# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 11:54:36 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 1-(pyridin-3-yl)-1,4-diazepane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CNCCN(C1)c2cccnc2
#
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
 09O  09O  1-(pyridin-3-yl)-1,4-diazepane  ligand  28  13  .  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_09O
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
 09O  C1   C  CH2   0  -0.360  -1.0922   0.8812  -1.0788
 09O  C2   C  CH2   0  -0.297  -1.9184   1.5770   0.0071
 09O  N1   N  NH1   0  -0.579  -3.0980   0.8696   0.4609
 09O  C3   C  CH2   0  -0.306  -2.8969  -0.5147   0.8507
 09O  C4   C  CH2   0  -0.495  -2.4396  -1.4796  -0.2530
 09O  C5   C  CH2   0  -0.287  -0.9316  -1.5362  -0.4644
 09O  N2   N  NT    0  -0.508  -0.3086  -0.2309  -0.5842
 09O  C6   C  CR16  0  -0.121   3.6511   0.1629   0.5306
 09O  N3   N  N     0  -0.386   3.1308  -1.0439   0.3473
 09O  C7   C  CR16  0  -0.172   1.8634  -1.1533  -0.0167
 09O  C8   C  CR6   0   0.321   0.9972  -0.0570  -0.2190
 09O  C9   C  CR16  0  -0.262   1.5733   1.2110  -0.0259
 09O  C10  C  CR16  0  -0.306   2.9002   1.3138   0.3464
 09O  H1   H  HCH2  0   0.258  -1.7514   0.5290  -1.8762
 09O  H2   H  HCH2  0   0.255  -0.4294   1.6022  -1.5607
 09O  H3   H  HCH2  0   0.220  -1.2711   1.7727   0.8685
 09O  H4   H  HCH2  0   0.233  -2.2403   2.5516  -0.3680
 09O  H5   H  HNH1  0   0.341  -3.8024   0.9037  -0.2659
 09O  H7   H  HCH2  0   0.221  -2.1850  -0.5436   1.6831
 09O  H8   H  HCH2  0   0.236  -3.8469  -0.8763   1.2507
 09O  H9   H  HCH2  0   0.250  -2.7485  -2.4949   0.0084
 09O  H10  H  HCH2  0   0.234  -2.9638  -1.2427  -1.1829
 09O  H11  H  HCH2  0   0.235  -0.5037  -2.0400   0.4059
 09O  H12  H  HCH2  0   0.231  -0.7092  -2.1719  -1.3309
 09O  H14  H  HCR6  0   0.261   1.5092  -2.1652  -0.1730
 09O  H15  H  HCR6  0   0.271   0.9932   2.1158  -0.1424
 09O  H16  H  HCR6  0   0.262   3.3446   2.2877   0.5038
 09O  H13  H  HCR6  0   0.249   4.6927   0.2144   0.8261

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
 09O  C3   C4   single    1.536  0.020  1.536
 09O  C3   N1   single    1.452  0.020  1.452
 09O  C4   C5   single    1.524  0.020  1.524
 09O  N1   C2   single    1.448  0.020  1.448
 09O  C5   N2   single    1.451  0.020  1.451
 09O  C2   C1   single    1.532  0.020  1.532
 09O  N2   C1   single    1.448  0.020  1.448
 09O  N2   C8   single    1.367  0.020  1.367
 09O  C9   C8   aromatic  1.406  0.020  1.406
 09O  C9   C10  aromatic  1.382  0.020  1.382
 09O  C8   C7   aromatic  1.412  0.020  1.412
 09O  C10  C6   aromatic  1.387  0.020  1.387
 09O  C7   N3   aromatic  1.323  0.020  1.323
 09O  C6   N3   aromatic  1.327  0.020  1.327
 09O  C1   H1   single    0.970  0.020  1.090
 09O  C1   H2   single    0.970  0.020  1.090
 09O  C2   H3   single    0.970  0.020  1.090
 09O  C2   H4   single    0.970  0.020  1.090
 09O  N1   H5   single    0.890  0.020  1.040
 09O  C3   H7   single    0.970  0.020  1.090
 09O  C3   H8   single    0.970  0.020  1.090
 09O  C4   H9   single    0.970  0.020  1.090
 09O  C4   H10  single    0.970  0.020  1.090
 09O  C5   H11  single    0.970  0.020  1.090
 09O  C5   H12  single    0.970  0.020  1.090
 09O  C6   H13  single    0.930  0.020  1.080
 09O  C7   H14  single    0.930  0.020  1.080
 09O  C9   H15  single    0.930  0.020  1.080
 09O  C10  H16  single    0.930  0.020  1.080

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
 09O  H2   C1   H1   104.89  3.000
 09O  H2   C1   N2   109.25  3.000
 09O  H1   C1   N2   109.16  3.000
 09O  H2   C1   C2   109.90  3.000
 09O  H1   C1   C2   109.77  3.000
 09O  N2   C1   C2   113.50  3.000
 09O  H4   C2   H3   106.54  3.000
 09O  H4   C2   N1   107.66  3.000
 09O  H3   C2   N1   108.79  3.000
 09O  H4   C2   C1   108.71  3.000
 09O  H3   C2   C1   108.66  3.000
 09O  N1   C2   C1   116.08  3.000
 09O  H5   N1   C3   108.73  3.000
 09O  H5   N1   C2   108.97  3.000
 09O  C3   N1   C2   115.91  3.000
 09O  H8   C3   H7   106.15  3.000
 09O  H8   C3   C4   108.31  3.000
 09O  H7   C3   C4   109.63  3.000
 09O  H8   C3   N1   107.07  3.000
 09O  H7   C3   N1   108.61  3.000
 09O  C4   C3   N1   116.57  3.000
 09O  H10  C4   H9   105.62  3.000
 09O  H10  C4   C5   111.38  3.000
 09O  H9   C4   C5   106.16  3.000
 09O  H10  C4   C3   109.41  3.000
 09O  H9   C4   C3   109.12  3.000
 09O  C5   C4   C3   114.69  3.000
 09O  H12  C5   H11  106.40  3.000
 09O  H12  C5   N2   111.64  3.000
 09O  H11  C5   N2   108.19  3.000
 09O  H12  C5   C4   109.37  3.000
 09O  H11  C5   C4   107.10  3.000
 09O  N2   C5   C4   113.76  3.000
 09O  C8   N2   C5   120.16  3.000
 09O  C8   N2   C1   120.70  3.000
 09O  C5   N2   C1   119.13  3.000
 09O  H13  C6   C10  121.15  3.000
 09O  H13  C6   N3   117.24  3.000
 09O  C10  C6   N3   121.62  3.000
 09O  C7   N3   C6   119.26  3.000
 09O  H14  C7   C8   120.27  3.000
 09O  H14  C7   N3   115.47  3.000
 09O  C8   C7   N3   124.26  3.000
 09O  C9   C8   C7   115.42  3.000
 09O  C7   C8   N2   121.71  3.000
 09O  C9   C8   N2   122.87  3.000
 09O  H15  C9   C10  118.81  3.000
 09O  H15  C9   C8   121.34  3.000
 09O  C10  C9   C8   119.84  3.000
 09O  H16  C10  C9   120.04  3.000
 09O  H16  C10  C6   120.35  3.000
 09O  C9   C10  C6   119.60  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
 09O  CONST_01  C8   C9   C10  C6    0.00  0.0  0
 09O  CONST_02  C8   C7   N3   C6    0.00  0.0  0
 09O  CONST_03  C9   C8   C7   N3    0.00  0.0  0
 09O  CONST_04  C9   C10  C6   N3    0.00  0.0  0
 09O  CONST_05  C10  C9   C8   C7    0.00  0.0  0
 09O  CONST_06  C10  C6   N3   C7    0.00  0.0  0
 09O  CONST_07  C10  C9   C8   N2  180.00  0.0  0
 09O  CONST_08  N3   C7   C8   N2  180.00  0.0  0
 09O  CONST_09  H15  C9   C8   N2    0.00  0.0  0
 09O  CONST_10  H14  C7   C8   N2    0.00  0.0  0
 09O  CONST_11  H16  C10  C6   N3  180.00  0.0  0
 09O  CONST_12  H13  C6   N3   C7  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
 09O  plan-1  N2   0.020
 09O  plan-1  C6   0.020
 09O  plan-1  N3   0.020
 09O  plan-1  C7   0.020
 09O  plan-1  C8   0.020
 09O  plan-1  C9   0.020
 09O  plan-1  C10  0.020
 09O  plan-1  H14  0.020
 09O  plan-1  H15  0.020
 09O  plan-1  H16  0.020
 09O  plan-1  H13  0.020

