# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 14:39:31 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-(6-methylpyrimidin-4-yl)azepane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(ncn1)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
 46S  46S  1-(6-methylpyrimidin-4-yl)azepane  ligand  31  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_46S
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
 46S  C4   C  CR16  0   0.067   2.0347   1.4677   0.8888
 46S  N1   N  N     0  -0.451   2.8670   0.4547   1.0367
 46S  N2   N  NT    0  -0.473  -0.6955   0.3445  -0.9840
 46S  C1   C  CR6   0   0.283   2.4703  -0.7042   0.4839
 46S  N    N  N     0  -0.471   0.8732   1.4806   0.2631
 46S  C3   C  CR6   0   0.574   0.4691   0.3362  -0.3065
 46S  C2   C  CR16  0  -0.408   1.2780  -0.8166  -0.1939
 46S  H1   H  HCR6  0   0.231   2.3373   2.4094   1.3383
 46S  H12  H  HCH3  0   0.248   4.3715  -1.6442   0.2349
 46S  H13  H  HCH3  0   0.248   3.5279  -2.1033   1.7032
 46S  H14  H  HCH3  0   0.227   3.0062  -2.7642   0.1496
 46S  H15  H  HCR6  0   0.232   0.9843  -1.7693  -0.6088
 46S  C7   C  CH2   0  -0.309  -1.5734   1.5048  -0.9592
 46S  C5   C  CH2   0  -0.427  -2.5502   1.4965   0.2082
 46S  C8   C  CH2   0  -0.436  -3.3952   0.2289   0.3305
 46S  C9   C  CH2   0  -0.430  -2.5938  -1.0232   0.6990
 46S  C10  C  CH2   0  -0.435  -1.9361  -1.7733  -0.4597
 46S  C11  C  CH2   0  -0.333  -1.2730  -0.8767  -1.5107
 46S  H2   H  HCH2  0   0.265  -0.9725   2.4112  -0.9386
 46S  H3   H  HCH2  0   0.220  -2.1247   1.5089  -1.9021
 46S  H4   H  HCH2  0   0.229  -1.9966   1.6439   1.1405
 46S  H5   H  HCH2  0   0.224  -3.2064   2.3645   0.0983
 46S  H6   H  HCH2  0   0.234  -4.1393   0.4020   1.1117
 46S  H7   H  HCH2  0   0.205  -3.9673   0.0638  -0.5895
 46S  H8   H  HCH2  0   0.223  -1.8293  -0.7452   1.4317
 46S  H9   H  HCH2  0   0.232  -3.2463  -1.7286   1.2190
 46S  H10  H  HCH2  0   0.225  -1.2089  -2.4751  -0.0445
 46S  H11  H  HCH2  0   0.225  -2.6797  -2.3842  -0.9784
 46S  H16  H  HCH2  0   0.242  -2.0143  -0.5749  -2.2505
 46S  H17  H  HCH2  0   0.245  -0.5213  -1.4389  -2.0688
 46S  C    C  CH3   0  -0.706   3.3876  -1.8740   0.6459

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
 46S  C    C1   single    1.495  0.020  1.495
 46S  C1   C2   aromatic  1.376  0.020  1.376
 46S  C1   N1   aromatic  1.344  0.020  1.344
 46S  C2   C3   aromatic  1.413  0.020  1.413
 46S  N1   C4   aromatic  1.319  0.020  1.319
 46S  C3   N2   single    1.347  0.020  1.347
 46S  C3   N    aromatic  1.341  0.020  1.341
 46S  C4   N    aromatic  1.319  0.020  1.319
 46S  C4   H1   single    0.930  0.020  1.080
 46S  C    H12  single    0.970  0.020  1.090
 46S  C    H13  single    0.970  0.020  1.090
 46S  C    H14  single    0.970  0.020  1.090
 46S  C2   H15  single    0.930  0.020  1.080
 46S  N2   C7   single    1.455  0.020  1.455
 46S  C7   C5   single    1.522  0.020  1.522
 46S  C5   C8   single    1.528  0.020  1.528
 46S  C8   C9   single    1.532  0.020  1.532
 46S  C9   C10  single    1.529  0.020  1.529
 46S  C10  C11  single    1.532  0.020  1.532
 46S  C11  N2   single    1.450  0.020  1.450
 46S  C7   H2   single    0.970  0.020  1.090
 46S  C7   H3   single    0.970  0.020  1.090
 46S  C5   H4   single    0.970  0.020  1.090
 46S  C5   H5   single    0.970  0.020  1.090
 46S  C8   H6   single    0.970  0.020  1.090
 46S  C8   H7   single    0.970  0.020  1.090
 46S  C9   H8   single    0.970  0.020  1.090
 46S  C9   H9   single    0.970  0.020  1.090
 46S  C10  H10  single    0.970  0.020  1.090
 46S  C10  H11  single    0.970  0.020  1.090
 46S  C11  H16  single    0.970  0.020  1.090
 46S  C11  H17  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
 46S  H1   C4   N    115.66  3.000
 46S  H1   C4   N1   116.32  3.000
 46S  N    C4   N1   128.02  3.000
 46S  C1   N1   C4   115.45  3.000
 46S  C11  N2   C7   115.95  3.000
 46S  C11  N2   C3   121.44  3.000
 46S  C7   N2   C3   121.19  3.000
 46S  C2   C1   C    121.40  3.000
 46S  C2   C1   N1   121.92  3.000
 46S  C    C1   N1   116.68  3.000
 46S  C3   N    C4   117.29  3.000
 46S  C2   C3   N    119.34  3.000
 46S  N    C3   N2   117.96  3.000
 46S  C2   C3   N2   122.69  3.000
 46S  H15  C2   C3   122.24  3.000
 46S  H15  C2   C1   119.80  3.000
 46S  C3   C2   C1   117.96  3.000
 46S  H3   C7   H2   106.98  3.000
 46S  H3   C7   C5   109.76  3.000
 46S  H2   C7   C5   110.15  3.000
 46S  H3   C7   N2   107.02  3.000
 46S  H2   C7   N2   109.36  3.000
 46S  C5   C7   N2   113.32  3.000
 46S  H5   C5   H4   106.40  3.000
 46S  H5   C5   C8   109.55  3.000
 46S  H4   C5   C8   108.86  3.000
 46S  H5   C5   C7   107.68  3.000
 46S  H4   C5   C7   109.15  3.000
 46S  C8   C5   C7   114.88  3.000
 46S  H7   C8   H6   105.58  3.000
 46S  H7   C8   C9   110.61  3.000
 46S  H6   C8   C9   108.29  3.000
 46S  H7   C8   C5   110.27  3.000
 46S  H6   C8   C5   107.60  3.000
 46S  C9   C8   C5   114.08  3.000
 46S  H9   C9   H8   105.22  3.000
 46S  H9   C9   C10  107.51  3.000
 46S  H8   C9   C10  109.35  3.000
 46S  H9   C9   C8   109.26  3.000
 46S  H8   C9   C8   108.59  3.000
 46S  C10  C9   C8   116.34  3.000
 46S  H11  C10  H10  105.90  3.000
 46S  H11  C10  C11  107.21  3.000
 46S  H10  C10  C11  110.39  3.000
 46S  H11  C10  C9   109.95  3.000
 46S  H10  C10  C9   108.26  3.000
 46S  C11  C10  C9   114.77  3.000
 46S  H17  C11  H16  105.30  3.000
 46S  H17  C11  C10  110.32  3.000
 46S  H16  C11  C10  109.46  3.000
 46S  H17  C11  N2   110.19  3.000
 46S  H16  C11  N2   106.51  3.000
 46S  C10  C11  N2   114.59  3.000
 46S  H14  C    H13  108.37  3.000
 46S  H14  C    H12  108.46  3.000
 46S  H13  C    H12  107.07  3.000
 46S  H14  C    C1   112.06  3.000
 46S  H13  C    C1   110.38  3.000
 46S  H12  C    C1   110.35  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
 46S  CONST_01  C2   C1  N1  C4    0.00   0.0  0
 46S  CONST_02  C2   C3  N   C4    0.00   0.0  0
 46S  CONST_03  C3   C2  C1  N1    0.00   0.0  0
 46S  CONST_04  C3   N   C4  N1    0.00   0.0  0
 46S  CONST_05  N    C3  C2  C1    0.00   0.0  0
 46S  CONST_06  N    C4  N1  C1    0.00   0.0  0
 46S  CONST_07  N2   C3  N   C4  180.00   0.0  0
 46S  CONST_08  C1   C2  C3  N2  180.00   0.0  0
 46S  CONST_09  C    C1  N1  C4  180.00   0.0  0
 46S  CONST_10  C3   C2  C1  C   180.00   0.0  0
 46S  CONST_11  H15  C2  C1  N1  180.00   0.0  0
 46S  CONST_12  H1   C4  N1  C1  180.00   0.0  0
 46S  Var_01    H12  C   C1  N1  -57.59  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
 46S  plan-1  C4   0.020
 46S  plan-1  N1   0.020
 46S  plan-1  N2   0.020
 46S  plan-1  C1   0.020
 46S  plan-1  N    0.020
 46S  plan-1  C3   0.020
 46S  plan-1  C2   0.020
 46S  plan-1  H1   0.020
 46S  plan-1  H15  0.020
 46S  plan-1  C    0.020

