# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 14:38:47 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 3-{2-[(3-{[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]methyl}oxetan-3-yl)methoxy]phenyl}propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1OCC2(COC2)COc3ccccc3CCC(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
 H9I  H9I  "3-{2-[(3-{[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]methyl}oxetan-3-yl)methoxy]phenyl}propanoic acid"  ligand  54  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_H9I
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
 H9I  C10   C  CR6    0   0.125   8.6612   3.8717  15.1276
 H9I  C12   C  CH2    0  -0.152   7.9858   2.5226  13.3204
 H9I  C13   C  C      0  -0.253   7.8418   1.0555  12.9791
 H9I  C14   C  CH2    0  -0.172   6.9562   0.3104  13.9575
 H9I  C20   C  C1     0  -0.302   2.4015   0.7366  15.3574
 H9I  C21   C  C      0   0.032   3.4263   1.0618  14.4796
 H9I  C22   C  CH2    0  -0.488   3.1727   1.9471  13.2919
 H9I  C23   C  CH2    0  -0.577   2.9682   1.1400  12.0109
 H9I  C24   C  C      0   0.411   2.6956   1.9648  10.7363
 H9I  C01   C  CH3    0  -0.669   5.2149   4.1972  15.6326
 H9I  C02   C  CH2    0  -0.506   6.4543   3.6401  16.3301
 H9I  C03   C  CR6    0   0.226   7.6949   4.3984  15.9572
 H9I  C05   C  CR6    0   0.509   8.8963   6.3197  16.1403
 H9I  C08   C  CR6    0   0.435   9.7884   4.6774  14.8539
 H9I  C16   C  C      0   0.357   4.6897   0.4918  14.7068
 H9I  C17   C  C1     0  -0.374   4.8928  -0.3858  15.7671
 H9I  C18   C  C1     0  -0.260   3.8419  -0.6928  16.6252
 H9I  C19   C  C1     0  -0.266   2.5932  -0.1300  16.4289
 H9I  C27   C  C      0  -0.118   7.5264   0.7713  11.5029
 H9I  C29   C  C      0  -0.121   9.1560   0.3218  12.6727
 H9I  N04   N  N      0  -0.498   7.8103   5.6299  16.4699
 H9I  N06   N  NH2    0  -0.825   8.9929   7.5898  16.6139
 H9I  N07   N  N      0  -0.500   9.8950   5.8980  15.3630
 H9I  N09   N  NH2    0  -0.826  10.7763   4.2353  14.0500
 H9I  O11   O  O2     0  -0.498   8.5885   2.6107  14.6067
 H9I  O15   O  O2     0  -0.479   5.6600   0.8573  13.8416
 H9I  O25   O  O      0  -0.622   2.4285   1.3018   9.7126
 H9I  O26   O  OC    -1  -0.602   2.7714   3.2065  10.8208
 H9I  O28   O  O      0  -0.501   8.7327   0.0177  11.3398
 H9I  H122  H  HCH2   0   0.243   7.0123   3.0241  13.3137
 H9I  H121  H  HCH2   0   0.233   8.6126   3.0184  12.5692
 H9I  H141  H  HCH2   0   0.241   7.3469   0.4166  14.9750
 H9I  H142  H  HCH2   0   0.240   6.9422  -0.7608  13.7202
 H9I  H201  H  H      0   0.241   1.4235   1.1754  15.1947
 H9I  H221  H  HCH2   0   0.224   2.2811   2.5479  13.4856
 H9I  H222  H  HCH2   0   0.228   3.9899   2.6569  13.1545
 H9I  H232  H  HCH2   0   0.228   3.8454   0.5112  11.8237
 H9I  H231  H  HCH2   0   0.219   2.1417   0.4361  12.1550
 H9I  H012  H  HCH3   0   0.235   4.3235   3.6516  15.9425
 H9I  H011  H  HCH3   0   0.229   5.0694   5.2499  15.8736
 H9I  H013  H  HCH3   0   0.232   5.2961   4.1079  14.5491
 H9I  H021  H  HCH2   0   0.247   6.3239   3.7196  17.4118
 H9I  H022  H  HCH2   0   0.251   6.5634   2.5808  16.1016
 H9I  H171  H  H      0   0.272   5.8590  -0.8409  15.9390
 H9I  H181  H  H      0   0.250   4.0137  -1.3762  17.4468
 H9I  H191  H  H      0   0.244   1.7734  -0.3624  17.0959
 H9I  H272  H  H      0   0.227   6.6278   0.1772  11.3138
 H9I  H271  H  H      0   0.220   7.4977   1.6594  10.8627
 H9I  H291  H  H      0   0.223   9.3546  -0.5755  13.2671
 H9I  H292  H  H      0   0.224  10.0478   0.9571  12.6950
 H9I  H062  H  HNH2   0   0.384   8.4077   7.8343  17.3945
 H9I  H061  H  HNH2   0   0.384   9.9032   8.0175  16.6053
 H9I  H092  H  HNH2   0   0.392  11.6338   4.7614  14.0286
 H9I  H091  H  HNH2   0   0.403  10.8547   3.2514  13.8561

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
 H9I  C02  C01   single    1.527  0.020  1.527
 H9I  C03  C02   single    1.501  0.020  1.501
 H9I  N04  C03   aromatic  1.339  0.020  1.339
 H9I  C05  N04   aromatic  1.328  0.020  1.328
 H9I  N06  C05   single    1.359  0.020  1.359
 H9I  N07  C05   aromatic  1.334  0.020  1.334
 H9I  C08  N07   aromatic  1.327  0.020  1.327
 H9I  N09  C08   single    1.348  0.020  1.348
 H9I  C10  C08   aromatic  1.412  0.020  1.412
 H9I  O11  C10   single    1.366  0.020  1.366
 H9I  C12  O11   single    1.423  0.020  1.423
 H9I  C13  C12   single    1.513  0.020  1.513
 H9I  O15  C14   single    1.412  0.020  1.412
 H9I  C16  O15   single    1.350  0.020  1.350
 H9I  C17  C16   aromatic  1.391  0.020  1.391
 H9I  C18  C17   aromatic  1.391  0.020  1.391
 H9I  C19  C18   aromatic  1.384  0.020  1.384
 H9I  C20  C19   aromatic  1.391  0.020  1.391
 H9I  C21  C20   aromatic  1.388  0.020  1.388
 H9I  C22  C21   single    1.503  0.020  1.503
 H9I  C23  C22   single    1.528  0.020  1.528
 H9I  C24  C23   single    1.542  0.020  1.542
 H9I  O25  C24   deloc     1.249  0.020  1.249
 H9I  O26  C24   deloc     1.247  0.020  1.247
 H9I  C14  C13   single    1.516  0.020  1.516
 H9I  C27  C13   single    1.536  0.020  1.536
 H9I  O28  C27   single    1.432  0.020  1.432
 H9I  C29  O28   single    1.431  0.020  1.431
 H9I  C03  C10   aromatic  1.378  0.020  1.378
 H9I  C13  C29   single    1.536  0.020  1.536
 H9I  C16  C21   aromatic  1.405  0.020  1.405
 H9I  C12  H122  single    0.970  0.020  1.090
 H9I  C12  H121  single    0.970  0.020  1.090
 H9I  C14  H141  single    0.970  0.020  1.090
 H9I  C14  H142  single    0.970  0.020  1.090
 H9I  C20  H201  single    0.930  0.020  1.080
 H9I  C22  H221  single    0.970  0.020  1.090
 H9I  C22  H222  single    0.970  0.020  1.090
 H9I  C23  H232  single    0.970  0.020  1.090
 H9I  C23  H231  single    0.970  0.020  1.090
 H9I  C01  H012  single    0.970  0.020  1.090
 H9I  C01  H011  single    0.970  0.020  1.090
 H9I  C01  H013  single    0.970  0.020  1.090
 H9I  C02  H021  single    0.970  0.020  1.090
 H9I  C02  H022  single    0.970  0.020  1.090
 H9I  C17  H171  single    0.930  0.020  1.080
 H9I  C18  H181  single    0.930  0.020  1.080
 H9I  C19  H191  single    0.930  0.020  1.080
 H9I  C27  H272  single    0.970  0.020  1.090
 H9I  C27  H271  single    0.970  0.020  1.090
 H9I  C29  H291  single    0.970  0.020  1.090
 H9I  C29  H292  single    0.970  0.020  1.090
 H9I  N06  H062  single    0.890  0.020  1.040
 H9I  N06  H061  single    0.890  0.020  1.040
 H9I  N09  H092  single    0.890  0.020  1.040
 H9I  N09  H091  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
 H9I  O11   C10  C08   119.68  3.000
 H9I  O11   C10  C03   123.01  3.000
 H9I  C08   C10  C03   117.28  3.000
 H9I  H121  C12  H122  107.27  3.000
 H9I  H121  C12  O11   110.43  3.000
 H9I  H122  C12  O11   110.71  3.000
 H9I  H121  C12  C13   109.76  3.000
 H9I  H122  C12  C13   110.98  3.000
 H9I  O11   C12  C13   107.70  3.000
 H9I  C29   C13  C27    84.00  3.000
 H9I  C29   C13  C14   113.19  3.000
 H9I  C27   C13  C14   114.17  3.000
 H9I  C29   C13  C12   115.26  3.000
 H9I  C27   C13  C12   114.56  3.000
 H9I  C14   C13  C12   112.75  3.000
 H9I  H142  C14  H141  107.47  3.000
 H9I  H142  C14  O15   110.41  3.000
 H9I  H141  C14  O15   111.49  3.000
 H9I  H142  C14  C13   110.35  3.000
 H9I  H141  C14  C13   110.10  3.000
 H9I  O15   C14  C13   107.04  3.000
 H9I  H201  C20  C19   119.47  3.000
 H9I  H201  C20  C21   118.44  3.000
 H9I  C19   C20  C21   122.09  3.000
 H9I  C16   C21  C22   121.24  3.000
 H9I  C16   C21  C20   117.82  3.000
 H9I  C22   C21  C20   120.88  3.000
 H9I  H222  C22  H221  106.01  3.000
 H9I  H222  C22  C23   109.77  3.000
 H9I  H221  C22  C23   109.27  3.000
 H9I  H222  C22  C21   110.87  3.000
 H9I  H221  C22  C21   108.76  3.000
 H9I  C23   C22  C21   111.96  3.000
 H9I  H231  C23  H232  104.95  3.000
 H9I  H231  C23  C24   108.61  3.000
 H9I  H232  C23  C24   107.89  3.000
 H9I  H231  C23  C22   109.28  3.000
 H9I  H232  C23  C22   109.83  3.000
 H9I  C24   C23  C22   115.72  3.000
 H9I  O26   C24  O25   126.68  3.000
 H9I  O26   C24  C23   117.76  3.000
 H9I  O25   C24  C23   115.56  3.000
 H9I  H013  C01  H011  107.99  3.000
 H9I  H013  C01  H012  107.60  3.000
 H9I  H011  C01  H012  108.15  3.000
 H9I  H013  C01  C02   111.32  3.000
 H9I  H011  C01  C02   111.08  3.000
 H9I  H012  C01  C02   110.56  3.000
 H9I  H022  C02  H021  106.88  3.000
 H9I  H022  C02  C03   110.89  3.000
 H9I  H021  C02  C03   107.93  3.000
 H9I  H022  C02  C01   109.89  3.000
 H9I  H021  C02  C01   109.19  3.000
 H9I  C03   C02  C01   111.90  3.000
 H9I  N04   C03  C02   116.15  3.000
 H9I  N04   C03  C10   121.44  3.000
 H9I  C02   C03  C10   122.41  3.000
 H9I  N07   C05  N06   116.44  3.000
 H9I  N07   C05  N04   126.34  3.000
 H9I  N06   C05  N04   117.20  3.000
 H9I  N09   C08  N07   118.14  3.000
 H9I  N09   C08  C10   120.88  3.000
 H9I  N07   C08  C10   120.97  3.000
 H9I  O15   C16  C17   123.65  3.000
 H9I  C17   C16  C21   120.70  3.000
 H9I  O15   C16  C21   115.65  3.000
 H9I  H171  C17  C18   118.94  3.000
 H9I  H171  C17  C16   121.13  3.000
 H9I  C18   C17  C16   119.93  3.000
 H9I  H181  C18  C19   120.51  3.000
 H9I  H181  C18  C17   119.19  3.000
 H9I  C19   C18  C17   120.30  3.000
 H9I  H191  C19  C18   120.59  3.000
 H9I  H191  C19  C20   120.27  3.000
 H9I  C18   C19  C20   119.14  3.000
 H9I  H271  C27  H272  108.54  3.000
 H9I  H271  C27  O28   112.48  3.000
 H9I  H272  C27  O28   112.75  3.000
 H9I  H271  C27  C13   114.65  3.000
 H9I  H272  C27  C13   115.81  3.000
 H9I  O28   C27  C13    91.94  3.000
 H9I  H292  C29  H291  108.46  3.000
 H9I  H292  C29  O28   112.52  3.000
 H9I  H291  C29  O28   112.66  3.000
 H9I  H292  C29  C13   114.55  3.000
 H9I  H291  C29  C13   116.01  3.000
 H9I  O28   C29  C13    91.97  3.000
 H9I  C05   N04  C03   116.95  3.000
 H9I  H061  N06  H062  115.46  3.000
 H9I  H061  N06  C05   117.31  3.000
 H9I  H062  N06  C05   117.15  3.000
 H9I  C08   N07  C05   117.02  3.000
 H9I  H091  N09  H092  116.16  3.000
 H9I  H091  N09  C08   119.53  3.000
 H9I  H092  N09  C08   117.75  3.000
 H9I  C12   O11  C10   115.10  3.000
 H9I  C16   O15  C14   120.15  3.000
 H9I  C29   O28  C27    91.79  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
 H9I  CONST_01  C05   N07  C08  C10     0.00   0.0  0
 H9I  CONST_02  C05   N04  C03  C10     0.00   0.0  0
 H9I  CONST_03  C17   C18  C19  C20     0.00   0.0  0
 H9I  CONST_04  C17   C16  C21  C20     0.00   0.0  0
 H9I  CONST_05  C18   C19  C20  C21     0.00   0.0  0
 H9I  CONST_06  C18   C17  C16  C21     0.00   0.0  0
 H9I  CONST_07  N07   C05  N04  C03     0.00   0.0  0
 H9I  CONST_08  N07   C08  C10  C03     0.00   0.0  0
 H9I  CONST_09  N04   C05  N07  C08     0.00   0.0  0
 H9I  CONST_10  N04   C03  C10  C08     0.00   0.0  0
 H9I  CONST_11  C19   C18  C17  C16     0.00   0.0  0
 H9I  CONST_12  C19   C20  C21  C16     0.00   0.0  0
 H9I  CONST_13  O15   C16  C21  C20   180.00   0.0  0
 H9I  CONST_14  C19   C20  C21  C22   180.00   0.0  0
 H9I  CONST_15  C17   C16  C21  C22   180.00   0.0  0
 H9I  CONST_16  C05   N04  C03  C02   180.00   0.0  0
 H9I  CONST_17  C08   C10  C03  C02   180.00   0.0  0
 H9I  CONST_18  N06   C05  N04  C03   180.00   0.0  0
 H9I  CONST_19  N09   C08  C10  C03   180.00   0.0  0
 H9I  CONST_20  N09   C08  N07  C05   180.00   0.0  0
 H9I  CONST_21  N06   C05  N07  C08   180.00   0.0  0
 H9I  CONST_22  O15   C16  C17  C18   180.00   0.0  0
 H9I  CONST_23  O11   C10  C03  N04   180.00   0.0  0
 H9I  CONST_24  O11   C10  C08  N07   180.00   0.0  0
 H9I  CONST_25  H181  C18  C19  C20   180.00   0.0  0
 H9I  CONST_26  H191  C19  C20  C21   180.00   0.0  0
 H9I  CONST_27  H171  C17  C16  C21   180.00   0.0  0
 H9I  CONST_28  H181  C18  C17  C16   180.00   0.0  0
 H9I  CONST_29  H201  C20  C21  C16   180.00   0.0  0
 H9I  CONST_30  H191  C19  C18  C17   180.00   0.0  0
 H9I  CONST_31  H201  C20  C19  C18   180.00   0.0  0
 H9I  CONST_32  H171  C17  C18  C19   180.00   0.0  0
 H9I  CONST_33  H092  N09  C08  C10   180.00   0.0  0
 H9I  CONST_39  H092  N09  C08  N07     0.00   0.0  0
 H9I  Var_01    C29   O28  C27  C13    -4.28  30.0  1
 H9I  Var_02    H291  C29  O28  C27   123.61  30.0  1
 H9I  Var_03    H292  C29  O28  C27  -113.39  30.0  1
 H9I  Var_04    H272  C27  O28  C29  -123.39  30.0  1
 H9I  Var_05    H271  C27  O28  C29   113.47  30.0  1
 H9I  Var_06    C13   C12  O11  C10  -173.37  30.0  1
 H9I  Var_07    C01   C02  C03  C10  -107.35  30.0  2
 H9I  Var_08    C08   C10  O11  C12   -89.14  30.0  2
 H9I  Var_09    C03   C10  O11  C12    93.00  30.0  2
 H9I  Var_10    C16   O15  C14  C13  -172.34  30.0  1
 H9I  Var_11    C17   C16  O15  C14     2.09  30.0  2
 H9I  Var_12    C21   C16  O15  C14  -178.11  30.0  2
 H9I  Var_13    C23   C22  C21  C20   -98.36  30.0  2
 H9I  Var_14    C16   C21  C22  C23    78.92  30.0  2
 H9I  Var_15    N04   C03  C02  C01    72.17  30.0  1
 H9I  Var_16    H021  C02  C03  C10   132.49  30.0  2
 H9I  Var_17    H022  C02  C03  C10    15.74  30.0  2
 H9I  Var_18    H221  C22  C21  C20    22.48  30.0  2
 H9I  Var_19    H222  C22  C21  C20   138.67  30.0  2
 H9I  Var_20    H221  C22  C21  C16  -160.24  30.0  2
 H9I  Var_21    H222  C22  C21  C16   -44.05  30.0  2
 H9I  Var_22    H021  C02  C03  N04   -47.99  30.0  2
 H9I  Var_23    H022  C02  C03  N04  -164.75  30.0  2
 H9I  Var_24    C24   C23  C22  C21   179.78  30.0  1
 H9I  Var_25    H122  C12  O11  C10   -51.87  30.0  1
 H9I  Var_26    H121  C12  O11  C10    66.78  30.0  1
 H9I  Var_27    H232  C23  C22  C21   -57.78  30.0  1
 H9I  Var_28    H231  C23  C22  C21    56.84  30.0  1
 H9I  Var_29    H012  C01  C02  C03  -178.22  30.0  3
 H9I  Var_30    H011  C01  C02  C03   -58.15  30.0  3
 H9I  Var_31    H013  C01  C02  C03    62.24  30.0  3
 H9I  Var_32    H141  C14  O15  C16   -51.88  30.0  3
 H9I  Var_33    H142  C14  O15  C16    67.51  30.0  3
 H9I  Var_34    O25   C24  C23  C22  -174.78  30.0  2
 H9I  Var_35    O26   C24  C23  C22     5.76  30.0  2
 H9I  Var_36    H221  C22  C23  C24    59.24  30.0  3
 H9I  Var_37    H222  C22  C23  C24   -56.63  30.0  3
 H9I  Var_38    H232  C23  C24  O25    61.77  30.0  3
 H9I  Var_39    H231  C23  C24  O25   -51.48  30.0  3
 H9I  Var_40    H232  C23  C24  O26  -117.69  30.0  3
 H9I  Var_41    H231  C23  C24  O26   129.06  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
 H9I  chir_01  C13  C14  C27  C29  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
 H9I  plan-1  C20   0.020
 H9I  plan-1  C21   0.020
 H9I  plan-1  C22   0.020
 H9I  plan-1  C16   0.020
 H9I  plan-1  C17   0.020
 H9I  plan-1  C18   0.020
 H9I  plan-1  C19   0.020
 H9I  plan-1  O15   0.020
 H9I  plan-1  H201  0.020
 H9I  plan-1  H171  0.020
 H9I  plan-1  H181  0.020
 H9I  plan-1  H191  0.020
 H9I  plan-2  C10   0.020
 H9I  plan-2  C02   0.020
 H9I  plan-2  C03   0.020
 H9I  plan-2  C05   0.020
 H9I  plan-2  C08   0.020
 H9I  plan-2  N04   0.020
 H9I  plan-2  N06   0.020
 H9I  plan-2  N07   0.020
 H9I  plan-2  N09   0.020
 H9I  plan-2  O11   0.020
 H9I  plan-3  C05   0.020
 H9I  plan-3  N06   0.020
 H9I  plan-3  H062  0.020
 H9I  plan-3  H061  0.020
 H9I  plan-4  C08   0.020
 H9I  plan-4  N09   0.020
 H9I  plan-4  H092  0.020
 H9I  plan-4  H091  0.020
 H9I  plan-5  C23   0.020
 H9I  plan-5  C24   0.020
 H9I  plan-5  O25   0.020
 H9I  plan-5  O26   0.020

