# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 10:39:42 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (3S)-N-(pyrimidin-2-yl)azepan-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC[C@@H](CNC1)Nc2ncccn2
#
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
 LES  LES  (3S)-N-(pyrimidin-2-yl)azepan-3-amine  ligand  30  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LES
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
 LES  N1   N  NH1   0  -0.665   0.4722   0.9464  -0.3101
 LES  N3   N  N     0  -0.463   2.7364   1.0790  -0.5698
 LES  C4   C  CH2   0  -0.274  -1.1813  -0.6884  -1.0379
 LES  C5   C  CH2   0  -0.302  -3.5801  -0.8633  -0.4979
 LES  C6   C  CR6   0   0.597   1.6794   0.3883  -0.1119
 LES  C7   C  CR16  0  -0.010   2.9496  -1.2839   0.7319
 LES  C8   C  CR16  0  -0.395   4.1086  -0.6576   0.3069
 LES  N    N  NH1   0  -0.598  -2.2985  -1.5304  -0.6715
 LES  C    C  CH2   0  -0.433  -3.7033  -0.2235   0.8807
 LES  C1   C  CH2   0  -0.432  -3.0396   1.1497   1.0532
 LES  C2   C  CH2   0  -0.476  -1.8371   1.4565   0.1627
 LES  C3   C  CH1   0  -0.046  -0.7991   0.3390   0.0347
 LES  C9   C  CR16  0  -0.021   3.9258   0.5495  -0.3539
 LES  N2   N  N     0  -0.464   1.7408  -0.7832   0.5312
 LES  H1   H  HNH1  0   0.389   0.4625   1.7957  -0.8530
 LES  H2   H  HCH2  0   0.231  -0.3247  -1.3459  -1.2060
 LES  H3   H  HCH2  0   0.182  -1.3466  -0.1328  -1.9771
 LES  H4   H  HCH2  0   0.192  -3.7904  -0.1230  -1.2872
 LES  H5   H  HCH2  0   0.233  -4.3508  -1.6311  -0.5886
 LES  H6   H  HCR6  0   0.267   2.9945  -2.2328   1.2566
 LES  H7   H  HCR6  0   0.268   5.0874  -1.0798   0.4754
 LES  H8   H  HNH1  0   0.353  -2.3953  -2.2448  -1.3799
 LES  H10  H  HCH2  0   0.227  -4.7618  -0.1269   1.1337
 LES  H11  H  HCH2  0   0.217  -3.2849  -0.9339   1.5979
 LES  H12  H  HCH2  0   0.227  -3.7792   1.9340   0.8755
 LES  H13  H  HCH2  0   0.225  -2.7397   1.2599   2.0982
 LES  H14  H  HCH2  0   0.227  -2.1727   1.7303  -0.8428
 LES  H15  H  HCH2  0   0.243  -1.3490   2.3470   0.5677
 LES  H16  H  HCH1  0   0.236  -0.6810  -0.1733   0.9933
 LES  H17  H  HCR6  0   0.268   4.7774   1.1116  -0.7232

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
 LES  C9  C8   aromatic  1.388  0.020  1.388
 LES  C9  N3   aromatic  1.320  0.020  1.320
 LES  C8  C7   aromatic  1.384  0.020  1.384
 LES  N3  C6   aromatic  1.343  0.020  1.343
 LES  C7  N2   aromatic  1.324  0.020  1.324
 LES  C6  N2   aromatic  1.338  0.020  1.338
 LES  C6  N1   single    1.345  0.020  1.345
 LES  N1  C3   single    1.451  0.020  1.451
 LES  C2  C3   single    1.531  0.020  1.531
 LES  C2  C1   single    1.527  0.020  1.527
 LES  C3  C4   single    1.534  0.020  1.534
 LES  C1  C    single    1.535  0.020  1.535
 LES  C4  N    single    1.446  0.020  1.446
 LES  C   C5   single    1.525  0.020  1.525
 LES  N   C5   single    1.455  0.020  1.455
 LES  N1  H1   single    0.860  0.020  1.020
 LES  C4  H2   single    0.970  0.020  1.090
 LES  C4  H3   single    0.970  0.020  1.090
 LES  C5  H4   single    0.970  0.020  1.090
 LES  C5  H5   single    0.970  0.020  1.090
 LES  C7  H6   single    0.930  0.020  1.080
 LES  C8  H7   single    0.930  0.020  1.080
 LES  N   H8   single    0.890  0.020  1.040
 LES  C   H10  single    0.970  0.020  1.090
 LES  C   H11  single    0.970  0.020  1.090
 LES  C1  H12  single    0.970  0.020  1.090
 LES  C1  H13  single    0.970  0.020  1.090
 LES  C2  H14  single    0.970  0.020  1.090
 LES  C2  H15  single    0.970  0.020  1.090
 LES  C3  H16  single    0.970  0.020  1.090
 LES  C9  H17  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
 LES  H1   N1  C3   118.19  3.000
 LES  H1   N1  C6   115.96  3.000
 LES  C3   N1  C6   125.31  3.000
 LES  C9   N3  C6   116.56  3.000
 LES  H3   C4  H2   106.82  3.000
 LES  H3   C4  C3   107.17  3.000
 LES  H2   C4  C3   108.38  3.000
 LES  H3   C4  N    113.14  3.000
 LES  H2   C4  N    107.11  3.000
 LES  C3   C4  N    113.92  3.000
 LES  H5   C5  H4   106.15  3.000
 LES  H5   C5  C    108.26  3.000
 LES  H4   C5  C    110.50  3.000
 LES  H5   C5  N    106.82  3.000
 LES  H4   C5  N    112.98  3.000
 LES  C    C5  N    111.80  3.000
 LES  N2   C6  N3   125.31  3.000
 LES  N2   C6  N1   118.40  3.000
 LES  N3   C6  N1   116.29  3.000
 LES  H6   C7  N2   116.23  3.000
 LES  H6   C7  C8   120.62  3.000
 LES  N2   C7  C8   123.15  3.000
 LES  H7   C8  C9   122.27  3.000
 LES  H7   C8  C7   122.31  3.000
 LES  C9   C8  C7   115.42  3.000
 LES  H8   N   C5   108.86  3.000
 LES  H8   N   C4   107.94  3.000
 LES  C5   N   C4   116.34  3.000
 LES  H11  C   H10  106.05  3.000
 LES  H11  C   C1   110.02  3.000
 LES  H10  C   C1   108.29  3.000
 LES  H11  C   C5   106.83  3.000
 LES  H10  C   C5   108.95  3.000
 LES  C1   C   C5   116.24  3.000
 LES  H13  C1  H12  105.60  3.000
 LES  H13  C1  C2   108.74  3.000
 LES  H12  C1  C2   107.09  3.000
 LES  H13  C1  C    108.44  3.000
 LES  H12  C1  C    109.34  3.000
 LES  C2   C1  C    117.04  3.000
 LES  H15  C2  H14  105.87  3.000
 LES  H15  C2  C3   108.84  3.000
 LES  H14  C2  C3   108.28  3.000
 LES  H15  C2  C1   107.41  3.000
 LES  H14  C2  C1   110.14  3.000
 LES  C3   C2  C1   115.85  3.000
 LES  H16  C3  C2   110.00  3.000
 LES  H16  C3  C4   109.04  3.000
 LES  C2   C3  C4   112.24  3.000
 LES  H16  C3  N1   108.06  3.000
 LES  C4   C3  N1   109.43  3.000
 LES  C2   C3  N1   107.97  3.000
 LES  H17  C9  C8   120.60  3.000
 LES  H17  C9  N3   116.34  3.000
 LES  C8   C9  N3   123.06  3.000
 LES  C7   N2  C6   116.49  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
 LES  CONST_01  C7   C8  C9  N3    0.00  0.0  0
 LES  CONST_02  C7   N2  C6  N3    0.00  0.0  0
 LES  CONST_03  C8   C9  N3  C6    0.00  0.0  0
 LES  CONST_04  C8   C7  N2  C6    0.00  0.0  0
 LES  CONST_05  N2   C7  C8  C9    0.00  0.0  0
 LES  CONST_06  N2   C6  N3  C9    0.00  0.0  0
 LES  CONST_07  C9   N3  C6  N1  180.00  0.0  0
 LES  CONST_08  C7   N2  C6  N1  180.00  0.0  0
 LES  CONST_09  C3   N1  C6  N3  180.00  0.0  0
 LES  CONST_10  N2   C6  N1  C3    0.00  0.0  0
 LES  CONST_11  H7   C8  C9  N3  180.00  0.0  0
 LES  CONST_12  H17  C9  N3  C6  180.00  0.0  0
 LES  CONST_13  H6   C7  N2  C6  180.00  0.0  0
 LES  CONST_14  H1   N1  C6  N3    0.00  0.0  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 LES  chir_01  C3  N1  C2  C4  negativ

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
 LES  plan-1  N1   0.020
 LES  plan-1  N3   0.020
 LES  plan-1  C6   0.020
 LES  plan-1  C7   0.020
 LES  plan-1  C8   0.020
 LES  plan-1  C9   0.020
 LES  plan-1  N2   0.020
 LES  plan-1  H6   0.020
 LES  plan-1  H7   0.020
 LES  plan-1  H17  0.020
 LES  plan-2  N1   0.020
 LES  plan-2  C6   0.020
 LES  plan-2  C3   0.020
 LES  plan-2  H1   0.020

