# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 19:44:32 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1cc(cnc1Br)N2CCCNCC2
#
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
 09S  09S  1-(6-bromo-5-ethoxypyridin-3-yl)-1,4-diazepane  ligand  35  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_09S
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
 09S  C1   C   CH2   0  -0.382  -3.0059   0.6888   1.3574
 09S  C2   C   CH2   0  -0.304  -3.6416   1.5803   0.2689
 09S  N1   N   NH1   0  -0.587  -4.2028   0.9002  -0.8770
 09S  C3   C   CH2   0  -0.303  -4.9888  -0.2977  -0.6377
 09S  C4   C   CH2   0  -0.445  -4.1852  -1.5935  -0.5086
 09S  C5   C   CH2   0  -0.353  -3.2911  -1.6517   0.7235
 09S  N2   N   NT    0  -0.493  -2.3907  -0.5183   0.8513
 09S  C6   C   CR6   0  -0.080   1.1529  -0.4522  -1.2277
 09S  N3   N   N     0  -0.354   0.4200  -1.5278  -1.2346
 09S  C7   C   CR16  0  -0.188  -0.7359  -1.5613  -0.5914
 09S  C8   C   CR6   0   0.355  -1.2289  -0.4615   0.1367
 09S  C9   C   CR16  0  -0.416  -0.4338   0.6999   0.1149
 09S  C10  C   CR6   0   0.438   0.7746   0.7203  -0.5628
 09S  O1   O   O2    0  -0.455   1.5940   1.7695  -0.6310
 09S  C11  C   CH2   0  -0.196   1.2370   2.9758   0.0401
 09S  C12  C   CH3   0  -0.681   2.3333   3.9848  -0.1978
 09S  H1   H   HCH2  0   0.258  -2.2950   1.2728   1.9475
 09S  H2   H   HCH2  0   0.262  -3.7728   0.3777   2.0668
 09S  H3   H   HCH2  0   0.231  -4.4133   2.1813   0.7608
 09S  H4   H   HCH2  0   0.232  -2.9082   2.2919  -0.1147
 09S  H5   H   HNH1  0   0.345  -3.4813   0.7087  -1.5593
 09S  H7   H   HCH2  0   0.224  -5.6055  -0.1435   0.2537
 09S  H8   H   HCH2  0   0.235  -5.6932  -0.4211  -1.4657
 09S  H9   H   HCH2  0   0.234  -4.8719  -2.4440  -0.4747
 09S  H10  H   HCH2  0   0.225  -3.5830  -1.7204  -1.4148
 09S  H11  H   HCH2  0   0.256  -3.9110  -1.6693   1.6224
 09S  H12  H   HCH2  0   0.258  -2.7247  -2.5835   0.7430
 09S  H13  H   HCR6  0   0.266  -1.2821  -2.4923  -0.6599
 09S  H14  H   HCR6  0   0.300  -0.7594   1.5882   0.6352
 09S  H15  H   HCH2  0   0.231   0.2815   3.3473  -0.3441
 09S  H16  H   HCH2  0   0.233   1.1168   2.7858   1.1113
 09S  H17  H   HCH3  0   0.241   2.0742   4.9166   0.3038
 09S  H18  H   HCH3  0   0.238   3.2863   3.6410   0.2036
 09S  H19  H   HCH3  0   0.238   2.4561   4.1986  -1.2592
 09S  BR1  BR  BR    0  -0.066   2.7932  -0.4964  -2.1781

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
 09S  C3   N1   single    1.453  0.020  1.453
 09S  C3   C4   single    1.530  0.020  1.530
 09S  N1   C2   single    1.446  0.020  1.446
 09S  C4   C5   single    1.523  0.020  1.523
 09S  C2   C1   single    1.544  0.020  1.544
 09S  C12  C11  single    1.509  0.020  1.509
 09S  C11  O1   single    1.426  0.020  1.426
 09S  C5   N2   single    1.453  0.020  1.453
 09S  C1   N2   single    1.446  0.020  1.446
 09S  N2   C8   single    1.365  0.020  1.365
 09S  C9   C8   aromatic  1.408  0.020  1.408
 09S  C9   C10  aromatic  1.386  0.020  1.386
 09S  O1   C10  single    1.333  0.020  1.333
 09S  C8   C7   aromatic  1.408  0.020  1.408
 09S  C10  C6   aromatic  1.400  0.020  1.400
 09S  C7   N3   aromatic  1.323  0.020  1.323
 09S  C6   N3   aromatic  1.302  0.020  1.302
 09S  C6   BR1  single    1.896  0.020  1.896
 09S  C1   H1   single    0.970  0.020  1.090
 09S  C1   H2   single    0.970  0.020  1.090
 09S  C2   H3   single    0.970  0.020  1.090
 09S  C2   H4   single    0.970  0.020  1.090
 09S  N1   H5   single    0.890  0.020  1.040
 09S  C3   H7   single    0.970  0.020  1.090
 09S  C3   H8   single    0.970  0.020  1.090
 09S  C4   H9   single    0.970  0.020  1.090
 09S  C4   H10  single    0.970  0.020  1.090
 09S  C5   H11  single    0.970  0.020  1.090
 09S  C5   H12  single    0.970  0.020  1.090
 09S  C7   H13  single    0.930  0.020  1.080
 09S  C9   H14  single    0.930  0.020  1.080
 09S  C11  H15  single    0.970  0.020  1.090
 09S  C11  H16  single    0.970  0.020  1.090
 09S  C12  H17  single    0.970  0.020  1.090
 09S  C12  H18  single    0.970  0.020  1.090
 09S  C12  H19  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
 09S  H2   C1   H1   105.00  3.000
 09S  H2   C1   N2   106.79  3.000
 09S  H1   C1   N2   110.99  3.000
 09S  H2   C1   C2   109.51  3.000
 09S  H1   C1   C2   109.87  3.000
 09S  N2   C1   C2   114.23  3.000
 09S  H4   C2   H3   105.88  3.000
 09S  H4   C2   N1   106.79  3.000
 09S  H3   C2   N1   109.92  3.000
 09S  H4   C2   C1   110.34  3.000
 09S  H3   C2   C1   106.88  3.000
 09S  N1   C2   C1   116.55  3.000
 09S  H5   N1   C3   109.94  3.000
 09S  H5   N1   C2   110.29  3.000
 09S  C3   N1   C2   117.86  3.000
 09S  H8   C3   H7   105.64  3.000
 09S  H8   C3   C4   107.85  3.000
 09S  H7   C3   C4   110.26  3.000
 09S  H8   C3   N1   108.47  3.000
 09S  H7   C3   N1   108.83  3.000
 09S  C4   C3   N1   115.34  3.000
 09S  H10  C4   H9   106.30  3.000
 09S  H10  C4   C5   110.00  3.000
 09S  H9   C4   C5   108.29  3.000
 09S  H10  C4   C3   108.48  3.000
 09S  H9   C4   C3   109.35  3.000
 09S  C5   C4   C3   114.13  3.000
 09S  H12  C5   H11  105.44  3.000
 09S  H12  C5   N2   110.06  3.000
 09S  H11  C5   N2   106.98  3.000
 09S  H12  C5   C4   110.60  3.000
 09S  H11  C5   C4   109.46  3.000
 09S  N2   C5   C4   113.89  3.000
 09S  C8   N2   C5   120.91  3.000
 09S  C8   N2   C1   120.69  3.000
 09S  C5   N2   C1   114.72  3.000
 09S  BR1  C6   C10  119.43  3.000
 09S  BR1  C6   N3   117.72  3.000
 09S  C10  C6   N3   122.85  3.000
 09S  C7   N3   C6   120.68  3.000
 09S  H13  C7   C8   121.88  3.000
 09S  H13  C7   N3   115.61  3.000
 09S  C8   C7   N3   122.51  3.000
 09S  C9   C8   C7   116.02  3.000
 09S  C7   C8   N2   122.42  3.000
 09S  C9   C8   N2   121.54  3.000
 09S  H14  C9   C10  119.11  3.000
 09S  H14  C9   C8   120.07  3.000
 09S  C10  C9   C8   120.82  3.000
 09S  O1   C10  C9   124.94  3.000
 09S  O1   C10  C6   117.96  3.000
 09S  C9   C10  C6   117.11  3.000
 09S  C11  O1   C10  119.21  3.000
 09S  H16  C11  H15  107.84  3.000
 09S  H16  C11  C12  110.50  3.000
 09S  H15  C11  C12  110.60  3.000
 09S  H16  C11  O1   109.95  3.000
 09S  H15  C11  O1   109.91  3.000
 09S  C12  C11  O1   108.04  3.000
 09S  H19  C12  H18  108.80  3.000
 09S  H19  C12  H17  107.90  3.000
 09S  H18  C12  H17  107.95  3.000
 09S  H19  C12  C11  111.51  3.000
 09S  H18  C12  C11  111.49  3.000
 09S  H17  C12  C11  109.06  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
 09S  CONST_01  C8   C9   C10  C6     0.00   0.0  0
 09S  CONST_02  C8   C7   N3   C6     0.00   0.0  0
 09S  CONST_03  C9   C8   C7   N3     0.00   0.0  0
 09S  CONST_04  C9   C10  C6   N3     0.00   0.0  0
 09S  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 09S  CONST_06  C10  C6   N3   C7     0.00   0.0  0
 09S  CONST_07  C10  C9   C8   N2   180.00   0.0  0
 09S  CONST_08  N3   C7   C8   N2   180.00   0.0  0
 09S  CONST_09  O1   C10  C6   N3   180.00   0.0  0
 09S  CONST_10  BR1  C6   N3   C7   180.00   0.0  0
 09S  CONST_11  O1   C10  C9   C8   180.00   0.0  0
 09S  CONST_12  BR1  C6   C10  C9   180.00   0.0  0
 09S  CONST_13  H14  C9   C8   N2     0.00   0.0  0
 09S  CONST_14  H13  C7   C8   N2     0.00   0.0  0
 09S  Var_01    C12  C11  O1   C10  179.82  30.0  2
 09S  Var_02    H17  C12  C11  O1   179.67  30.0  3

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
 09S  plan-1  N2   0.020
 09S  plan-1  C6   0.020
 09S  plan-1  N3   0.020
 09S  plan-1  C7   0.020
 09S  plan-1  C8   0.020
 09S  plan-1  C9   0.020
 09S  plan-1  C10  0.020
 09S  plan-1  O1   0.020
 09S  plan-1  H13  0.020
 09S  plan-1  H14  0.020
 09S  plan-1  BR1  0.020

