# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 16:26:16 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 1-(5-phenylpyridin-3-yl)-1,4-diazepane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CNCCN(C1)c2cncc(c2)c3ccccc3
#
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
 09Q  09Q  1-(5-phenylpyridin-3-yl)-1,4-diazepane  ligand  38  19  .  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_09Q
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
 09Q  C1   C  CR6   0   0.079   2.7798  -0.0855  -0.0014
 09Q  C2   C  CR16  0  -0.309   2.8828  -1.3323  -0.6213
 09Q  C3   C  CR16  0  -0.240   4.0261  -2.1038  -0.4760
 09Q  C4   C  CR16  0  -0.265   5.0882  -1.6427   0.2909
 09Q  C5   C  CR16  0  -0.240   4.9965  -0.4045   0.9133
 09Q  C6   C  CR16  0  -0.309   3.8525   0.3667   0.7689
 09Q  C7   C  CR16  0  -0.170  -0.6145   2.3409  -0.4671
 09Q  C8   C  CR16  0  -0.153   1.6553   2.1259  -0.2843
 09Q  C9   C  CR6   0   0.029   1.5676   0.7394  -0.1630
 09Q  C10  C  CR16  0  -0.316   0.3048   0.1643  -0.1908
 09Q  C11  C  CR6   0   0.342  -0.8422   0.9551  -0.3566
 09Q  C12  C  CH2   0  -0.305  -3.2881   1.2014  -0.1802
 09Q  C13  C  CH2   0  -0.448  -4.3146   0.5390   0.7374
 09Q  C14  C  CH2   0  -0.320  -4.9366  -0.7496   0.1966
 09Q  C15  C  CH2   0  -0.272  -2.7453  -1.9273   0.2103
 09Q  C16  C  CH2   0  -0.366  -2.2983  -0.9491  -0.8716
 09Q  N1   N  NT    0  -0.514  -2.0978   0.4062  -0.3973
 09Q  N2   N  NH1   0  -0.600  -4.1924  -1.9862   0.3728
 09Q  N3   N  N     0  -0.381   0.5864   2.8935  -0.4250
 09Q  H1   H  HCR6  0   0.253   2.0712  -1.6964  -1.2393
 09Q  H2   H  HCR6  0   0.259   4.0901  -3.0644  -0.9705
 09Q  H3   H  HCR6  0   0.259   5.9805  -2.2449   0.4025
 09Q  H4   H  HCR6  0   0.259   5.8151  -0.0394   1.5199
 09Q  H5   H  HCR6  0   0.254   3.7867   1.3206   1.2771
 09Q  H7   H  HCR6  0   0.249   2.6192   2.6231  -0.2933
 09Q  H8   H  HCR6  0   0.269   0.2131  -0.9036  -0.0389
 09Q  H9   H  HCH2  0   0.221  -3.7701   1.4481  -1.1363
 09Q  H10  H  HCH2  0   0.250  -3.0050   2.1446   0.2821
 09Q  H11  H  HCH2  0   0.230  -3.8790   0.3717   1.7271
 09Q  H12  H  HCH2  0   0.239  -5.1154   1.2713   0.8715
 09Q  H13  H  HCH2  0   0.242  -5.9064  -0.9038   0.6729
 09Q  H14  H  HCH2  0   0.211  -5.1587  -0.5995  -0.8663
 09Q  H15  H  HCH2  0   0.227  -2.3911  -2.9271  -0.0578
 09Q  H16  H  HCH2  0   0.207  -2.2228  -1.6524   1.1363
 09Q  H17  H  HCH2  0   0.266  -1.3713  -1.3093  -1.3143
 09Q  H18  H  HCH2  0   0.257  -3.0237  -0.9429  -1.6941
 09Q  H19  H  HNH1  0   0.349  -4.3964  -2.3671   1.2857
 09Q  H6   H  HCR6  0   0.261  -1.4398   3.0278  -0.6096

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
 09Q  N2   C14  single    1.454  0.020  1.454
 09Q  N2   C15  single    1.457  0.020  1.457
 09Q  C14  C13  single    1.530  0.020  1.530
 09Q  C13  C12  single    1.528  0.020  1.528
 09Q  C15  C16  single    1.526  0.020  1.526
 09Q  C3   C2   aromatic  1.387  0.020  1.387
 09Q  C3   C4   aromatic  1.389  0.020  1.389
 09Q  C2   C1   aromatic  1.396  0.020  1.396
 09Q  C16  N1   single    1.450  0.020  1.450
 09Q  C12  N1   single    1.448  0.020  1.448
 09Q  C4   C5   aromatic  1.389  0.020  1.389
 09Q  N1   C11  single    1.371  0.020  1.371
 09Q  C10  C11  aromatic  1.403  0.020  1.403
 09Q  C10  C9   aromatic  1.388  0.020  1.388
 09Q  C11  C7   aromatic  1.409  0.020  1.409
 09Q  C1   C9   single    1.475  0.020  1.475
 09Q  C1   C6   aromatic  1.396  0.020  1.396
 09Q  C9   C8   aromatic  1.395  0.020  1.395
 09Q  C7   N3   aromatic  1.323  0.020  1.323
 09Q  C5   C6   aromatic  1.387  0.020  1.387
 09Q  C8   N3   aromatic  1.323  0.020  1.323
 09Q  C2   H1   single    0.930  0.020  1.080
 09Q  C3   H2   single    0.930  0.020  1.080
 09Q  C4   H3   single    0.930  0.020  1.080
 09Q  C5   H4   single    0.930  0.020  1.080
 09Q  C6   H5   single    0.930  0.020  1.080
 09Q  C7   H6   single    0.930  0.020  1.080
 09Q  C8   H7   single    0.930  0.020  1.080
 09Q  C10  H8   single    0.930  0.020  1.080
 09Q  C12  H9   single    0.970  0.020  1.090
 09Q  C12  H10  single    0.970  0.020  1.090
 09Q  C13  H11  single    0.970  0.020  1.090
 09Q  C13  H12  single    0.970  0.020  1.090
 09Q  C14  H13  single    0.970  0.020  1.090
 09Q  C14  H14  single    0.970  0.020  1.090
 09Q  C15  H15  single    0.970  0.020  1.090
 09Q  C15  H16  single    0.970  0.020  1.090
 09Q  C16  H17  single    0.970  0.020  1.090
 09Q  C16  H18  single    0.970  0.020  1.090
 09Q  N2   H19  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
 09Q  C9   C1   C6   120.71  3.000
 09Q  C6   C1   C2   118.53  3.000
 09Q  C9   C1   C2   120.76  3.000
 09Q  H1   C2   C3   119.37  3.000
 09Q  H1   C2   C1   119.88  3.000
 09Q  C3   C2   C1   120.73  3.000
 09Q  H2   C3   C4   120.12  3.000
 09Q  H2   C3   C2   119.64  3.000
 09Q  C4   C3   C2   120.23  3.000
 09Q  H3   C4   C5   120.28  3.000
 09Q  H3   C4   C3   120.18  3.000
 09Q  C5   C4   C3   119.54  3.000
 09Q  H4   C5   C6   119.64  3.000
 09Q  H4   C5   C4   120.13  3.000
 09Q  C6   C5   C4   120.22  3.000
 09Q  H5   C6   C5   119.40  3.000
 09Q  H5   C6   C1   119.85  3.000
 09Q  C5   C6   C1   120.74  3.000
 09Q  H6   C7   N3   115.53  3.000
 09Q  H6   C7   C11  120.73  3.000
 09Q  N3   C7   C11  123.73  3.000
 09Q  H7   C8   N3   116.81  3.000
 09Q  H7   C8   C9   120.82  3.000
 09Q  N3   C8   C9   122.35  3.000
 09Q  C10  C9   C8   117.87  3.000
 09Q  C8   C9   C1   120.92  3.000
 09Q  C10  C9   C1   121.20  3.000
 09Q  H8   C10  C11  120.22  3.000
 09Q  H8   C10  C9   118.89  3.000
 09Q  C11  C10  C9   120.84  3.000
 09Q  N1   C11  C10  121.77  3.000
 09Q  C10  C11  C7   115.57  3.000
 09Q  N1   C11  C7   122.66  3.000
 09Q  H10  C12  H9   106.82  3.000
 09Q  H10  C12  N1   109.03  3.000
 09Q  H9   C12  N1   110.70  3.000
 09Q  H10  C12  C13  107.19  3.000
 09Q  H9   C12  C13  108.97  3.000
 09Q  N1   C12  C13  113.85  3.000
 09Q  H12  C13  H11  106.44  3.000
 09Q  H12  C13  C14  108.04  3.000
 09Q  H11  C13  C14  110.66  3.000
 09Q  H12  C13  C12  105.98  3.000
 09Q  H11  C13  C12  110.01  3.000
 09Q  C14  C13  C12  115.22  3.000
 09Q  H14  C14  H13  105.22  3.000
 09Q  H14  C14  N2   109.73  3.000
 09Q  H13  C14  N2   106.37  3.000
 09Q  H14  C14  C13  108.05  3.000
 09Q  H13  C14  C13  109.03  3.000
 09Q  N2   C14  C13  117.74  3.000
 09Q  H16  C15  H15  106.34  3.000
 09Q  H16  C15  N2   112.86  3.000
 09Q  H15  C15  N2   108.17  3.000
 09Q  H16  C15  C16  107.34  3.000
 09Q  H15  C15  C16  108.50  3.000
 09Q  N2   C15  C16  113.33  3.000
 09Q  H18  C16  H17  105.08  3.000
 09Q  H18  C16  N1   109.36  3.000
 09Q  H17  C16  N1   108.94  3.000
 09Q  H18  C16  C15  109.98  3.000
 09Q  H17  C16  C15  109.01  3.000
 09Q  N1   C16  C15  114.07  3.000
 09Q  C16  N1   C12  116.67  3.000
 09Q  C12  N1   C11  121.90  3.000
 09Q  C16  N1   C11  120.71  3.000
 09Q  H19  N2   C15  108.46  3.000
 09Q  H19  N2   C14  109.07  3.000
 09Q  C15  N2   C14  117.41  3.000
 09Q  C8   N3   C7   119.63  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
 09Q  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 09Q  CONST_02  C11  C10  C9   C1   180.00  0.0  0
 09Q  CONST_03  N3   C8   C9   C1   180.00  0.0  0
 09Q  CONST_04  C4   C5   C6   C1     0.00  0.0  0
 09Q  CONST_05  C5   C4   C3   C2     0.00  0.0  0
 09Q  CONST_08  C5   C6   C1   C2     0.00  0.0  0
 09Q  CONST_09  C9   C1   C2   C3   180.00  0.0  0
 09Q  CONST_10  C6   C1   C2   C3     0.00  0.0  0
 09Q  CONST_11  C6   C5   C4   C3     0.00  0.0  0
 09Q  CONST_12  C9   C1   C6   C5   180.00  0.0  0
 09Q  CONST_15  C9   C10  C11  C7     0.00  0.0  0
 09Q  CONST_16  C9   C8   N3   C7     0.00  0.0  0
 09Q  CONST_17  C11  C10  C9   C8     0.00  0.0  0
 09Q  CONST_18  C11  C7   N3   C8     0.00  0.0  0
 09Q  CONST_19  N3   C7   C11  C10    0.00  0.0  0
 09Q  CONST_20  N3   C8   C9   C10    0.00  0.0  0
 09Q  CONST_21  N1   C11  C10  C9   180.00  0.0  0
 09Q  CONST_22  N3   C7   C11  N1   180.00  0.0  0
 09Q  CONST_23  H2   C3   C2   C1   180.00  0.0  0
 09Q  CONST_24  H8   C10  C9   C1     0.00  0.0  0
 09Q  CONST_25  H7   C8   C9   C1     0.00  0.0  0
 09Q  CONST_26  H4   C5   C6   C1   180.00  0.0  0
 09Q  CONST_27  H3   C4   C3   C2   180.00  0.0  0
 09Q  CONST_28  H5   C6   C1   C2   180.00  0.0  0
 09Q  CONST_29  H1   C2   C3   C4   180.00  0.0  0
 09Q  CONST_30  H6   C7   N3   C8   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
 09Q  plan-1  C1   0.020
 09Q  plan-1  C2   0.020
 09Q  plan-1  C3   0.020
 09Q  plan-1  C4   0.020
 09Q  plan-1  C5   0.020
 09Q  plan-1  C6   0.020
 09Q  plan-1  C9   0.020
 09Q  plan-1  H1   0.020
 09Q  plan-1  H2   0.020
 09Q  plan-1  H3   0.020
 09Q  plan-1  H4   0.020
 09Q  plan-1  H5   0.020
 09Q  plan-2  C1   0.020
 09Q  plan-2  C7   0.020
 09Q  plan-2  C8   0.020
 09Q  plan-2  C9   0.020
 09Q  plan-2  C10  0.020
 09Q  plan-2  C11  0.020
 09Q  plan-2  N1   0.020
 09Q  plan-2  N3   0.020
 09Q  plan-2  H7   0.020
 09Q  plan-2  H8   0.020
 09Q  plan-2  H6   0.020

