# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 13:51:12 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 1-(6-bromopyridin-3-yl)-1,4-diazepane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccc(cn1)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
 09R  09R  1-(6-bromopyridin-3-yl)-1,4-diazepane  ligand  28  14  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_09R
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
 09R  C1    C   CR16  0  -0.158   0.3028   1.1003   0.3408
 09R  C2    C   CR6   0   0.322   0.9556  -0.1455   0.4293
 09R  C3    C   CR16  0  -0.243   0.2524  -1.2325  -0.1233
 09R  C4    C   CR16  0  -0.251  -1.0015  -1.0533  -0.6707
 09R  C5    C   CR6   0   0.039  -1.5331   0.2266  -0.6691
 09R  N1    N   N     0  -0.372  -0.9018   1.2641  -0.1857
 09R  BR1   BR  BR    0  -0.070  -3.2567   0.5328  -1.4085
 09R  N2    N   NT    0  -0.499   2.1718  -0.2826   1.0348
 09R  C6    C   CH2   0  -0.355   2.9314  -1.5143   0.9222
 09R  C7    C   CH2   0  -0.301   3.7196  -1.6217  -0.3830
 09R  N3    N   NH1   0  -0.588   4.6074  -0.5170  -0.6814
 09R  C8    C   CH2   0  -0.292   3.9634   0.7524  -0.9707
 09R  C9    C   CH2   0  -0.466   3.5837   1.6391   0.2199
 09R  C10   C   CH2   0  -0.350   2.9541   0.8842   1.3975
 09R  H1    H   HCR6  0   0.270   0.7666   2.0042   0.7122
 09R  H2    H   HCR6  0   0.283   0.6700  -2.2288  -0.1290
 09R  H3    H   HCR6  0   0.286  -1.5370  -1.8947  -1.0879
 09R  H4    H   HCH2  0   0.255   3.6233  -1.5468   1.7667
 09R  H5    H   HCH2  0   0.252   2.2803  -2.3821   1.0433
 09R  H6    H   HCH2  0   0.237   4.3034  -2.5463  -0.3521
 09R  H7    H   HCH2  0   0.224   3.0255  -1.7271  -1.2231
 09R  H8    H   HNH1  0   0.342   5.3173  -0.4142   0.0335
 09R  H11   H   HCH2  0   0.259   2.3571   1.5663   2.0073
 09R  H12   H   HCH2  0   0.257   3.7449   0.5258   2.0557
 09R  H9    H   HCH2  0   0.232   4.6151   1.3413  -1.6235
 09R  H121  H   HCH2  0   0.220   3.0730   0.5352  -1.5672
 09R  H10   H   HCH2  0   0.239   4.4727   2.1512   0.5978
 09R  H14   H   HCH2  0   0.231   2.9189   2.4275  -0.1441

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
 09R  C1   N1    aromatic  1.325  0.020  1.325
 09R  C1   H1    single    0.930  0.020  1.080
 09R  C2   C1    aromatic  1.409  0.020  1.409
 09R  C3   C4    aromatic  1.380  0.020  1.380
 09R  C3   C2    aromatic  1.408  0.020  1.408
 09R  C3   H2    single    0.930  0.020  1.080
 09R  C4   C5    aromatic  1.386  0.020  1.386
 09R  C4   H3    single    0.930  0.020  1.080
 09R  C5   N1    aromatic  1.307  0.020  1.307
 09R  C5   BR1   single    1.900  0.020  1.900
 09R  N2   C2    single    1.366  0.020  1.366
 09R  N2   C6    single    1.451  0.020  1.451
 09R  C6   H4    single    0.970  0.020  1.090
 09R  C6   H5    single    0.970  0.020  1.090
 09R  C7   C6    single    1.528  0.020  1.528
 09R  C7   H6    single    0.970  0.020  1.090
 09R  C7   H7    single    0.970  0.020  1.090
 09R  N3   C7    single    1.448  0.020  1.448
 09R  N3   H8    single    0.890  0.020  1.040
 09R  C8   N3    single    1.453  0.020  1.453
 09R  C9   C8    single    1.532  0.020  1.532
 09R  C9   C10   single    1.534  0.020  1.534
 09R  C10  N2    single    1.451  0.020  1.451
 09R  C10  H11   single    0.970  0.020  1.090
 09R  C10  H12   single    0.970  0.020  1.090
 09R  C8   H9    single    0.970  0.020  1.090
 09R  C8   H121  single    0.970  0.020  1.090
 09R  C9   H10   single    0.970  0.020  1.090
 09R  C9   H14   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
 09R  H1    C1   N1   115.03  3.000
 09R  H1    C1   C2   121.24  3.000
 09R  N1    C1   C2   123.74  3.000
 09R  N2    C2   C3   122.79  3.000
 09R  N2    C2   C1   121.95  3.000
 09R  C3    C2   C1   115.25  3.000
 09R  H2    C3   C4   117.96  3.000
 09R  H2    C3   C2   121.41  3.000
 09R  C4    C3   C2   120.63  3.000
 09R  H3    C4   C5   121.95  3.000
 09R  H3    C4   C3   120.14  3.000
 09R  C5    C4   C3   117.90  3.000
 09R  BR1   C5   N1   117.00  3.000
 09R  BR1   C5   C4   119.75  3.000
 09R  N1    C5   C4   123.24  3.000
 09R  C5    N1   C1   119.21  3.000
 09R  C10   N2   C6   114.81  3.000
 09R  C10   N2   C2   120.69  3.000
 09R  C6    N2   C2   121.12  3.000
 09R  H5    C6   H4   105.56  3.000
 09R  H5    C6   C7   110.27  3.000
 09R  H4    C6   C7   109.36  3.000
 09R  C7    C6   N2   113.32  3.000
 09R  H5    C6   N2   110.72  3.000
 09R  H4    C6   N2   107.26  3.000
 09R  H7    C7   H6   106.18  3.000
 09R  H7    C7   N3   107.69  3.000
 09R  H6    C7   N3   108.87  3.000
 09R  N3    C7   C6   116.00  3.000
 09R  H7    C7   C6   109.58  3.000
 09R  H6    C7   C6   108.09  3.000
 09R  H8    N3   C8   111.27  3.000
 09R  C8    N3   C7   115.84  3.000
 09R  H8    N3   C7   111.20  3.000
 09R  H121  C8   H9   105.45  3.000
 09R  H121  C8   C9   109.70  3.000
 09R  H9    C8   C9   107.43  3.000
 09R  H121  C8   N3   107.22  3.000
 09R  H9    C8   N3   108.97  3.000
 09R  C9    C8   N3   117.44  3.000
 09R  H14   C9   H10  105.76  3.000
 09R  H14   C9   C10  111.15  3.000
 09R  H10   C9   C10  107.39  3.000
 09R  H14   C9   C8   108.01  3.000
 09R  H10   C9   C8   109.76  3.000
 09R  C10   C9   C8   114.42  3.000
 09R  H12   C10  H11  105.36  3.000
 09R  H12   C10  C9   109.13  3.000
 09R  H11   C10  C9   110.21  3.000
 09R  H12   C10  N2   106.13  3.000
 09R  H11   C10  N2   110.30  3.000
 09R  C9    C10  N2   115.16  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
 09R  CONST_01  C4   C5  N1  C1    0.00  0.0  0
 09R  CONST_02  C4   C3  C2  C1    0.00  0.0  0
 09R  CONST_03  C5   N1  C1  C2    0.00  0.0  0
 09R  CONST_04  C5   C4  C3  C2    0.00  0.0  0
 09R  CONST_05  N1   C5  C4  C3    0.00  0.0  0
 09R  CONST_06  N1   C1  C2  C3    0.00  0.0  0
 09R  CONST_07  N2   C2  C3  C4  180.00  0.0  0
 09R  CONST_08  N2   C2  C1  N1  180.00  0.0  0
 09R  CONST_09  BR1  C5  N1  C1  180.00  0.0  0
 09R  CONST_10  BR1  C5  C4  C3  180.00  0.0  0
 09R  CONST_11  H2   C3  C2  C1  180.00  0.0  0
 09R  CONST_12  H3   C4  C3  C2  180.00  0.0  0
 09R  CONST_13  H1   C1  C2  C3  180.00  0.0  0

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
 09R  plan-1  C1   0.020
 09R  plan-1  C2   0.020
 09R  plan-1  C3   0.020
 09R  plan-1  C4   0.020
 09R  plan-1  C5   0.020
 09R  plan-1  N1   0.020
 09R  plan-1  BR1  0.020
 09R  plan-1  N2   0.020
 09R  plan-1  H1   0.020
 09R  plan-1  H2   0.020
 09R  plan-1  H3   0.020

