# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 23:51:20 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-[3-chloranyl-5-(trifluoromethyl)pyridin-2-yl]-1,4-diazepane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cnc(N2CCCNCC2)c(Cl)c1
#
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
 A5K  A5K  1-[3-chloranyl-5-(trifluoromethyl)pyridin-2-yl]-1,4-diazepane  ligand  31  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A5K
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
 A5K  C10  C   CR16  0  -0.086   1.4323  -0.7617   0.5659
 A5K  C9   C   CR6   0  -0.187   0.0836  -0.5610   0.7282
 A5K  C8   C   CH2   0  -0.304  -2.4808   1.8505  -0.5861
 A5K  C7   C   CH2   0  -0.274  -3.4545   1.1227  -1.4955
 A5K  C4   C   CH2   0  -0.309  -2.5777   0.6983   1.5732
 A5K  C5   C   CH2   0  -0.420  -3.7486  -0.2943   1.4500
 A5K  C6   C   CH2   0  -0.286  -4.1480  -0.6518   0.0256
 A5K  C3   C   CR6   0   0.604  -0.5312   0.5887   0.1605
 A5K  C2   C   CR16  0  -0.030   1.4895   1.1498  -0.8218
 A5K  C1   C   CR6   0  -0.349   2.1819   0.1230  -0.2043
 A5K  CL   CL  CL    0  -0.089  -0.8103  -1.8226   1.5061
 A5K  C    C   CT    0   1.060   3.6403  -0.0966  -0.3837
 A5K  F2   F   F     0  -0.306   4.2199   0.8828  -1.0852
 A5K  F1   F   F     0  -0.320   4.2823  -0.1703   0.7952
 A5K  F    F   F     0  -0.311   3.9086  -1.2465  -1.0203
 A5K  N    N   N     0  -0.449   0.2041   1.3635  -0.6383
 A5K  N1   N   NT    0  -0.493  -1.8264   0.9468   0.3518
 A5K  N2   N   NH1   0  -0.571  -4.5401   0.5011  -0.7676
 A5K  H1   H   HCR6  0   0.270   1.8864  -1.6363   1.0138
 A5K  H3   H   HCH2  0   0.222  -3.0163   2.6127  -0.0146
 A5K  H4   H   HCH2  0   0.223  -3.8796   1.8571  -2.1840
 A5K  H5   H   HCH2  0   0.188  -2.8852   0.4032  -2.1076
 A5K  H6   H   HCH2  0   0.244  -2.9677   1.6705   1.8840
 A5K  H7   H   HCH2  0   0.251  -1.8997   0.3979   2.3689
 A5K  H8   H   HCH2  0   0.219  -3.5076  -1.2217   1.9714
 A5K  H9   H   HCH2  0   0.224  -4.6149   0.1308   1.9604
 A5K  H10  H   HCH2  0   0.190  -3.3360  -1.2228  -0.4505
 A5K  H11  H   HCH2  0   0.225  -5.0012  -1.3301   0.0848
 A5K  H12  H   HCR6  0   0.254   1.9865   1.8414  -1.4917
 A5K  H13  H   HNH1  0   0.335  -5.2504   0.2223  -1.4279
 A5K  H2   H   HCH2  0   0.275  -1.7309   2.3575  -1.1866

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
 A5K  C6   C5   single    1.522  0.020  1.522
 A5K  C6   N2   single    1.453  0.020  1.453
 A5K  C5   C4   single    1.540  0.020  1.540
 A5K  C4   N1   single    1.455  0.020  1.455
 A5K  N2   C7   single    1.447  0.020  1.447
 A5K  C7   C8   single    1.518  0.020  1.518
 A5K  N1   C8   single    1.458  0.020  1.458
 A5K  N1   C3   single    1.357  0.020  1.357
 A5K  C3   N    aromatic  1.334  0.020  1.334
 A5K  C3   C9   aromatic  1.422  0.020  1.422
 A5K  N    C2   aromatic  1.316  0.020  1.316
 A5K  CL   C9   single    1.731  0.020  1.731
 A5K  C9   C10  aromatic  1.373  0.020  1.373
 A5K  C2   C1   aromatic  1.384  0.020  1.384
 A5K  C10  C1   aromatic  1.392  0.020  1.392
 A5K  C1   C    single    1.486  0.020  1.486
 A5K  F2   C    single    1.337  0.020  1.337
 A5K  C    F    single    1.341  0.020  1.341
 A5K  C    F1   single    1.344  0.020  1.344
 A5K  C10  H1   single    0.930  0.020  1.080
 A5K  C8   H2   single    0.970  0.020  1.090
 A5K  C8   H3   single    0.970  0.020  1.090
 A5K  C7   H4   single    0.970  0.020  1.090
 A5K  C7   H5   single    0.970  0.020  1.090
 A5K  C4   H6   single    0.970  0.020  1.090
 A5K  C4   H7   single    0.970  0.020  1.090
 A5K  C5   H8   single    0.970  0.020  1.090
 A5K  C5   H9   single    0.970  0.020  1.090
 A5K  C6   H10  single    0.970  0.020  1.090
 A5K  C6   H11  single    0.970  0.020  1.090
 A5K  C2   H12  single    0.930  0.020  1.080
 A5K  N2   H13  single    0.890  0.020  1.040

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
 A5K  H1   C10  C1   121.09  3.000
 A5K  H1   C10  C9   118.77  3.000
 A5K  C1   C10  C9   120.09  3.000
 A5K  CL   C9   C3   123.05  3.000
 A5K  CL   C9   C10  116.99  3.000
 A5K  C3   C9   C10  119.71  3.000
 A5K  H3   C8   H2   107.56  3.000
 A5K  H3   C8   N1   108.41  3.000
 A5K  H2   C8   N1   109.58  3.000
 A5K  H3   C8   C7   109.48  3.000
 A5K  H2   C8   C7   109.60  3.000
 A5K  N1   C8   C7   112.09  3.000
 A5K  H5   C7   H4   106.82  3.000
 A5K  H5   C7   N2   112.71  3.000
 A5K  H4   C7   N2   108.28  3.000
 A5K  H5   C7   C8   108.31  3.000
 A5K  H4   C7   C8   107.74  3.000
 A5K  N2   C7   C8   112.69  3.000
 A5K  H7   C4   H6   105.08  3.000
 A5K  H7   C4   N1   109.83  3.000
 A5K  H6   C4   N1   105.72  3.000
 A5K  H7   C4   C5   110.76  3.000
 A5K  H6   C4   C5   108.96  3.000
 A5K  N1   C4   C5   115.81  3.000
 A5K  H9   C5   H8   106.43  3.000
 A5K  H9   C5   C6   108.71  3.000
 A5K  H8   C5   C6   107.80  3.000
 A5K  H9   C5   C4   108.36  3.000
 A5K  H8   C5   C4   109.98  3.000
 A5K  C6   C5   C4   115.20  3.000
 A5K  H11  C6   H10  106.13  3.000
 A5K  H11  C6   N2   108.16  3.000
 A5K  H10  C6   N2   111.99  3.000
 A5K  H11  C6   C5   107.48  3.000
 A5K  H10  C6   C5   109.45  3.000
 A5K  N2   C6   C5   113.28  3.000
 A5K  N1   C3   N    117.21  3.000
 A5K  N    C3   C9   118.06  3.000
 A5K  N1   C3   C9   124.72  3.000
 A5K  H12  C2   N    115.50  3.000
 A5K  H12  C2   C1   121.33  3.000
 A5K  N    C2   C1   123.17  3.000
 A5K  C    C1   C2   123.15  3.000
 A5K  C    C1   C10  120.10  3.000
 A5K  C2   C1   C10  116.68  3.000
 A5K  F    C    F1   105.88  3.000
 A5K  F1   C    F2   107.05  3.000
 A5K  F    C    F2   106.99  3.000
 A5K  F1   C    C1   111.77  3.000
 A5K  F    C    C1   112.36  3.000
 A5K  F2   C    C1   112.38  3.000
 A5K  C2   N    C3   121.84  3.000
 A5K  C3   N1   C4   124.46  3.000
 A5K  C3   N1   C8   120.09  3.000
 A5K  C4   N1   C8   114.47  3.000
 A5K  H13  N2   C6   109.14  3.000
 A5K  H13  N2   C7   108.51  3.000
 A5K  C6   N2   C7   114.38  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
 A5K  CONST_01  N    C3   C9   C10     0.00   0.0  0
 A5K  CONST_02  N    C2   C1   C10     0.00   0.0  0
 A5K  CONST_03  C2   N    C3   C9      0.00   0.0  0
 A5K  CONST_04  C2   C1   C10  C9      0.00   0.0  0
 A5K  CONST_05  C1   C2   N    C3      0.00   0.0  0
 A5K  CONST_06  C1   C10  C9   C3      0.00   0.0  0
 A5K  CONST_07  N1   C3   C9   C10   180.00   0.0  0
 A5K  CONST_08  N1   C3   N    C2    180.00   0.0  0
 A5K  CONST_09  C    C1   C10  C9    180.00   0.0  0
 A5K  CONST_10  CL   C9   C10  C1    180.00   0.0  0
 A5K  CONST_11  N1   C3   C9   CL      0.00   0.0  0
 A5K  CONST_12  N    C3   C9   CL    180.00   0.0  0
 A5K  CONST_13  N    C2   C1   C     180.00   0.0  0
 A5K  CONST_14  H12  C2   C1   C10   180.00   0.0  0
 A5K  CONST_15  H1   C10  C9   C3    180.00   0.0  0
 A5K  Var_01    F2   C    C1   C10  -176.43  30.0  2

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
 A5K  plan-1  C10  0.020
 A5K  plan-1  C9   0.020
 A5K  plan-1  C3   0.020
 A5K  plan-1  C2   0.020
 A5K  plan-1  C1   0.020
 A5K  plan-1  CL   0.020
 A5K  plan-1  C    0.020
 A5K  plan-1  N    0.020
 A5K  plan-1  N1   0.020
 A5K  plan-1  H1   0.020
 A5K  plan-1  H12  0.020

