    0.970  0.020  1.090
 HIK  C12  H121  single    0.970  0.020  1.090
 HIK  C18  H182  single    0.970  0.020  1.090
 HIK  C18  H181  single    0.970  0.020  1.090
 HIK  C01  H012  single    0.970  0.020  1.090
 HIK  C01  H011  single    0.970  0.020  1.090
 HIK  C01  H013  single    0.970  0.020  1.090
 HIK  C02  H021  single    0.970  0.020  1.090
 HIK  C02  H022  single    0.970  0.020  1.090
 HIK  C19  H192  single    0.970  0.020  1.090
 HIK  C19  H191  single    0.970  0.020  1.090
 HIK  C20  H202  single    0.970  0.020  1.090
 HIK  C20  H201  single    0.970  0.020  1.090
 HIK  C22  H221  single    0.930  0.020  1.080
 HIK  C23  H231  single    0.930  0.020  1.080
 HIK  C24  H241  single    0.930  0.020  1.080
 HIK  N06  H062  single    0.890  0.020  1.040
 HIK  N06  H061  single    0.890  0.020  1.040
 HIK  N09  H092  single    0.890  0.020  1.040
 HIK  N09  H091  single    0.890  0.020  1.040
 HIK  O21  H211  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
 HIK  H141  C14  H142  107.31  3.000
 HIK  H141  C14  O15   110.66  3.000
 HIK  H142  C14  O15   109.86  3.000
 HIK  H141  C14  C13   110.97  3.000
 HIK  H142  C14  C13   110.40  3.000
 HIK  O15   C14  C13   107.65  3.000
 HIK  H131  C13  H132  106.23  3.000
 HIK  H131  C13  C12   109.69  3.000
 HIK  H132  C13  C12   108.39  3.000
 HIK  H131  C13  C14   108.03  3.000
 HIK  H132  C13  C14   110.06  3.000
 HIK  C12   C13  C14   114.15  3.000
 HIK  H121  C12  H122  107.25  3.000
 HIK  H121  C12  O11   110.30  3.000
 HIK  H122  C12  O11   110.18  3.000
 HIK  H121  C12  C13   109.82  3.000
 HIK  H122  C12  C13   110.82  3.000
 HIK  O11   C12  C13   108.47  3.000
 HIK  O15   C16  N25   119.28  3.000
 HIK  N25   C16  C17   124.07  3.000
 HIK  O15   C16  C17   116.65  3.000
 HIK  C22   C17  C16   115.90  3.000
 HIK  C22   C17  C18   122.01  3.000
 HIK  C16   C17  C18   122.06  3.000
 HIK  O11   C10  C08   119.77  3.000
 HIK  O11   C10  C03   123.10  3.000
 HIK  C08   C10  C03   117.10  3.000
 HIK  H013  C01  H011  107.92  3.000
 HIK  H013  C01  H012  107.63  3.000
 HIK  H011  C01  H012  108.09  3.000
 HIK  H013  C01  C02   111.30  3.000
 HIK  H011  C01  C02   111.12  3.000
 HIK  H012  C01  C02   110.63  3.000
 HIK  N04   C03  C02   116.04  3.000
 HIK  N04   C03  C10   121.52  3.000
 HIK  C02   C03  C10   122.44  3.000
 HIK  N07   C05  N06   116.46  3.000
 HIK  N07   C05  N04   126.32  3.000
 HIK  N06   C05  N04   117.21  3.000
 HIK  N09   C08  N07   118.13  3.000
 HIK  N09   C08  C10   120.77  3.000
 HIK  N07   C08  C10   121.09  3.000
 HIK  H191  C19  H192  106.21  3.000
 HIK  H191  C19  C20   107.94  3.000
 HIK  H192  C19  C20   109.34  3.000
 HIK  H191  C19  C18   109.88  3.000
 HIK  H192  C19  C18   108.76  3.000
 HIK  C20   C19  C18   114.40  3.000
 HIK  H201  C20  H202  106.58  3.000
 HIK  H201  C20  O21   111.31  3.000
 HIK  H202  C20  O21   111.30  3.000
 HIK  H201  C20  C19   109.67  3.000
 HIK  H202  C20  C19   108.63  3.000
 HIK  O21   C20  C19   109.28  3.000
 HIK  H221  C22  C23   120.09  3.000
 HIK  H221  C22  C17   119.11  3.000
 HIK  C23   C22  C17   120.80  3.000
 HIK  H231  C23  C24   120.86  3.000
 HIK  H231  C23  C22   121.46  3.000
 HIK  C24   C23  C22   117.68  3.000
 HIK  H241  C24  N25   116.17  3.000
 HIK  H241  C24  C23   120.85  3.000
 HIK  N25   C24  C23   122.98  3.000
 HIK  C05   N04  C03   116.96  3.000
 HIK  H061  N06  H062  115.49  3.000
 HIK  H061  N06  C05   117.29  3.000
 HIK  H062  N06  C05   117.08  3.000
 HIK  C08   N07  C05   116.98  3.000
 HIK  H091  N09  H092  115.94  3.000
 HIK  H091  N09  C08   119.04  3.000
 HIK  H092  N09  C08   117.63  3.000
 HIK  C24   N25  C16   118.56  3.000
 HIK  C10   O11  C12   114.91  3.000
 HIK  C16   O15  C14   119.36  3.000
 HIK  H211  O21  C20   108.21  3.000
 HIK  H022  C02  H021  106.79  3.000
 HIK  H022  C02  C03   110.88  3.000
 HIK  H021  C02  C03   107.97  3.000
 HIK  H022  C02  C01   110.05  3.000
 HIK  H021  C02  C01   109.17  3.000
 HIK  C03   C02  C01   111.82  3.000
 HIK  H181  C18  H182  106.19  3.000
 HIK  H181  C18  C19   109.51  3.000
 HIK  H182  C18  C19   108.64  3.000
 HIK  H181  C18  C17   108.84  3.000
 HIK  H182  C18  C17   110.31  3.000
 HIK  C19   C18  C17   113.11  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
 HIK  CONST_01  C23   C22  C17  C16     0.00   0.0  0
 HIK  CONST_02  C23   C24  N25  C16     0.00   0.0  0
 HIK  CONST_03  C24   N25  C16  C17     0.00   0.0  0
 HIK  CONST_04  C24   C23  C22  C17     0.00   0.0  0
 HIK  CONST_05  C05   N07  C08  C10     0.00   0.0  0
 HIK  CONST_06  C05   N04  C03  C10     0.00   0.0  0
 HIK  CONST_07  N07   C05  N04  C03     0.00   0.0  0
 HIK  CONST_08  N07   C08  C10  C03     0.00   0.0  0
 HIK  CONST_09  N04   C05  N07  C08     0.00   0.0  0
 HIK  CONST_10  N04   C03  C10  C08     0.00   0.0  0
 HIK  CONST_11  N25   C16  C17  C22     0.00   0.0  0
 HIK  CONST_12  N25   C24  C23  C22     0.00   0.0  0
 HIK  CONST_13  N25   C16  C17  C18   180.00   0.0  0
 HIK  CONST_14  C23   C22  C17  C18   180.00   0.0  0
 HIK  CONST_15  C05   N04  C03  C02   180.00   0.0  0
 HIK  CONST_16  C08   C10  C03  C02   180.00   0.0  0
 HIK  CONST_17  N06   C05  N04  C03   180.00   0.0  0
 HIK  CONST_18  N09   C08  C10  C03   180.00   0.0  0
 HIK  CONST_19  N09   C08  N07  C05   180.00   0.0  0
 HIK  CONST_20  N06   C05  N07  C08   180.00   0.0  0
 HIK  CONST_21  O15   C16  C17  C22   180.00   0.0  0
 HIK  CONST_22  O15   C16  N25  C24   180.00   0.0  0
 HIK  CONST_23  O11   C10  C03  N04   180.00   0.0  0
 HIK  CONST_24  O11   C10  C08  N07   180.00   0.0  0
 HIK  CONST_25  H221  C22  C17  C16   180.00   0.0  0
 HIK  CONST_26  H241  C24  N25  C16   180.00   0.0  0
 HIK  CONST_27  H231  C23  C22  C17   180.00   0.0  0
 HIK  CONST_28  H241  C24  C23  C22   180.00   0.0  0
 HIK  CONST_29  H221  C22  C23  C24   180.00   0.0  0
 HIK  CONST_30  H231  C23  C24  N25   180.00   0.0  0
 HIK  CONST_31  H092  N09  C08  C10   180.00   0.0  0
 HIK  CONST_37  H092  N09  C08  N07     0.00   0.0  0
 HIK  Var_01    C17   C16  O15  C14   179.31  30.0  1
 HIK  Var_02    N25   C16  O15  C14    -0.57  30.0  1
 HIK  Var_03    C08   C10  O11  C12   -88.66  30.0  2
 HIK  Var_04    C03   C10  O11  C12    93.32  30.0  2
 HIK  Var_05    C19   C18  C17  C16    79.98  30.0  2
 HIK  Var_06    C01   C02  C03  C10  -107.78  30.0  2
 HIK  Var_07    N04   C03  C02  C01    71.77  30.0  2
 HIK  Var_08    C22   C17  C18  C19   -98.12  30.0  2
 HIK  Var_09    H182  C18  C17  C16   -41.93  30.0  2
 HIK  Var_10    H181  C18  C17  C16  -158.06  30.0  2
 HIK  Var_11    H021  C02  C03  C10   132.10  30.0  2
 HIK  Var_12    H022  C02  C03  C10    15.44  30.0  2
 HIK  Var_13    H182  C18  C17  C22   139.97  30.0  2
 HIK  Var_14    H181  C18  C17  C22    23.84  30.0  2
 HIK  Var_15    H021  C02  C03  N04   -48.34  30.0  2
 HIK  Var_16    H022  C02  C03  N04  -165.00  30.0  2
 HIK  Var_17    C10   O11  C12  C13  -171.85  30.0  3
 HIK  Var_18    C16   O15  C14  C13  -168.19  30.0  2
 HIK  Var_19    C20   C19  C18  C17    61.21  30.0  1
 HIK  Var_20    H142  C14  O15  C16    71.55  30.0  3
 HIK  Var_21    H141  C14  O15  C16   -46.76  30.0  3
 HIK  Var_22    H192  C19  C18  C17  -176.24  30.0  1
 HIK  Var_23    H191  C19  C18  C17   -60.37  30.0  1
 HIK  Var_24    H122  C12  O11  C10   -50.38  30.0  1
 HIK  Var_25    H121  C12  O11  C10    67.84  30.0  1
 HIK  Var_26    H012  C01  C02  C03  -178.77  30.0  3
 HIK  Var_27    H011  C01  C02  C03   -58.69  30.0  3
 HIK  Var_28    H013  C01  C02  C03    61.62  30.0  3
 HIK  Var_29    O11   C12  C13  C14    62.99  30.0  3
 HIK  Var_30    O15   C14  C13  C12    64.43  30.0  1
 HIK  Var_31    O21   C20  C19  C18    60.02  30.0  2
 HIK  Var_32    H122  C12  C13  C14   -58.09  30.0  3
 HIK  Var_33    H121  C12  C13  C14  -176.40  30.0  3
 HIK  Var_34    H142  C14  C13  C12  -175.65  30.0  1
 HIK  Var_35    H141  C14  C13  C12   -56.80  30.0  1
 HIK  Var_36    H202  C20  C19  C18  -178.38  30.0  2
 HIK  Var_37    H201  C20  C19  C18   -62.25  30.0  2
 HIK  Var_38    H182  C18  C19  C20  -175.95  30.0  3
 HIK  Var_39    H181  C18  C19  C20   -60.38  30.0  3
 HIK  Var_40    H132  C13  C12  O11  -173.98  30.0  1
 HIK  Var_41    H131  C13  C12  O11   -58.39  30.0  1
 HIK  Var_42    H132  C13  C14  O15   -57.69  30.0  3
 HIK  Var_43    H131  C13  C14  O15  -173.27  30.0  3
 HIK  Var_44    H192  C19  C20  O21   -62.22  30.0  3
 HIK  Var_45    H191  C19  C20  O21  -177.34  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
 HIK  plan-1  C16   0.020
 HIK  plan-1  C17   0.020
 HIK  plan-1  C22   0.020
 HIK  plan-1  C23   0.020
 HIK  plan-1  C24   0.020
 HIK  plan-1  N25   0.020
 HIK  plan-1  O15   0.020
 HIK  plan-1  H221  0.020
 HIK  plan-1  H231  0.020
 HIK  plan-1  H241  0.020
 HIK  plan-1  C18   0.020
 HIK  plan-2  C10   0.020
 HIK  plan-2  C03   0.020
 HIK  plan-2  C05   0.020
 HIK  plan-2  C08   0.020
 HIK  plan-2  N04   0.020
 HIK  plan-2  N06   0.020
 HIK  plan-2  N07   0.020
 HIK  plan-2  N09   0.020
 HIK  plan-2  O11   0.020
 HIK  plan-2  C02   0.020
 HIK  plan-3  C05   0.020
 HIK  plan-3  N06   0.020
 HIK  plan-3  H062  0.020
 HIK  plan-3  H061  0.020
 HIK  plan-4  C08   0.020
 HIK  plan-4  N09   0.020
 HIK  plan-4  H092  0.020
 HIK  plan-4  H091  0.020

