# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 10:15:58 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-(2-methyl-8-phenylmethoxy-imidazo[1,2-a]pyridin-3-yl)ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2n(cccc2OCc3ccccc3)c1CC#N
#
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
 8WX  8WX  2-(2-methyl-8-phenylmethoxy-imidazo[1,2-a]pyridin-3-yl)ethanenitrile  ligand  36  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8WX
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
 8WX  C10  C  CH2   0  -0.659  -4.5974   0.3318  -0.5492
 8WX  C11  C  CR16  0  -0.314  -0.1739  -2.3430  -0.1272
 8WX  C12  C  CR16  0  -0.369  -1.5127  -2.8055  -0.2086
 8WX  C13  C  CH3   0  -0.745  -2.7099   3.0166  -0.4919
 8WX  C14  C  CH2   0  -0.271   2.4328  -1.2462   0.0421
 8WX  C15  C  CR6   0   0.096   3.6308  -0.3497   0.1099
 8WX  C16  C  CR16  0  -0.287   3.9925   0.2478   1.3145
 8WX  C17  C  CR16  0  -0.295   4.3767  -0.0782  -1.0325
 8WX  C18  C  CSP   0   0.136  -5.2016  -0.0765   0.7174
 8WX  C19  C  CR16  0  -0.242   5.0849   1.1008   1.3768
 8WX  C20  C  CR16  0  -0.241   5.4722   0.7734  -0.9733
 8WX  C21  C  CR16  0  -0.261   5.8268   1.3647   0.2318
 8WX  C5   C  CR5   0   0.275  -3.1211   0.4783  -0.4472
 8WX  C6   C  CR56  0   0.453  -1.0039  -0.0947  -0.2668
 8WX  C7   C  CR5   0   0.098  -2.3059   1.5861  -0.4224
 8WX  C8   C  CR6   0   0.260   0.0877  -0.9999  -0.1568
 8WX  C9   C  CR16  0  -0.003  -2.5508  -1.9437  -0.3144
 8WX  N2   N  N     0  -0.544  -2.2787  -0.6021  -0.3428
 8WX  N3   N  N     0  -0.479  -1.0043   1.2224  -0.3148
 8WX  N4   N  NS    0  -0.263  -5.6602  -0.4042   1.7199
 8WX  O1   O  O2    0  -0.449   1.2859  -0.4109  -0.0927
 8WX  H1   H  HCH2  0   0.339  -4.8885  -0.3928  -1.3156
 8WX  H2   H  HCH2  0   0.345  -5.0456   1.2814  -0.8449
 8WX  H3   H  HCR6  0   0.298   0.6188  -3.0726  -0.0456
 8WX  H4   H  HCR6  0   0.283  -1.7123  -3.8667  -0.1856
 8WX  H5   H  HCH3  0   0.254  -2.4490   3.5389   0.4297
 8WX  H6   H  HCH3  0   0.253  -2.1987   3.5248  -1.3100
 8WX  H7   H  HCH3  0   0.242  -3.7816   3.1317  -0.6445
 8WX  H8   H  HCH2  0   0.249   2.5070  -1.9268  -0.8116
 8WX  H9   H  HCH2  0   0.248   2.3496  -1.8511   0.9507
 8WX  H10  H  HCR6  0   0.255   3.4205   0.0394   2.2112
 8WX  H11  H  HCR6  0   0.256   4.1039  -0.5392  -1.9745
 8WX  H14  H  HCR6  0   0.259   5.3595   1.5577   2.3188
 8WX  H15  H  HCR6  0   0.259   6.0486   0.9726  -1.8674
 8WX  H16  H  HCR6  0   0.260   6.6816   2.0266   0.2809
 8WX  H17  H  HCR6  0   0.305  -3.5836  -2.2497  -0.3817

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
 8WX  C12  C11  aromatic  1.419  0.020  1.419
 8WX  C12  C9   aromatic  1.353  0.020  1.353
 8WX  C11  C8   aromatic  1.369  0.020  1.369
 8WX  N4   C18  triple    1.150  0.020  1.150
 8WX  C9   N2   aromatic  1.369  0.020  1.369
 8WX  C8   O1   single    1.337  0.020  1.337
 8WX  C8   C6   aromatic  1.422  0.020  1.422
 8WX  N2   C6   aromatic  1.374  0.020  1.374
 8WX  N2   C5   aromatic  1.374  0.020  1.374
 8WX  C18  C10  single    1.462  0.020  1.462
 8WX  C14  O1   single    1.425  0.020  1.425
 8WX  C14  C15  single    1.498  0.020  1.498
 8WX  C17  C15  aromatic  1.391  0.020  1.391
 8WX  C17  C20  aromatic  1.389  0.020  1.389
 8WX  C6   N3   aromatic  1.318  0.020  1.318
 8WX  C5   C10  single    1.487  0.020  1.487
 8WX  C5   C7   aromatic  1.376  0.020  1.376
 8WX  C15  C16  aromatic  1.392  0.020  1.392
 8WX  C20  C21  aromatic  1.388  0.020  1.388
 8WX  N3   C7   aromatic  1.356  0.020  1.356
 8WX  C7   C13  single    1.488  0.020  1.488
 8WX  C16  C19  aromatic  1.387  0.020  1.387
 8WX  C21  C19  aromatic  1.390  0.020  1.390
 8WX  C10  H1   single    0.970  0.020  1.090
 8WX  C10  H2   single    0.970  0.020  1.090
 8WX  C11  H3   single    0.930  0.020  1.080
 8WX  C12  H4   single    0.930  0.020  1.080
 8WX  C13  H5   single    0.970  0.020  1.090
 8WX  C13  H6   single    0.970  0.020  1.090
 8WX  C13  H7   single    0.970  0.020  1.090
 8WX  C14  H8   single    0.970  0.020  1.090
 8WX  C14  H9   single    0.970  0.020  1.090
 8WX  C16  H10  single    0.930  0.020  1.080
 8WX  C17  H11  single    0.930  0.020  1.080
 8WX  C19  H14  single    0.930  0.020  1.080
 8WX  C20  H15  single    0.930  0.020  1.080
 8WX  C21  H16  single    0.930  0.020  1.080
 8WX  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
 8WX  H2   C10  H1   106.10  3.000
 8WX  H2   C10  C5   109.92  3.000
 8WX  H1   C10  C5   112.17  3.000
 8WX  H2   C10  C18  107.96  3.000
 8WX  H1   C10  C18  108.18  3.000
 8WX  C5   C10  C18  112.24  3.000
 8WX  H3   C11  C8   121.60  3.000
 8WX  H3   C11  C12  118.46  3.000
 8WX  C8   C11  C12  119.93  3.000
 8WX  H4   C12  C9   119.05  3.000
 8WX  H4   C12  C11  119.57  3.000
 8WX  C9   C12  C11  121.38  3.000
 8WX  H7   C13  H6   107.88  3.000
 8WX  H7   C13  H5   107.65  3.000
 8WX  H6   C13  H5   107.37  3.000
 8WX  H7   C13  C7   112.05  3.000
 8WX  H6   C13  C7   110.85  3.000
 8WX  H5   C13  C7   110.85  3.000
 8WX  H9   C14  H8   108.00  3.000
 8WX  H9   C14  O1   109.95  3.000
 8WX  H8   C14  O1   110.20  3.000
 8WX  H9   C14  C15  110.73  3.000
 8WX  H8   C14  C15  110.69  3.000
 8WX  O1   C14  C15  107.29  3.000
 8WX  C17  C15  C16  119.17  3.000
 8WX  C16  C15  C14  120.25  3.000
 8WX  C17  C15  C14  120.57  3.000
 8WX  H10  C16  C19  119.78  3.000
 8WX  H10  C16  C15  119.74  3.000
 8WX  C19  C16  C15  120.48  3.000
 8WX  H11  C17  C20  119.77  3.000
 8WX  H11  C17  C15  119.72  3.000
 8WX  C20  C17  C15  120.51  3.000
 8WX  N4   C18  C10  180.00  3.000
 8WX  H14  C19  C21  120.10  3.000
 8WX  H14  C19  C16  119.90  3.000
 8WX  C21  C19  C16  120.00  3.000
 8WX  H15  C20  C21  120.18  3.000
 8WX  H15  C20  C17  119.85  3.000
 8WX  C21  C20  C17  119.97  3.000
 8WX  H16  C21  C20  120.11  3.000
 8WX  H16  C21  C19  120.02  3.000
 8WX  C20  C21  C19  119.87  3.000
 8WX  N2   C5   C7   105.58  3.000
 8WX  C7   C5   C10  131.98  3.000
 8WX  N2   C5   C10  122.45  3.000
 8WX  N3   C6   N2   111.51  3.000
 8WX  N3   C6   C8   129.72  3.000
 8WX  N2   C6   C8   118.77  3.000
 8WX  N3   C7   C5   110.75  3.000
 8WX  N3   C7   C13  121.48  3.000
 8WX  C5   C7   C13  127.77  3.000
 8WX  O1   C8   C6   114.28  3.000
 8WX  C6   C8   C11  118.66  3.000
 8WX  O1   C8   C11  127.06  3.000
 8WX  H17  C9   N2   117.82  3.000
 8WX  H17  C9   C12  123.94  3.000
 8WX  N2   C9   C12  118.24  3.000
 8WX  C9   N2   C6   123.02  3.000
 8WX  C6   N2   C5   106.42  3.000
 8WX  C9   N2   C5   130.55  3.000
 8WX  C7   N3   C6   105.74  3.000
 8WX  C8   O1   C14  117.88  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
 8WX  CONST_01  N2   C9   C12  C11    0.00   0.0  0
 8WX  CONST_02  N2   C6   C8   C11    0.00   0.0  0
 8WX  CONST_03  N3   C6   C8   C11  180.00   0.0  0
 8WX  CONST_04  C6   C8   C11  C12    0.00   0.0  0
 8WX  CONST_05  C6   N2   C9   C12    0.00   0.0  0
 8WX  CONST_06  C5   N2   C9   C12  180.00   0.0  0
 8WX  CONST_07  C21  C20  C17  C15    0.00   0.0  0
 8WX  CONST_08  C21  C19  C16  C15    0.00   0.0  0
 8WX  CONST_09  C20  C17  C15  C16    0.00   0.0  0
 8WX  CONST_10  C20  C21  C19  C16    0.00   0.0  0
 8WX  CONST_11  C19  C16  C15  C17    0.00   0.0  0
 8WX  CONST_12  C19  C21  C20  C17    0.00   0.0  0
 8WX  CONST_13  C8   C6   N2   C5   180.00   0.0  0
 8WX  CONST_14  N3   C6   N2   C5     0.00   0.0  0
 8WX  CONST_15  C6   N3   C7   C5     0.00   0.0  0
 8WX  CONST_16  C7   C5   N2   C6     0.00   0.0  0
 8WX  CONST_17  C9   N2   C5   C7   180.00   0.0  0
 8WX  CONST_18  C8   C6   N3   C7   180.00   0.0  0
 8WX  CONST_19  N2   C6   N3   C7     0.00   0.0  0
 8WX  CONST_20  C9   C12  C11  C8     0.00   0.0  0
 8WX  CONST_21  C9   N2   C6   C8     0.00   0.0  0
 8WX  CONST_22  N3   C6   N2   C9   180.00   0.0  0
 8WX  CONST_23  N3   C7   C5   N2     0.00   0.0  0
 8WX  CONST_24  C9   N2   C5   C10    0.00   0.0  0
 8WX  CONST_25  C6   N2   C5   C10  180.00   0.0  0
 8WX  CONST_26  N3   C7   C5   C10  180.00   0.0  0
 8WX  CONST_27  O1   C8   C11  C12  180.00   0.0  0
 8WX  CONST_28  N2   C5   C7   C13  180.00   0.0  0
 8WX  CONST_29  C6   N3   C7   C13  180.00   0.0  0
 8WX  CONST_30  C20  C17  C15  C14  180.00   0.0  0
 8WX  CONST_31  C19  C16  C15  C14  180.00   0.0  0
 8WX  CONST_32  O1   C8   C6   N2   180.00   0.0  0
 8WX  CONST_33  O1   C8   C6   N3     0.00   0.0  0
 8WX  CONST_34  H17  C9   C12  C11  180.00   0.0  0
 8WX  CONST_35  H15  C20  C17  C15  180.00   0.0  0
 8WX  CONST_36  H14  C19  C16  C15  180.00   0.0  0
 8WX  CONST_37  H11  C17  C15  C16  180.00   0.0  0
 8WX  CONST_38  H16  C21  C19  C16  180.00   0.0  0
 8WX  CONST_39  H10  C16  C15  C17  180.00   0.0  0
 8WX  CONST_40  H3   C11  C8   C6   180.00   0.0  0
 8WX  CONST_41  H4   C12  C11  C8   180.00   0.0  0
 8WX  Var_01    C6   C8   O1   C14  178.94  30.0  2
 8WX  Var_02    O1   C14  C15  C16   82.32  30.0  2
 8WX  Var_03    N2   C5   C10  C18   72.48  30.0  3
 8WX  Var_04    H5   C13  C7   C5   116.06  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
 8WX  plan-1  C14  0.020
 8WX  plan-1  C15  0.020
 8WX  plan-1  C16  0.020
 8WX  plan-1  C17  0.020
 8WX  plan-1  C19  0.020
 8WX  plan-1  C20  0.020
 8WX  plan-1  C21  0.020
 8WX  plan-1  H10  0.020
 8WX  plan-1  H11  0.020
 8WX  plan-1  H14  0.020
 8WX  plan-1  H15  0.020
 8WX  plan-1  H16  0.020
 8WX  plan-2  C10  0.020
 8WX  plan-2  C11  0.020
 8WX  plan-2  C12  0.020
 8WX  plan-2  C13  0.020
 8WX  plan-2  C5   0.020
 8WX  plan-2  C6   0.020
 8WX  plan-2  C7   0.020
 8WX  plan-2  C8   0.020
 8WX  plan-2  C9   0.020
 8WX  plan-2  N2   0.020
 8WX  plan-2  N3   0.020
 8WX  plan-2  O1   0.020
 8WX  plan-2  H3   0.020
 8WX  plan-2  H4   0.020
 8WX  plan-2  H17  0.020

