# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:27:19 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: ~{N}-[6-(4-ethylpiperazin-1-yl)-2-methyl-pyrimidin-4-yl]-5-pyridin-4-yl-1,3-thiazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1CCN(CC1)c2cc(Nc3sc(cn3)c4ccncc4)nc(C)n2
#
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
 DJX  DJX  ~{N}-[6-(4-ethylpiperazin-1-yl)-2-methyl-pyrimidin-4-yl]-5-pyridin-4-yl-1,3-thiazol-2-amine  ligand  50  27  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DJX
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
 DJX  C10  C  CH2   0  -0.307   5.2187   1.1993  -0.5461
 DJX  N12  N  NT    0  -0.420   6.7770  -0.6681  -0.2961
 DJX  C13  C  CH2   0  -0.283   5.6586  -1.5550  -0.0530
 DJX  C15  C  CH2   0  -0.269   8.0113  -1.1463   0.3039
 DJX  C17  C  CR5   0   0.316  -1.9724   0.0808  -0.2219
 DJX  C20  C  CR15  0  -0.018  -3.8352   1.2195  -0.1994
 DJX  C22  C  CR6   0   0.254  -5.8156  -0.3689  -0.0438
 DJX  C24  C  CR16  0  -0.058  -8.1302   0.2254   0.1618
 DJX  C26  C  CR16  0  -0.057  -7.6079  -1.9657  -0.0615
 DJX  C1   C  CR6   0   0.545   0.4650   0.5344  -0.2018
 DJX  C2   C  CR16  0  -0.541   1.6980  -0.0747  -0.3883
 DJX  C3   C  CR6   0   0.587   2.8262   0.7500  -0.2866
 DJX  C5   C  CR6   0   0.356   1.4476   2.5320   0.0988
 DJX  C7   C  CH3   0  -0.728   1.3000   3.9940   0.3847
 DJX  C11  C  CH2   0  -0.287   6.4399   0.6608   0.1726
 DJX  C14  C  CH2   0  -0.306   4.4053  -1.0755  -0.7647
 DJX  C16  C  CH3   0  -0.679   8.5578  -2.4007  -0.3573
 DJX  C19  C  CR5   0  -0.274  -4.4092  -0.0129  -0.1091
 DJX  C23  C  CR16  0  -0.402  -6.8029   0.6087   0.1089
 DJX  C27  C  CR16  0  -0.405  -6.2518  -1.6916  -0.1294
 DJX  N4   N  N     0  -0.500   2.6708   2.0656  -0.0559
 DJX  N6   N  N     0  -0.461   0.3203   1.8285   0.0458
 DJX  N9   N  NT    0  -0.507   4.0940   0.2914  -0.3998
 DJX  N21  N  N     0  -0.392  -2.4797   1.2720  -0.2660
 DJX  N25  N  N     0  -0.412  -8.5443  -1.0360   0.0804
 DJX  S18  S  S2    0   0.195  -3.1436  -1.2037  -0.0907
 DJX  H1   H  HCH2  0   0.272   4.9536   2.1714  -0.1428
 DJX  H2   H  HCH2  0   0.249   5.8844  -2.5555  -0.4243
 DJX  H3   H  HCH2  0   0.230   8.7522  -0.3489   0.2063
 DJX  H4   H  HCH2  0   0.191   7.8900  -1.3228   1.3861
 DJX  H5   H  HCR5  0   0.280  -4.3919   2.1462  -0.2348
 DJX  H6   H  HCR6  0   0.268  -8.8985   0.9810   0.2808
 DJX  H7   H  HCR6  0   0.267  -7.9477  -2.9934  -0.1272
 DJX  H8   H  HCR6  0   0.284   1.7538  -1.1302  -0.6056
 DJX  H9   H  HCH3  0   0.256   1.0455   4.1450   1.4356
 DJX  H10  H  HCH3  0   0.245   2.2212   4.5327   0.1768
 DJX  H11  H  HCH3  0   0.249   0.4906   4.4220  -0.2053
 DJX  H12  H  HCH2  0   0.244   7.2770   1.3352  -0.0222
 DJX  H13  H  HCH2  0   0.236   4.5432  -1.1555  -1.8498
 DJX  H14  H  HCH3  0   0.227   7.9036  -3.2631  -0.2273
 DJX  H15  H  HCH3  0   0.223   8.7048  -2.2450  -1.4266
 DJX  H16  H  HCH3  0   0.233   9.5217  -2.6588   0.0812
 DJX  H17  H  HCR6  0   0.269  -6.5538   1.6575   0.1938
 DJX  H18  H  HCR6  0   0.267  -5.5581  -2.5136  -0.2530
 DJX  H19  H  HNH1  0   0.429  -0.4666  -1.2534  -0.3755
 DJX  H20  H  HCH2  0   0.228   5.4497   1.3305  -1.6106
 DJX  H21  H  HCH2  0   0.197   5.4453  -1.6513   1.0262
 DJX  H22  H  HCH2  0   0.196   6.2560   0.6788   1.2611
 DJX  H23  H  HCH2  0   0.263   3.5942  -1.7434  -0.4864
 DJX  N8   N  NH1   0  -0.751  -0.6575  -0.2679  -0.2753

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
 DJX  C15  N12  single    1.453  0.020  1.453
 DJX  C15  C16  single    1.520  0.020  1.520
 DJX  N12  C11  single    1.449  0.020  1.449
 DJX  N12  C13  single    1.448  0.020  1.448
 DJX  C11  C10  single    1.516  0.020  1.516
 DJX  C13  C14  single    1.519  0.020  1.519
 DJX  C10  N9   single    1.453  0.020  1.453
 DJX  C14  N9   single    1.449  0.020  1.449
 DJX  N9   C3   single    1.353  0.020  1.353
 DJX  C3   C2   aromatic  1.401  0.020  1.401
 DJX  C3   N4   aromatic  1.345  0.020  1.345
 DJX  C2   C1   aromatic  1.388  0.020  1.388
 DJX  N4   C5   aromatic  1.318  0.020  1.318
 DJX  C1   N8   single    1.382  0.020  1.382
 DJX  C1   N6   aromatic  1.326  0.020  1.326
 DJX  N8   C17  single    1.361  0.020  1.361
 DJX  C5   N6   aromatic  1.330  0.020  1.330
 DJX  C5   C7   single    1.497  0.020  1.497
 DJX  C17  N21  aromatic  1.295  0.020  1.295
 DJX  C17  S18  aromatic  1.743  0.020  1.743
 DJX  N21  C20  aromatic  1.358  0.020  1.358
 DJX  C20  C19  aromatic  1.362  0.020  1.362
 DJX  S18  C19  aromatic  1.738  0.020  1.738
 DJX  C19  C22  single    1.452  0.020  1.452
 DJX  C22  C27  aromatic  1.395  0.020  1.395
 DJX  C22  C23  aromatic  1.398  0.020  1.398
 DJX  C27  C26  aromatic  1.385  0.020  1.385
 DJX  C23  C24  aromatic  1.382  0.020  1.382
 DJX  C26  N25  aromatic  1.327  0.020  1.327
 DJX  C24  N25  aromatic  1.330  0.020  1.330
 DJX  C10  H1   single    0.970  0.020  1.090
 DJX  C13  H2   single    0.970  0.020  1.090
 DJX  C15  H3   single    0.970  0.020  1.090
 DJX  C15  H4   single    0.970  0.020  1.090
 DJX  C20  H5   single    0.930  0.020  1.080
 DJX  C24  H6   single    0.930  0.020  1.080
 DJX  C26  H7   single    0.930  0.020  1.080
 DJX  C2   H8   single    0.930  0.020  1.080
 DJX  C7   H9   single    0.970  0.020  1.090
 DJX  C7   H10  single    0.970  0.020  1.090
 DJX  C7   H11  single    0.970  0.020  1.090
 DJX  C11  H12  single    0.970  0.020  1.090
 DJX  C14  H13  single    0.970  0.020  1.090
 DJX  C16  H14  single    0.970  0.020  1.090
 DJX  C16  H15  single    0.970  0.020  1.090
 DJX  C16  H16  single    0.970  0.020  1.090
 DJX  C23  H17  single    0.930  0.020  1.080
 DJX  C27  H18  single    0.930  0.020  1.080
 DJX  N8   H19  single    0.860  0.020  1.020
 DJX  C10  H20  single    0.970  0.020  1.090
 DJX  C13  H21  single    0.970  0.020  1.090
 DJX  C11  H22  single    0.970  0.020  1.090
 DJX  C14  H23  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
 DJX  H20  C10  H1   107.75  3.000
 DJX  H20  C10  N9   109.60  3.000
 DJX  H1   C10  N9   109.46  3.000
 DJX  H20  C10  C11  109.45  3.000
 DJX  H1   C10  C11  109.80  3.000
 DJX  N9   C10  C11  110.72  3.000
 DJX  C11  N12  C15  111.46  3.000
 DJX  C11  N12  C13  109.13  3.000
 DJX  C15  N12  C13  112.65  3.000
 DJX  H21  C13  H2   107.02  3.000
 DJX  H21  C13  C14  109.03  3.000
 DJX  H2   C13  C14  107.51  3.000
 DJX  H21  C13  N12  111.51  3.000
 DJX  H2   C13  N12  110.16  3.000
 DJX  C14  C13  N12  111.42  3.000
 DJX  H4   C15  H3   106.19  3.000
 DJX  H4   C15  C16  109.53  3.000
 DJX  H3   C15  C16  108.64  3.000
 DJX  H4   C15  N12  111.36  3.000
 DJX  H3   C15  N12  107.39  3.000
 DJX  C16  C15  N12  113.42  3.000
 DJX  S18  C17  N21  114.65  3.000
 DJX  S18  C17  N8   117.59  3.000
 DJX  N21  C17  N8   127.76  3.000
 DJX  H5   C20  N21  118.62  3.000
 DJX  H5   C20  C19  124.08  3.000
 DJX  N21  C20  C19  117.30  3.000
 DJX  C27  C22  C23  116.67  3.000
 DJX  C23  C22  C19  121.17  3.000
 DJX  C27  C22  C19  122.16  3.000
 DJX  H6   C24  N25  116.55  3.000
 DJX  H6   C24  C23  119.43  3.000
 DJX  N25  C24  C23  124.02  3.000
 DJX  H7   C26  N25  116.69  3.000
 DJX  H7   C26  C27  119.43  3.000
 DJX  N25  C26  C27  123.88  3.000
 DJX  N8   C1   N6   119.22  3.000
 DJX  N6   C1   C2   123.41  3.000
 DJX  N8   C1   C2   117.37  3.000
 DJX  H8   C2   C3   123.28  3.000
 DJX  H8   C2   C1   120.15  3.000
 DJX  C3   C2   C1   116.57  3.000
 DJX  N9   C3   N4   117.02  3.000
 DJX  N4   C3   C2   119.68  3.000
 DJX  N9   C3   C2   123.29  3.000
 DJX  N6   C5   N4   126.50  3.000
 DJX  N6   C5   C7   116.14  3.000
 DJX  N4   C5   C7   117.35  3.000
 DJX  H11  C7   H10  109.36  3.000
 DJX  H11  C7   H9   107.09  3.000
 DJX  H10  C7   H9   108.24  3.000
 DJX  H11  C7   C5   110.71  3.000
 DJX  H10  C7   C5   111.34  3.000
 DJX  H9   C7   C5   109.99  3.000
 DJX  H22  C11  H12  107.06  3.000
 DJX  H22  C11  N12  111.88  3.000
 DJX  H12  C11  N12  109.28  3.000
 DJX  H22  C11  C10  109.12  3.000
 DJX  H12  C11  C10  108.27  3.000
 DJX  N12  C11  C10  111.09  3.000
 DJX  H23  C14  H13  107.60  3.000
 DJX  H23  C14  N9   110.79  3.000
 DJX  H13  C14  N9   110.19  3.000
 DJX  H23  C14  C13  107.56  3.000
 DJX  H13  C14  C13  109.68  3.000
 DJX  N9   C14  C13  110.92  3.000
 DJX  H16  C16  H15  108.00  3.000
 DJX  H16  C16  H14  107.17  3.000
 DJX  H15  C16  H14  108.10  3.000
 DJX  H16  C16  C15  109.79  3.000
 DJX  H15  C16  C15  110.93  3.000
 DJX  H14  C16  C15  112.66  3.000
 DJX  S18  C19  C22  122.47  3.000
 DJX  C22  C19  C20  129.25  3.000
 DJX  S18  C19  C20  108.28  3.000
 DJX  H17  C23  C24  119.15  3.000
 DJX  H17  C23  C22  121.61  3.000
 DJX  C24  C23  C22  119.24  3.000
 DJX  H18  C27  C26  118.86  3.000
 DJX  H18  C27  C22  121.76  3.000
 DJX  C26  C27  C22  119.38  3.000
 DJX  C5   N4   C3   118.27  3.000
 DJX  C5   N6   C1   115.55  3.000
 DJX  C14  N9   C3   122.84  3.000
 DJX  C3   N9   C10  121.47  3.000
 DJX  C14  N9   C10  113.45  3.000
 DJX  C20  N21  C17  110.71  3.000
 DJX  C26  N25  C24  116.82  3.000
 DJX  C19  S18  C17   89.06  3.000
 DJX  H19  N8   C1   114.76  3.000
 DJX  H19  N8   C17  115.90  3.000
 DJX  C1   N8   C17  129.34  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
 DJX  CONST_01  C19  C20  N21  C17     0.00   0.0  0
 DJX  CONST_02  C20  C19  S18  C17     0.00   0.0  0
 DJX  CONST_03  C22  C19  S18  C17   180.00   0.0  0
 DJX  CONST_04  S18  C17  N21  C20     0.00   0.0  0
 DJX  CONST_05  C27  C22  C19  C20   180.00   0.0  0
 DJX  CONST_06  C23  C22  C19  C20     0.00   0.0  0
 DJX  CONST_07  N21  C20  C19  C22   180.00   0.0  0
 DJX  CONST_08  N25  C26  C27  C22     0.00   0.0  0
 DJX  CONST_09  N25  C24  C23  C22     0.00   0.0  0
 DJX  CONST_10  C19  C22  C23  C24   180.00   0.0  0
 DJX  CONST_11  C27  C22  C23  C24     0.00   0.0  0
 DJX  CONST_12  C27  C26  N25  C24     0.00   0.0  0
 DJX  CONST_13  C19  C22  C27  C26   180.00   0.0  0
 DJX  CONST_14  C23  C22  C27  C26     0.00   0.0  0
 DJX  CONST_15  C23  C24  N25  C26     0.00   0.0  0
 DJX  CONST_16  N4   C3   C2   C1      0.00   0.0  0
 DJX  CONST_17  N4   C5   N6   C1      0.00   0.0  0
 DJX  CONST_18  C5   N4   C3   C2      0.00   0.0  0
 DJX  CONST_19  C5   N6   C1   C2      0.00   0.0  0
 DJX  CONST_20  N6   C1   C2   C3      0.00   0.0  0
 DJX  CONST_21  N6   C5   N4   C3      0.00   0.0  0
 DJX  CONST_22  N21  C17  S18  C19     0.00   0.0  0
 DJX  CONST_23  S18  C19  C22  C23   180.00   0.0  0
 DJX  CONST_24  S18  C19  C22  C27     0.00   0.0  0
 DJX  CONST_25  S18  C19  C20  N21     0.00   0.0  0
 DJX  CONST_26  N9   C3   C2   C1    180.00   0.0  0
 DJX  CONST_27  N9   C3   N4   C5    180.00   0.0  0
 DJX  CONST_28  N8   C17  N21  C20   180.00   0.0  0
 DJX  CONST_29  C7   C5   N6   C1    180.00   0.0  0
 DJX  CONST_30  N8   C1   C2   C3    180.00   0.0  0
 DJX  CONST_31  C7   C5   N4   C3    180.00   0.0  0
 DJX  CONST_32  N8   C1   N6   C5    180.00   0.0  0
 DJX  CONST_33  N8   C17  S18  C19   180.00   0.0  0
 DJX  CONST_34  H5   C20  N21  C17   180.00   0.0  0
 DJX  CONST_35  H7   C26  C27  C22   180.00   0.0  0
 DJX  CONST_36  H6   C24  C23  C22   180.00   0.0  0
 DJX  CONST_37  H18  C27  C22  C19     0.00   0.0  0
 DJX  CONST_38  H17  C23  C22  C19     0.00   0.0  0
 DJX  CONST_39  H8   C2   C3   N4    180.00   0.0  0
 DJX  Var_01    C13  N12  C11  C10   -59.83  30.0  1
 DJX  Var_02    C13  C14  N9   C10    51.25  30.0  1
 DJX  Var_03    C2   C3   N9   C10   167.97  30.0  2
 DJX  Var_04    N9   C10  C11  N12    56.01  30.0  1
 DJX  Var_05    N9   C14  C13  N12   -54.89  30.0  1
 DJX  Var_06    C11  C10  N9   C3    144.68  30.0  1
 DJX  Var_07    C14  C13  N12  C11    59.25  30.0  1
 DJX  Var_08    C2   C1   N8   C17  -175.10  30.0  2
 DJX  Var_09    N21  C17  N8   C1     10.01  30.0  2
 DJX  Var_10    C16  C15  N12  C13    68.68  30.0  2
 DJX  Var_11    H9   C7   C5   N4   -105.36  30.0  2
 DJX  Var_12    H14  C16  C15  N12   -65.35  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
 DJX  plan-1  C17  0.020
 DJX  plan-1  C20  0.020
 DJX  plan-1  C22  0.020
 DJX  plan-1  C19  0.020
 DJX  plan-1  N21  0.020
 DJX  plan-1  S18  0.020
 DJX  plan-1  H5   0.020
 DJX  plan-1  N8   0.020
 DJX  plan-2  C22  0.020
 DJX  plan-2  C24  0.020
 DJX  plan-2  C26  0.020
 DJX  plan-2  C19  0.020
 DJX  plan-2  C23  0.020
 DJX  plan-2  C27  0.020
 DJX  plan-2  N25  0.020
 DJX  plan-2  H6   0.020
 DJX  plan-2  H7   0.020
 DJX  plan-2  H17  0.020
 DJX  plan-2  H18  0.020
 DJX  plan-3  C1   0.020
 DJX  plan-3  C2   0.020
 DJX  plan-3  C3   0.020
 DJX  plan-3  C5   0.020
 DJX  plan-3  C7   0.020
 DJX  plan-3  N4   0.020
 DJX  plan-3  N6   0.020
 DJX  plan-3  N9   0.020
 DJX  plan-3  H8   0.020
 DJX  plan-3  N8   0.020

