# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:50:04 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3-azanyl-5-(azepan-1-yl)-~{N}-[bis(azanyl)methylidene]-6-chloranyl-pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(N)=NC(=O)c1nc(Cl)c(nc1N)N2CCCCCC2
#
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
 HMX  HMX  3-azanyl-5-(azepan-1-yl)-~{N}-[bis(azanyl)methylidene]-6-chloranyl-pyrazine-2-carboxamide  ligand  39  21  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HMX
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
 HMX  C1   C   CR6   0   0.005   0.4190  -0.7878   0.9595
 HMX  N1   N   N     0  -0.484   0.7627   1.4849   0.5071
 HMX  C2   C   CR6   0   0.573   1.2977   0.3454   0.9286
 HMX  N2   N   N     0  -0.315  -0.8289  -0.6735   0.6537
 HMX  C3   C   CR6   0   0.453  -0.5205   1.6001   0.1804
 HMX  C4   C   CR6   0  -0.052  -1.3791   0.4745   0.2774
 HMX  C5   C   C     0   0.475  -2.8291   0.5159  -0.0185
 HMX  C6   C   CH2   0  -0.339   3.4451  -0.6824   1.7437
 HMX  C7   C   CH2   0  -0.427   4.1602  -1.4121   0.6157
 HMX  C8   C   CH2   0  -0.444   4.9617  -0.5130  -0.3261
 HMX  C9   C   CH2   0  -0.442   4.1000   0.4443  -1.1570
 HMX  C10  C   CH2   0  -0.440   3.7372   1.7673  -0.4811
 HMX  C11  C   CH2   0  -0.315   3.3344   1.6369   0.9877
 HMX  C12  C   C     0   0.665  -4.7688  -0.7711  -0.0815
 HMX  O1   O   O     0  -0.543  -3.3395   1.6021  -0.3525
 HMX  N5   N   N     0  -0.561  -3.4604  -0.6616   0.1157
 HMX  N7   N   NH2   0  -0.816  -5.6049   0.2170  -0.4031
 HMX  N6   N   NH2   0  -0.819  -5.2850  -2.0005   0.0482
 HMX  CL1  CL  CL    0  -0.132   0.9064  -2.4228   1.3578
 HMX  N3   N   NH2   0  -0.835  -0.9165   2.8048  -0.2556
 HMX  N4   N   NT    0  -0.485   2.5973   0.4128   1.2898
 HMX  H1   H   HCH2  0   0.260   2.8859  -1.3750   2.3626
 HMX  H2   H   HCH2  0   0.253   4.1893  -0.2345   2.4047
 HMX  H3   H   HCH2  0   0.233   4.8254  -2.1483   1.0760
 HMX  H4   H   HCH2  0   0.218   3.4341  -1.9795   0.0268
 HMX  H5   H   HCH2  0   0.218   5.7215   0.0453   0.2324
 HMX  H6   H   HCH2  0   0.236   5.5144  -1.1633  -1.0080
 HMX  H7   H   HCH2  0   0.235   4.6176   0.6790  -2.0902
 HMX  H8   H   HCH2  0   0.217   3.1860  -0.0796  -1.4558
 HMX  H9   H   HCH2  0   0.229   4.5915   2.4485  -0.5216
 HMX  H10  H   HCH2  0   0.233   2.9343   2.2438  -1.0458
 HMX  H11  H   HCH2  0   0.245   4.2277   1.6132   1.6106
 HMX  H12  H   HCH2  0   0.261   2.7599   2.5075   1.2990
 HMX  H14  H   HNH2  0   0.426  -5.2256   1.1437  -0.5146
 HMX  H15  H   HNH2  0   0.406  -6.5930   0.0628  -0.5078
 HMX  H16  H   HNH2  0   0.405  -4.6870  -2.7407   0.3695
 HMX  H17  H   HNH2  0   0.388  -0.2827   3.5798  -0.1643
 HMX  H18  H   HNH2  0   0.408  -1.8991   2.9729  -0.3926
 HMX  H13  H   HNH2  0   0.406  -6.2740  -2.1760   0.0107

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
 HMX  N3   C3   single    1.341  0.020  1.341
 HMX  O1   C5   double    1.246  0.020  1.246
 HMX  C3   N1   aromatic  1.329  0.020  1.329
 HMX  C3   C4   aromatic  1.419  0.020  1.419
 HMX  N6   C12  single    1.340  0.020  1.340
 HMX  C5   C4   single    1.480  0.020  1.480
 HMX  C5   N5   single    1.343  0.020  1.343
 HMX  N1   C2   aromatic  1.328  0.020  1.328
 HMX  C4   N2   aromatic  1.327  0.020  1.327
 HMX  C10  C11  single    1.529  0.020  1.529
 HMX  C10  C9   single    1.529  0.020  1.529
 HMX  C12  N5   double    1.328  0.020  1.328
 HMX  C12  N7   single    1.334  0.020  1.334
 HMX  C11  N4   single    1.461  0.020  1.461
 HMX  C2   N4   single    1.351  0.020  1.351
 HMX  C2   C1   aromatic  1.434  0.020  1.434
 HMX  C9   C8   single    1.533  0.020  1.533
 HMX  N2   C1   aromatic  1.290  0.020  1.290
 HMX  N4   C6   single    1.457  0.020  1.457
 HMX  C1   CL1  single    1.752  0.020  1.752
 HMX  C8   C7   single    1.529  0.020  1.529
 HMX  C6   C7   single    1.522  0.020  1.522
 HMX  C6   H1   single    0.970  0.020  1.090
 HMX  C6   H2   single    0.970  0.020  1.090
 HMX  C7   H3   single    0.970  0.020  1.090
 HMX  C7   H4   single    0.970  0.020  1.090
 HMX  C8   H5   single    0.970  0.020  1.090
 HMX  C8   H6   single    0.970  0.020  1.090
 HMX  C9   H7   single    0.970  0.020  1.090
 HMX  C9   H8   single    0.970  0.020  1.090
 HMX  C10  H9   single    0.970  0.020  1.090
 HMX  C10  H10  single    0.970  0.020  1.090
 HMX  C11  H11  single    0.970  0.020  1.090
 HMX  C11  H12  single    0.970  0.020  1.090
 HMX  N7   H14  single    0.860  0.020  1.020
 HMX  N7   H15  single    0.860  0.020  1.020
 HMX  N6   H16  single    0.860  0.020  1.020
 HMX  N3   H17  single    0.860  0.020  1.020
 HMX  N3   H18  single    0.860  0.020  1.020
 HMX  N6   H13  single    0.860  0.020  1.020

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
 HMX  CL1  C1   N2   113.94  3.000
 HMX  CL1  C1   C2   124.87  3.000
 HMX  N2   C1   C2   121.17  3.000
 HMX  C3   N1   C2   122.78  3.000
 HMX  N4   C2   N1   115.46  3.000
 HMX  N4   C2   C1   128.55  3.000
 HMX  N1   C2   C1   115.98  3.000
 HMX  C4   N2   C1   123.01  3.000
 HMX  N3   C3   C4   123.79  3.000
 HMX  C4   C3   N1   119.91  3.000
 HMX  N3   C3   N1   116.28  3.000
 HMX  C5   C4   C3   123.83  3.000
 HMX  C5   C4   N2   119.13  3.000
 HMX  C3   C4   N2   117.04  3.000
 HMX  N5   C5   O1   126.78  3.000
 HMX  N5   C5   C4   114.58  3.000
 HMX  O1   C5   C4   118.64  3.000
 HMX  H2   C6   H1   105.55  3.000
 HMX  H2   C6   N4   106.07  3.000
 HMX  H1   C6   N4   110.97  3.000
 HMX  H2   C6   C7   108.98  3.000
 HMX  H1   C6   C7   111.05  3.000
 HMX  N4   C6   C7   113.75  3.000
 HMX  H4   C7   H3   106.32  3.000
 HMX  H4   C7   C8   108.75  3.000
 HMX  H3   C7   C8   109.65  3.000
 HMX  H4   C7   C6   109.63  3.000
 HMX  H3   C7   C6   107.25  3.000
 HMX  C8   C7   C6   114.89  3.000
 HMX  H6   C8   H5   105.70  3.000
 HMX  H6   C8   C9   108.53  3.000
 HMX  H5   C8   C9   110.36  3.000
 HMX  H6   C8   C7   107.44  3.000
 HMX  H5   C8   C7   110.43  3.000
 HMX  C9   C8   C7   113.99  3.000
 HMX  H8   C9   H7   105.38  3.000
 HMX  H8   C9   C10  109.66  3.000
 HMX  H7   C9   C10  107.70  3.000
 HMX  H8   C9   C8   108.56  3.000
 HMX  H7   C9   C8   109.32  3.000
 HMX  C10  C9   C8   115.72  3.000
 HMX  H10  C10  H9   106.49  3.000
 HMX  H10  C10  C11  109.92  3.000
 HMX  H9   C10  C11  107.14  3.000
 HMX  H10  C10  C9   108.88  3.000
 HMX  H9   C10  C9   109.70  3.000
 HMX  C11  C10  C9   114.42  3.000
 HMX  H12  C11  H11  106.66  3.000
 HMX  H12  C11  N4   110.17  3.000
 HMX  H11  C11  N4   106.11  3.000
 HMX  H12  C11  C10  110.22  3.000
 HMX  H11  C11  C10  109.58  3.000
 HMX  N4   C11  C10  113.78  3.000
 HMX  N6   C12  N7   117.49  3.000
 HMX  N7   C12  N5   126.34  3.000
 HMX  N6   C12  N5   116.17  3.000
 HMX  C12  N5   C5   121.39  3.000
 HMX  H15  N7   H14  119.96  3.000
 HMX  H15  N7   C12  121.85  3.000
 HMX  H14  N7   C12  118.17  3.000
 HMX  H13  N6   H16  117.98  3.000
 HMX  H13  N6   C12  122.40  3.000
 HMX  H16  N6   C12  118.55  3.000
 HMX  H18  N3   H17  119.94  3.000
 HMX  H18  N3   C3   118.86  3.000
 HMX  H17  N3   C3   118.48  3.000
 HMX  C11  N4   C6   113.62  3.000
 HMX  C6   N4   C2   127.27  3.000
 HMX  C11  N4   C2   118.17  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
 HMX  CONST_01  C3   N1   C2   C1     0.00   0.0  0
 HMX  CONST_02  C3   C4   N2   C1     0.00   0.0  0
 HMX  CONST_03  N2   C4   C3   N1     0.00   0.0  0
 HMX  CONST_04  N2   C1   C2   N1     0.00   0.0  0
 HMX  CONST_05  C4   C3   N1   C2     0.00   0.0  0
 HMX  CONST_06  C4   N2   C1   C2     0.00   0.0  0
 HMX  CONST_07  N4   C2   C1   N2   180.00   0.0  0
 HMX  CONST_08  N4   C2   N1   C3   180.00   0.0  0
 HMX  CONST_09  C5   C4   N2   C1   180.00   0.0  0
 HMX  CONST_10  C5   C4   C3   N1   180.00   0.0  0
 HMX  CONST_11  CL1  C1   C2   N1   180.00   0.0  0
 HMX  CONST_12  N3   C3   N1   C2   180.00   0.0  0
 HMX  CONST_13  N3   C3   C4   N2   180.00   0.0  0
 HMX  CONST_14  CL1  C1   N2   C4   180.00   0.0  0
 HMX  CONST_15  N4   C2   C1   CL1    0.00   0.0  0
 HMX  CONST_16  H17  N3   C3   N1     0.00   0.0  0
 HMX  CONST_17  H18  N3   C3   N1   180.00   0.0  0
 HMX  CONST_18  C12  N5   C5   C4   180.00   0.0  0
 HMX  CONST_19  O1   C5   N5   C12    0.00   0.0  0
 HMX  CONST_20  N6   C12  N5   C5   180.00   0.0  0
 HMX  CONST_21  N7   C12  N5   C5     0.00   0.0  0
 HMX  CONST_22  H16  N6   C12  N5     0.00   0.0  0
 HMX  CONST_23  H13  N6   C12  N5   180.00   0.0  0
 HMX  CONST_24  H14  N7   C12  N5     0.00   0.0  0
 HMX  CONST_25  H15  N7   C12  N5   180.00   0.0  0
 HMX  Var_01    O1   C5   C4   N2   179.00  30.0  2

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
 HMX  plan-1  C1   0.020
 HMX  plan-1  N1   0.020
 HMX  plan-1  C2   0.020
 HMX  plan-1  N2   0.020
 HMX  plan-1  C3   0.020
 HMX  plan-1  C4   0.020
 HMX  plan-1  C5   0.020
 HMX  plan-1  CL1  0.020
 HMX  plan-1  N3   0.020
 HMX  plan-1  N4   0.020
 HMX  plan-2  C4   0.020
 HMX  plan-2  C5   0.020
 HMX  plan-2  C12  0.020
 HMX  plan-2  O1   0.020
 HMX  plan-2  N5   0.020
 HMX  plan-2  N7   0.020
 HMX  plan-2  N6   0.020
 HMX  plan-2  H14  0.020
 HMX  plan-2  H15  0.020
 HMX  plan-2  H16  0.020
 HMX  plan-2  H13  0.020
 HMX  plan-3  C3   0.020
 HMX  plan-3  N3   0.020
 HMX  plan-3  H17  0.020
 HMX  plan-3  H18  0.020

