# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 10:57:30 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: [4-[cyclopentyl(pyrazin-2-ylmethyl)amino]-6-morpholin-4-yl-1,3,5-triazin-2-yl]methylideneazanide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [N-]=Cc1nc(nc(n1)N(Cc2cnccn2)C3CCCC3)N4CCOCC4
#
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
 7KN  7KN  '[4-[cyclopentyl(pyrazin-2-ylmethyl)amino]-6-morpholin-4-yl-1,3,5-triazin-2-yl]methylideneazanide'  ligand  50  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7KN
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
 7KN  C16  C  CH2    0  -0.439  -3.0413  -2.0550  -1.4371
 7KN  C12  C  CR16   0  -0.118  -3.2711   3.3509   1.0609
 7KN  C11  C  CR16   0  -0.103  -2.2460   3.9561   1.7725
 7KN  C15  C  CH2    0  -0.422  -1.4655   1.2179  -1.2769
 7KN  C14  C  CR6    0   0.224  -1.7536   2.2255  -0.1955
 7KN  C9   C  CR16   0  -0.106  -0.7298   2.8433   0.5217
 7KN  C1   C  CH2    0  -0.323   3.0908   1.4794  -0.4478
 7KN  C2   C  CH2    0  -0.180   4.3293   1.6875  -1.3012
 7KN  C4   C  CH2    0  -0.187   5.4342  -0.0842  -0.2864
 7KN  C5   C  CH2    0  -0.314   4.2497  -0.3750   0.6163
 7KN  O3   O  O2     0  -0.485   5.5028   1.2811  -0.6342
 7KN  N6   N  NT     0  -0.509   3.0295   0.1021  -0.0032
 7KN  C8   C  C1     0  -0.290   0.6760  -3.8568   1.1687
 7KN  N10  N  N      0  -0.353  -0.9731   3.7043   1.4979
 7KN  N13  N  N      0  -0.365  -3.0251   2.4942   0.0798
 7KN  C17  C  CH2    0  -0.456  -4.4137  -2.5109  -0.9344
 7KN  C18  C  CH2    0  -0.450  -4.5323  -1.9838   0.5189
 7KN  C19  C  CH2    0  -0.443  -3.2856  -1.1199   0.7671
 7KN  C20  C  CR15   0  -0.066  -2.8052  -0.7693  -0.6437
 7KN  N21  N  NT     0  -0.507  -1.4915  -0.1448  -0.7715
 7KN  N22  N  N      0  -0.543   0.7658   0.0183  -0.3719
 7KN  C23  C  CR6    0   0.647  -0.3486  -0.7088  -0.3126
 7KN  N24  N  N      0  -0.498  -0.4054  -1.9546   0.1656
 7KN  C25  C  CR6    0   0.315   0.7421  -2.4557   0.6102
 7KN  N26  N  N      0  -0.495   1.9059  -1.8158   0.5936
 7KN  C27  C  CR6    0   0.628   1.8667  -0.5850   0.0770
 7KN  H1   H  HCH2   0   0.239  -2.2728  -2.7869  -1.1917
 7KN  H2   H  HCH2   0   0.226  -3.0189  -1.8879  -2.5156
 7KN  H3   H  HCR6   0   0.275  -4.3078   3.5700   1.2868
 7KN  H4   H  HCR6   0   0.276  -2.4614   4.6561   2.5707
 7KN  H5   H  HCH2   0   0.278  -2.2226   1.3076  -2.0563
 7KN  H6   H  HCH2   0   0.282  -0.4994   1.4202  -1.7319
 7KN  H7   H  HCR6   0   0.279   0.3061   2.6257   0.2916
 7KN  H9   H  HCH2   0   0.272   2.2068   1.7185  -1.0331
 7KN  H10  H  HCH2   0   0.205   4.2139   1.1364  -2.2456
 7KN  H11  H  HCH2   0   0.241   4.4370   2.7464  -1.5408
 7KN  H12  H  HCH2   0   0.241   6.3611  -0.3381   0.2297
 7KN  H13  H  HCH2   0   0.205   5.3674  -0.7074  -1.1896
 7KN  H14  H  HCH2   0   0.272   4.1736  -1.4440   0.7959
 7KN  H15  H  HCH2   0   0.230   4.3949   0.1172   1.5864
 7KN  H17  H  H      0   0.040  -0.4005  -4.1856   1.0860
 7KN  H18  H  HCH2   0   0.225  -5.2021  -2.0794  -1.5541
 7KN  H19  H  HCH2   0   0.230  -4.5289  -3.5937  -0.9922
 7KN  H20  H  HCH2   0   0.226  -5.4441  -1.3963   0.6352
 7KN  H21  H  HCH2   0   0.228  -4.5925  -2.7996   1.2397
 7KN  H22  H  HCH2   0   0.226  -3.4985  -0.2280   1.3587
 7KN  H23  H  HCH2   0   0.241  -2.5189  -1.6959   1.2828
 7KN  H24  H  HCR5   0   0.246  -3.5014  -0.0232  -1.0348
 7KN  H8   H  HCH2   0   0.231   3.1128   2.1544   0.4175
 7KN  N7   N  N     -1  -0.577   1.6241  -4.5150   1.6309

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
 7KN  N7   C8   double    1.243  0.020  1.243
 7KN  C8   C25  single    1.510  0.020  1.510
 7KN  C25  N26  aromatic  1.328  0.020  1.328
 7KN  C25  N24  aromatic  1.329  0.020  1.329
 7KN  N26  C27  aromatic  1.335  0.020  1.335
 7KN  C5   C4   single    1.517  0.020  1.517
 7KN  C5   N6   single    1.449  0.020  1.449
 7KN  C4   O3   single    1.411  0.020  1.411
 7KN  N24  C23  aromatic  1.336  0.020  1.336
 7KN  C27  N6   single    1.353  0.020  1.353
 7KN  C27  N22  aromatic  1.333  0.020  1.333
 7KN  N6   C1   single    1.449  0.020  1.449
 7KN  O3   C2   single    1.410  0.020  1.410
 7KN  C23  N22  aromatic  1.332  0.020  1.332
 7KN  C23  N21  single    1.355  0.020  1.355
 7KN  C19  C20  single    1.531  0.020  1.531
 7KN  C19  C18  single    1.537  0.020  1.537
 7KN  C1   C2   single    1.518  0.020  1.518
 7KN  C20  N21  single    1.460  0.020  1.460
 7KN  C20  C16  single    1.529  0.020  1.529
 7KN  C18  C17  single    1.551  0.020  1.551
 7KN  N21  C15  single    1.454  0.020  1.454
 7KN  C16  C17  single    1.531  0.020  1.531
 7KN  C15  C14  single    1.506  0.020  1.506
 7KN  C9   C14  aromatic  1.394  0.020  1.394
 7KN  C9   N10  aromatic  1.324  0.020  1.324
 7KN  C14  N13  aromatic  1.328  0.020  1.328
 7KN  N10  C11  aromatic  1.326  0.020  1.326
 7KN  N13  C12  aromatic  1.326  0.020  1.326
 7KN  C11  C12  aromatic  1.387  0.020  1.387
 7KN  C16  H1   single    0.970  0.020  1.090
 7KN  C16  H2   single    0.970  0.020  1.090
 7KN  C12  H3   single    0.930  0.020  1.080
 7KN  C11  H4   single    0.930  0.020  1.080
 7KN  C15  H5   single    0.970  0.020  1.090
 7KN  C15  H6   single    0.970  0.020  1.090
 7KN  C9   H7   single    0.930  0.020  1.080
 7KN  C1   H8   single    0.970  0.020  1.090
 7KN  C1   H9   single    0.970  0.020  1.090
 7KN  C2   H10  single    0.970  0.020  1.090
 7KN  C2   H11  single    0.970  0.020  1.090
 7KN  C4   H12  single    0.970  0.020  1.090
 7KN  C4   H13  single    0.970  0.020  1.090
 7KN  C5   H14  single    0.970  0.020  1.090
 7KN  C5   H15  single    0.970  0.020  1.090
 7KN  C8   H17  single    0.930  0.020  1.080
 7KN  C17  H18  single    0.970  0.020  1.090
 7KN  C17  H19  single    0.970  0.020  1.090
 7KN  C18  H20  single    0.970  0.020  1.090
 7KN  C18  H21  single    0.970  0.020  1.090
 7KN  C19  H22  single    0.970  0.020  1.090
 7KN  C19  H23  single    0.970  0.020  1.090
 7KN  C20  H24  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
 7KN  H2   C16  H1   108.12  3.000
 7KN  H2   C16  C20  112.38  3.000
 7KN  H1   C16  C20  109.82  3.000
 7KN  H2   C16  C17  112.86  3.000
 7KN  H1   C16  C17  111.00  3.000
 7KN  C20  C16  C17  102.62  3.000
 7KN  H3   C12  N13  117.56  3.000
 7KN  H3   C12  C11  120.80  3.000
 7KN  N13  C12  C11  121.64  3.000
 7KN  H4   C11  N10  117.77  3.000
 7KN  H4   C11  C12  120.87  3.000
 7KN  N10  C11  C12  121.36  3.000
 7KN  H6   C15  H5   107.62  3.000
 7KN  H6   C15  N21  109.63  3.000
 7KN  H5   C15  N21  108.26  3.000
 7KN  H6   C15  C14  110.25  3.000
 7KN  H5   C15  C14  108.99  3.000
 7KN  N21  C15  C14  111.97  3.000
 7KN  N13  C14  C9   120.43  3.000
 7KN  N13  C14  C15  117.86  3.000
 7KN  C9   C14  C15  121.69  3.000
 7KN  H7   C9   N10  117.57  3.000
 7KN  H7   C9   C14  120.26  3.000
 7KN  N10  C9   C14  122.17  3.000
 7KN  H9   C1   H8   107.79  3.000
 7KN  H9   C1   N6   109.88  3.000
 7KN  H8   C1   N6   110.10  3.000
 7KN  H9   C1   C2   109.30  3.000
 7KN  H8   C1   C2   110.03  3.000
 7KN  N6   C1   C2   109.71  3.000
 7KN  H11  C2   H10  107.95  3.000
 7KN  H11  C2   O3   107.55  3.000
 7KN  H10  C2   O3   110.44  3.000
 7KN  H11  C2   C1   109.69  3.000
 7KN  H10  C2   C1   109.18  3.000
 7KN  O3   C2   C1   111.94  3.000
 7KN  H13  C4   H12  107.96  3.000
 7KN  H13  C4   O3   110.43  3.000
 7KN  H12  C4   O3   107.49  3.000
 7KN  H13  C4   C5   109.43  3.000
 7KN  H12  C4   C5   109.71  3.000
 7KN  O3   C4   C5   111.72  3.000
 7KN  H15  C5   H14  107.72  3.000
 7KN  H15  C5   N6   109.98  3.000
 7KN  H14  C5   N6   109.61  3.000
 7KN  H15  C5   C4   109.67  3.000
 7KN  H14  C5   C4   109.97  3.000
 7KN  N6   C5   C4   109.87  3.000
 7KN  C4   O3   C2   110.81  3.000
 7KN  C27  N6   C5   122.08  3.000
 7KN  C27  N6   C1   122.51  3.000
 7KN  C5   N6   C1   114.11  3.000
 7KN  H17  C8   C25  106.56  3.000
 7KN  H17  C8   N7   126.89  3.000
 7KN  C25  C8   N7   126.54  3.000
 7KN  C9   N10  C11  116.90  3.000
 7KN  C14  N13  C12  117.51  3.000
 7KN  H19  C17  H18  106.62  3.000
 7KN  H19  C17  C18  112.28  3.000
 7KN  H18  C17  C18  110.02  3.000
 7KN  H19  C17  C16  111.90  3.000
 7KN  H18  C17  C16  110.08  3.000
 7KN  C18  C17  C16  105.97  3.000
 7KN  H21  C18  H20  106.64  3.000
 7KN  H21  C18  C19  111.02  3.000
 7KN  H20  C18  C19  110.98  3.000
 7KN  H21  C18  C17  111.69  3.000
 7KN  H20  C18  C17  110.30  3.000
 7KN  C19  C18  C17  106.29  3.000
 7KN  H23  C19  H22  108.25  3.000
 7KN  H23  C19  C20  109.67  3.000
 7KN  H22  C19  C20  111.94  3.000
 7KN  H23  C19  C18  110.50  3.000
 7KN  H22  C19  C18  112.87  3.000
 7KN  C20  C19  C18  103.56  3.000
 7KN  H24  C20  N21  104.47  3.000
 7KN  H24  C20  C19  106.63  3.000
 7KN  N21  C20  C19  117.44  3.000
 7KN  H24  C20  C16  106.86  3.000
 7KN  N21  C20  C16  116.95  3.000
 7KN  C19  C20  C16  103.72  3.000
 7KN  C23  N21  C20  123.46  3.000
 7KN  C20  N21  C15  116.58  3.000
 7KN  C23  N21  C15  119.54  3.000
 7KN  C27  N22  C23  115.39  3.000
 7KN  N24  C23  N22  124.11  3.000
 7KN  N22  C23  N21  117.61  3.000
 7KN  N24  C23  N21  118.28  3.000
 7KN  C25  N24  C23  115.77  3.000
 7KN  N26  C25  N24  124.81  3.000
 7KN  N24  C25  C8   115.84  3.000
 7KN  N26  C25  C8   119.35  3.000
 7KN  C27  N26  C25  115.04  3.000
 7KN  N26  C27  N22  124.86  3.000
 7KN  N22  C27  N6   117.38  3.000
 7KN  N26  C27  N6   117.76  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
 7KN  CONST_01  C9   C14  N13  C12     0.00   0.0  0
 7KN  CONST_02  C9   N10  C11  C12     0.00   0.0  0
 7KN  CONST_03  C14  C9   N10  C11     0.00   0.0  0
 7KN  CONST_04  C14  N13  C12  C11     0.00   0.0  0
 7KN  CONST_05  N13  C14  C9   N10     0.00   0.0  0
 7KN  CONST_06  N13  C12  C11  N10     0.00   0.0  0
 7KN  CONST_07  C25  N26  C27  N22     0.00   0.0  0
 7KN  CONST_08  C25  N24  C23  N22     0.00   0.0  0
 7KN  CONST_09  N26  C25  N24  C23     0.00   0.0  0
 7KN  CONST_10  N26  C27  N22  C23     0.00   0.0  0
 7KN  CONST_11  C27  N26  C25  N24     0.00   0.0  0
 7KN  CONST_12  C27  N22  C23  N24     0.00   0.0  0
 7KN  CONST_13  C25  N26  C27  N6    180.00   0.0  0
 7KN  CONST_14  C23  N22  C27  N6    180.00   0.0  0
 7KN  CONST_15  C15  C14  N13  C12   180.00   0.0  0
 7KN  CONST_16  N10  C9   C14  C15   180.00   0.0  0
 7KN  CONST_17  C27  N26  C25  C8    180.00   0.0  0
 7KN  CONST_18  C23  N24  C25  C8    180.00   0.0  0
 7KN  CONST_19  C25  N24  C23  N21   180.00   0.0  0
 7KN  CONST_20  C27  N22  C23  N21   180.00   0.0  0
 7KN  CONST_21  N24  C23  N21  C20     0.00   0.0  0
 7KN  CONST_22  N22  C23  N21  C20   180.00   0.0  0
 7KN  CONST_23  H7   C9   N10  C11   180.00   0.0  0
 7KN  CONST_24  H3   C12  N13  C14   180.00   0.0  0
 7KN  CONST_25  H4   C11  N10  C9    180.00   0.0  0
 7KN  CONST_26  N24  C23  N21  C15   180.00   0.0  0
 7KN  CONST_27  N22  C23  N21  C15     0.00   0.0  0
 7KN  Var_01    C19  C18  C17  C16     5.50  30.0  1
 7KN  Var_02    C4   C5   N6   C1    -51.31  30.0  1
 7KN  Var_03    N26  C27  N6   C1   -175.07  30.0  2
 7KN  Var_04    C5   C4   O3   C2    -59.20  30.0  1
 7KN  Var_05    C5   N6   C1   C2     51.13  30.0  1
 7KN  Var_06    N6   C5   C4   O3     54.38  30.0  1
 7KN  Var_07    N6   C1   C2   O3    -54.26  30.0  1
 7KN  Var_08    C20  C19  C18  C17    20.22  30.0  1
 7KN  Var_09    C20  C16  C17  C18   -29.02  30.0  1
 7KN  Var_10    H10  C2   O3   C4    -62.64  30.0  1
 7KN  Var_11    C23  N21  C15  C14   -90.87  30.0  2
 7KN  Var_12    N21  C15  C14  C9     93.86  30.0  1
 7KN  Var_13    N26  C25  C8   N7     -0.31  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
 7KN  chir_01  C20  C19  N21  C16  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
 7KN  plan-1  C12  0.020
 7KN  plan-1  C11  0.020
 7KN  plan-1  C15  0.020
 7KN  plan-1  C14  0.020
 7KN  plan-1  C9   0.020
 7KN  plan-1  N10  0.020
 7KN  plan-1  N13  0.020
 7KN  plan-1  H3   0.020
 7KN  plan-1  H4   0.020
 7KN  plan-1  H7   0.020
 7KN  plan-2  N6   0.020
 7KN  plan-2  C8   0.020
 7KN  plan-2  N21  0.020
 7KN  plan-2  N22  0.020
 7KN  plan-2  C23  0.020
 7KN  plan-2  N24  0.020
 7KN  plan-2  C25  0.020
 7KN  plan-2  N26  0.020
 7KN  plan-2  C27  0.020
 7KN  plan-3  C15  0.020
 7KN  plan-3  C20  0.020
 7KN  plan-3  N21  0.020
 7KN  plan-3  C23  0.020
 7KN  plan-4  C8   0.020
 7KN  plan-4  C25  0.020
 7KN  plan-4  H17  0.020
 7KN  plan-4  N7   0.020

