# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 07:06:29 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-[2-(morpholin-4-yl)-6-(pyridin-3-ylamino)pyrimidin-4-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(c1)c2cc(Nc3cccnc3)nc(n2)N4CCOCC4
#
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
 P2B  P2B  3-[2-(morpholin-4-yl)-6-(pyridin-3-ylamino)pyrimidin-4-yl]phenol  ligand  45  26  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P2B
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
 P2B  C1    C  CR6   0   0.581   0.7225   1.3134   0.0322
 P2B  N2    N  NH1   0  -0.778   1.6644   2.2823   0.2086
 P2B  C4    C  CR6   0   0.269   3.0492   2.1745   0.1898
 P2B  N5    N  N     0  -0.534   1.1075   0.0708  -0.1909
 P2B  C6    C  CR6   0   0.651   0.1446  -0.8433  -0.3598
 P2B  N7    N  NT    0  -0.515   0.5376  -2.1198  -0.5750
 P2B  N8    N  N     0  -0.532  -1.1641  -0.5968  -0.3367
 P2B  C9    C  CR6   0   0.303  -1.5445   0.6613  -0.1159
 P2B  C10   C  CR6   0   0.075  -3.0045   0.9113  -0.0845
 P2B  C11   C  CR16  0  -0.515  -0.6328   1.6781   0.0885
 P2B  C13   C  CR16  0  -0.190   3.7684   1.0389   0.5577
 P2B  C15   C  CR16  0  -0.321   5.1523   1.0934   0.5213
 P2B  C17   C  CR16  0  -0.086   5.7804   2.2675   0.1386
 P2B  N19   N  N     0  -0.391   5.1023   3.3596  -0.1963
 P2B  C20   C  CR16  0  -0.144   3.7821   3.3088  -0.1755
 P2B  C22   C  CH2   0  -0.324  -0.3960  -3.1996  -0.8217
 P2B  C25   C  CH2   0  -0.183  -0.0299  -4.3945   0.0418
 P2B  O28   O  O2    0  -0.485   1.3115  -4.7876  -0.1495
 P2B  C29   C  CH2   0  -0.183   2.1991  -3.7318   0.1447
 P2B  C32   C  CH2   0  -0.324   1.9242  -2.5128  -0.7184
 P2B  C35   C  CR16  0  -0.347  -3.5264   2.1893  -0.2751
 P2B  C37   C  CR16  0  -0.227  -4.8993   2.3861  -0.2360
 P2B  C39   C  CR16  0  -0.342  -5.7653   1.3298  -0.0056
 P2B  C41   C  CR6   0   0.389  -5.2472   0.0499   0.1821
 P2B  O42   O  OH1   0  -0.633  -6.1197  -0.9534   0.4056
 P2B  C44   C  CR16  0  -0.436  -3.8736  -0.1561   0.1346
 P2B  HN2   H  HNH1  0   0.415   1.3080   3.2254   0.2321
 P2B  H11   H  HCR6  0   0.272  -0.9278   2.6945   0.3036
 P2B  H13   H  HCR6  0   0.283   3.2652   0.1399   0.8744
 P2B  H15   H  HCR6  0   0.272   5.7379   0.2281   0.8007
 P2B  H17   H  HCR6  0   0.262   6.8617   2.3316   0.1041
 P2B  H20   H  HCR6  0   0.270   3.2543   4.2156  -0.4587
 P2B  H22   H  HCH2  0   0.277  -1.4072  -2.8750  -0.5936
 P2B  H22A  H  HCH2  0   0.235  -0.3639  -3.4812  -1.8812
 P2B  H25   H  HCH2  0   0.206  -0.2108  -4.1461   1.0971
 P2B  H25A  H  HCH2  0   0.241  -0.6604  -5.2461  -0.2181
 P2B  H29   H  HCH2  0   0.206   2.1254  -3.4496   1.2047
 P2B  H29A  H  HCH2  0   0.242   3.2113  -4.0948  -0.0390
 P2B  H32   H  HCH2  0   0.238   2.1330  -2.7472  -1.7693
 P2B  H32A  H  HCH2  0   0.274   2.5781  -1.6958  -0.4272
 P2B  H35   H  HCR6  0   0.252  -2.8764   3.0304  -0.4740
 P2B  H37   H  HCR6  0   0.261  -5.3024   3.3780  -0.3932
 P2B  H39   H  HCR6  0   0.267  -6.8358   1.4887   0.0262
 P2B  HO42  H  HOH1  0   0.475  -5.6510  -1.7887   0.5102
 P2B  H44   H  HCR6  0   0.275  -3.4656  -1.1504   0.2758

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
 P2B  N2   C1    single    1.363  0.020  1.363
 P2B  C11  C1    aromatic  1.405  0.020  1.405
 P2B  C1   N5    aromatic  1.320  0.020  1.320
 P2B  N2   C4    single    1.389  0.020  1.389
 P2B  N2   HN2   single    0.860  0.020  1.020
 P2B  C20  C4    aromatic  1.399  0.020  1.399
 P2B  C4   C13   aromatic  1.394  0.020  1.394
 P2B  N5   C6    aromatic  1.338  0.020  1.338
 P2B  N8   C6    aromatic  1.332  0.020  1.332
 P2B  C6   N7    single    1.353  0.020  1.353
 P2B  C22  N7    single    1.449  0.020  1.449
 P2B  N7   C32   single    1.448  0.020  1.448
 P2B  C9   N8    aromatic  1.333  0.020  1.333
 P2B  C11  C9    aromatic  1.381  0.020  1.381
 P2B  C10  C9    single    1.482  0.020  1.482
 P2B  C35  C10   aromatic  1.394  0.020  1.394
 P2B  C10  C44   aromatic  1.394  0.020  1.394
 P2B  C11  H11   single    0.930  0.020  1.080
 P2B  C13  C15   aromatic  1.385  0.020  1.385
 P2B  C13  H13   single    0.930  0.020  1.080
 P2B  C17  C15   aromatic  1.385  0.020  1.385
 P2B  C15  H15   single    0.930  0.020  1.080
 P2B  N19  C17   aromatic  1.328  0.020  1.328
 P2B  C17  H17   single    0.930  0.020  1.080
 P2B  C20  N19   aromatic  1.321  0.020  1.321
 P2B  C20  H20   single    0.930  0.020  1.080
 P2B  C22  C25   single    1.519  0.020  1.519
 P2B  C22  H22   single    0.970  0.020  1.090
 P2B  C22  H22A  single    0.970  0.020  1.090
 P2B  C25  O28   single    1.411  0.020  1.411
 P2B  C25  H25   single    0.970  0.020  1.090
 P2B  C25  H25A  single    0.970  0.020  1.090
 P2B  O28  C29   single    1.410  0.020  1.410
 P2B  C32  C29   single    1.519  0.020  1.519
 P2B  C29  H29   single    0.970  0.020  1.090
 P2B  C29  H29A  single    0.970  0.020  1.090
 P2B  C32  H32   single    0.970  0.020  1.090
 P2B  C32  H32A  single    0.970  0.020  1.090
 P2B  C37  C35   aromatic  1.387  0.020  1.387
 P2B  C35  H35   single    0.930  0.020  1.080
 P2B  C37  C39   aromatic  1.385  0.020  1.385
 P2B  C37  H37   single    0.930  0.020  1.080
 P2B  C39  C41   aromatic  1.393  0.020  1.393
 P2B  C39  H39   single    0.930  0.020  1.080
 P2B  C41  C44   aromatic  1.390  0.020  1.390
 P2B  C41  O42   single    1.348  0.020  1.348
 P2B  O42  HO42  single    0.850  0.020  0.980
 P2B  C44  H44   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
 P2B  C11   C1   N5   122.19  3.000
 P2B  N5    C1   N2   119.32  3.000
 P2B  C11   C1   N2   118.50  3.000
 P2B  HN2   N2   C4   115.16  3.000
 P2B  HN2   N2   C1   115.07  3.000
 P2B  C4    N2   C1   129.20  3.000
 P2B  C20   C4   C13  117.33  3.000
 P2B  C13   C4   N2   125.04  3.000
 P2B  C20   C4   N2   117.57  3.000
 P2B  C6    N5   C1   117.03  3.000
 P2B  N8    C6   N7   117.57  3.000
 P2B  N7    C6   N5   117.10  3.000
 P2B  N8    C6   N5   125.34  3.000
 P2B  C32   N7   C22  113.45  3.000
 P2B  C32   N7   C6   123.36  3.000
 P2B  C22   N7   C6   122.90  3.000
 P2B  C9    N8   C6   117.26  3.000
 P2B  C11   C9   C10  121.55  3.000
 P2B  C10   C9   N8   116.36  3.000
 P2B  C11   C9   N8   122.09  3.000
 P2B  C44   C10  C35  119.36  3.000
 P2B  C44   C10  C9   119.25  3.000
 P2B  C35   C10  C9   121.39  3.000
 P2B  H11   C11  C9   122.83  3.000
 P2B  H11   C11  C1   121.05  3.000
 P2B  C9    C11  C1   116.10  3.000
 P2B  H13   C13  C15  120.46  3.000
 P2B  H13   C13  C4   121.08  3.000
 P2B  C15   C13  C4   118.46  3.000
 P2B  H15   C15  C17  120.26  3.000
 P2B  H15   C15  C13  120.17  3.000
 P2B  C17   C15  C13  119.57  3.000
 P2B  H17   C17  N19  116.92  3.000
 P2B  H17   C17  C15  120.75  3.000
 P2B  N19   C17  C15  122.34  3.000
 P2B  C20   N19  C17  118.32  3.000
 P2B  H20   C20  N19  116.68  3.000
 P2B  H20   C20  C4   119.34  3.000
 P2B  N19   C20  C4   123.97  3.000
 P2B  H22A  C22  H22  107.87  3.000
 P2B  H22A  C22  C25  109.89  3.000
 P2B  H22   C22  C25  109.88  3.000
 P2B  H22A  C22  N7   109.70  3.000
 P2B  H22   C22  N7   109.96  3.000
 P2B  C25   C22  N7   109.53  3.000
 P2B  H25A  C25  H25  108.06  3.000
 P2B  H25A  C25  O28  107.44  3.000
 P2B  H25   C25  O28  110.46  3.000
 P2B  H25A  C25  C22  109.84  3.000
 P2B  H25   C25  C22  109.17  3.000
 P2B  O28   C25  C22  111.79  3.000
 P2B  C29   O28  C25  111.19  3.000
 P2B  H29A  C29  H29  108.06  3.000
 P2B  H29A  C29  C32  109.84  3.000
 P2B  H29   C29  C32  109.25  3.000
 P2B  H29A  C29  O28  107.44  3.000
 P2B  H29   C29  O28  110.56  3.000
 P2B  C32   C29  O28  111.62  3.000
 P2B  H32A  C32  H32  107.64  3.000
 P2B  H32A  C32  C29  110.03  3.000
 P2B  H32   C32  C29  109.79  3.000
 P2B  H32A  C32  N7   110.22  3.000
 P2B  H32   C32  N7   109.58  3.000
 P2B  C29   C32  N7   109.56  3.000
 P2B  H35   C35  C37  119.32  3.000
 P2B  H35   C35  C10  120.88  3.000
 P2B  C37   C35  C10  119.79  3.000
 P2B  H37   C37  C39  119.36  3.000
 P2B  H37   C37  C35  119.63  3.000
 P2B  C39   C37  C35  121.01  3.000
 P2B  H39   C39  C41  119.90  3.000
 P2B  H39   C39  C37  120.74  3.000
 P2B  C41   C39  C37  119.37  3.000
 P2B  C44   C41  O42  122.34  3.000
 P2B  O42   C41  C39  117.72  3.000
 P2B  C44   C41  C39  119.93  3.000
 P2B  HO42  O42  C41  110.38  3.000
 P2B  H44   C44  C41  120.24  3.000
 P2B  H44   C44  C10  119.22  3.000
 P2B  C41   C44  C10  120.54  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
 P2B  CONST_01  N8   C9   C11  C1      0.00   0.0  0
 P2B  CONST_02  C10  C9   C11  C1    180.00   0.0  0
 P2B  CONST_03  N8   C6   N5   C1      0.00   0.0  0
 P2B  CONST_04  C17  N19  C20  C4      0.00   0.0  0
 P2B  CONST_05  C17  C15  C13  C4      0.00   0.0  0
 P2B  CONST_06  C9   C11  C1   N5      0.00   0.0  0
 P2B  CONST_07  C9   N8   C6   N5      0.00   0.0  0
 P2B  CONST_08  C11  C1   N5   C6      0.00   0.0  0
 P2B  CONST_09  C11  C9   N8   C6      0.00   0.0  0
 P2B  CONST_10  C10  C9   N8   C6    180.00   0.0  0
 P2B  CONST_13  C37  C35  C10  C9    180.00   0.0  0
 P2B  CONST_14  C41  C44  C10  C9    180.00   0.0  0
 P2B  CONST_15  C39  C37  C35  C10     0.00   0.0  0
 P2B  CONST_16  C39  C41  C44  C10     0.00   0.0  0
 P2B  CONST_19  N19  C20  C4   C13     0.00   0.0  0
 P2B  CONST_20  N19  C17  C15  C13     0.00   0.0  0
 P2B  CONST_21  C20  C4   C13  C15     0.00   0.0  0
 P2B  CONST_22  C20  N19  C17  C15     0.00   0.0  0
 P2B  CONST_23  C41  C44  C10  C35     0.00   0.0  0
 P2B  CONST_24  C41  C39  C37  C35     0.00   0.0  0
 P2B  CONST_25  C44  C10  C35  C37     0.00   0.0  0
 P2B  CONST_26  C44  C41  C39  C37     0.00   0.0  0
 P2B  CONST_27  N7   C6   N5   C1    180.00   0.0  0
 P2B  CONST_28  C9   N8   C6   N7    180.00   0.0  0
 P2B  CONST_29  C9   C11  C1   N2    180.00   0.0  0
 P2B  CONST_30  C6   N5   C1   N2    180.00   0.0  0
 P2B  CONST_31  N19  C20  C4   N2    180.00   0.0  0
 P2B  CONST_32  C15  C13  C4   N2    180.00   0.0  0
 P2B  CONST_33  O42  C41  C44  C10   180.00   0.0  0
 P2B  CONST_34  O42  C41  C39  C37   180.00   0.0  0
 P2B  CONST_35  H15  C15  C13  C4    180.00   0.0  0
 P2B  CONST_36  H11  C11  C1   N5    180.00   0.0  0
 P2B  CONST_37  H35  C35  C10  C9      0.00   0.0  0
 P2B  CONST_38  H44  C44  C10  C9      0.00   0.0  0
 P2B  CONST_39  H37  C37  C35  C10   180.00   0.0  0
 P2B  CONST_40  H20  C20  C4   C13   180.00   0.0  0
 P2B  CONST_41  H17  C17  C15  C13   180.00   0.0  0
 P2B  CONST_42  H13  C13  C15  C17   180.00   0.0  0
 P2B  CONST_43  H39  C39  C37  C35   180.00   0.0  0
 P2B  Var_01    C22  N7   C6   N5   -177.70  30.0  2
 P2B  Var_02    C25  C22  N7   C6   -133.06  30.0  1
 P2B  Var_03    C29  C32  N7   C6    132.87  30.0  1
 P2B  Var_04    O28  C25  C22  N7    -54.67  30.0  1
 P2B  Var_05    O28  C29  C32  N7     55.03  30.0  1
 P2B  Var_06    C32  C29  O28  C25   -58.58  30.0  1
 P2B  Var_07    C20  C4   N2   C1    153.03  30.0  2
 P2B  Var_08    C11  C1   N2   C4   -179.58  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
 P2B  plan-1  C1   0.020
 P2B  plan-1  N2   0.020
 P2B  plan-1  N5   0.020
 P2B  plan-1  C6   0.020
 P2B  plan-1  N7   0.020
 P2B  plan-1  N8   0.020
 P2B  plan-1  C9   0.020
 P2B  plan-1  C10  0.020
 P2B  plan-1  C11  0.020
 P2B  plan-1  H11  0.020
 P2B  plan-2  N2   0.020
 P2B  plan-2  C4   0.020
 P2B  plan-2  C13  0.020
 P2B  plan-2  C15  0.020
 P2B  plan-2  C17  0.020
 P2B  plan-2  N19  0.020
 P2B  plan-2  C20  0.020
 P2B  plan-2  H13  0.020
 P2B  plan-2  H15  0.020
 P2B  plan-2  H17  0.020
 P2B  plan-2  H20  0.020
 P2B  plan-3  C9   0.020
 P2B  plan-3  C10  0.020
 P2B  plan-3  C35  0.020
 P2B  plan-3  C37  0.020
 P2B  plan-3  C39  0.020
 P2B  plan-3  C41  0.020
 P2B  plan-3  O42  0.020
 P2B  plan-3  C44  0.020
 P2B  plan-3  H35  0.020
 P2B  plan-3  H37  0.020
 P2B  plan-3  H39  0.020
 P2B  plan-3  H44  0.020

