# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 16:08:35 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: N~4~-{5-[2-(3,5-dimethoxyphenyl)ethyl]-1H-pyrazol-3-yl}-N~2~-[(3-methyl-1,2-oxazol-5-yl)methyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CCc2[nH]nc(Nc3ccnc(NCc4onc(C)c4)n3)c2)cc(OC)c1
#
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
 2K5  2K5  N~4~-{5-[2-(3,5-dimethoxyphenyl)ethyl]-1H-pyrazol-3-yl}-N~2~-[(3-methyl-1,2-oxazol-5-yl)methyl]pyrimidine-2,4-diamine  ligand  57  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2K5
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
 2K5  C21  C  CH3   0  -0.438   8.4958  -2.4171   0.0851
 2K5  O2   O  O2    0  -0.475   7.1567  -2.7095   0.4293
 2K5  C16  C  CR6   0   0.432   6.2213  -1.7518   0.2826
 2K5  C15  C  CR16  0  -0.432   4.9293  -2.0911   0.6755
 2K5  C17  C  CR16  0  -0.547   6.4971  -0.4835  -0.2284
 2K5  C18  C  CR6   0   0.433   5.4584   0.4404  -0.3398
 2K5  O1   O  O2    0  -0.475   5.6265   1.6895  -0.8147
 2K5  C20  C  CH3   0  -0.439   6.9175   2.1007  -1.2172
 2K5  C19  C  CR16  0  -0.436   4.1656   0.1028   0.0519
 2K5  C14  C  CR6   0   0.156   3.9024  -1.1624   0.5603
 2K5  C13  C  CH2   0  -0.514   2.4996  -1.5471   0.9393
 2K5  C12  C  CH2   0  -0.517   1.7698  -2.2246  -0.2315
 2K5  C11  C  CR5   0   0.434   0.3777  -2.6157   0.1230
 2K5  C10  C  CR15  0  -0.555  -0.8202  -1.9599  -0.0769
 2K5  N5   N  NR15  0  -0.484   0.0817  -3.7374   0.7964
 2K5  N6   N  N     0  -0.328  -1.2204  -3.8744   1.0539
 2K5  C9   C  CR5   0   0.456  -1.7783  -2.7981   0.5286
 2K5  N4   N  NH1   0  -0.755  -3.1525  -2.6740   0.6505
 2K5  C8   C  CR6   0   0.560  -3.9562  -1.6746   0.2159
 2K5  C7   C  CR16  0  -0.464  -5.3419  -1.7485   0.4665
 2K5  C6   C  CR16  0  -0.019  -6.0881  -0.6979  -0.0005
 2K5  N2   N  N     0  -0.494  -5.5773   0.3456  -0.6548
 2K5  N3   N  N     0  -0.523  -3.4271  -0.6510  -0.4341
 2K5  C5   C  CR6   0   0.614  -4.2621   0.3096  -0.8441
 2K5  N1   N  NH1   0  -0.656  -3.6856   1.3182  -1.5400
 2K5  C4   C  CH2   0  -0.397  -4.3693   2.5187  -1.9329
 2K5  C3   C  CR5   0   0.447  -4.2716   3.6144  -0.9226
 2K5  C2   C  CR15  0  -0.517  -3.8912   4.9087  -1.0144
 2K5  O    O  O     0  -0.340  -4.6049   3.3406   0.3401
 2K5  N    N  N     0  -0.183  -4.4447   4.4584   1.1097
 2K5  C1   C  CR5   0   0.260  -4.0250   5.3986   0.3128
 2K5  C    C  CH3   0  -0.733  -3.7400   6.7681   0.8153
 2K5  H1   H  HCH3  0   0.228   8.8989  -1.5918   0.6777
 2K5  H2   H  HCH3  0   0.261   9.0722  -3.3139   0.2992
 2K5  H3   H  HCH3  0   0.228   8.6040  -2.1759  -0.9755
 2K5  H4   H  HCR6  0   0.249   4.7339  -3.0802   1.0734
 2K5  H5   H  HCR6  0   0.299   7.5004  -0.2199  -0.5297
 2K5  H6   H  HCH3  0   0.229   7.2965   1.5017  -2.0492
 2K5  H7   H  HCH3  0   0.261   6.8247   3.1331  -1.5449
 2K5  H8   H  HCH3  0   0.228   7.6360   2.0561  -0.3949
 2K5  H9   H  HCR6  0   0.249   3.3724   0.8356  -0.0379
 2K5  H10  H  HCH2  0   0.255   2.5178  -2.2250   1.7956
 2K5  H11  H  HCH2  0   0.257   1.9363  -0.6631   1.2454
 2K5  H12  H  HCH2  0   0.268   1.7363  -1.5416  -1.0814
 2K5  H13  H  HCH2  0   0.265   2.3356  -3.1022  -0.5549
 2K5  H14  H  HCR5  0   0.272  -0.9758  -1.0247  -0.5811
 2K5  H15  H  HNR5  0   0.416   0.7224  -4.4524   1.1013
 2K5  H16  H  HNH1  0   0.409  -3.6028  -3.4350   1.1357
 2K5  H17  H  HCR6  0   0.272  -5.7893  -2.5785   0.9940
 2K5  H18  H  HCR6  0   0.264  -7.1611  -0.6841   0.1586
 2K5  H19  H  HNH1  0   0.396  -2.6795   1.3138  -1.5827
 2K5  H20  H  HCH2  0   0.290  -3.9436   2.8847  -2.8667
 2K5  H21  H  HCH2  0   0.284  -5.4160   2.2848  -2.1286
 2K5  H22  H  HCR5  0   0.277  -3.5582   5.4411  -1.8895
 2K5  H23  H  HCH3  0   0.259  -4.3540   7.5035   0.2957
 2K5  H24  H  HCH3  0   0.257  -3.9391   6.8454   1.8823
 2K5  H25  H  HCH3  0   0.259  -2.6967   7.0307   0.6399

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
 2K5  C6   C7   aromatic  1.371  0.020  1.371
 2K5  C6   N2   aromatic  1.333  0.020  1.333
 2K5  C7   C8   aromatic  1.410  0.020  1.410
 2K5  N2   C5   aromatic  1.329  0.020  1.329
 2K5  C8   N4   single    1.354  0.020  1.354
 2K5  C8   N3   aromatic  1.323  0.020  1.323
 2K5  C5   N3   aromatic  1.337  0.020  1.337
 2K5  C5   N1   single    1.354  0.020  1.354
 2K5  N4   C9   single    1.385  0.020  1.385
 2K5  N1   C4   single    1.436  0.020  1.436
 2K5  C9   N6   aromatic  1.321  0.020  1.321
 2K5  C9   C10  aromatic  1.410  0.020  1.410
 2K5  C4   C3   single    1.494  0.020  1.494
 2K5  N6   N5   aromatic  1.334  0.020  1.334
 2K5  C10  C11  aromatic  1.380  0.020  1.380
 2K5  C3   C2   aromatic  1.352  0.020  1.352
 2K5  C3   O    aromatic  1.334  0.020  1.334
 2K5  N5   C11  aromatic  1.341  0.020  1.341
 2K5  C11  C12  single    1.489  0.020  1.489
 2K5  C2   C1   aromatic  1.421  0.020  1.421
 2K5  O    N    aromatic  1.367  0.020  1.367
 2K5  C12  C13  single    1.537  0.020  1.537
 2K5  C1   N    aromatic  1.302  0.020  1.302
 2K5  C1   C    single    1.486  0.020  1.486
 2K5  C13  C14  single    1.503  0.020  1.503
 2K5  C14  C19  aromatic  1.389  0.020  1.389
 2K5  C14  C15  aromatic  1.389  0.020  1.389
 2K5  C19  C18  aromatic  1.392  0.020  1.392
 2K5  C15  C16  aromatic  1.392  0.020  1.392
 2K5  C18  O1   single    1.347  0.020  1.347
 2K5  C18  C17  aromatic  1.395  0.020  1.395
 2K5  O1   C20  single    1.414  0.020  1.414
 2K5  C16  C17  aromatic  1.395  0.020  1.395
 2K5  C16  O2   single    1.347  0.020  1.347
 2K5  O2   C21  single    1.413  0.020  1.413
 2K5  C21  H1   single    0.970  0.020  1.090
 2K5  C21  H2   single    0.970  0.020  1.090
 2K5  C21  H3   single    0.970  0.020  1.090
 2K5  C15  H4   single    0.930  0.020  1.080
 2K5  C17  H5   single    0.930  0.020  1.080
 2K5  C20  H6   single    0.970  0.020  1.090
 2K5  C20  H7   single    0.970  0.020  1.090
 2K5  C20  H8   single    0.970  0.020  1.090
 2K5  C19  H9   single    0.930  0.020  1.080
 2K5  C13  H10  single    0.970  0.020  1.090
 2K5  C13  H11  single    0.970  0.020  1.090
 2K5  C12  H12  single    0.970  0.020  1.090
 2K5  C12  H13  single    0.970  0.020  1.090
 2K5  C10  H14  single    0.930  0.020  1.080
 2K5  N5   H15  single    0.860  0.020  1.020
 2K5  N4   H16  single    0.860  0.020  1.020
 2K5  C7   H17  single    0.930  0.020  1.080
 2K5  C6   H18  single    0.930  0.020  1.080
 2K5  N1   H19  single    0.860  0.020  1.020
 2K5  C4   H20  single    0.970  0.020  1.090
 2K5  C4   H21  single    0.970  0.020  1.090
 2K5  C2   H22  single    0.930  0.020  1.080
 2K5  C    H23  single    0.970  0.020  1.090
 2K5  C    H24  single    0.970  0.020  1.090
 2K5  C    H25  single    0.970  0.020  1.090

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
 2K5  H3   C21  H2   108.70  3.000
 2K5  H3   C21  H1   108.84  3.000
 2K5  H2   C21  H1   108.69  3.000
 2K5  H3   C21  O2   112.07  3.000
 2K5  H2   C21  O2   106.49  3.000
 2K5  H1   C21  O2   111.94  3.000
 2K5  C16  O2   C21  118.98  3.000
 2K5  C17  C16  C15  120.56  3.000
 2K5  C17  C16  O2   123.31  3.000
 2K5  C15  C16  O2   116.13  3.000
 2K5  H4   C15  C14  120.47  3.000
 2K5  H4   C15  C16  119.55  3.000
 2K5  C14  C15  C16  119.97  3.000
 2K5  H5   C17  C18  120.52  3.000
 2K5  H5   C17  C16  120.51  3.000
 2K5  C18  C17  C16  118.97  3.000
 2K5  C19  C18  O1   116.10  3.000
 2K5  O1   C18  C17  123.34  3.000
 2K5  C19  C18  C17  120.56  3.000
 2K5  C20  O1   C18  118.96  3.000
 2K5  H8   C20  H7   108.76  3.000
 2K5  H8   C20  H6   108.82  3.000
 2K5  H7   C20  H6   108.70  3.000
 2K5  H8   C20  O1   111.98  3.000
 2K5  H7   C20  O1   106.50  3.000
 2K5  H6   C20  O1   111.96  3.000
 2K5  H9   C19  C14  120.51  3.000
 2K5  H9   C19  C18  119.49  3.000
 2K5  C14  C19  C18  120.00  3.000
 2K5  C13  C14  C19  120.16  3.000
 2K5  C19  C14  C15  119.95  3.000
 2K5  C13  C14  C15  119.86  3.000
 2K5  H11  C13  H10  106.93  3.000
 2K5  H11  C13  C12  108.99  3.000
 2K5  H10  C13  C12  109.36  3.000
 2K5  H11  C13  C14  110.18  3.000
 2K5  H10  C13  C14  109.93  3.000
 2K5  C12  C13  C14  111.33  3.000
 2K5  H13  C12  H12  106.75  3.000
 2K5  H13  C12  C11  110.09  3.000
 2K5  H12  C12  C11  108.74  3.000
 2K5  H13  C12  C13  109.48  3.000
 2K5  H12  C12  C13  109.40  3.000
 2K5  C11  C12  C13  112.23  3.000
 2K5  N5   C11  C10  106.17  3.000
 2K5  N5   C11  C12  123.07  3.000
 2K5  C10  C11  C12  130.71  3.000
 2K5  H14  C10  C9   128.39  3.000
 2K5  H14  C10  C11  127.41  3.000
 2K5  C9   C10  C11  104.19  3.000
 2K5  H15  N5   N6   119.30  3.000
 2K5  H15  N5   C11  127.24  3.000
 2K5  N6   N5   C11  113.46  3.000
 2K5  C9   N6   N5   104.58  3.000
 2K5  N4   C9   N6   117.19  3.000
 2K5  N6   C9   C10  111.60  3.000
 2K5  N4   C9   C10  131.21  3.000
 2K5  H16  N4   C8   116.51  3.000
 2K5  H16  N4   C9   114.68  3.000
 2K5  C8   N4   C9   128.81  3.000
 2K5  N3   C8   C7   121.39  3.000
 2K5  N3   C8   N4   119.43  3.000
 2K5  C7   C8   N4   119.18  3.000
 2K5  H17  C7   C6   121.99  3.000
 2K5  H17  C7   C8   122.27  3.000
 2K5  C6   C7   C8   115.74  3.000
 2K5  H18  C6   N2   116.16  3.000
 2K5  H18  C6   C7   119.89  3.000
 2K5  N2   C6   C7   123.95  3.000
 2K5  C5   N2   C6   115.32  3.000
 2K5  C5   N3   C8   117.18  3.000
 2K5  N1   C5   N3   115.26  3.000
 2K5  N1   C5   N2   118.31  3.000
 2K5  N3   C5   N2   126.41  3.000
 2K5  H19  N1   C4   117.87  3.000
 2K5  H19  N1   C5   116.35  3.000
 2K5  C4   N1   C5   124.09  3.000
 2K5  H21  C4   H20  107.06  3.000
 2K5  H21  C4   C3   109.97  3.000
 2K5  H20  C4   C3   107.92  3.000
 2K5  H21  C4   N1   109.07  3.000
 2K5  H20  C4   N1   109.23  3.000
 2K5  C3   C4   N1   113.39  3.000
 2K5  O    C3   C2   109.33  3.000
 2K5  O    C3   C4   118.24  3.000
 2K5  C2   C3   C4   132.43  3.000
 2K5  H22  C2   C1   128.14  3.000
 2K5  H22  C2   C3   127.97  3.000
 2K5  C1   C2   C3   103.89  3.000
 2K5  N    O    C3   109.62  3.000
 2K5  C1   N    O    106.49  3.000
 2K5  C    C1   N    121.35  3.000
 2K5  C    C1   C2   127.98  3.000
 2K5  N    C1   C2   110.67  3.000
 2K5  H25  C    H24  108.41  3.000
 2K5  H25  C    H23  107.45  3.000
 2K5  H24  C    H23  108.46  3.000
 2K5  H25  C    C1   110.55  3.000
 2K5  H24  C    C1   111.22  3.000
 2K5  H23  C    C1   110.64  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
 2K5  CONST_01  C19  C14  C15  C16     0.00   0.0  0
 2K5  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 2K5  CONST_03  C18  C19  C14  C15     0.00   0.0  0
 2K5  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 2K5  CONST_05  C14  C19  C18  C17     0.00   0.0  0
 2K5  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 2K5  CONST_07  N6   C9   C10  C11     0.00   0.0  0
 2K5  CONST_08  C9   N6   N5   C11     0.00   0.0  0
 2K5  CONST_09  N5   N6   C9   C10     0.00   0.0  0
 2K5  CONST_10  N6   N5   C11  C10     0.00   0.0  0
 2K5  CONST_11  C9   C10  C11  N5      0.00   0.0  0
 2K5  CONST_12  N2   C6   C7   C8      0.00   0.0  0
 2K5  CONST_13  N2   C5   N3   C8      0.00   0.0  0
 2K5  CONST_14  C5   N2   C6   C7      0.00   0.0  0
 2K5  CONST_15  C5   N3   C8   C7      0.00   0.0  0
 2K5  CONST_16  N3   C8   C7   C6      0.00   0.0  0
 2K5  CONST_17  N3   C5   N2   C6      0.00   0.0  0
 2K5  CONST_18  N    C1   C2   C3      0.00   0.0  0
 2K5  CONST_19  C1   N    O    C3      0.00   0.0  0
 2K5  CONST_20  N    O    C3   C2      0.00   0.0  0
 2K5  CONST_21  O    N    C1   C2      0.00   0.0  0
 2K5  CONST_22  C1   C2   C3   O       0.00   0.0  0
 2K5  CONST_23  C14  C15  C16  O2    180.00   0.0  0
 2K5  CONST_24  C18  C17  C16  O2    180.00   0.0  0
 2K5  CONST_25  C13  C14  C15  C16   180.00   0.0  0
 2K5  CONST_26  O1   C18  C17  C16   180.00   0.0  0
 2K5  CONST_27  C13  C14  C19  C18   180.00   0.0  0
 2K5  CONST_28  C14  C19  C18  O1    180.00   0.0  0
 2K5  CONST_29  C9   C10  C11  C12   180.00   0.0  0
 2K5  CONST_30  N6   N5   C11  C12   180.00   0.0  0
 2K5  CONST_31  N4   C9   C10  C11   180.00   0.0  0
 2K5  CONST_32  N4   C9   N6   N5    180.00   0.0  0
 2K5  CONST_33  C6   C7   C8   N4    180.00   0.0  0
 2K5  CONST_34  C5   N3   C8   N4    180.00   0.0  0
 2K5  CONST_35  N1   C5   N3   C8    180.00   0.0  0
 2K5  CONST_36  N1   C5   N2   C6    180.00   0.0  0
 2K5  CONST_37  C1   C2   C3   C4    180.00   0.0  0
 2K5  CONST_38  N    O    C3   C4    180.00   0.0  0
 2K5  CONST_39  C    C1   C2   C3    180.00   0.0  0
 2K5  CONST_40  C    C1   N    O     180.00   0.0  0
 2K5  CONST_41  H9   C19  C14  C15   180.00   0.0  0
 2K5  CONST_42  H5   C17  C16  C15   180.00   0.0  0
 2K5  CONST_43  H4   C15  C16  C17   180.00   0.0  0
 2K5  CONST_44  H15  N5   C11  C10   180.00   0.0  0
 2K5  CONST_45  H14  C10  C11  N5    180.00   0.0  0
 2K5  CONST_46  H18  C6   C7   C8    180.00   0.0  0
 2K5  CONST_47  H17  C7   C6   N2    180.00   0.0  0
 2K5  CONST_48  H22  C2   C3   O     180.00   0.0  0
 2K5  CONST_49  C4   N1   C5   N2      0.00   0.0  0
 2K5  CONST_50  C4   N1   C5   N3    180.00   0.0  0
 2K5  CONST_51  H19  N1   C5   N2    180.00   0.0  0
 2K5  Var_01    C8   N4   C9   C10    -0.74  30.0  2
 2K5  Var_02    C7   C8   N4   C9   -179.23  30.0  3
 2K5  Var_03    C15  C16  O2   C21  -178.21  30.0  3
 2K5  Var_04    C12  C13  C14  C15   -85.62  30.0  3
 2K5  Var_05    C19  C18  O1   C20   179.37  30.0  2
 2K5  Var_06    C11  C12  C13  C14   179.93  30.0  2
 2K5  Var_07    C10  C11  C12  C13    95.41  30.0  2
 2K5  Var_08    C3   C4   N1   C5     90.31  30.0  3
 2K5  Var_09    C2   C3   C4   N1    127.98  30.0  2
 2K5  Var_10    H23  C    C1   C2     59.31  30.0  2
 2K5  Var_11    H1   C21  O2   C16    60.24  30.0  3
 2K5  Var_12    H6   C20  O1   C18    62.27  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
 2K5  plan-1  C12  0.020
 2K5  plan-1  C11  0.020
 2K5  plan-1  C10  0.020
 2K5  plan-1  N5   0.020
 2K5  plan-1  N6   0.020
 2K5  plan-1  C9   0.020
 2K5  plan-1  N4   0.020
 2K5  plan-1  H14  0.020
 2K5  plan-1  H15  0.020
 2K5  plan-2  C4   0.020
 2K5  plan-2  C3   0.020
 2K5  plan-2  C2   0.020
 2K5  plan-2  O    0.020
 2K5  plan-2  N    0.020
 2K5  plan-2  C1   0.020
 2K5  plan-2  C    0.020
 2K5  plan-2  H22  0.020
 2K5  plan-3  O2   0.020
 2K5  plan-3  C16  0.020
 2K5  plan-3  C15  0.020
 2K5  plan-3  C17  0.020
 2K5  plan-3  C18  0.020
 2K5  plan-3  O1   0.020
 2K5  plan-3  C19  0.020
 2K5  plan-3  C14  0.020
 2K5  plan-3  C13  0.020
 2K5  plan-3  H4   0.020
 2K5  plan-3  H5   0.020
 2K5  plan-3  H9   0.020
 2K5  plan-4  N4   0.020
 2K5  plan-4  C8   0.020
 2K5  plan-4  C7   0.020
 2K5  plan-4  C6   0.020
 2K5  plan-4  N2   0.020
 2K5  plan-4  N3   0.020
 2K5  plan-4  C5   0.020
 2K5  plan-4  N1   0.020
 2K5  plan-4  H17  0.020
 2K5  plan-4  H18  0.020
 2K5  plan-5  C5   0.020
 2K5  plan-5  N1   0.020
 2K5  plan-5  C4   0.020
 2K5  plan-5  H19  0.020

