# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 11:51:42 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CN2CCNC2=N)cn1
#
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
 N2Y  N2Y  (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine  ligand  25  14  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N2Y
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
 N2Y  N2   N   N     0  -0.723  -3.3502  -1.8933   0.9249
 N2Y  N3   N   NT    0  -0.487  -2.1110  -0.0141   0.2930
 N2Y  C1   C   C     0   0.604  -3.2181  -0.8263   0.2341
 N2Y  N4   N   NH1   0  -0.671  -4.0936  -0.2531  -0.6610
 N2Y  C2   C   CH2   0  -0.293  -3.4251   0.7954  -1.4105
 N2Y  C3   C   CH2   0  -0.282  -2.3502   1.2225  -0.4192
 N2Y  C4   C   CR6   0   0.154   2.8344   0.2875   0.2044
 N2Y  CL1  CL  CL    0  -0.111   4.5076   0.4571  -0.2333
 N2Y  N6   N   N     0  -0.386   2.4220   0.9918   1.2265
 N2Y  C5   C   CR16  0  -0.107   1.1429   0.8781   1.5774
 N2Y  C6   C   CR6   0   0.013   0.2364   0.0559   0.9271
 N2Y  C7   C   CR16  0  -0.163   0.7074  -0.6745  -0.1610
 N2Y  C8   C   CR16  0  -0.262   2.0318  -0.5659  -0.5400
 N2Y  H1   H   H     0   0.322  -4.2286  -2.3489   0.7090
 N2Y  H3   H   HCH2  0   0.237  -2.9779   0.4188  -2.3360
 N2Y  H4   H   HCH2  0   0.234  -2.7157   2.0079   0.2546
 N2Y  H5   H   HCR6  0   0.272   0.8260   1.4787   2.4235
 N2Y  H6   H   HCR6  0   0.278   0.0395  -1.3232  -0.7136
 N2Y  H7   H   HCR6  0   0.293   2.4276  -1.1195  -1.3792
 N2Y  H8   H   HCH2  0   0.248  -1.4007   0.7423   2.1173
 N2Y  H9   H   HCH2  0   0.281  -1.3354  -1.0022   1.9121
 N2Y  H2   H   HNH1  0   0.390  -4.7157  -0.8711  -1.1583
 N2Y  H10  H   HCH2  0   0.248  -4.1040   1.6086  -1.6627
 N2Y  H11  H   HCH2  0   0.252  -1.4492   1.5899  -0.9104
 N2Y  C9   C   CH2   0  -0.342  -1.1906  -0.0538   1.3917

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
 N2Y  C8   C7   aromatic  1.382  0.020  1.382
 N2Y  C8   C4   aromatic  1.388  0.020  1.388
 N2Y  C3   C2   single    1.523  0.020  1.523
 N2Y  C3   N3   single    1.447  0.020  1.447
 N2Y  C7   C6   aromatic  1.393  0.020  1.393
 N2Y  CL1  C4   single    1.738  0.020  1.738
 N2Y  C4   N6   aromatic  1.308  0.020  1.308
 N2Y  C2   N4   single    1.452  0.020  1.452
 N2Y  C6   C9   single    1.505  0.020  1.505
 N2Y  C6   C5   aromatic  1.386  0.020  1.386
 N2Y  C9   N3   single    1.434  0.020  1.434
 N2Y  N3   C1   single    1.374  0.020  1.374
 N2Y  N6   C5   aromatic  1.331  0.020  1.331
 N2Y  N4   C1   single    1.377  0.020  1.377
 N2Y  C1   N2   double    1.278  0.020  1.278
 N2Y  N2   H1   single    0.890  0.020  1.040
 N2Y  C2   H3   single    0.970  0.020  1.090
 N2Y  C3   H4   single    0.970  0.020  1.090
 N2Y  C5   H5   single    0.930  0.020  1.080
 N2Y  C7   H6   single    0.930  0.020  1.080
 N2Y  C8   H7   single    0.930  0.020  1.080
 N2Y  C9   H8   single    0.970  0.020  1.090
 N2Y  C9   H9   single    0.970  0.020  1.090
 N2Y  N4   H2   single    0.890  0.020  1.040
 N2Y  C2   H10  single    0.970  0.020  1.090
 N2Y  C3   H11  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
 N2Y  H1   N2  C1   110.48  3.000
 N2Y  C9   N3  C3   120.46  3.000
 N2Y  C9   N3  C1   122.25  3.000
 N2Y  C3   N3  C1   110.53  3.000
 N2Y  N4   C1  N3   107.10  3.000
 N2Y  N4   C1  N2   129.29  3.000
 N2Y  N3   C1  N2   123.60  3.000
 N2Y  H2   N4  C2   118.18  3.000
 N2Y  H2   N4  C1   117.25  3.000
 N2Y  C2   N4  C1   110.08  3.000
 N2Y  H10  C2  H3   108.41  3.000
 N2Y  H10  C2  C3   112.41  3.000
 N2Y  H3   C2  C3   111.00  3.000
 N2Y  H10  C2  N4   111.83  3.000
 N2Y  H3   C2  N4   112.09  3.000
 N2Y  C3   C2  N4   101.04  3.000
 N2Y  H11  C3  H4   108.10  3.000
 N2Y  H11  C3  C2   112.62  3.000
 N2Y  H4   C3  C2   111.42  3.000
 N2Y  H11  C3  N3   111.91  3.000
 N2Y  H4   C3  N3   111.38  3.000
 N2Y  C2   C3  N3   101.38  3.000
 N2Y  C8   C4  N6   124.60  3.000
 N2Y  N6   C4  CL1  116.60  3.000
 N2Y  C8   C4  CL1  118.79  3.000
 N2Y  C5   N6  C4   117.57  3.000
 N2Y  H5   C5  C6   120.22  3.000
 N2Y  H5   C5  N6   116.03  3.000
 N2Y  C6   C5  N6   123.74  3.000
 N2Y  C9   C6  C7   121.59  3.000
 N2Y  C9   C6  C5   121.24  3.000
 N2Y  C7   C6  C5   117.17  3.000
 N2Y  H6   C7  C8   119.89  3.000
 N2Y  H6   C7  C6   120.29  3.000
 N2Y  C8   C7  C6   119.82  3.000
 N2Y  H7   C8  C7   121.59  3.000
 N2Y  H7   C8  C4   121.31  3.000
 N2Y  C7   C8  C4   117.09  3.000
 N2Y  H9   C9  H8   106.84  3.000
 N2Y  H9   C9  C6   109.65  3.000
 N2Y  H8   C9  C6   109.44  3.000
 N2Y  H9   C9  N3   107.71  3.000
 N2Y  H8   C9  N3   111.33  3.000
 N2Y  C6   C9  N3   111.72  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
 N2Y  CONST_01  C6  C7  C8  C4     0.00   0.0  0
 N2Y  CONST_02  C6  C5  N6  C4     0.00   0.0  0
 N2Y  CONST_03  C7  C8  C4  N6     0.00   0.0  0
 N2Y  CONST_04  C7  C6  C5  N6     0.00   0.0  0
 N2Y  CONST_05  C8  C7  C6  C5     0.00   0.0  0
 N2Y  CONST_06  C8  C4  N6  C5     0.00   0.0  0
 N2Y  CONST_08  C2  N4  C1  N3     0.00   0.0  0
 N2Y  CONST_11  C3  N3  C1  N4     0.00   0.0  0
 N2Y  CONST_12  C7  C8  C4  CL1  180.00   0.0  0
 N2Y  CONST_13  C5  N6  C4  CL1  180.00   0.0  0
 N2Y  CONST_14  C9  C6  C5  N6   180.00   0.0  0
 N2Y  CONST_15  C9  C6  C7  C8   180.00   0.0  0
 N2Y  CONST_16  C3  N3  C1  N2   180.00   0.0  0
 N2Y  CONST_17  C2  N4  C1  N2   180.00   0.0  0
 N2Y  CONST_19  C9  N3  C3  C2   180.00   0.0  0
 N2Y  CONST_20  H6  C7  C8  C4   180.00   0.0  0
 N2Y  CONST_21  H5  C5  N6  C4   180.00   0.0  0
 N2Y  CONST_22  H7  C8  C4  N6   180.00   0.0  0
 N2Y  CONST_25  H1  N2  C1  N3   180.00   0.0  0
 N2Y  Var_01    C7  C6  C9  N3   -44.85  30.0  2
 N2Y  Var_02    C6  C9  N3  C1   139.37  30.0  2
 N2Y  Var_03    H3  C2  C3  N3   -88.99  30.0  1
 N2Y  Var_04    H4  C3  N3  C1    93.49  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
 N2Y  plan-1  C4   0.020
 N2Y  plan-1  CL1  0.020
 N2Y  plan-1  N6   0.020
 N2Y  plan-1  C5   0.020
 N2Y  plan-1  C6   0.020
 N2Y  plan-1  C7   0.020
 N2Y  plan-1  C8   0.020
 N2Y  plan-1  H5   0.020
 N2Y  plan-1  H6   0.020
 N2Y  plan-1  H7   0.020
 N2Y  plan-1  C9   0.020
 N2Y  plan-2  N2   0.020
 N2Y  plan-2  N3   0.020
 N2Y  plan-2  C1   0.020
 N2Y  plan-2  N4   0.020
 N2Y  plan-2  C2   0.020
 N2Y  plan-2  C3   0.020
 N2Y  plan-2  H1   0.020
 N2Y  plan-2  H2   0.020
 N2Y  plan-2  C9   0.020

