# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 17:38:09 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 1-(5-ethoxypyridin-3-yl)-1,4-diazepane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1cncc(c1)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
 09P  09P  1-(5-ethoxypyridin-3-yl)-1,4-diazepane  ligand  35  16  .  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_09P
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
 09P  C1   C  CH2   0  -0.298   2.3254   1.9389   0.2270
 09P  N1   N  NH1   0  -0.599   3.4661   1.1615   0.6816
 09P  C2   C  CH2   0  -0.298   3.1216  -0.1925   1.0974
 09P  C3   C  CH2   0  -0.435   3.2665  -1.2308  -0.0133
 09P  C4   C  CH2   0  -0.343   2.7105  -0.7677  -1.3648
 09P  N2   N  NT    0  -0.508   1.5553   0.1071  -1.2791
 09P  C5   C  CH2   0  -0.337   1.8705   1.5187  -1.1639
 09P  C6   C  CR16  0  -0.241  -2.0922  -1.4864  -0.1355
 09P  C7   C  CR6   0   0.350  -1.9525  -0.1005  -0.1601
 09P  C8   C  CR16  0  -0.385  -0.7270   0.4488  -0.5196
 09P  C9   C  CR6   0   0.338   0.3427  -0.3811  -0.8695
 09P  C10  C  CR16  0  -0.175   0.0896  -1.7709  -0.8013
 09P  N3   N  N     0  -0.372  -1.0743  -2.2789  -0.4528
 09P  C11  C  CH2   0  -0.187  -4.1982   0.2737   0.5467
 09P  C12  C  CH3   0  -0.682  -5.1011   1.4565   0.8047
 09P  H1   H  HCH2  0   0.199   1.4777   1.8744   0.9275
 09P  H2   H  HCH2  0   0.237   2.6149   2.9914   0.1810
 09P  H3   H  HNH1  0   0.356   3.8841   1.6454   1.4636
 09P  H5   H  HCH2  0   0.239   3.7779  -0.4816   1.9204
 09P  H6   H  HCH2  0   0.198   2.0984  -0.2347   1.5000
 09P  H7   H  HCH2  0   0.231   4.3201  -1.4833  -0.1573
 09P  H8   H  HCH2  0   0.225   2.7751  -2.1493   0.3161
 09P  H9   H  HCH2  0   0.254   3.4792  -0.2051  -1.8932
 09P  H10  H  HCH2  0   0.253   2.4884  -1.6282  -2.0000
 09P  H11  H  HCH2  0   0.251   1.0179   2.1231  -1.4771
 09P  H12  H  HCH2  0   0.254   2.6680   1.7316  -1.8782
 09P  H13  H  HCR6  0   0.264  -3.0183  -1.9724   0.1457
 09P  H14  H  HCR6  0   0.272  -0.6351   1.5264  -0.5161
 09P  H15  H  HCR6  0   0.256   0.8656  -2.4891  -1.0362
 09P  H16  H  HCH2  0   0.225  -4.6191  -0.3621  -0.2394
 09P  H17  H  HCH2  0   0.225  -4.1000  -0.3374   1.4502
 09P  H18  H  HCH3  0   0.235  -5.2339   2.0587  -0.0943
 09P  H19  H  HCH3  0   0.238  -6.0823   1.1009   1.1173
 09P  H20  H  HCH3  0   0.235  -4.7071   2.0932   1.5968
 09P  O1   O  O2    0  -0.473  -2.9263   0.7720   0.1504

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
 09P  C2   C3   single    1.527  0.020  1.527
 09P  C2   N1   single    1.458  0.020  1.458
 09P  C3   C4   single    1.533  0.020  1.533
 09P  N1   C1   single    1.453  0.020  1.453
 09P  C4   N2   single    1.452  0.020  1.452
 09P  C1   C5   single    1.523  0.020  1.523
 09P  C11  C12  single    1.510  0.020  1.510
 09P  C11  O1   single    1.422  0.020  1.422
 09P  N2   C5   single    1.451  0.020  1.451
 09P  N2   C9   single    1.370  0.020  1.370
 09P  C8   C9   aromatic  1.398  0.020  1.398
 09P  C8   C7   aromatic  1.390  0.020  1.390
 09P  O1   C7   single    1.344  0.020  1.344
 09P  C9   C10  aromatic  1.414  0.020  1.414
 09P  C7   C6   aromatic  1.393  0.020  1.393
 09P  C10  N3   aromatic  1.317  0.020  1.317
 09P  C6   N3   aromatic  1.328  0.020  1.328
 09P  C1   H1   single    0.970  0.020  1.090
 09P  C1   H2   single    0.970  0.020  1.090
 09P  N1   H3   single    0.890  0.020  1.040
 09P  C2   H5   single    0.970  0.020  1.090
 09P  C2   H6   single    0.970  0.020  1.090
 09P  C3   H7   single    0.970  0.020  1.090
 09P  C3   H8   single    0.970  0.020  1.090
 09P  C4   H9   single    0.970  0.020  1.090
 09P  C4   H10  single    0.970  0.020  1.090
 09P  C5   H11  single    0.970  0.020  1.090
 09P  C5   H12  single    0.970  0.020  1.090
 09P  C6   H13  single    0.930  0.020  1.080
 09P  C8   H14  single    0.930  0.020  1.080
 09P  C10  H15  single    0.930  0.020  1.080
 09P  C11  H16  single    0.970  0.020  1.090
 09P  C11  H17  single    0.970  0.020  1.090
 09P  C12  H18  single    0.970  0.020  1.090
 09P  C12  H19  single    0.970  0.020  1.090
 09P  C12  H20  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
 09P  H2   C1   H1   106.69  3.000
 09P  H2   C1   C5   107.85  3.000
 09P  H1   C1   C5   109.57  3.000
 09P  H2   C1   N1   108.69  3.000
 09P  H1   C1   N1   111.94  3.000
 09P  C5   C1   N1   111.88  3.000
 09P  H3   N1   C2   108.78  3.000
 09P  H3   N1   C1   108.10  3.000
 09P  C2   N1   C1   113.61  3.000
 09P  H6   C2   H5   105.85  3.000
 09P  H6   C2   C3   109.16  3.000
 09P  H5   C2   C3   108.13  3.000
 09P  H6   C2   N1   111.08  3.000
 09P  H5   C2   N1   108.60  3.000
 09P  C3   C2   N1   113.68  3.000
 09P  H8   C3   H7   106.21  3.000
 09P  H8   C3   C4   110.90  3.000
 09P  H7   C3   C4   107.65  3.000
 09P  H8   C3   C2   108.04  3.000
 09P  H7   C3   C2   110.14  3.000
 09P  C4   C3   C2   113.66  3.000
 09P  H10  C4   H9   105.56  3.000
 09P  H10  C4   N2   110.31  3.000
 09P  H9   C4   N2   106.20  3.000
 09P  H10  C4   C3   110.39  3.000
 09P  H9   C4   C3   109.13  3.000
 09P  N2   C4   C3   114.75  3.000
 09P  C9   N2   C5   121.01  3.000
 09P  C9   N2   C4   120.49  3.000
 09P  C5   N2   C4   114.72  3.000
 09P  H12  C5   H11  105.96  3.000
 09P  H12  C5   N2   107.24  3.000
 09P  H11  C5   N2   110.27  3.000
 09P  H12  C5   C1   109.00  3.000
 09P  H11  C5   C1   110.05  3.000
 09P  N2   C5   C1   113.95  3.000
 09P  H13  C6   N3   116.71  3.000
 09P  H13  C6   C7   122.46  3.000
 09P  N3   C6   C7   120.82  3.000
 09P  O1   C7   C8   116.23  3.000
 09P  O1   C7   C6   124.69  3.000
 09P  C8   C7   C6   119.08  3.000
 09P  H14  C8   C9   121.81  3.000
 09P  H14  C8   C7   117.89  3.000
 09P  C9   C8   C7   120.30  3.000
 09P  C10  C9   C8   115.74  3.000
 09P  C10  C9   N2   121.53  3.000
 09P  C8   C9   N2   122.72  3.000
 09P  H15  C10  N3   115.78  3.000
 09P  H15  C10  C9   120.86  3.000
 09P  N3   C10  C9   123.37  3.000
 09P  C10  N3   C6   120.68  3.000
 09P  H17  C11  H16  107.62  3.000
 09P  H17  C11  C12  110.47  3.000
 09P  H16  C11  C12  110.34  3.000
 09P  H17  C11  O1   110.19  3.000
 09P  H16  C11  O1   110.31  3.000
 09P  C12  C11  O1   107.93  3.000
 09P  H20  C12  H19  107.92  3.000
 09P  H20  C12  H18  108.70  3.000
 09P  H19  C12  H18  107.89  3.000
 09P  H20  C12  C11  111.44  3.000
 09P  H19  C12  C11  109.38  3.000
 09P  H18  C12  C11  111.38  3.000
 09P  C11  O1   C7   119.01  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
 09P  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 09P  CONST_02  C9   C10  N3   C6     0.00   0.0  0
 09P  CONST_03  C10  C9   C8   C7     0.00   0.0  0
 09P  CONST_04  C10  N3   C6   C7     0.00   0.0  0
 09P  CONST_05  N3   C10  C9   C8     0.00   0.0  0
 09P  CONST_06  N3   C6   C7   C8     0.00   0.0  0
 09P  CONST_07  C7   C8   C9   N2   180.00   0.0  0
 09P  CONST_08  N3   C10  C9   N2   180.00   0.0  0
 09P  CONST_09  O1   C7   C8   C9   180.00   0.0  0
 09P  CONST_10  O1   C7   C6   N3   180.00   0.0  0
 09P  CONST_11  H14  C8   C9   N2     0.00   0.0  0
 09P  CONST_12  H15  C10  C9   N2     0.00   0.0  0
 09P  CONST_13  H13  C6   C7   C8   180.00   0.0  0
 09P  Var_01    C12  C11  O1   C7  -178.78  30.0  1
 09P  Var_02    H18  C12  C11  O1    61.22  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
 09P  plan-1  N2   0.020
 09P  plan-1  C6   0.020
 09P  plan-1  C7   0.020
 09P  plan-1  C8   0.020
 09P  plan-1  C9   0.020
 09P  plan-1  C10  0.020
 09P  plan-1  N3   0.020
 09P  plan-1  H13  0.020
 09P  plan-1  H14  0.020
 09P  plan-1  H15  0.020
 09P  plan-1  O1   0.020

