# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:43:22 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 6-chloranyl-~{N}-(cyclopropylmethyl)-3-(2~{H}-indazol-5-yl)imidazo[1,2-b]pyridazin-8-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(NCC2CC2)c3ncc(n3n1)c4ccc5n[nH]cc5c4
#
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
 GXK  GXK  6-chloranyl-~{N}-(cyclopropylmethyl)-3-(2~{H}-indazol-5-yl)imidazo[1,2-b]pyridazin-8-amine  ligand  39  24  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GXK
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
 GXK  C2   C   CR6   0   0.152   1.2190   1.9498   0.2387
 GXK  C3   C   CR16  0  -0.370   2.4900   1.3619   0.1583
 GXK  C4   C   CR6   0   0.382   2.5612  -0.0068  -0.0540
 GXK  C6   C   CH2   0  -0.277   5.0096  -0.1467  -0.0324
 GXK  C7   C   CH1   0  -0.290   6.0460  -1.1602  -0.4203
 GXK  C8   C   CH2   0  -0.490   7.3794  -1.1330   0.2567
 GXK  C12  C   CR15  0  -0.245  -0.2877  -2.0534  -0.3809
 GXK  C15  C   CR16  0  -0.376  -3.1917  -1.3075   0.4394
 GXK  C16  C   CR56  0  -0.079  -4.5630  -0.9878   0.4061
 GXK  C17  C   CR15  0  -0.019  -5.7259  -1.5760   0.8971
 GXK  C21  C   CR16  0  -0.281  -4.0953   1.0586  -0.8697
 GXK  CL1  CL  CL    0  -0.090   1.1425   3.6542   0.5140
 GXK  N5   N   NH1   0  -0.671   3.6838  -0.7138  -0.1592
 GXK  C9   C   CH2   0  -0.484   6.4151  -2.2401   0.5537
 GXK  C10  C   CR56  0   0.451   1.3104  -0.6837  -0.1666
 GXK  N11  N   N     0  -0.451   1.0600  -1.9617  -0.3512
 GXK  C13  C   CR5   0   0.299  -0.8915  -0.8237  -0.2130
 GXK  C14  C   CR6   0   0.021  -2.3036  -0.4598  -0.1781
 GXK  N18  N   NR15  0  -0.398  -6.7161  -0.7610   0.5307
 GXK  N19  N   N     0  -0.314  -6.3473   0.3132  -0.1522
 GXK  C20  C   CR56  0   0.239  -5.0209   0.1938  -0.2409
 GXK  C22  C   CR16  0  -0.289  -2.7737   0.7249  -0.8322
 GXK  N23  N   N     0  -0.418   0.1579   0.0465  -0.0786
 GXK  N24  N   N     0  -0.267   0.0679   1.3661   0.1379
 GXK  H1   H   HCR6  0   0.303   3.3736   1.9715   0.2682
 GXK  H2   H   HCH2  0   0.243   5.1829   0.1935   0.9953
 GXK  H3   H   HCH2  0   0.255   5.0864   0.7335  -0.6772
 GXK  H4   H   HCH1  0   0.272   6.0409  -1.4335  -1.4703
 GXK  H5   H   HCH2  0   0.258   8.2542  -1.3592  -0.3385
 GXK  H6   H   HCH2  0   0.251   7.5438  -0.3844   1.0225
 GXK  H7   H   HCR5  0   0.268  -0.7904  -2.9955  -0.5411
 GXK  H8   H   HCR6  0   0.257  -2.8453  -2.1986   0.9480
 GXK  H9   H   HCR5  0   0.298  -5.9035  -2.4803   1.4548
 GXK  H10  H   HCR6  0   0.260  -4.4284   1.9570  -1.3727
 GXK  H11  H   HNH1  0   0.407   3.6014  -1.7165  -0.2346
 GXK  H12  H   HCH2  0   0.251   5.9249  -2.2406   1.5200
 GXK  H13  H   HCH2  0   0.256   6.6299  -3.2266   0.1644
 GXK  H14  H   HNR5  0   0.433  -7.6957  -0.9013   0.7293
 GXK  H15  H   HCR6  0   0.255  -2.0578   1.3704  -1.3216

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
 GXK  C8   C9   single    1.498  0.020  1.498
 GXK  C8   C7   single    1.496  0.020  1.496
 GXK  C9   C7   single    1.500  0.020  1.500
 GXK  C7   C6   single    1.501  0.020  1.501
 GXK  C6   N5   single    1.448  0.020  1.448
 GXK  N5   C4   single    1.331  0.020  1.331
 GXK  N11  C10  aromatic  1.315  0.020  1.315
 GXK  N11  C12  aromatic  1.351  0.020  1.351
 GXK  C4   C10  aromatic  1.427  0.020  1.427
 GXK  C4   C3   aromatic  1.387  0.020  1.387
 GXK  C10  N23  aromatic  1.367  0.020  1.367
 GXK  C3   C2   aromatic  1.403  0.020  1.403
 GXK  C12  C13  aromatic  1.380  0.020  1.380
 GXK  N23  C13  aromatic  1.370  0.020  1.370
 GXK  N23  N24  aromatic  1.340  0.020  1.340
 GXK  C13  C14  single    1.459  0.020  1.459
 GXK  C2   N24  aromatic  1.295  0.020  1.295
 GXK  C2   CL1  single    1.728  0.020  1.728
 GXK  C22  C14  aromatic  1.433  0.020  1.433
 GXK  C22  C21  aromatic  1.364  0.020  1.364
 GXK  C14  C15  aromatic  1.374  0.020  1.374
 GXK  C21  C20  aromatic  1.414  0.020  1.414
 GXK  C15  C16  aromatic  1.408  0.020  1.408
 GXK  C20  C16  aromatic  1.423  0.020  1.423
 GXK  C20  N19  aromatic  1.335  0.020  1.335
 GXK  C16  C17  aromatic  1.393  0.020  1.393
 GXK  N19  N18  aromatic  1.325  0.020  1.325
 GXK  C17  N18  aromatic  1.334  0.020  1.334
 GXK  C3   H1   single    0.930  0.020  1.080
 GXK  C6   H2   single    0.970  0.020  1.090
 GXK  C6   H3   single    0.970  0.020  1.090
 GXK  C7   H4   single    0.970  0.020  1.090
 GXK  C8   H5   single    0.970  0.020  1.090
 GXK  C8   H6   single    0.970  0.020  1.090
 GXK  C12  H7   single    0.930  0.020  1.080
 GXK  C15  H8   single    0.930  0.020  1.080
 GXK  C17  H9   single    0.930  0.020  1.080
 GXK  C21  H10  single    0.930  0.020  1.080
 GXK  N5   H11  single    0.860  0.020  1.020
 GXK  C9   H12  single    0.970  0.020  1.090
 GXK  C9   H13  single    0.970  0.020  1.090
 GXK  N18  H14  single    0.860  0.020  1.020
 GXK  C22  H15  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
 GXK  N24  C2   CL1  114.69  3.000
 GXK  CL1  C2   C3   117.56  3.000
 GXK  N24  C2   C3   127.75  3.000
 GXK  H1   C3   C4   122.08  3.000
 GXK  H1   C3   C2   119.95  3.000
 GXK  C4   C3   C2   117.96  3.000
 GXK  C10  C4   N5   118.76  3.000
 GXK  C10  C4   C3   115.81  3.000
 GXK  N5   C4   C3   125.43  3.000
 GXK  H3   C6   H2   106.97  3.000
 GXK  H3   C6   N5   109.15  3.000
 GXK  H2   C6   N5   110.39  3.000
 GXK  H3   C6   C7   110.04  3.000
 GXK  H2   C6   C7   110.04  3.000
 GXK  N5   C6   C7   110.20  3.000
 GXK  H4   C7   C9   116.62  3.000
 GXK  H4   C7   C8   116.54  3.000
 GXK  C9   C7   C8    60.00  3.000
 GXK  H4   C7   C6   114.65  3.000
 GXK  C9   C7   C6   119.23  3.000
 GXK  C8   C7   C6   119.11  3.000
 GXK  H6   C8   H5   114.24  3.000
 GXK  H6   C8   C9   117.92  3.000
 GXK  H5   C8   C9   118.36  3.000
 GXK  H6   C8   C7   117.89  3.000
 GXK  H5   C8   C7   117.91  3.000
 GXK  C9   C8   C7    60.16  3.000
 GXK  H7   C12  C13  126.28  3.000
 GXK  H7   C12  N11  121.80  3.000
 GXK  C13  C12  N11  111.91  3.000
 GXK  H8   C15  C14  120.79  3.000
 GXK  H8   C15  C16  120.62  3.000
 GXK  C14  C15  C16  118.59  3.000
 GXK  C20  C16  C17  104.02  3.000
 GXK  C17  C16  C15  135.14  3.000
 GXK  C20  C16  C15  120.84  3.000
 GXK  H9   C17  N18  122.19  3.000
 GXK  H9   C17  C16  132.44  3.000
 GXK  N18  C17  C16  105.36  3.000
 GXK  H10  C21  C22  120.95  3.000
 GXK  H10  C21  C20  120.86  3.000
 GXK  C22  C21  C20  118.20  3.000
 GXK  H11  N5   C6   118.08  3.000
 GXK  H11  N5   C4   117.71  3.000
 GXK  C6   N5   C4   123.88  3.000
 GXK  H13  C9   H12  114.22  3.000
 GXK  H13  C9   C8   118.34  3.000
 GXK  H12  C9   C8   117.93  3.000
 GXK  H13  C9   C7   118.13  3.000
 GXK  H12  C9   C7   117.90  3.000
 GXK  C8   C9   C7    59.85  3.000
 GXK  N23  C10  N11  111.56  3.000
 GXK  N23  C10  C4   118.72  3.000
 GXK  N11  C10  C4   129.72  3.000
 GXK  C10  N11  C12  105.01  3.000
 GXK  N23  C13  C14  125.51  3.000
 GXK  C14  C13  C12  130.44  3.000
 GXK  N23  C13  C12  104.05  3.000
 GXK  C22  C14  C13  120.87  3.000
 GXK  C22  C14  C15  120.21  3.000
 GXK  C13  C14  C15  118.85  3.000
 GXK  H14  N18  N19  118.96  3.000
 GXK  H14  N18  C17  125.55  3.000
 GXK  N19  N18  C17  115.49  3.000
 GXK  C20  N19  N18  103.78  3.000
 GXK  N19  C20  C21  128.70  3.000
 GXK  N19  C20  C16  111.34  3.000
 GXK  C21  C20  C16  119.96  3.000
 GXK  H15  C22  C14  118.89  3.000
 GXK  H15  C22  C21  118.90  3.000
 GXK  C14  C22  C21  122.20  3.000
 GXK  N24  N23  C13  126.15  3.000
 GXK  N24  N23  C10  126.36  3.000
 GXK  C13  N23  C10  107.46  3.000
 GXK  N23  N24  C2   113.38  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
 GXK  CONST_01  C10  C4   C3   C2      0.00   0.0  0
 GXK  CONST_02  C10  N23  N24  C2      0.00   0.0  0
 GXK  CONST_03  C13  N23  N24  C2    180.00   0.0  0
 GXK  CONST_04  N11  C10  C4   C3    180.00   0.0  0
 GXK  CONST_05  N23  C10  C4   C3      0.00   0.0  0
 GXK  CONST_06  N23  N24  C2   C3      0.00   0.0  0
 GXK  CONST_07  C12  N11  C10  C4    180.00   0.0  0
 GXK  CONST_08  C13  N23  C10  C4    180.00   0.0  0
 GXK  CONST_09  N24  N23  C10  C4      0.00   0.0  0
 GXK  CONST_10  N24  C2   C3   C4      0.00   0.0  0
 GXK  CONST_11  N23  C10  N11  C12     0.00   0.0  0
 GXK  CONST_12  C10  N23  C13  C12     0.00   0.0  0
 GXK  CONST_13  N24  N23  C13  C12   180.00   0.0  0
 GXK  CONST_17  C21  C22  C14  C15     0.00   0.0  0
 GXK  CONST_18  C21  C20  C16  C15     0.00   0.0  0
 GXK  CONST_19  N19  C20  C16  C15   180.00   0.0  0
 GXK  CONST_20  N18  C17  C16  C15   180.00   0.0  0
 GXK  CONST_21  C13  C14  C15  C16   180.00   0.0  0
 GXK  CONST_22  C22  C14  C15  C16     0.00   0.0  0
 GXK  CONST_23  C22  C21  C20  C16     0.00   0.0  0
 GXK  CONST_24  N18  N19  C20  C16     0.00   0.0  0
 GXK  CONST_25  N19  N18  C17  C16     0.00   0.0  0
 GXK  CONST_26  C14  C15  C16  C17   180.00   0.0  0
 GXK  CONST_27  C21  C20  C16  C17   180.00   0.0  0
 GXK  CONST_28  N19  C20  C16  C17     0.00   0.0  0
 GXK  CONST_29  C20  N19  N18  C17     0.00   0.0  0
 GXK  CONST_30  C13  C14  C22  C21   180.00   0.0  0
 GXK  CONST_31  N18  N19  C20  C21   180.00   0.0  0
 GXK  CONST_32  C13  C12  N11  C10     0.00   0.0  0
 GXK  CONST_33  C14  C13  N23  C10   180.00   0.0  0
 GXK  CONST_34  C13  N23  C10  N11     0.00   0.0  0
 GXK  CONST_35  N24  N23  C10  N11   180.00   0.0  0
 GXK  CONST_36  N23  C13  C12  N11     0.00   0.0  0
 GXK  CONST_37  C14  C13  C12  N11   180.00   0.0  0
 GXK  CONST_38  N24  N23  C13  C14     0.00   0.0  0
 GXK  CONST_39  C20  C21  C22  C14     0.00   0.0  0
 GXK  CONST_40  C20  C16  C15  C14     0.00   0.0  0
 GXK  CONST_41  C20  C16  C17  N18     0.00   0.0  0
 GXK  CONST_42  C22  C21  C20  N19   180.00   0.0  0
 GXK  CONST_44  N5   C4   C3   C2    180.00   0.0  0
 GXK  CONST_45  CL1  C2   C3   C4    180.00   0.0  0
 GXK  CONST_46  N23  N24  C2   CL1   180.00   0.0  0
 GXK  CONST_47  N11  C10  C4   N5      0.00   0.0  0
 GXK  CONST_48  N23  C10  C4   N5    180.00   0.0  0
 GXK  CONST_49  H15  C22  C14  C15   180.00   0.0  0
 GXK  CONST_50  H9   C17  C16  C15     0.00   0.0  0
 GXK  CONST_51  H10  C21  C20  C16   180.00   0.0  0
 GXK  CONST_52  H14  N18  C17  C16   180.00   0.0  0
 GXK  CONST_53  H8   C15  C16  C17     0.00   0.0  0
 GXK  CONST_54  H7   C12  N11  C10   180.00   0.0  0
 GXK  CONST_55  H1   C3   C4   C10   180.00   0.0  0
 GXK  CONST_56  C6   N5   C4   C3      0.00   0.0  0
 GXK  CONST_57  C10  C4   N5   C6    180.00   0.0  0
 GXK  CONST_58  H11  N5   C4   C3    180.00   0.0  0
 GXK  Var_01    C9   C8   C7   C6    108.89  30.0  1
 GXK  Var_02    H12  C9   C8   C7   -107.73  30.0  1
 GXK  Var_03    C7   C6   N5   C4   -170.91  30.0  1
 GXK  Var_04    N5   C6   C7   C8   -147.99  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 GXK  chir_01  C7  C8  C9  C6  both

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
 GXK  plan-1  C2   0.020
 GXK  plan-1  C3   0.020
 GXK  plan-1  C4   0.020
 GXK  plan-1  C12  0.020
 GXK  plan-1  CL1  0.020
 GXK  plan-1  N5   0.020
 GXK  plan-1  C10  0.020
 GXK  plan-1  N11  0.020
 GXK  plan-1  C13  0.020
 GXK  plan-1  C14  0.020
 GXK  plan-1  N23  0.020
 GXK  plan-1  N24  0.020
 GXK  plan-1  H1   0.020
 GXK  plan-1  H7   0.020
 GXK  plan-2  C15  0.020
 GXK  plan-2  C16  0.020
 GXK  plan-2  C17  0.020
 GXK  plan-2  C21  0.020
 GXK  plan-2  C13  0.020
 GXK  plan-2  C14  0.020
 GXK  plan-2  N18  0.020
 GXK  plan-2  N19  0.020
 GXK  plan-2  C20  0.020
 GXK  plan-2  C22  0.020
 GXK  plan-2  H8   0.020
 GXK  plan-2  H9   0.020
 GXK  plan-2  H10  0.020
 GXK  plan-2  H14  0.020
 GXK  plan-2  H15  0.020
 GXK  plan-3  C4   0.020
 GXK  plan-3  C6   0.020
 GXK  plan-3  N5   0.020
 GXK  plan-3  H11  0.020

