# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 21:43:35 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: 1-cyano-2-(2-methylbutan-2-yl)-3-pyridin-3-yl-guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(C)(C)N=C(NC#N)Nc1cccnc1
#
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
 ESV  ESV  "1-cyano-2-(2-methylbutan-2-yl)-3-pyridin-3-yl-guanidine"
  ligand  34  17  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ESV
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
 ESV  C10  C  CH3   0  -0.664  140.6228  130.1488  113.2762
 ESV  C13  C  CR16  0  -0.194  134.4636  132.4330  113.9053
 ESV  C15  C  CR16  0  -0.316  133.5148  131.7608  114.6535
 ESV  C17  C  CSP   0   0.294  137.6327  133.6314  115.5457
 ESV  C6   C  CT    0   0.036  140.3747  132.6219  112.5332
 ESV  C7   C  CH2   0  -0.435  141.0773  131.5914  113.4426
 ESV  C8   C  CH3   0  -0.638  140.8586  132.4314  111.0923
 ESV  C9   C  CH3   0  -0.648  140.7560  134.0405  112.9738
 ESV  C11  C  C     0   0.579  138.1066  132.6278  113.4170
 ESV  C12  C  CR6   0   0.216  135.7818  131.9897  113.9361
 ESV  C14  C  CR16  0  -0.097  136.0771  130.8788  114.7258
 ESV  C16  C  CR16  0  -0.079  133.9174  130.6830  115.4289
 ESV  N1   N  N     0  -0.406  138.9278  132.4349  112.4846
 ESV  N2   N  NH1   0  -0.730  136.7497  132.6523  113.1683
 ESV  N3   N  NH1   0  -0.691  138.4062  132.8892  114.7710
 ESV  N4   N  N     0  -0.389  135.1719  130.2522  115.4627
 ESV  N5   N  NS    0  -0.300  136.9663  134.2775  116.2340
 ESV  H1   H  HCH3  0   0.231  141.2143  129.4916  113.9138
 ESV  H2   H  HCH3  0   0.226  139.5765  130.0164  113.5538
 ESV  H3   H  HCH3  0   0.225  140.7394  129.7986  112.2503
 ESV  H5   H  HCR6  0   0.274  132.4803  132.0759  114.6489
 ESV  H6   H  HCH2  0   0.238  142.1492  131.6626  113.2386
 ESV  H7   H  HCH2  0   0.218  140.9822  131.8776  114.4960
 ESV  H8   H  HCH3  0   0.217  141.9392  132.5632  111.0236
 ESV  H9   H  HCH3  0   0.229  140.6128  131.4388  110.7136
 ESV  H10  H  HCH3  0   0.227  140.3871  133.1623  110.4337
 ESV  H11  H  HCH3  0   0.225  140.4843  134.2523  114.0079
 ESV  H12  H  HCH3  0   0.233  141.8352  134.1749  112.8870
 ESV  H13  H  HCH3  0   0.234  140.2736  134.7839  112.3376
 ESV  H14  H  HCR6  0   0.275  137.0857  130.4785  114.7585
 ESV  H15  H  HCR6  0   0.264  133.2000  130.1436  116.0361
 ESV  H16  H  HNH1  0   0.407  136.5258  132.7796  112.1912
 ESV  H17  H  HNH1  0   0.456  139.3020  132.6124  115.1460
 ESV  H4   H  HCR6  0   0.283  134.1920  133.2912  113.3031

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
 ESV  C8   C6   single    1.532  0.020  1.532
 ESV  N1   C6   single    1.460  0.020  1.460
 ESV  N1   C11  double    1.257  0.020  1.257
 ESV  C6   C9   single    1.534  0.020  1.534
 ESV  C6   C7   single    1.543  0.020  1.543
 ESV  N2   C11  single    1.380  0.020  1.380
 ESV  N2   C12  single    1.402  0.020  1.402
 ESV  C10  C7   single    1.522  0.020  1.522
 ESV  C11  N3   single    1.411  0.020  1.411
 ESV  C13  C12  aromatic  1.391  0.020  1.391
 ESV  C13  C15  aromatic  1.383  0.020  1.383
 ESV  C12  C14  aromatic  1.395  0.020  1.395
 ESV  C15  C16  aromatic  1.387  0.020  1.387
 ESV  N3   C17  single    1.323  0.020  1.323
 ESV  C14  N4   aromatic  1.325  0.020  1.325
 ESV  C16  N4   aromatic  1.327  0.020  1.327
 ESV  C17  N5   triple    1.156  0.020  1.156
 ESV  C10  H1   single    0.970  0.020  1.090
 ESV  C10  H2   single    0.970  0.020  1.090
 ESV  C10  H3   single    0.970  0.020  1.090
 ESV  C13  H4   single    0.930  0.020  1.080
 ESV  C15  H5   single    0.930  0.020  1.080
 ESV  C7   H6   single    0.970  0.020  1.090
 ESV  C7   H7   single    0.970  0.020  1.090
 ESV  C8   H8   single    0.970  0.020  1.090
 ESV  C8   H9   single    0.970  0.020  1.090
 ESV  C8   H10  single    0.970  0.020  1.090
 ESV  C9   H11  single    0.970  0.020  1.090
 ESV  C9   H12  single    0.970  0.020  1.090
 ESV  C9   H13  single    0.970  0.020  1.090
 ESV  C14  H14  single    0.930  0.020  1.080
 ESV  C16  H15  single    0.930  0.020  1.080
 ESV  N2   H16  single    0.890  0.020  1.040
 ESV  N3   H17  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
 ESV  H3   C10  H2   107.65  3.000
 ESV  H3   C10  H1   107.37  3.000
 ESV  H2   C10  H1   107.36  3.000
 ESV  H3   C10  C7   112.05  3.000
 ESV  H2   C10  C7   111.96  3.000
 ESV  H1   C10  C7   110.22  3.000
 ESV  H4   C13  C12  120.16  3.000
 ESV  H4   C13  C15  120.94  3.000
 ESV  C12  C13  C15  118.91  3.000
 ESV  H5   C15  C16  120.42  3.000
 ESV  H5   C15  C13  120.82  3.000
 ESV  C16  C15  C13  118.75  3.000
 ESV  N5   C17  N3   180.00  3.000
 ESV  N1   C6   C9   111.99  3.000
 ESV  C9   C6   C8   107.86  3.000
 ESV  N1   C6   C8   105.42  3.000
 ESV  C9   C6   C7   109.58  3.000
 ESV  N1   C6   C7   112.66  3.000
 ESV  C8   C6   C7   109.11  3.000
 ESV  H7   C7   H6   104.32  3.000
 ESV  H7   C7   C6   110.65  3.000
 ESV  H6   C7   C6   107.03  3.000
 ESV  H7   C7   C10  109.07  3.000
 ESV  H6   C7   C10  109.52  3.000
 ESV  C6   C7   C10  115.63  3.000
 ESV  H10  C8   H9   107.62  3.000
 ESV  H10  C8   H8   108.01  3.000
 ESV  H9   C8   H8   108.15  3.000
 ESV  H10  C8   C6   110.36  3.000
 ESV  H9   C8   C6   111.63  3.000
 ESV  H8   C8   C6   110.92  3.000
 ESV  H13  C9   H12  107.88  3.000
 ESV  H13  C9   H11  108.09  3.000
 ESV  H12  C9   H11  107.34  3.000
 ESV  H13  C9   C6   110.67  3.000
 ESV  H12  C9   C6   109.70  3.000
 ESV  H11  C9   C6   112.98  3.000
 ESV  N3   C11  N2   112.24  3.000
 ESV  N3   C11  N1   126.97  3.000
 ESV  N2   C11  N1   120.75  3.000
 ESV  N2   C12  C14  122.71  3.000
 ESV  C14  C12  C13  117.84  3.000
 ESV  N2   C12  C13  119.45  3.000
 ESV  H14  C14  N4   116.34  3.000
 ESV  H14  C14  C12  120.49  3.000
 ESV  N4   C14  C12  123.17  3.000
 ESV  H15  C16  N4   116.74  3.000
 ESV  H15  C16  C15  120.51  3.000
 ESV  N4   C16  C15  122.74  3.000
 ESV  C11  N1   C6   127.08  3.000
 ESV  H16  N2   C12  115.85  3.000
 ESV  H16  N2   C11  113.23  3.000
 ESV  C12  N2   C11  124.89  3.000
 ESV  H17  N3   C11  119.59  3.000
 ESV  H17  N3   C17  117.07  3.000
 ESV  C11  N3   C17  122.81  3.000
 ESV  C16  N4   C14  118.57  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
 ESV  CONST_01  N4   C14  C12  C13     0.00   0.0  0
 ESV  CONST_02  N4   C16  C15  C13     0.00   0.0  0
 ESV  CONST_03  C14  C12  C13  C15     0.00   0.0  0
 ESV  CONST_04  C14  N4   C16  C15     0.00   0.0  0
 ESV  CONST_05  C16  C15  C13  C12     0.00   0.0  0
 ESV  CONST_06  C16  N4   C14  C12     0.00   0.0  0
 ESV  CONST_07  N2   C12  C13  C15   180.00   0.0  0
 ESV  CONST_08  N4   C14  C12  N2    180.00   0.0  0
 ESV  CONST_09  H14  C14  C12  C13   180.00   0.0  0
 ESV  CONST_10  H15  C16  C15  C13   180.00   0.0  0
 ESV  CONST_11  H5   C15  C13  C12   180.00   0.0  0
 ESV  CONST_12  H4   C13  C12  C14   180.00   0.0  0
 ESV  CONST_13  H15  C16  N4   C14   180.00   0.0  0
 ESV  CONST_14  H4   C13  C15  C16   180.00   0.0  0
 ESV  CONST_15  H14  C14  N4   C16   180.00   0.0  0
 ESV  CONST_16  H5   C15  C16  N4    180.00   0.0  0
 ESV  CONST_25  N2   C11  N1   C6    180.00   0.0  0
 ESV  CONST_26  N3   C11  N1   C6      0.00   0.0  0
 ESV  Var_01    C8   C6   C7   C10   -71.67  30.0  1
 ESV  Var_02    N1   C6   C7   C10    45.05  30.0  1
 ESV  Var_03    C9   C6   C7   C10   170.45  30.0  1
 ESV  Var_04    C11  N1   C6   C7     68.53  30.0  3
 ESV  Var_05    C11  N1   C6   C8   -172.59  30.0  3
 ESV  Var_06    C11  N1   C6   C9    -55.55  30.0  3
 ESV  Var_07    N5   C17  N3   C11   179.43  30.0  3
 ESV  Var_08    H1   C10  C7   C6    176.63  30.0  3
 ESV  Var_09    H2   C10  C7   C6    -63.94  30.0  3
 ESV  Var_10    H3   C10  C7   C6     57.12  30.0  3
 ESV  Var_11    H8   C8   C6   C7    -59.34  30.0  3
 ESV  Var_12    H9   C8   C6   C7     61.35  30.0  3
 ESV  Var_13    H10  C8   C6   C7   -179.01  30.0  3
 ESV  Var_14    H11  C9   C6   C7    -59.02  30.0  3
 ESV  Var_15    H12  C9   C6   C7     60.70  30.0  3
 ESV  Var_16    H13  C9   C6   C7    179.62  30.0  3
 ESV  Var_17    H11  C9   C6   C8   -177.68  30.0  3
 ESV  Var_18    H12  C9   C6   C8    -57.96  30.0  3
 ESV  Var_19    H13  C9   C6   C8     60.96  30.0  3
 ESV  Var_20    H6   C7   C6   C8     50.65  30.0  3
 ESV  Var_21    H7   C7   C6   C8    163.72  30.0  3
 ESV  Var_22    H8   C8   C6   C9     59.62  30.0  3
 ESV  Var_23    H9   C8   C6   C9   -179.69  30.0  3
 ESV  Var_24    H10  C8   C6   C9    -60.04  30.0  3
 ESV  Var_25    H6   C7   C6   C9    -67.24  30.0  3
 ESV  Var_26    H7   C7   C6   C9     45.83  30.0  3
 ESV  Var_27    H8   C8   C6   N1    179.43  30.0  3
 ESV  Var_28    H9   C8   C6   N1    -59.88  30.0  3
 ESV  Var_29    H10  C8   C6   N1     59.76  30.0  3
 ESV  Var_30    H11  C9   C6   N1     66.76  30.0  3
 ESV  Var_31    H12  C9   C6   N1   -173.52  30.0  3
 ESV  Var_32    H13  C9   C6   N1    -54.60  30.0  3
 ESV  Var_33    H6   C7   C6   N1    167.36  30.0  3
 ESV  Var_34    H7   C7   C6   N1    -79.57  30.0  3
 ESV  Var_35    H17  N3   C17  N5     -8.96  30.0  1

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
 ESV  plan-1  C13  0.020
 ESV  plan-1  C15  0.020
 ESV  plan-1  C12  0.020
 ESV  plan-1  C14  0.020
 ESV  plan-1  C16  0.020
 ESV  plan-1  N2   0.020
 ESV  plan-1  N4   0.020
 ESV  plan-1  H5   0.020
 ESV  plan-1  H14  0.020
 ESV  plan-1  H15  0.020
 ESV  plan-1  H4   0.020
 ESV  plan-2  C17  0.020
 ESV  plan-2  C6   0.020
 ESV  plan-2  C11  0.020
 ESV  plan-2  C12  0.020
 ESV  plan-2  N1   0.020
 ESV  plan-2  N2   0.020
 ESV  plan-2  N3   0.020
 ESV  plan-2  H16  0.020
 ESV  plan-2  H17  0.020

