# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:53:21 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 6-[(1S)-1-(azepan-1-yl)ethyl]-N,N-dimethyl-1,3,5-triazine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N1CCCCCC1)c2nc(N)nc(n2)N(C)C
#
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
 487  487  6-[(1S)-1-(azepan-1-yl)ethyl]-N,N-dimethyl-1,3,5-triazine-2,4-diamine  ligand  43  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_487
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
 487  C4   C  CR6   0   0.638  -2.6954   0.1638   0.0914
 487  C5   C  CH3   0  -0.525  -3.7915   2.0745   1.1469
 487  C6   C  CH3   0  -0.517  -5.0054  -0.0301   0.8296
 487  N1   N  NH2   0  -0.827  -1.6824  -2.8777  -1.2432
 487  C7   C  CH2   0  -0.300   3.1164   1.1445  -0.6389
 487  C8   C  CH2   0  -0.457   4.4063   0.3601  -0.4123
 487  N2   N  N     0  -0.518  -2.7680  -1.1124  -0.2837
 487  C9   C  CH2   0  -0.452   4.7681   0.1236   1.0521
 487  C10  C  CH2   0  -0.418   4.1034  -1.0986   1.6801
 487  C11  C  CH2   0  -0.438   2.6350  -1.2993   1.2930
 487  C12  C  CH2   0  -0.287   1.8279  -0.0271   1.0418
 487  N3   N  NT    0  -0.482  -3.8030   0.7379   0.5962
 487  N4   N  N     0  -0.489  -1.5842   0.9151  -0.0030
 487  C3   C  CR6   0   0.534  -1.6564  -1.6079  -0.8253
 487  N    N  N     0  -0.449  -0.5109  -0.9307  -0.9943
 487  C2   C  CR6   0   0.318  -0.5433   0.3113  -0.5487
 487  C1   C  CH1   0  -0.073   0.7007   1.1568  -0.7276
 487  C    C  CH3   0  -0.690   0.7127   1.5983  -2.1938
 487  N5   N  NT    0  -0.406   1.8927   0.4156  -0.3469
 487  H1   H  HCH3  0   0.267  -2.8907   2.5984   0.8483
 487  H2   H  HCH3  0   0.236  -4.6582   2.6285   0.7836
 487  H3   H  HCH3  0   0.231  -3.8385   2.0528   2.2392
 487  H4   H  HCH3  0   0.232  -5.0179  -0.4681   1.8318
 487  H5   H  HCH3  0   0.238  -5.8685   0.6286   0.7389
 487  H6   H  HCH3  0   0.258  -5.1025  -0.8314   0.1045
 487  H7   H  HNH2  0   0.404  -2.4834  -3.4539  -1.0516
 487  H8   H  HNH2  0   0.414  -0.8305  -3.3225  -1.5400
 487  H9   H  HCH2  0   0.195   3.1733   2.0815  -0.0551
 487  H10  H  HCH2  0   0.249   3.1025   1.4304  -1.6901
 487  H11  H  HCH2  0   0.236   4.3632  -0.5849  -0.9628
 487  H12  H  HCH2  0   0.238   5.2063   0.9385  -0.8825
 487  H13  H  HCH2  0   0.228   5.8514   0.0219   1.1549
 487  H14  H  HCH2  0   0.215   4.5055   1.0198   1.6231
 487  H15  H  HCH2  0   0.207   4.6620  -1.9973   1.4042
 487  H16  H  HCH2  0   0.208   4.1910  -1.0198   2.7673
 487  H17  H  HCH2  0   0.228   2.5555  -1.9024   0.3864
 487  H18  H  HCH2  0   0.215   2.1453  -1.8792   2.0798
 487  H19  H  HCH2  0   0.239   0.7899  -0.2490   1.2881
 487  H20  H  HCH2  0   0.194   2.1248   0.7770   1.7366
 487  H21  H  HCH1  0   0.204   0.5609   2.0580  -0.1072
 487  H22  H  HCH3  0   0.236  -0.2701   1.9783  -2.4735
 487  H23  H  HCH3  0   0.237   1.4254   2.3995  -2.3786
 487  H24  H  HCH3  0   0.230   0.9530   0.7574  -2.8448

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
 487  N1   C3   single    1.337  0.020  1.337
 487  C3   N2   aromatic  1.332  0.020  1.332
 487  C3   N    aromatic  1.341  0.020  1.341
 487  N2   C4   aromatic  1.332  0.020  1.332
 487  N    C2   aromatic  1.320  0.020  1.320
 487  C    C1   single    1.531  0.020  1.531
 487  C5   N3   single    1.446  0.020  1.446
 487  C4   N3   single    1.346  0.020  1.346
 487  C4   N4   aromatic  1.345  0.020  1.345
 487  C2   N4   aromatic  1.321  0.020  1.321
 487  C2   C1   single    1.515  0.020  1.515
 487  N3   C6   single    1.446  0.020  1.446
 487  C1   N5   single    1.454  0.020  1.454
 487  C7   N5   single    1.454  0.020  1.454
 487  C7   C8   single    1.527  0.020  1.527
 487  N5   C12  single    1.459  0.020  1.459
 487  C8   C9   single    1.527  0.020  1.527
 487  C12  C11  single    1.527  0.020  1.527
 487  C9   C10  single    1.526  0.020  1.526
 487  C10  C11  single    1.532  0.020  1.532
 487  C5   H1   single    0.970  0.020  1.090
 487  C5   H2   single    0.970  0.020  1.090
 487  C5   H3   single    0.970  0.020  1.090
 487  C6   H4   single    0.970  0.020  1.090
 487  C6   H5   single    0.970  0.020  1.090
 487  C6   H6   single    0.970  0.020  1.090
 487  N1   H7   single    0.860  0.020  1.020
 487  N1   H8   single    0.860  0.020  1.020
 487  C7   H9   single    0.970  0.020  1.090
 487  C7   H10  single    0.970  0.020  1.090
 487  C8   H11  single    0.970  0.020  1.090
 487  C8   H12  single    0.970  0.020  1.090
 487  C9   H13  single    0.970  0.020  1.090
 487  C9   H14  single    0.970  0.020  1.090
 487  C10  H15  single    0.970  0.020  1.090
 487  C10  H16  single    0.970  0.020  1.090
 487  C11  H17  single    0.970  0.020  1.090
 487  C11  H18  single    0.970  0.020  1.090
 487  C12  H19  single    0.970  0.020  1.090
 487  C12  H20  single    0.970  0.020  1.090
 487  C1   H21  single    0.970  0.020  1.090
 487  C    H22  single    0.970  0.020  1.090
 487  C    H23  single    0.970  0.020  1.090
 487  C    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
 487  N4   C4   N3   117.91  3.000
 487  N4   C4   N2   124.09  3.000
 487  N3   C4   N2   118.00  3.000
 487  H3   C5   H2   107.97  3.000
 487  H3   C5   H1   108.69  3.000
 487  H2   C5   H1   108.84  3.000
 487  H3   C5   N3   111.22  3.000
 487  H2   C5   N3   109.65  3.000
 487  H1   C5   N3   110.40  3.000
 487  H6   C6   H5   108.66  3.000
 487  H6   C6   H4   108.39  3.000
 487  H5   C6   H4   108.01  3.000
 487  H6   C6   N3   111.03  3.000
 487  H5   C6   N3   108.93  3.000
 487  H4   C6   N3   111.73  3.000
 487  H8   N1   H7   118.54  3.000
 487  H8   N1   C3   119.72  3.000
 487  H7   N1   C3   120.01  3.000
 487  H10  C7   H9   106.73  3.000
 487  H10  C7   N5   108.33  3.000
 487  H9   C7   N5   111.23  3.000
 487  H10  C7   C8   106.78  3.000
 487  H9   C7   C8   108.29  3.000
 487  N5   C7   C8   115.07  3.000
 487  H12  C8   H11  105.63  3.000
 487  H12  C8   C9   108.72  3.000
 487  H11  C8   C9   110.98  3.000
 487  H12  C8   C7   106.41  3.000
 487  H11  C8   C7   109.62  3.000
 487  C9   C8   C7   114.96  3.000
 487  C3   N2   C4   115.18  3.000
 487  H14  C9   H13  105.36  3.000
 487  H14  C9   C10  109.66  3.000
 487  H13  C9   C10  108.56  3.000
 487  H14  C9   C8   108.46  3.000
 487  H13  C9   C8   109.85  3.000
 487  C10  C9   C8   114.54  3.000
 487  H16  C10  H15  105.61  3.000
 487  H16  C10  C11  109.73  3.000
 487  H15  C10  C11  108.56  3.000
 487  H16  C10  C9   108.44  3.000
 487  H15  C10  C9   109.38  3.000
 487  C11  C10  C9   114.73  3.000
 487  H18  C11  H17  105.78  3.000
 487  H18  C11  C12  108.87  3.000
 487  H17  C11  C12  106.56  3.000
 487  H18  C11  C10  108.48  3.000
 487  H17  C11  C10  110.61  3.000
 487  C12  C11  C10  116.04  3.000
 487  H20  C12  H19  105.21  3.000
 487  H20  C12  N5   111.49  3.000
 487  H19  C12  N5   108.61  3.000
 487  H20  C12  C11  111.18  3.000
 487  H19  C12  C11  107.25  3.000
 487  N5   C12  C11  112.70  3.000
 487  C6   N3   C5   115.87  3.000
 487  C6   N3   C4   121.23  3.000
 487  C5   N3   C4   122.05  3.000
 487  C2   N4   C4   115.13  3.000
 487  N    C3   N2   125.17  3.000
 487  N    C3   N1   117.17  3.000
 487  N2   C3   N1   117.65  3.000
 487  C2   N    C3   114.30  3.000
 487  C1   C2   N    117.72  3.000
 487  C1   C2   N4   116.15  3.000
 487  N    C2   N4   126.07  3.000
 487  H21  C1   N5   111.91  3.000
 487  H21  C1   C    107.70  3.000
 487  N5   C1   C    113.03  3.000
 487  H21  C1   C2   106.59  3.000
 487  N5   C1   C2   110.96  3.000
 487  C    C1   C2   106.29  3.000
 487  H24  C    H23  108.79  3.000
 487  H24  C    H22  108.32  3.000
 487  H23  C    H22  106.87  3.000
 487  H24  C    C1   110.55  3.000
 487  H23  C    C1   112.34  3.000
 487  H22  C    C1   109.82  3.000
 487  C1   N5   C12  111.56  3.000
 487  C12  N5   C7   112.37  3.000
 487  C1   N5   C7   112.44  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
 487  CONST_01  N   C3  N2  C4    0.00   0.0  0
 487  CONST_02  N   C2  N4  C4    0.00   0.0  0
 487  CONST_03  C2  N   C3  N2    0.00   0.0  0
 487  CONST_04  C2  N4  C4  N2    0.00   0.0  0
 487  CONST_05  C3  N2  C4  N4    0.00   0.0  0
 487  CONST_06  C3  N   C2  N4    0.00   0.0  0
 487  CONST_07  N1  C3  N2  C4  180.00   0.0  0
 487  CONST_08  C1  C2  N4  C4  180.00   0.0  0
 487  CONST_09  C2  N   C3  N1  180.00   0.0  0
 487  CONST_10  C3  N2  C4  N3  180.00   0.0  0
 487  CONST_11  C2  N4  C4  N3  180.00   0.0  0
 487  CONST_12  C1  C2  N   C3  180.00   0.0  0
 487  CONST_13  N2  C4  N3  C5  180.00   0.0  0
 487  CONST_14  N4  C4  N3  C5    0.00   0.0  0
 487  CONST_15  N2  C4  N3  C6    0.00   0.0  0
 487  CONST_16  N4  C4  N3  C6  180.00   0.0  0
 487  CONST_17  H7  N1  C3  N2    0.00   0.0  0
 487  CONST_18  H8  N1  C3  N2  180.00   0.0  0
 487  Var_01    H1  C5  N3  C4   15.36  30.0  3
 487  Var_02    H4  C6  N3  C4   89.30  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
 487  chir_01  C1  C  C2  N5  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
 487  plan-1  C4  0.020
 487  plan-1  N1  0.020
 487  plan-1  N2  0.020
 487  plan-1  N3  0.020
 487  plan-1  N4  0.020
 487  plan-1  C3  0.020
 487  plan-1  N   0.020
 487  plan-1  C2  0.020
 487  plan-1  C1  0.020
 487  plan-2  N1  0.020
 487  plan-2  C3  0.020
 487  plan-2  H7  0.020
 487  plan-2  H8  0.020
 487  plan-3  C4  0.020
 487  plan-3  C5  0.020
 487  plan-3  C6  0.020
 487  plan-3  N3  0.020

