# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:32:36 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 4-({4-amino-6-[4-(2-hydroxyethyl)-1H-imidazol-1-yl]pyrimidin-2-yl}amino)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(nc(Nc2ccc(cc2)C#N)n1)n3cnc(CCO)c3
#
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
 J9D  J9D  4-({4-amino-6-[4-(2-hydroxyethyl)-1H-imidazol-1-yl]pyrimidin-2-yl}amino)benzonitrile  ligand  39  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J9D
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
 J9D  C10  C  CR6   0   0.515  -0.3179   2.6476  -0.1900
 J9D  C13  C  CR6   0   0.552   1.4410   1.1178   0.1338
 J9D  C15  C  CR15  0   0.091   3.8534   1.5955   0.4246
 J9D  C17  C  CR5   0   0.160   4.6308  -0.3962   0.4509
 J9D  C21  C  CR15  0  -0.115   3.2862  -0.5234   0.2951
 J9D  C24  C  CR16  0  -0.208  -5.1355   0.0672  -0.3827
 J9D  C03  C  CR6   0  -0.121  -5.6711  -1.1912  -0.1121
 J9D  C04  C  CR16  0  -0.170  -4.8146  -2.2351   0.2440
 J9D  C05  C  CR16  0  -0.375  -3.4594  -2.0141   0.3247
 J9D  C06  C  CR6   0   0.406  -2.9120  -0.7486   0.0564
 J9D  C08  C  CR6   0   0.546  -0.6999   0.4327   0.0671
 J9D  C12  C  CR16  0  -0.496   1.0652   2.4274  -0.0657
 J9D  C18  C  CH2   0  -0.591   5.6615  -1.4705   0.4988
 J9D  C19  C  CH2   0  -0.119   6.5671  -1.4285  -0.7240
 J9D  C23  C  CR16  0  -0.247  -3.7751   0.2942  -0.3013
 J9D  N01  N  NS    0  -0.210  -8.2125  -1.5866  -0.2593
 J9D  N07  N  NH1   0  -0.722  -1.5416  -0.6427   0.1565
 J9D  N09  N  N     0  -0.320  -1.1956   1.6400  -0.1222
 J9D  N11  N  NH2   0  -0.844  -0.8105   3.8723  -0.3914
 J9D  N14  N  NR5   0  -0.540   2.7859   0.7613   0.2753
 J9D  N16  N  N     0  -0.386   4.9666   0.9364   0.5338
 J9D  N22  N  N     0  -0.572   0.5846   0.1099   0.2013
 J9D  O20  O  OH1   0  -0.677   7.5199  -2.4625  -0.6133
 J9D  H1   H  HCR5  0   0.272   3.7552   2.6688   0.4631
 J9D  H2   H  HCR5  0   0.299   2.6520  -1.3859   0.1927
 J9D  H3   H  HCR6  0   0.255  -5.7890   0.8830  -0.6618
 J9D  H4   H  HCR6  0   0.284  -5.2101  -3.2184   0.4596
 J9D  H5   H  HCR6  0   0.223  -2.8062  -2.8322   0.6025
 J9D  H6   H  HCR6  0   0.262   1.7639   3.2467  -0.1373
 J9D  H7   H  HCH2  0   0.218   6.2710  -1.3599   1.4008
 J9D  H8   H  HCH2  0   0.232   5.1702  -2.4442   0.5588
 J9D  H9   H  HCH2  0   0.167   5.9533  -1.5389  -1.6272
 J9D  H10  H  HCH2  0   0.242   7.0460  -0.4429  -0.7825
 J9D  H11  H  HCR6  0   0.278  -3.3876   1.2761  -0.5132
 J9D  H12  H  HNH1  0   0.446  -1.0537  -1.5038   0.3556
 J9D  H13  H  HNH2  0   0.383  -1.8038   4.0182  -0.4413
 J9D  H14  H  HNH2  0   0.397  -0.2141   4.6809  -0.4132
 J9D  H15  H  HOH1  0   0.455   8.0535  -2.4651  -1.4129
 J9D  C02  C  CSP   0   0.030  -7.0745  -1.4088  -0.1961

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
 J9D  N11  C10  single    1.335  0.020  1.335
 J9D  C10  N09  aromatic  1.338  0.020  1.338
 J9D  C10  C12  aromatic  1.406  0.020  1.406
 J9D  N09  C08  aromatic  1.319  0.020  1.319
 J9D  O20  C19  single    1.410  0.020  1.410
 J9D  C12  C13  aromatic  1.377  0.020  1.377
 J9D  C08  N07  single    1.369  0.020  1.369
 J9D  C08  N22  aromatic  1.331  0.020  1.331
 J9D  N07  C06  single    1.378  0.020  1.378
 J9D  C05  C06  aromatic  1.405  0.020  1.405
 J9D  C05  C04  aromatic  1.376  0.020  1.376
 J9D  C13  N22  aromatic  1.324  0.020  1.324
 J9D  C13  N14  single    1.399  0.020  1.399
 J9D  C06  C23  aromatic  1.400  0.020  1.400
 J9D  C21  N14  aromatic  1.379  0.020  1.379
 J9D  C21  C17  aromatic  1.360  0.020  1.360
 J9D  C04  C03  aromatic  1.396  0.020  1.396
 J9D  N14  C15  aromatic  1.363  0.020  1.363
 J9D  C19  C18  single    1.522  0.020  1.522
 J9D  C17  C18  single    1.490  0.020  1.490
 J9D  C17  N16  aromatic  1.377  0.020  1.377
 J9D  C23  C24  aromatic  1.382  0.020  1.382
 J9D  C15  N16  aromatic  1.298  0.020  1.298
 J9D  C03  C24  aromatic  1.394  0.020  1.394
 J9D  C03  C02  single    1.423  0.020  1.423
 J9D  C02  N01  triple    1.154  0.020  1.154
 J9D  C15  H1   single    0.930  0.020  1.080
 J9D  C21  H2   single    0.930  0.020  1.080
 J9D  C24  H3   single    0.930  0.020  1.080
 J9D  C04  H4   single    0.930  0.020  1.080
 J9D  C05  H5   single    0.930  0.020  1.080
 J9D  C12  H6   single    0.930  0.020  1.080
 J9D  C18  H7   single    0.970  0.020  1.090
 J9D  C18  H8   single    0.970  0.020  1.090
 J9D  C19  H9   single    0.970  0.020  1.090
 J9D  C19  H10  single    0.970  0.020  1.090
 J9D  C23  H11  single    0.930  0.020  1.080
 J9D  N07  H12  single    0.860  0.020  1.020
 J9D  N11  H13  single    0.860  0.020  1.020
 J9D  N11  H14  single    0.860  0.020  1.020
 J9D  O20  H15  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
 J9D  N11  C10  N09  117.16  3.000
 J9D  N09  C10  C12  121.52  3.000
 J9D  N11  C10  C12  121.32  3.000
 J9D  N22  C13  N14  115.01  3.000
 J9D  N14  C13  C12  121.30  3.000
 J9D  N22  C13  C12  123.69  3.000
 J9D  H1   C15  N16  125.47  3.000
 J9D  H1   C15  N14  122.80  3.000
 J9D  N16  C15  N14  111.71  3.000
 J9D  N16  C17  C18  121.83  3.000
 J9D  N16  C17  C21  109.80  3.000
 J9D  C18  C17  C21  128.36  3.000
 J9D  H2   C21  N14  122.13  3.000
 J9D  H2   C21  C17  132.01  3.000
 J9D  N14  C21  C17  105.86  3.000
 J9D  H3   C24  C23  119.08  3.000
 J9D  H3   C24  C03  119.91  3.000
 J9D  C23  C24  C03  121.00  3.000
 J9D  C04  C03  C02  120.38  3.000
 J9D  C02  C03  C24  120.37  3.000
 J9D  C04  C03  C24  119.25  3.000
 J9D  H4   C04  C05  119.65  3.000
 J9D  H4   C04  C03  120.41  3.000
 J9D  C05  C04  C03  119.94  3.000
 J9D  H5   C05  C06  119.64  3.000
 J9D  H5   C05  C04  119.20  3.000
 J9D  C06  C05  C04  121.17  3.000
 J9D  N07  C06  C23  125.05  3.000
 J9D  C23  C06  C05  118.66  3.000
 J9D  N07  C06  C05  116.29  3.000
 J9D  N22  C08  N09  126.81  3.000
 J9D  N22  C08  N07  113.35  3.000
 J9D  N09  C08  N07  119.84  3.000
 J9D  H6   C12  C13  123.71  3.000
 J9D  H6   C12  C10  120.81  3.000
 J9D  C13  C12  C10  115.48  3.000
 J9D  H8   C18  H7   107.18  3.000
 J9D  H8   C18  C19  109.65  3.000
 J9D  H7   C18  C19  109.15  3.000
 J9D  H8   C18  C17  109.48  3.000
 J9D  H7   C18  C17  109.82  3.000
 J9D  C19  C18  C17  111.46  3.000
 J9D  H10  C19  H9   106.89  3.000
 J9D  H10  C19  O20  111.58  3.000
 J9D  H9   C19  O20  111.63  3.000
 J9D  H10  C19  C18  109.10  3.000
 J9D  H9   C19  C18  109.00  3.000
 J9D  O20  C19  C18  108.58  3.000
 J9D  H11  C23  C06  120.50  3.000
 J9D  H11  C23  C24  119.51  3.000
 J9D  C06  C23  C24  119.98  3.000
 J9D  H12  N07  C08  112.70  3.000
 J9D  H12  N07  C06  115.43  3.000
 J9D  C08  N07  C06  131.85  3.000
 J9D  C08  N09  C10  116.76  3.000
 J9D  H14  N11  H13  117.94  3.000
 J9D  H14  N11  C10  121.49  3.000
 J9D  H13  N11  C10  120.34  3.000
 J9D  C21  N14  C15  106.53  3.000
 J9D  C15  N14  C13  127.46  3.000
 J9D  C21  N14  C13  126.01  3.000
 J9D  C17  N16  C15  106.09  3.000
 J9D  C08  N22  C13  115.74  3.000
 J9D  H15  O20  C19  108.16  3.000
 J9D  N01  C02  C03  180.00  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
 J9D  CONST_01  N22  C08  N09  C10     0.00   0.0  0
 J9D  CONST_02  N22  C13  C12  C10     0.00   0.0  0
 J9D  CONST_03  N14  C13  C12  C10   180.00   0.0  0
 J9D  CONST_04  N09  C10  C12  C13     0.00   0.0  0
 J9D  CONST_05  N09  C08  N22  C13     0.00   0.0  0
 J9D  CONST_06  C17  C21  N14  C13   180.00   0.0  0
 J9D  CONST_07  N16  C15  N14  C13   180.00   0.0  0
 J9D  CONST_08  C12  C13  N14  C15     0.00   0.0  0
 J9D  CONST_09  N22  C13  N14  C15   180.00   0.0  0
 J9D  CONST_10  C17  C21  N14  C15     0.00   0.0  0
 J9D  CONST_11  C21  C17  N16  C15     0.00   0.0  0
 J9D  CONST_12  N14  C15  N16  C17     0.00   0.0  0
 J9D  CONST_13  C12  C13  N14  C21   180.00   0.0  0
 J9D  CONST_14  N22  C13  N14  C21     0.00   0.0  0
 J9D  CONST_15  N16  C15  N14  C21     0.00   0.0  0
 J9D  CONST_16  C05  C06  C23  C24     0.00   0.0  0
 J9D  CONST_17  C05  C04  C03  C24     0.00   0.0  0
 J9D  CONST_18  C06  C05  C04  C03     0.00   0.0  0
 J9D  CONST_19  C06  C23  C24  C03     0.00   0.0  0
 J9D  CONST_20  C23  C06  C05  C04     0.00   0.0  0
 J9D  CONST_21  C23  C24  C03  C04     0.00   0.0  0
 J9D  CONST_22  C12  C10  N09  C08     0.00   0.0  0
 J9D  CONST_23  C12  C13  N22  C08     0.00   0.0  0
 J9D  CONST_24  N14  C13  N22  C08   180.00   0.0  0
 J9D  CONST_25  N16  C17  C21  N14     0.00   0.0  0
 J9D  CONST_26  N07  C08  N09  C10   180.00   0.0  0
 J9D  CONST_27  N11  C10  C12  C13   180.00   0.0  0
 J9D  CONST_28  N07  C08  N22  C13   180.00   0.0  0
 J9D  CONST_29  C18  C17  N16  C15   180.00   0.0  0
 J9D  CONST_30  N07  C06  C23  C24   180.00   0.0  0
 J9D  CONST_31  C05  C04  C03  C02   180.00   0.0  0
 J9D  CONST_32  C23  C24  C03  C02   180.00   0.0  0
 J9D  CONST_33  N07  C06  C05  C04   180.00   0.0  0
 J9D  CONST_34  N11  C10  N09  C08   180.00   0.0  0
 J9D  CONST_35  N14  C21  C17  C18   180.00   0.0  0
 J9D  CONST_36  H2   C21  N14  C13     0.00   0.0  0
 J9D  CONST_37  H1   C15  N14  C13     0.00   0.0  0
 J9D  CONST_38  H4   C04  C03  C24   180.00   0.0  0
 J9D  CONST_39  H5   C05  C04  C03   180.00   0.0  0
 J9D  CONST_40  H11  C23  C24  C03   180.00   0.0  0
 J9D  CONST_41  H3   C24  C03  C04   180.00   0.0  0
 J9D  CONST_42  H6   C12  C10  N09   180.00   0.0  0
 J9D  CONST_43  H13  N11  C10  C12   180.00   0.0  0
 J9D  CONST_44  H14  N11  C10  C12     0.00   0.0  0
 J9D  Var_01    C08  N07  C06  C05  -174.36  30.0  2
 J9D  Var_02    N09  C08  N07  C06     1.63  30.0  1
 J9D  Var_03    C19  C18  C17  C21   111.87  30.0  2
 J9D  Var_04    O20  C19  C18  C17   179.71  30.0  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
 J9D  plan-1  C13  0.020
 J9D  plan-1  C15  0.020
 J9D  plan-1  C17  0.020
 J9D  plan-1  C21  0.020
 J9D  plan-1  C18  0.020
 J9D  plan-1  N14  0.020
 J9D  plan-1  N16  0.020
 J9D  plan-1  H1   0.020
 J9D  plan-1  H2   0.020
 J9D  plan-2  C10  0.020
 J9D  plan-2  C13  0.020
 J9D  plan-2  C08  0.020
 J9D  plan-2  C12  0.020
 J9D  plan-2  N07  0.020
 J9D  plan-2  N09  0.020
 J9D  plan-2  N11  0.020
 J9D  plan-2  N14  0.020
 J9D  plan-2  N22  0.020
 J9D  plan-2  H6   0.020
 J9D  plan-3  C24  0.020
 J9D  plan-3  C03  0.020
 J9D  plan-3  C04  0.020
 J9D  plan-3  C05  0.020
 J9D  plan-3  C06  0.020
 J9D  plan-3  C23  0.020
 J9D  plan-3  N01  0.020
 J9D  plan-3  N07  0.020
 J9D  plan-3  H3   0.020
 J9D  plan-3  H4   0.020
 J9D  plan-3  H5   0.020
 J9D  plan-3  H11  0.020
 J9D  plan-3  C02  0.020
 J9D  plan-4  C10  0.020
 J9D  plan-4  N11  0.020
 J9D  plan-4  H13  0.020
 J9D  plan-4  H14  0.020

