# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:28:23 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5-{4-[3-(2-methylpyrimidin-5-yl)phenyl]piperazin-1-yl}pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(cn1)c2cccc(c2)N3CCN(CC3)c4cnc(N)nc4N
#
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
 K9A  K9A  5-{4-[3-(2-methylpyrimidin-5-yl)phenyl]piperazin-1-yl}pyrimidine-2,4-diamine  ligand  49  27  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K9A
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
 K9A  N7   N  NH2   0  -0.823   7.9929   1.6858   0.1693
 K9A  C17  C  CR6   0   0.523   6.7087   1.2483   0.1185
 K9A  N4   N  N     0  -0.486   5.8083   1.9178   0.8343
 K9A  C16  C  CR16  0  -0.065   4.5533   1.4724   0.7430
 K9A  N5   N  N     0  -0.500   6.4645   0.2093  -0.6826
 K9A  C18  C  CR6   0   0.461   5.2087  -0.2086  -0.7742
 K9A  N6   N  NH2   0  -0.816   4.9361  -1.2657  -1.5614
 K9A  C15  C  CR6   0   0.096   4.1669   0.4125  -0.0405
 K9A  N3   N  NT    0  -0.516   2.8539  -0.0906  -0.1670
 K9A  C12  C  CH2   0  -0.300   2.5412  -1.1613   0.7659
 K9A  C11  C  CH2   0  -0.315   1.2480  -1.8517   0.3768
 K9A  C13  C  CH2   0  -0.300   1.7847   0.8869  -0.1787
 K9A  C14  C  CH2   0  -0.306   0.4906   0.2213  -0.6045
 K9A  N2   N  NT    0  -0.524   0.1609  -0.8985   0.2677
 K9A  C9   C  CR6   0   0.407  -1.1383  -1.3947   0.2268
 K9A  C8   C  CR16  0  -0.370  -1.4163  -2.7680   0.2840
 K9A  C7   C  CR16  0  -0.225  -2.7252  -3.2281   0.2845
 K9A  C6   C  CR16  0  -0.349  -3.7958  -2.3549   0.2115
 K9A  C10  C  CR16  0  -0.416  -2.2331  -0.5206   0.1500
 K9A  C5   C  CR6   0   0.118  -3.5435  -0.9840   0.1400
 K9A  C3   C  CR6   0  -0.050  -4.6581  -0.0265   0.0580
 K9A  C2   C  CR16  0  -0.055  -4.6462   1.2078   0.6996
 K9A  N    N  N     0  -0.405  -5.6478   2.0695   0.6234
 K9A  C4   C  CR16  0  -0.054  -5.8155  -0.2881  -0.6690
 K9A  N1   N  N     0  -0.405  -6.8255   0.5629  -0.7479
 K9A  C1   C  CR6   0   0.350  -6.7068   1.7184  -0.1001
 K9A  C    C  CH3   0  -0.729  -7.8293   2.6981  -0.2137
 K9A  H1   H  HNH2  0   0.386   8.2424   2.2909   0.9329
 K9A  H2   H  HNH2  0   0.386   8.7107   1.0480  -0.1300
 K9A  H3   H  HCR6  0   0.259   3.8159   2.0122   1.3302
 K9A  H4   H  HNH2  0   0.393   3.9727  -1.4135  -1.8157
 K9A  H5   H  HNH2  0   0.391   5.6335  -1.5598  -2.2242
 K9A  H6   H  HCH2  0   0.255   3.3425  -1.9018   0.7573
 K9A  H7   H  HCH2  0   0.218   2.4587  -0.7799   1.7955
 K9A  H8   H  HCH2  0   0.218   1.3956  -2.4076  -0.5616
 K9A  H9   H  HCH2  0   0.256   1.0208  -2.5800   1.1558
 K9A  H10  H  HCH2  0   0.210   1.6356   1.3580   0.8050
 K9A  H11  H  HCH2  0   0.254   2.0226   1.6770  -0.8924
 K9A  H12  H  HCH2  0   0.259  -0.2938   0.9730  -0.5723
 K9A  H13  H  HCH2  0   0.222   0.5820  -0.1146  -1.6470
 K9A  H14  H  HCR6  0   0.272  -0.6202  -3.4973   0.3138
 K9A  H15  H  HCR6  0   0.257  -2.9040  -4.2945   0.3358
 K9A  H16  H  HCR6  0   0.251  -4.8105  -2.7311   0.2282
 K9A  H17  H  HCR6  0   0.262  -2.0685   0.5467   0.0901
 K9A  H18  H  HCR6  0   0.271  -3.8010   1.5033   1.3133
 K9A  H19  H  HCR6  0   0.271  -5.9220  -1.2193  -1.2167
 K9A  H20  H  HCH3  0   0.262  -7.6862   3.3316  -1.0922
 K9A  H21  H  HCH3  0   0.252  -8.7837   2.1890  -0.3311
 K9A  H22  H  HCH3  0   0.252  -7.8708   3.3482   0.6575

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
 K9A  C7   C8   aromatic  1.387  0.020  1.387
 K9A  C7   C6   aromatic  1.383  0.020  1.383
 K9A  C8   C9   aromatic  1.402  0.020  1.402
 K9A  C11  C12  single    1.517  0.020  1.517
 K9A  C11  N2   single    1.450  0.020  1.450
 K9A  C6   C5   aromatic  1.396  0.020  1.396
 K9A  C9   N2   single    1.391  0.020  1.391
 K9A  C9   C10  aromatic  1.403  0.020  1.403
 K9A  C12  N3   single    1.454  0.020  1.454
 K9A  N2   C14  single    1.457  0.020  1.457
 K9A  C5   C10  aromatic  1.390  0.020  1.390
 K9A  C5   C3   single    1.472  0.020  1.472
 K9A  C14  C13  single    1.516  0.020  1.516
 K9A  N6   C18  single    1.346  0.020  1.346
 K9A  C2   C3   aromatic  1.391  0.020  1.391
 K9A  C2   N    aromatic  1.324  0.020  1.324
 K9A  N3   C13  single    1.449  0.020  1.449
 K9A  N3   C15  single    1.412  0.020  1.412
 K9A  C3   C4   aromatic  1.392  0.020  1.392
 K9A  C18  C15  aromatic  1.418  0.020  1.418
 K9A  C18  N5   aromatic  1.327  0.020  1.327
 K9A  C15  C16  aromatic  1.374  0.020  1.374
 K9A  N    C1   aromatic  1.330  0.020  1.330
 K9A  C4   N1   aromatic  1.323  0.020  1.323
 K9A  N5   C17  aromatic  1.335  0.020  1.335
 K9A  C16  N4   aromatic  1.335  0.020  1.335
 K9A  C1   N1   aromatic  1.330  0.020  1.330
 K9A  C1   C    single    1.494  0.020  1.494
 K9A  C17  N4   aromatic  1.331  0.020  1.331
 K9A  C17  N7   single    1.358  0.020  1.358
 K9A  N7   H1   single    0.890  0.020  1.040
 K9A  N7   H2   single    0.890  0.020  1.040
 K9A  C16  H3   single    0.930  0.020  1.080
 K9A  N6   H4   single    0.890  0.020  1.040
 K9A  N6   H5   single    0.890  0.020  1.040
 K9A  C12  H6   single    0.970  0.020  1.090
 K9A  C12  H7   single    0.970  0.020  1.090
 K9A  C11  H8   single    0.970  0.020  1.090
 K9A  C11  H9   single    0.970  0.020  1.090
 K9A  C13  H10  single    0.970  0.020  1.090
 K9A  C13  H11  single    0.970  0.020  1.090
 K9A  C14  H12  single    0.970  0.020  1.090
 K9A  C14  H13  single    0.970  0.020  1.090
 K9A  C8   H14  single    0.930  0.020  1.080
 K9A  C7   H15  single    0.930  0.020  1.080
 K9A  C6   H16  single    0.930  0.020  1.080
 K9A  C10  H17  single    0.930  0.020  1.080
 K9A  C2   H18  single    0.930  0.020  1.080
 K9A  C4   H19  single    0.930  0.020  1.080
 K9A  C    H20  single    0.970  0.020  1.090
 K9A  C    H21  single    0.970  0.020  1.090
 K9A  C    H22  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
 K9A  H2   N7   H1   115.49  3.000
 K9A  H2   N7   C17  117.36  3.000
 K9A  H1   N7   C17  117.19  3.000
 K9A  N5   C17  N4   126.21  3.000
 K9A  N4   C17  N7   117.24  3.000
 K9A  N5   C17  N7   116.51  3.000
 K9A  C16  N4   C17  115.56  3.000
 K9A  H3   C16  C15  120.06  3.000
 K9A  H3   C16  N4   115.82  3.000
 K9A  C15  C16  N4   124.12  3.000
 K9A  C18  N5   C17  117.38  3.000
 K9A  C15  C18  N6   119.87  3.000
 K9A  C15  C18  N5   121.47  3.000
 K9A  N6   C18  N5   118.65  3.000
 K9A  H5   N6   H4   116.99  3.000
 K9A  H5   N6   C18  118.33  3.000
 K9A  H4   N6   C18  117.17  3.000
 K9A  N3   C15  C18  118.75  3.000
 K9A  C18  C15  C16  115.25  3.000
 K9A  N3   C15  C16  126.00  3.000
 K9A  C13  N3   C12  110.08  3.000
 K9A  C13  N3   C15  116.53  3.000
 K9A  C12  N3   C15  113.89  3.000
 K9A  H7   C12  H6   107.31  3.000
 K9A  H7   C12  C11  109.49  3.000
 K9A  H6   C12  C11  108.37  3.000
 K9A  H7   C12  N3   111.16  3.000
 K9A  H6   C12  N3   109.68  3.000
 K9A  C11  C12  N3   110.73  3.000
 K9A  H9   C11  H8   107.44  3.000
 K9A  H9   C11  N2   109.67  3.000
 K9A  H8   C11  N2   111.62  3.000
 K9A  H9   C11  C12  107.36  3.000
 K9A  H8   C11  C12  109.53  3.000
 K9A  N2   C11  C12  111.06  3.000
 K9A  H11  C13  H10  107.71  3.000
 K9A  H11  C13  C14  108.68  3.000
 K9A  H10  C13  C14  108.85  3.000
 K9A  H11  C13  N3   109.45  3.000
 K9A  H10  C13  N3   112.42  3.000
 K9A  C14  C13  N3   109.63  3.000
 K9A  H13  C14  H12  107.42  3.000
 K9A  H13  C14  N2   110.59  3.000
 K9A  H12  C14  N2   110.52  3.000
 K9A  H13  C14  C13  109.24  3.000
 K9A  H12  C14  C13  107.70  3.000
 K9A  N2   C14  C13  111.24  3.000
 K9A  C9   N2   C14  117.89  3.000
 K9A  C14  N2   C11  112.37  3.000
 K9A  C9   N2   C11  117.89  3.000
 K9A  C10  C9   C8   117.23  3.000
 K9A  C10  C9   N2   120.53  3.000
 K9A  C8   C9   N2   122.22  3.000
 K9A  H14  C8   C7   118.13  3.000
 K9A  H14  C8   C9   121.08  3.000
 K9A  C7   C8   C9   120.79  3.000
 K9A  H15  C7   C6   119.77  3.000
 K9A  H15  C7   C8   118.85  3.000
 K9A  C6   C7   C8   121.38  3.000
 K9A  H16  C6   C5   120.77  3.000
 K9A  H16  C6   C7   120.35  3.000
 K9A  C5   C6   C7   118.86  3.000
 K9A  H17  C10  C5   118.17  3.000
 K9A  H17  C10  C9   119.94  3.000
 K9A  C5   C10  C9   121.90  3.000
 K9A  C3   C5   C10  119.84  3.000
 K9A  C3   C5   C6   120.33  3.000
 K9A  C10  C5   C6   119.83  3.000
 K9A  C4   C3   C2   114.51  3.000
 K9A  C4   C3   C5   122.46  3.000
 K9A  C2   C3   C5   123.03  3.000
 K9A  H18  C2   N    116.39  3.000
 K9A  H18  C2   C3   120.60  3.000
 K9A  N    C2   C3   123.00  3.000
 K9A  C1   N    C2   117.53  3.000
 K9A  H19  C4   N1   116.54  3.000
 K9A  H19  C4   C3   120.43  3.000
 K9A  N1   C4   C3   123.03  3.000
 K9A  C1   N1   C4   117.49  3.000
 K9A  C    C1   N1   117.74  3.000
 K9A  C    C1   N    117.81  3.000
 K9A  N1   C1   N    124.44  3.000
 K9A  H22  C    H21  109.43  3.000
 K9A  H22  C    H20  107.60  3.000
 K9A  H21  C    H20  107.42  3.000
 K9A  H22  C    C1   111.07  3.000
 K9A  H21  C    C1   111.12  3.000
 K9A  H20  C    C1   110.05  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
 K9A  CONST_01  C15  C18  N5   C17     0.00   0.0  0
 K9A  CONST_02  C15  C16  N4   C17     0.00   0.0  0
 K9A  CONST_03  C18  C15  C16  N4      0.00   0.0  0
 K9A  CONST_04  C18  N5   C17  N4      0.00   0.0  0
 K9A  CONST_05  N5   C18  C15  C16     0.00   0.0  0
 K9A  CONST_06  N5   C17  N4   C16     0.00   0.0  0
 K9A  CONST_07  C6   C7   C8   C9      0.00   0.0  0
 K9A  CONST_08  C6   C5   C10  C9      0.00   0.0  0
 K9A  CONST_09  C3   C5   C10  C9    180.00   0.0  0
 K9A  CONST_10  C5   C6   C7   C8      0.00   0.0  0
 K9A  CONST_11  C5   C10  C9   C8      0.00   0.0  0
 K9A  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 K9A  CONST_13  C10  C5   C6   C7      0.00   0.0  0
 K9A  CONST_14  C3   C5   C6   C7    180.00   0.0  0
 K9A  CONST_19  N    C2   C3   C5    180.00   0.0  0
 K9A  CONST_20  N1   C4   C3   C5    180.00   0.0  0
 K9A  CONST_21  C1   N    C2   C3      0.00   0.0  0
 K9A  CONST_22  C1   N1   C4   C3      0.00   0.0  0
 K9A  CONST_23  N1   C4   C3   C2      0.00   0.0  0
 K9A  CONST_24  N1   C1   N    C2      0.00   0.0  0
 K9A  CONST_25  C4   C3   C2   N       0.00   0.0  0
 K9A  CONST_26  C4   N1   C1   N       0.00   0.0  0
 K9A  CONST_27  N3   C15  C16  N4    180.00   0.0  0
 K9A  CONST_28  N3   C15  C18  N5    180.00   0.0  0
 K9A  CONST_29  C7   C8   C9   N2    180.00   0.0  0
 K9A  CONST_30  C5   C10  C9   N2    180.00   0.0  0
 K9A  CONST_31  C18  N5   C17  N7    180.00   0.0  0
 K9A  CONST_32  C16  N4   C17  N7    180.00   0.0  0
 K9A  CONST_33  N6   C18  N5   C17   180.00   0.0  0
 K9A  CONST_34  N6   C18  C15  C16   180.00   0.0  0
 K9A  CONST_35  N3   C15  C18  N6      0.00   0.0  0
 K9A  CONST_36  C    C1   N    C2    180.00   0.0  0
 K9A  CONST_37  C    C1   N1   C4    180.00   0.0  0
 K9A  CONST_38  H3   C16  N4   C17   180.00   0.0  0
 K9A  CONST_39  H14  C8   C9   N2      0.00   0.0  0
 K9A  CONST_40  H17  C10  C9   N2      0.00   0.0  0
 K9A  CONST_41  H15  C7   C8   C9    180.00   0.0  0
 K9A  CONST_42  H16  C6   C7   C8    180.00   0.0  0
 K9A  CONST_43  H18  C2   C3   C5      0.00   0.0  0
 K9A  CONST_44  H19  C4   C3   C5      0.00   0.0  0
 K9A  CONST_48  H5   N6   C18  N5      0.00   0.0  0
 K9A  Var_01    C12  N3   C15  C16   -91.91  30.0  2
 K9A  Var_02    C11  C12  N3   C15  -167.49  30.0  1
 K9A  Var_03    C14  C13  N3   C15   168.34  30.0  1
 K9A  Var_04    N2   C11  C12  N3    -55.19  30.0  1
 K9A  Var_05    N2   C14  C13  N3     57.00  30.0  1
 K9A  Var_06    C9   N2   C11  C12  -165.34  30.0  1
 K9A  Var_07    C8   C9   N2   C11    -0.16  30.0  2
 K9A  Var_08    C13  C14  N2   C11   -53.69  30.0  1
 K9A  Var_09    H20  C    C1   N      91.39  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
 K9A  plan-1  N7   0.020
 K9A  plan-1  C17  0.020
 K9A  plan-1  N4   0.020
 K9A  plan-1  C16  0.020
 K9A  plan-1  N5   0.020
 K9A  plan-1  C18  0.020
 K9A  plan-1  N6   0.020
 K9A  plan-1  C15  0.020
 K9A  plan-1  N3   0.020
 K9A  plan-1  H3   0.020
 K9A  plan-2  N2   0.020
 K9A  plan-2  C9   0.020
 K9A  plan-2  C8   0.020
 K9A  plan-2  C7   0.020
 K9A  plan-2  C6   0.020
 K9A  plan-2  C10  0.020
 K9A  plan-2  C5   0.020
 K9A  plan-2  C3   0.020
 K9A  plan-2  H14  0.020
 K9A  plan-2  H15  0.020
 K9A  plan-2  H16  0.020
 K9A  plan-2  H17  0.020
 K9A  plan-3  C5   0.020
 K9A  plan-3  C3   0.020
 K9A  plan-3  C2   0.020
 K9A  plan-3  N    0.020
 K9A  plan-3  C4   0.020
 K9A  plan-3  N1   0.020
 K9A  plan-3  C1   0.020
 K9A  plan-3  C    0.020
 K9A  plan-3  H18  0.020
 K9A  plan-3  H19  0.020
 K9A  plan-4  N7   0.020
 K9A  plan-4  C17  0.020
 K9A  plan-4  H1   0.020
 K9A  plan-4  H2   0.020
 K9A  plan-5  C18  0.020
 K9A  plan-5  N6   0.020
 K9A  plan-5  H4   0.020
 K9A  plan-5  H5   0.020

