# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 09:59:06 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: [2-(cycloheptylamino)pyrimidin-4-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccnc(NC2CCCCCC2)n1
#
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
 LE4  LE4  '[2-(cycloheptylamino)pyrimidin-4-yl]methanol'  ligand  35  16  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LE4
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
 LE4  N1   N  N     0  -0.467   0.9497   1.0868  -0.7164
 LE4  N3   N  N     0  -0.489   2.0561  -0.7740   0.2665
 LE4  C4   C  CR16  0  -0.009   2.1295   1.6644  -0.8706
 LE4  C5   C  CR6   0   0.586   0.9614  -0.1279  -0.1539
 LE4  C6   C  CH1   0  -0.045  -1.5186  -0.2281  -0.2954
 LE4  C7   C  CH2   0  -0.442  -2.4437  -1.4035  -0.6014
 LE4  C8   C  CH2   0  -0.440  -3.9025  -1.0549  -0.8814
 LE4  C10  C  CH2   0  -0.425  -4.5754   0.9299   0.6316
 LE4  C11  C  CH2   0  -0.449  -3.1972   1.5631   0.4241
 LE4  C12  C  CH2   0  -0.433  -1.9985   0.7031   0.8255
 LE4  C2   C  CR6   0   0.239   3.2231  -0.1732   0.0999
 LE4  C3   C  CR16  0  -0.405   3.3259   1.0852  -0.4825
 LE4  C9   C  CH2   0  -0.443  -4.6702  -0.5691   0.3487
 LE4  N2   N  NH1   0  -0.665  -0.2074  -0.7770  -0.0051
 LE4  O1   O  OH1   0  -0.664   5.5913  -0.2235   0.3793
 LE4  H1   H  HCR6  0   0.264   2.1246   2.6480  -1.3295
 LE4  H2   H  HCH1  0   0.229  -1.4274   0.3760  -1.2030
 LE4  H3   H  HCH2  0   0.236  -2.0293  -1.9348  -1.4626
 LE4  H4   H  HCH2  0   0.216  -2.4142  -2.1087   0.2381
 LE4  H5   H  HCH2  0   0.219  -3.9726  -0.3241  -1.6948
 LE4  H6   H  HCH2  0   0.234  -4.3829  -1.9618  -1.2558
 LE4  H7   H  HCH2  0   0.218  -4.9018   1.1034   1.6609
 LE4  H8   H  HCH2  0   0.218  -5.2943   1.4607   0.0012
 LE4  H9   H  HCH2  0   0.228   4.2492  -1.1979   1.6381
 LE4  H10  H  HCH2  0   0.231   4.4204  -1.9091   0.0399
 LE4  H11  H  HCH2  0   0.215  -3.0765   1.8515  -0.6250
 LE4  H12  H  HCH2  0   0.232  -3.1686   2.5012   0.9832
 LE4  H13  H  HCH2  0   0.216  -2.2138   0.1237   1.7296
 LE4  H14  H  HCH2  0   0.235  -1.1645   1.3632   1.0743
 LE4  H15  H  HCR6  0   0.264   4.2674   1.5902  -0.6284
 LE4  H16  H  HCH2  0   0.230  -5.7272  -0.8258   0.2426
 LE4  H17  H  HCH2  0   0.214  -4.3185  -1.1316   1.2196
 LE4  H18  H  HNH1  0   0.383  -0.1624  -1.6488   0.4990
 LE4  H19  H  HOH1  0   0.466   6.3345  -0.7876   0.6095
 LE4  C1   C  CH2   0  -0.194   4.4124  -0.9535   0.5799

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
 LE4  C1   O1   single    1.401  0.020  1.401
 LE4  C1   C2   single    1.501  0.020  1.501
 LE4  C3   C2   aromatic  1.391  0.020  1.391
 LE4  C3   C4   aromatic  1.385  0.020  1.385
 LE4  C2   N3   aromatic  1.323  0.020  1.323
 LE4  C4   N1   aromatic  1.323  0.020  1.323
 LE4  N3   C5   aromatic  1.339  0.020  1.339
 LE4  N1   C5   aromatic  1.339  0.020  1.339
 LE4  C5   N2   single    1.345  0.020  1.345
 LE4  N2   C6   single    1.451  0.020  1.451
 LE4  C12  C6   single    1.534  0.020  1.534
 LE4  C12  C11  single    1.529  0.020  1.529
 LE4  C6   C7   single    1.527  0.020  1.527
 LE4  C11  C10  single    1.531  0.020  1.531
 LE4  C7   C8   single    1.526  0.020  1.526
 LE4  C10  C9   single    1.528  0.020  1.528
 LE4  C8   C9   single    1.529  0.020  1.529
 LE4  C4   H1   single    0.930  0.020  1.080
 LE4  C6   H2   single    0.970  0.020  1.090
 LE4  C7   H3   single    0.970  0.020  1.090
 LE4  C7   H4   single    0.970  0.020  1.090
 LE4  C8   H5   single    0.970  0.020  1.090
 LE4  C8   H6   single    0.970  0.020  1.090
 LE4  C10  H7   single    0.970  0.020  1.090
 LE4  C10  H8   single    0.970  0.020  1.090
 LE4  C1   H9   single    0.970  0.020  1.090
 LE4  C1   H10  single    0.970  0.020  1.090
 LE4  C11  H11  single    0.970  0.020  1.090
 LE4  C11  H12  single    0.970  0.020  1.090
 LE4  C12  H13  single    0.970  0.020  1.090
 LE4  C12  H14  single    0.970  0.020  1.090
 LE4  C3   H15  single    0.930  0.020  1.080
 LE4  C9   H16  single    0.970  0.020  1.090
 LE4  C9   H17  single    0.970  0.020  1.090
 LE4  N2   H18  single    0.860  0.020  1.020
 LE4  O1   H19  single    0.850  0.020  0.980

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
 LE4  C5   N1   C4   115.94  3.000
 LE4  C2   N3   C5   117.55  3.000
 LE4  H1   C4   C3   120.10  3.000
 LE4  H1   C4   N1   116.16  3.000
 LE4  C3   C4   N1   123.74  3.000
 LE4  N2   C5   N3   116.29  3.000
 LE4  N2   C5   N1   118.47  3.000
 LE4  N3   C5   N1   125.24  3.000
 LE4  H2   C6   N2   107.43  3.000
 LE4  H2   C6   C12  107.27  3.000
 LE4  N2   C6   C12  111.48  3.000
 LE4  H2   C6   C7   108.02  3.000
 LE4  C12  C6   C7   115.10  3.000
 LE4  N2   C6   C7   107.25  3.000
 LE4  H4   C7   H3   106.27  3.000
 LE4  H4   C7   C8   108.25  3.000
 LE4  H3   C7   C8   109.20  3.000
 LE4  H4   C7   C6   108.98  3.000
 LE4  H3   C7   C6   107.59  3.000
 LE4  C8   C7   C6   116.12  3.000
 LE4  H6   C8   H5   105.73  3.000
 LE4  H6   C8   C9   108.58  3.000
 LE4  H5   C8   C9   110.68  3.000
 LE4  H6   C8   C7   107.08  3.000
 LE4  H5   C8   C7   110.48  3.000
 LE4  C9   C8   C7   113.89  3.000
 LE4  H8   C10  H7   105.63  3.000
 LE4  H8   C10  C9   109.18  3.000
 LE4  H7   C10  C9   108.13  3.000
 LE4  H8   C10  C11  108.24  3.000
 LE4  H7   C10  C11  109.31  3.000
 LE4  C9   C10  C11  115.88  3.000
 LE4  H12  C11  H11  105.15  3.000
 LE4  H12  C11  C12  109.15  3.000
 LE4  H11  C11  C12  108.26  3.000
 LE4  H12  C11  C10  108.02  3.000
 LE4  H11  C11  C10  109.77  3.000
 LE4  C12  C11  C10  115.95  3.000
 LE4  H14  C12  H13  106.37  3.000
 LE4  H14  C12  C11  108.57  3.000
 LE4  H13  C12  C11  111.11  3.000
 LE4  H14  C12  C6   107.12  3.000
 LE4  H13  C12  C6   110.09  3.000
 LE4  C11  C12  C6   113.26  3.000
 LE4  C3   C2   C1   123.08  3.000
 LE4  C3   C2   N3   121.93  3.000
 LE4  C1   C2   N3   114.99  3.000
 LE4  H15  C3   C2   123.03  3.000
 LE4  H15  C3   C4   121.37  3.000
 LE4  C2   C3   C4   115.60  3.000
 LE4  H17  C9   H16  105.50  3.000
 LE4  H17  C9   C10  109.68  3.000
 LE4  H16  C9   C10  107.96  3.000
 LE4  H17  C9   C8   108.39  3.000
 LE4  H16  C9   C8   109.44  3.000
 LE4  C10  C9   C8   115.42  3.000
 LE4  H18  N2   C6   117.88  3.000
 LE4  H18  N2   C5   115.71  3.000
 LE4  C6   N2   C5   125.50  3.000
 LE4  H19  O1   C1   108.10  3.000
 LE4  H10  C1   H9   106.34  3.000
 LE4  H10  C1   O1   112.15  3.000
 LE4  H9   C1   O1   112.26  3.000
 LE4  H10  C1   C2   107.52  3.000
 LE4  H9   C1   C2   107.82  3.000
 LE4  O1   C1   C2   110.49  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
 LE4  CONST_01  C2   C3  C4  N1     0.00   0.0  0
 LE4  CONST_02  C2   N3  C5  N1     0.00   0.0  0
 LE4  CONST_03  C4   C3  C2  N3     0.00   0.0  0
 LE4  CONST_04  C4   N1  C5  N3     0.00   0.0  0
 LE4  CONST_05  C3   C2  N3  C5     0.00   0.0  0
 LE4  CONST_06  C3   C4  N1  C5     0.00   0.0  0
 LE4  CONST_07  C1   C2  C3  C4   180.00   0.0  0
 LE4  CONST_08  N2   C5  N1  C4   180.00   0.0  0
 LE4  CONST_09  C1   C2  N3  C5   180.00   0.0  0
 LE4  CONST_10  N2   C5  N3  C2   180.00   0.0  0
 LE4  CONST_11  C6   N2  C5  N1     0.00   0.0  0
 LE4  CONST_12  C6   N2  C5  N3   180.00   0.0  0
 LE4  CONST_13  H15  C3  C4  N1   180.00   0.0  0
 LE4  CONST_14  H1   C4  N1  C5   180.00   0.0  0
 LE4  CONST_15  H18  N2  C5  N1   180.00   0.0  0
 LE4  Var_01    O1   C1  C2  N3  -179.01  30.0  3

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
 LE4  chir_01  C6  N2  C12  C7  positiv

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
 LE4  plan-1  N1   0.020
 LE4  plan-1  N3   0.020
 LE4  plan-1  C4   0.020
 LE4  plan-1  C5   0.020
 LE4  plan-1  C2   0.020
 LE4  plan-1  C3   0.020
 LE4  plan-1  N2   0.020
 LE4  plan-1  H1   0.020
 LE4  plan-1  H15  0.020
 LE4  plan-1  C1   0.020
 LE4  plan-2  C5   0.020
 LE4  plan-2  C6   0.020
 LE4  plan-2  N2   0.020
 LE4  plan-2  H18  0.020

