# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 10:55:41 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 4-(cyclohexylamino)-6-piperazin-1-yl-1,3,5-triazine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1nc(NC2CCCCC2)nc(n1)N3CCNCC3
#
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
 ORG  ORG  4-(cyclohexylamino)-6-piperazin-1-yl-1,3,5-triazine-2-carbonitrile  ligand  42  21  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ORG
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
 ORG  N1    N  N     0  -0.483  -0.7954   1.2871  -0.1913
 ORG  C2    C  CR6   0   0.623  -0.5600  -0.0336  -0.3480
 ORG  N3    N  N     0  -0.522   0.6529  -0.5743  -0.4460
 ORG  C4    C  CR6   0   0.669   1.6876   0.2604  -0.3790
 ORG  N5    N  N     0  -0.490   1.5556   1.5987  -0.2099
 ORG  C6    C  CR6   0   0.381   0.3097   1.9937  -0.1343
 ORG  N7    N  NH1   0  -0.657  -1.6083  -0.8502  -0.4180
 ORG  N8    N  NT    0  -0.490   2.9255  -0.2296  -0.4891
 ORG  C9    C  CSP   0   0.060   0.1227   3.4243   0.0419
 ORG  C10   C  CH2   0  -0.321   4.1215   0.5911  -0.3880
 ORG  C11   C  CH2   0  -0.315   5.0237   0.0537   0.7198
 ORG  N12   N  NH1   0  -0.579   5.3295  -1.3595   0.5888
 ORG  C13   C  CH2   0  -0.317   4.1212  -2.1479   0.4287
 ORG  C14   C  CH2   0  -0.320   3.1993  -1.6443  -0.6786
 ORG  N15   N  NS    0  -0.221  -0.0256   4.5556   0.1789
 ORG  C16   C  CH1   0  -0.046  -2.9995  -0.4494  -0.2985
 ORG  C17   C  CH2   0  -0.451  -3.8790  -1.4932  -0.9799
 ORG  C18   C  CH2   0  -0.438  -5.3546  -1.1247  -0.8708
 ORG  C19   C  CH2   0  -0.431  -5.7767  -0.9031   0.5774
 ORG  C20   C  CH2   0  -0.440  -4.8898   0.1333   1.2590
 ORG  C21   C  CH2   0  -0.431  -3.4157  -0.2442   1.1575
 ORG  HN7   H  HNH1  0   0.397  -1.3993  -1.8345  -0.4884
 ORG  H10   H  HCH2  0   0.241   4.6524   0.5569  -1.3461
 ORG  H10A  H  HCH2  0   0.275   3.8466   1.6239  -0.1963
 ORG  H11   H  HCH2  0   0.247   5.9541   0.6240   0.7303
 ORG  H11A  H  HCH2  0   0.228   4.5366   0.2189   1.6860
 ORG  HN12  H  HNH1  0   0.345   5.9281  -1.4974  -0.2176
 ORG  H13   H  HCH2  0   0.247   4.3936  -3.1843   0.2230
 ORG  H13A  H  HCH2  0   0.228   3.5717  -2.1408   1.3753
 ORG  H14   H  HCH2  0   0.273   2.2674  -2.2025  -0.6885
 ORG  H14A  H  HCH2  0   0.241   3.6784  -1.7793  -1.6548
 ORG  H16   H  HCH1  0   0.239  -3.1169   0.4992  -0.8303
 ORG  H17   H  HCH2  0   0.244  -3.5888  -1.5914  -2.0290
 ORG  H17A  H  HCH2  0   0.221  -3.7099  -2.4698  -0.5110
 ORG  H18   H  HCH2  0   0.216  -5.5410  -0.2120  -1.4464
 ORG  H18A  H  HCH2  0   0.235  -5.9629  -1.9074  -1.3289
 ORG  H19   H  HCH2  0   0.230  -6.8231  -0.5917   0.6189
 ORG  H19A  H  HCH2  0   0.211  -5.7136  -1.8495   1.1255
 ORG  H20   H  HCH2  0   0.214  -5.0496   1.1120   0.7938
 ORG  H20A  H  HCH2  0   0.233  -5.1710   0.2437   2.3087
 ORG  H21   H  HCH2  0   0.215  -3.2323  -1.1700   1.7134
 ORG  H21A  H  HCH2  0   0.238  -2.7908   0.5287   1.6107

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
 ORG  N1   C2    aromatic  1.351  0.020  1.351
 ORG  N1   C6    aromatic  1.313  0.020  1.313
 ORG  C2   N3    aromatic  1.332  0.020  1.332
 ORG  C2   N7    single    1.331  0.020  1.331
 ORG  N3   C4    aromatic  1.331  0.020  1.331
 ORG  C4   N5    aromatic  1.355  0.020  1.355
 ORG  C4   N8    single    1.336  0.020  1.336
 ORG  N5   C6    aromatic  1.309  0.020  1.309
 ORG  C6   C9    single    1.454  0.020  1.454
 ORG  N7   C16   single    1.453  0.020  1.453
 ORG  N7   HN7   single    0.860  0.020  1.020
 ORG  N8   C10   single    1.454  0.020  1.454
 ORG  N8   C14   single    1.453  0.020  1.453
 ORG  C9   N15   triple    1.149  0.020  1.149
 ORG  C10  C11   single    1.526  0.020  1.526
 ORG  C10  H10   single    0.970  0.020  1.090
 ORG  C10  H10A  single    0.970  0.020  1.090
 ORG  C11  N12   single    1.452  0.020  1.452
 ORG  C11  H11   single    0.970  0.020  1.090
 ORG  C11  H11A  single    0.970  0.020  1.090
 ORG  N12  C13   single    1.452  0.020  1.452
 ORG  N12  HN12  single    0.890  0.020  1.040
 ORG  C13  C14   single    1.526  0.020  1.526
 ORG  C13  H13   single    0.970  0.020  1.090
 ORG  C13  H13A  single    0.970  0.020  1.090
 ORG  C14  H14   single    0.970  0.020  1.090
 ORG  C14  H14A  single    0.970  0.020  1.090
 ORG  C16  C17   single    1.525  0.020  1.525
 ORG  C16  C21   single    1.528  0.020  1.528
 ORG  C16  H16   single    0.970  0.020  1.090
 ORG  C17  C18   single    1.525  0.020  1.525
 ORG  C17  H17   single    0.970  0.020  1.090
 ORG  C17  H17A  single    0.970  0.020  1.090
 ORG  C18  C19   single    1.525  0.020  1.525
 ORG  C18  H18   single    0.970  0.020  1.090
 ORG  C18  H18A  single    0.970  0.020  1.090
 ORG  C19  C20   single    1.525  0.020  1.525
 ORG  C19  H19   single    0.970  0.020  1.090
 ORG  C19  H19A  single    0.970  0.020  1.090
 ORG  C20  C21   single    1.525  0.020  1.525
 ORG  C20  H20   single    0.970  0.020  1.090
 ORG  C20  H20A  single    0.970  0.020  1.090
 ORG  C21  H21   single    0.970  0.020  1.090
 ORG  C21  H21A  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
 ORG  C6    N1   C2   112.62  3.000
 ORG  N7    C2   N3   117.68  3.000
 ORG  N7    C2   N1   117.96  3.000
 ORG  N3    C2   N1   124.36  3.000
 ORG  C4    N3   C2   116.72  3.000
 ORG  N8    C4   N5   117.56  3.000
 ORG  N8    C4   N3   119.09  3.000
 ORG  N5    C4   N3   123.35  3.000
 ORG  C6    N5   C4   113.44  3.000
 ORG  C9    C6   N5   115.24  3.000
 ORG  C9    C6   N1   115.26  3.000
 ORG  N5    C6   N1   129.50  3.000
 ORG  HN7   N7   C16  118.26  3.000
 ORG  HN7   N7   C2   116.05  3.000
 ORG  C16   N7   C2   125.51  3.000
 ORG  C14   N8   C10  113.80  3.000
 ORG  C14   N8   C4   122.85  3.000
 ORG  C10   N8   C4   123.33  3.000
 ORG  N15   C9   C6   180.00  3.000
 ORG  H10A  C10  H10  107.85  3.000
 ORG  H10A  C10  C11  110.88  3.000
 ORG  H10   C10  C11  109.71  3.000
 ORG  H10A  C10  N8   109.93  3.000
 ORG  H10   C10  N8   108.67  3.000
 ORG  C11   C10  N8   109.75  3.000
 ORG  H11A  C11  H11  106.97  3.000
 ORG  H11A  C11  N12  108.68  3.000
 ORG  H11   C11  N12  109.26  3.000
 ORG  H11A  C11  C10  108.93  3.000
 ORG  H11   C11  C10  109.08  3.000
 ORG  N12   C11  C10  113.69  3.000
 ORG  HN12  N12  C13  109.26  3.000
 ORG  HN12  N12  C11  109.18  3.000
 ORG  C13   N12  C11  111.30  3.000
 ORG  H13A  C13  H13  107.13  3.000
 ORG  H13A  C13  C14  108.79  3.000
 ORG  H13   C13  C14  109.11  3.000
 ORG  H13A  C13  N12  108.60  3.000
 ORG  H13   C13  N12  109.20  3.000
 ORG  C14   C13  N12  113.80  3.000
 ORG  H14A  C14  H14  107.68  3.000
 ORG  H14A  C14  C13  109.97  3.000
 ORG  H14   C14  C13  110.81  3.000
 ORG  H14A  C14  N8   108.57  3.000
 ORG  H14   C14  N8   109.86  3.000
 ORG  C13   C14  N8   109.90  3.000
 ORG  H16   C16  C21  108.51  3.000
 ORG  H16   C16  C17  108.32  3.000
 ORG  C21   C16  C17  111.13  3.000
 ORG  H16   C16  N7   107.58  3.000
 ORG  C21   C16  N7   112.10  3.000
 ORG  C17   C16  N7   109.06  3.000
 ORG  H17A  C17  H17  106.83  3.000
 ORG  H17A  C17  C18  109.51  3.000
 ORG  H17   C17  C18  110.32  3.000
 ORG  H17A  C17  C16  109.24  3.000
 ORG  H17   C17  C16  109.70  3.000
 ORG  C18   C17  C16  111.14  3.000
 ORG  H18A  C18  H18  106.38  3.000
 ORG  H18A  C18  C19  110.39  3.000
 ORG  H18   C18  C19  109.33  3.000
 ORG  H18A  C18  C17  109.62  3.000
 ORG  H18   C18  C17  109.18  3.000
 ORG  C19   C18  C17  111.78  3.000
 ORG  H19A  C19  H19  106.40  3.000
 ORG  H19A  C19  C20  109.27  3.000
 ORG  H19   C19  C20  110.27  3.000
 ORG  H19A  C19  C18  109.50  3.000
 ORG  H19   C19  C18  110.04  3.000
 ORG  C20   C19  C18  111.25  3.000
 ORG  H20A  C20  H20  106.28  3.000
 ORG  H20A  C20  C21  109.74  3.000
 ORG  H20   C20  C21  109.51  3.000
 ORG  H20A  C20  C19  110.40  3.000
 ORG  H20   C20  C19  109.42  3.000
 ORG  C21   C20  C19  111.36  3.000
 ORG  H21A  C21  H21  106.96  3.000
 ORG  H21A  C21  C20  110.50  3.000
 ORG  H21   C21  C20  109.71  3.000
 ORG  H21A  C21  C16  109.54  3.000
 ORG  H21   C21  C16  108.93  3.000
 ORG  C20   C21  C16  111.09  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
 ORG  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 ORG  CONST_02  C4   N5   C6   N1      0.00   0.0  0
 ORG  CONST_03  N5   C6   N1   C2      0.00   0.0  0
 ORG  CONST_04  N5   C4   N3   C2      0.00   0.0  0
 ORG  CONST_05  C6   N1   C2   N3      0.00   0.0  0
 ORG  CONST_06  C6   N5   C4   N3      0.00   0.0  0
 ORG  CONST_07  N8   C4   N3   C2    180.00   0.0  0
 ORG  CONST_08  N8   C4   N5   C6    180.00   0.0  0
 ORG  CONST_09  C9   C6   N1   C2    180.00   0.0  0
 ORG  CONST_10  N7   C2   N3   C4    180.00   0.0  0
 ORG  CONST_11  C9   C6   N5   C4    180.00   0.0  0
 ORG  CONST_12  N7   C2   N1   C6    180.00   0.0  0
 ORG  CONST_13  C16  N7   C2   N1      0.00   0.0  0
 ORG  CONST_14  C16  N7   C2   N3    180.00   0.0  0
 ORG  CONST_15  HN7  N7   C2   N1    180.00   0.0  0
 ORG  Var_01    C10  N8   C4   N3   -178.04  30.0  2
 ORG  Var_02    C11  C10  N8   C4    123.27  30.0  1
 ORG  Var_03    C13  C14  N8   C4   -123.53  30.0  1
 ORG  Var_04    N12  C11  C10  N8     53.05  30.0  1
 ORG  Var_05    N12  C13  C14  N8    -52.51  30.0  1
 ORG  Var_06    C13  N12  C11  C10   -51.88  30.0  1
 ORG  Var_07    C14  C13  N12  C11    51.59  30.0  1
 ORG  Var_08    C19  C18  C17  C16   -54.92  30.0  1
 ORG  Var_09    C19  C20  C21  C16    55.68  30.0  1
 ORG  Var_10    C20  C19  C18  C17    54.63  30.0  1
 ORG  Var_11    C21  C20  C19  C18   -54.93  30.0  1

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
 ORG  chir_01  C16  N7  C17  C21  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
 ORG  plan-1  N1   0.020
 ORG  plan-1  C2   0.020
 ORG  plan-1  N3   0.020
 ORG  plan-1  C4   0.020
 ORG  plan-1  N5   0.020
 ORG  plan-1  C6   0.020
 ORG  plan-1  N7   0.020
 ORG  plan-1  N8   0.020
 ORG  plan-1  C9   0.020
 ORG  plan-1  N15  0.020
 ORG  plan-2  C2   0.020
 ORG  plan-2  N7   0.020
 ORG  plan-2  C16  0.020
 ORG  plan-2  HN7  0.020

