# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 16:05:57 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: ~{N}-cyclopentyl-~{N}-(imidazo[1,2-a]pyridin-2-ylmethyl)-4-(iminomethyl)-6-morpholin-4-yl-1,3,5-triazin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=Cc1nc(nc(n1)N(Cc2cn3ccccc3n2)C4CCCC4)N5CCOCC5
#
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
 7KH  7KH  ~{N}-cyclopentyl-~{N}-(imidazo[1,2-a]pyridin-2-ylmethyl)-4-(iminomethyl)-6-morpholin-4-yl-1,3,5-triazin-2-amine  ligand  56  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7KH
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
 7KH  C5   C  CH2   0  -0.317  -4.7316  -1.5043   0.0265
 7KH  C1   C  CH2   0  -0.320  -2.9183  -2.3299   1.4290
 7KH  C14  C  CH2   0  -0.439   0.6069   3.7503   1.1436
 7KH  C9   C  CR5   0   0.136   2.2114  -0.4498   1.0951
 7KH  C4   C  CH2   0  -0.188  -4.9926  -2.9420  -0.3825
 7KH  C13  C  CH2   0  -0.443   0.8266   4.6271  -0.0935
 7KH  C2   C  CH2   0  -0.187  -3.2684  -3.7283   0.9552
 7KH  C18  C  CR6   0   0.660  -0.7783   1.0066   0.4981
 7KH  N16  N  NT    0  -0.493   0.4222   1.1996   1.0697
 7KH  O3   O  O2    0  -0.483  -4.6362  -3.8485   0.6369
 7KH  N6   N  NT    0  -0.509  -3.3498  -1.3545   0.4450
 7KH  N7   N  N     0  -0.511  -4.0587   2.7363  -2.2906
 7KH  C10  C  CH2   0  -0.437   1.0595   0.1435   1.8383
 7KH  C11  C  CH2   0  -0.437   1.7718   2.4977  -0.6394
 7KH  C12  C  CH2   0  -0.451   2.0263   3.9926  -0.7994
 7KH  C15  C  CH1   0  -0.066   1.2412   2.3768   0.7994
 7KH  N17  N  N     0  -0.531  -1.4515  -0.1085   0.7718
 7KH  N19  N  N     0  -0.498  -1.2460   1.9778  -0.3082
 7KH  C20  C  CR6   0   0.357  -2.4359   1.7407  -0.8242
 7KH  N21  N  N     0  -0.489  -3.1889   0.6765  -0.6272
 7KH  C22  C  CR6   0   0.646  -2.6432  -0.2345   0.1954
 7KH  N23  N  N     0  -0.478   2.0431  -1.0901  -0.0885
 7KH  C24  C  CR56  0   0.523   3.2538  -1.4430  -0.4763
 7KH  N25  N  N     0  -0.506   4.2063  -1.0403   0.4470
 7KH  C26  C  CR15  0  -0.131   3.5333  -0.4005   1.4538
 7KH  C27  C  CR16  0   0.043   5.5381  -1.2809   0.2808
 7KH  C28  C  CR16  0  -0.400   5.9576  -1.9405  -0.8274
 7KH  C29  C  CR16  0  -0.156   5.0178  -2.3737  -1.7991
 7KH  C30  C  CR16  0  -0.399   3.6868  -2.1313  -1.6295
 7KH  H1   H  HCH2  0   0.275  -4.9395  -0.8410  -0.8086
 7KH  H2   H  HCH2  0   0.236  -5.3998  -1.2236   0.8499
 7KH  H3   H  H     0   0.243  -2.2487   3.6574  -1.8208
 7KH  H4   H  HCH2  0   0.236  -3.4033  -2.1247   2.3912
 7KH  H5   H  HCH2  0   0.278  -1.8444  -2.2541   1.5775
 7KH  H6   H  HCH2  0   0.229   1.1247   4.1734   2.0066
 7KH  H7   H  HCH2  0   0.238  -0.4445   3.6709   1.4113
 7KH  H8   H  HCH2  0   0.244  -6.0557  -3.0766  -0.5857
 7KH  H9   H  HCH2  0   0.208  -4.4399  -3.1670  -1.3056
 7KH  H10  H  HCH2  0   0.228  -0.0479   4.5720  -0.7448
 7KH  H11  H  HCH2  0   0.224   0.9859   5.6769   0.1571
 7KH  H12  H  HCH2  0   0.207  -2.6477  -3.9843   0.0848
 7KH  H13  H  HCH2  0   0.244  -3.0496  -4.4470   1.7460
 7KH  H14  H  H     0   0.358  -4.2211   3.5638  -2.8582
 7KH  H15  H  HCH2  0   0.291   0.3191  -0.6218   2.0578
 7KH  H16  H  HCH2  0   0.266   1.4061   0.5532   2.7895
 7KH  H17  H  HCH2  0   0.233   1.0104   2.1755  -1.3495
 7KH  H18  H  HCH2  0   0.233   2.6572   1.8801  -0.7966
 7KH  H19  H  HCH2  0   0.230   2.1220   4.2973  -1.8427
 7KH  H20  H  HCH2  0   0.215   2.9539   4.2766  -0.2931
 7KH  H21  H  HCH1  0   0.259   2.1068   2.2554   1.4528
 7KH  H22  H  HCR5  0   0.300   4.0349   0.0260   2.3062
 7KH  H23  H  HCR6  0   0.306   6.1979  -0.9235   1.0572
 7KH  H24  H  HCR6  0   0.279   7.0128  -2.1285  -0.9598
 7KH  H25  H  HCR6  0   0.273   5.3664  -2.8977  -2.6782
 7KH  H26  H  HCR6  0   0.276   2.9492  -2.4483  -2.3535
 7KH  C8   C  C1    0  -0.106  -2.9381   2.8174  -1.7181

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
 7KH  N7   C8   double    1.261  0.020  1.261
 7KH  C8   C20  single    1.487  0.020  1.487
 7KH  C20  N21  aromatic  1.319  0.020  1.319
 7KH  C20  N19  aromatic  1.318  0.020  1.318
 7KH  N21  C22  aromatic  1.343  0.020  1.343
 7KH  C5   C4   single    1.517  0.020  1.517
 7KH  C5   N6   single    1.452  0.020  1.452
 7KH  C4   O3   single    1.410  0.020  1.410
 7KH  N19  C18  aromatic  1.346  0.020  1.346
 7KH  C22  N6   single    1.348  0.020  1.348
 7KH  C22  N17  aromatic  1.330  0.020  1.330
 7KH  N6   C1   single    1.451  0.020  1.451
 7KH  O3   C2   single    1.410  0.020  1.410
 7KH  C18  N17  aromatic  1.331  0.020  1.331
 7KH  C18  N16  single    1.344  0.020  1.344
 7KH  C1   C2   single    1.517  0.020  1.517
 7KH  C14  C13  single    1.532  0.020  1.532
 7KH  C14  C15  single    1.552  0.020  1.552
 7KH  C13  C12  single    1.530  0.020  1.530
 7KH  C15  N16  single    1.459  0.020  1.459
 7KH  C15  C11  single    1.538  0.020  1.538
 7KH  N16  C10  single    1.453  0.020  1.453
 7KH  C12  C11  single    1.525  0.020  1.525
 7KH  C10  C9   single    1.494  0.020  1.494
 7KH  C26  C9   aromatic  1.371  0.020  1.371
 7KH  C26  N25  aromatic  1.370  0.020  1.370
 7KH  C9   N23  aromatic  1.356  0.020  1.356
 7KH  N25  C27  aromatic  1.364  0.020  1.364
 7KH  N25  C24  aromatic  1.386  0.020  1.386
 7KH  C27  C28  aromatic  1.356  0.020  1.356
 7KH  N23  C24  aromatic  1.319  0.020  1.319
 7KH  C24  C30  aromatic  1.411  0.020  1.411
 7KH  C28  C29  aromatic  1.419  0.020  1.419
 7KH  C30  C29  aromatic  1.363  0.020  1.363
 7KH  C5   H1   single    0.970  0.020  1.090
 7KH  C5   H2   single    0.970  0.020  1.090
 7KH  C8   H3   single    0.930  0.020  1.080
 7KH  C1   H4   single    0.970  0.020  1.090
 7KH  C1   H5   single    0.970  0.020  1.090
 7KH  C14  H6   single    0.970  0.020  1.090
 7KH  C14  H7   single    0.970  0.020  1.090
 7KH  C4   H8   single    0.970  0.020  1.090
 7KH  C4   H9   single    0.970  0.020  1.090
 7KH  C13  H10  single    0.970  0.020  1.090
 7KH  C13  H11  single    0.970  0.020  1.090
 7KH  C2   H12  single    0.970  0.020  1.090
 7KH  C2   H13  single    0.970  0.020  1.090
 7KH  N7   H14  single    0.890  0.020  1.040
 7KH  C10  H15  single    0.970  0.020  1.090
 7KH  C10  H16  single    0.970  0.020  1.090
 7KH  C11  H17  single    0.970  0.020  1.090
 7KH  C11  H18  single    0.970  0.020  1.090
 7KH  C12  H19  single    0.970  0.020  1.090
 7KH  C12  H20  single    0.970  0.020  1.090
 7KH  C15  H21  single    0.970  0.020  1.090
 7KH  C26  H22  single    0.930  0.020  1.080
 7KH  C27  H23  single    0.930  0.020  1.080
 7KH  C28  H24  single    0.930  0.020  1.080
 7KH  C29  H25  single    0.930  0.020  1.080
 7KH  C30  H26  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
 7KH  H2   C5   H1   107.71  3.000
 7KH  H2   C5   N6   109.70  3.000
 7KH  H1   C5   N6   109.92  3.000
 7KH  H2   C5   C4   109.88  3.000
 7KH  H1   C5   C4   109.78  3.000
 7KH  N6   C5   C4   109.83  3.000
 7KH  H5   C1   H4   107.70  3.000
 7KH  H5   C1   N6   109.85  3.000
 7KH  H4   C1   N6   109.73  3.000
 7KH  H5   C1   C2   109.56  3.000
 7KH  H4   C1   C2   110.14  3.000
 7KH  N6   C1   C2   109.82  3.000
 7KH  H7   C14  H6   106.99  3.000
 7KH  H7   C14  C15  112.65  3.000
 7KH  H6   C14  C15  108.93  3.000
 7KH  H7   C14  C13  112.28  3.000
 7KH  H6   C14  C13  110.40  3.000
 7KH  C15  C14  C13  105.60  3.000
 7KH  C26  C9   N23  111.42  3.000
 7KH  N23  C9   C10  121.73  3.000
 7KH  C26  C9   C10  126.82  3.000
 7KH  H9   C4   H8   107.96  3.000
 7KH  H9   C4   O3   110.39  3.000
 7KH  H8   C4   O3   107.56  3.000
 7KH  H9   C4   C5   109.50  3.000
 7KH  H8   C4   C5   109.56  3.000
 7KH  O3   C4   C5   111.77  3.000
 7KH  H11  C13  H10  107.61  3.000
 7KH  H11  C13  C12  112.99  3.000
 7KH  H10  C13  C12  109.39  3.000
 7KH  H11  C13  C14  112.71  3.000
 7KH  H10  C13  C14  109.75  3.000
 7KH  C12  C13  C14  104.34  3.000
 7KH  H13  C2   H12  107.90  3.000
 7KH  H13  C2   O3   107.59  3.000
 7KH  H12  C2   O3   110.44  3.000
 7KH  H13  C2   C1   109.55  3.000
 7KH  H12  C2   C1   109.37  3.000
 7KH  O3   C2   C1   111.90  3.000
 7KH  N19  C18  N17  123.50  3.000
 7KH  N17  C18  N16  119.00  3.000
 7KH  N19  C18  N16  117.49  3.000
 7KH  C15  N16  C10  115.98  3.000
 7KH  C10  N16  C18  120.82  3.000
 7KH  C15  N16  C18  122.59  3.000
 7KH  C2   O3   C4   110.72  3.000
 7KH  C22  N6   C1   121.89  3.000
 7KH  C1   N6   C5   114.15  3.000
 7KH  C22  N6   C5   122.11  3.000
 7KH  H14  N7   C8   110.06  3.000
 7KH  H16  C10  H15  107.72  3.000
 7KH  H16  C10  N16  109.09  3.000
 7KH  H15  C10  N16  108.64  3.000
 7KH  H16  C10  C9   109.73  3.000
 7KH  H15  C10  C9   110.25  3.000
 7KH  N16  C10  C9   111.33  3.000
 7KH  H18  C11  H17  107.80  3.000
 7KH  H18  C11  C15  111.73  3.000
 7KH  H17  C11  C15  110.20  3.000
 7KH  H18  C11  C12  113.85  3.000
 7KH  H17  C11  C12  109.75  3.000
 7KH  C15  C11  C12  103.46  3.000
 7KH  H20  C12  H19  107.20  3.000
 7KH  H20  C12  C11  110.33  3.000
 7KH  H19  C12  C11  112.88  3.000
 7KH  H20  C12  C13  110.10  3.000
 7KH  H19  C12  C13  113.21  3.000
 7KH  C11  C12  C13  103.14  3.000
 7KH  H21  C15  C11  107.17  3.000
 7KH  H21  C15  N16  104.16  3.000
 7KH  C11  C15  N16  115.48  3.000
 7KH  H21  C15  C14  106.86  3.000
 7KH  C11  C15  C14  106.20  3.000
 7KH  N16  C15  C14  116.33  3.000
 7KH  C22  N17  C18  116.33  3.000
 7KH  C20  N19  C18  114.72  3.000
 7KH  N21  C20  N19  127.02  3.000
 7KH  N19  C20  C8   114.20  3.000
 7KH  N21  C20  C8   118.78  3.000
 7KH  C22  N21  C20  114.01  3.000
 7KH  N21  C22  N17  124.42  3.000
 7KH  N17  C22  N6   117.93  3.000
 7KH  N21  C22  N6   117.65  3.000
 7KH  C24  N23  C9   105.60  3.000
 7KH  C30  C24  N25  118.37  3.000
 7KH  C30  C24  N23  130.71  3.000
 7KH  N25  C24  N23  110.92  3.000
 7KH  C27  N25  C26  130.69  3.000
 7KH  C27  N25  C24  122.59  3.000
 7KH  C26  N25  C24  106.72  3.000
 7KH  H22  C26  N25  122.54  3.000
 7KH  H22  C26  C9   132.11  3.000
 7KH  N25  C26  C9   105.35  3.000
 7KH  H23  C27  C28  124.02  3.000
 7KH  H23  C27  N25  116.80  3.000
 7KH  C28  C27  N25  119.18  3.000
 7KH  H24  C28  C29  120.65  3.000
 7KH  H24  C28  C27  119.15  3.000
 7KH  C29  C28  C27  120.20  3.000
 7KH  H25  C29  C30  120.14  3.000
 7KH  H25  C29  C28  119.41  3.000
 7KH  C30  C29  C28  120.46  3.000
 7KH  H26  C30  C29  122.05  3.000
 7KH  H26  C30  C24  118.75  3.000
 7KH  C29  C30  C24  119.21  3.000
 7KH  H3   C8   C20  113.62  3.000
 7KH  H3   C8   N7   124.61  3.000
 7KH  C20  C8   N7   121.77  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
 7KH  CONST_01  C27  N25  C26  C9    180.00   0.0  0
 7KH  CONST_02  C24  N25  C26  C9      0.00   0.0  0
 7KH  CONST_03  N25  C24  N23  C9      0.00   0.0  0
 7KH  CONST_04  C30  C24  N23  C9    180.00   0.0  0
 7KH  CONST_05  N21  C20  N19  C18     0.00   0.0  0
 7KH  CONST_06  N21  C22  N17  C18     0.00   0.0  0
 7KH  CONST_07  C20  N21  C22  N17     0.00   0.0  0
 7KH  CONST_08  C20  N19  C18  N17     0.00   0.0  0
 7KH  CONST_09  C22  N21  C20  N19     0.00   0.0  0
 7KH  CONST_10  C22  N17  C18  N19     0.00   0.0  0
 7KH  CONST_11  N25  C26  C9   N23     0.00   0.0  0
 7KH  CONST_12  C26  N25  C24  N23     0.00   0.0  0
 7KH  CONST_13  C27  N25  C24  N23   180.00   0.0  0
 7KH  CONST_14  C29  C30  C24  N23   180.00   0.0  0
 7KH  CONST_15  C28  C27  N25  C24     0.00   0.0  0
 7KH  CONST_16  C26  C9   N23  C24     0.00   0.0  0
 7KH  CONST_17  C28  C29  C30  C24     0.00   0.0  0
 7KH  CONST_18  C29  C28  C27  N25     0.00   0.0  0
 7KH  CONST_19  C29  C30  C24  N25     0.00   0.0  0
 7KH  CONST_20  C28  C27  N25  C26   180.00   0.0  0
 7KH  CONST_21  C30  C24  N25  C26   180.00   0.0  0
 7KH  CONST_22  C30  C24  N25  C27     0.00   0.0  0
 7KH  CONST_23  C30  C29  C28  C27     0.00   0.0  0
 7KH  CONST_24  N6   C22  N17  C18   180.00   0.0  0
 7KH  CONST_25  C20  N21  C22  N6    180.00   0.0  0
 7KH  CONST_26  C22  N21  C20  C8    180.00   0.0  0
 7KH  CONST_27  C18  N19  C20  C8    180.00   0.0  0
 7KH  CONST_28  C20  N19  C18  N16   180.00   0.0  0
 7KH  CONST_29  C22  N17  C18  N16   180.00   0.0  0
 7KH  CONST_30  N25  C26  C9   C10   180.00   0.0  0
 7KH  CONST_31  C24  N23  C9   C10   180.00   0.0  0
 7KH  CONST_32  N19  C18  N16  C15     0.00   0.0  0
 7KH  CONST_33  N17  C18  N16  C15   180.00   0.0  0
 7KH  CONST_34  H22  C26  C9   N23   180.00   0.0  0
 7KH  CONST_35  H26  C30  C24  N23     0.00   0.0  0
 7KH  CONST_36  H23  C27  N25  C24   180.00   0.0  0
 7KH  CONST_37  H25  C29  C30  C24   180.00   0.0  0
 7KH  CONST_38  H24  C28  C27  N25   180.00   0.0  0
 7KH  CONST_39  N19  C18  N16  C10   180.00   0.0  0
 7KH  CONST_40  N17  C18  N16  C10     0.00   0.0  0
 7KH  Var_01    N21  C22  N6   C5     -9.53  30.0  3
 7KH  Var_02    C2   C1   N6   C5     50.72  30.0  1
 7KH  Var_03    C4   C5   N6   C1    -50.87  30.0  1
 7KH  Var_04    C11  C12  C13  C14    39.69  30.0  1
 7KH  Var_05    C15  C11  C12  C13   -40.29  30.0  1
 7KH  Var_06    N6   C5   C4   O3     54.40  30.0  1
 7KH  Var_07    N6   C1   C2   O3    -54.18  30.0  1
 7KH  Var_08    C15  C14  C13  C12   -23.35  30.0  1
 7KH  Var_09    H12  C2   O3   C4    -62.58  30.0  1
 7KH  Var_10    H8   C4   O3   C2   -179.89  30.0  1
 7KH  Var_11    C18  N16  C10  C9    107.01  30.0  3
 7KH  Var_12    C26  C9   C10  N16   115.17  30.0  2
 7KH  Var_13    N21  C20  C8   N7     -0.13  30.0  2

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
 7KH  chir_01  C15  C14  N16  C11  negativ

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
 7KH  plan-1  C18  0.020
 7KH  plan-1  N16  0.020
 7KH  plan-1  N6   0.020
 7KH  plan-1  N17  0.020
 7KH  plan-1  N19  0.020
 7KH  plan-1  C20  0.020
 7KH  plan-1  N21  0.020
 7KH  plan-1  C22  0.020
 7KH  plan-1  C8   0.020
 7KH  plan-2  C9   0.020
 7KH  plan-2  C10  0.020
 7KH  plan-2  N23  0.020
 7KH  plan-2  C24  0.020
 7KH  plan-2  N25  0.020
 7KH  plan-2  C26  0.020
 7KH  plan-2  C27  0.020
 7KH  plan-2  C28  0.020
 7KH  plan-2  C29  0.020
 7KH  plan-2  C30  0.020
 7KH  plan-2  H22  0.020
 7KH  plan-2  H23  0.020
 7KH  plan-2  H24  0.020
 7KH  plan-2  H25  0.020
 7KH  plan-2  H26  0.020
 7KH  plan-3  C18  0.020
 7KH  plan-3  N16  0.020
 7KH  plan-3  C10  0.020
 7KH  plan-3  C15  0.020
 7KH  plan-4  N7   0.020
 7KH  plan-4  C20  0.020
 7KH  plan-4  H3   0.020
 7KH  plan-4  H14  0.020
 7KH  plan-4  C8   0.020

