# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 09:43:08 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 2-chloro-5-{[(2E)-2-(nitromethylidene)imidazolidin-1-yl]methyl}pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)\C=C\1NCCN\1Cc2ccc(Cl)nc2
#
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
 N1Y  N1Y  2-chloro-5-{[(2E)-2-(nitromethylidene)imidazolidin-1-yl]methyl}pyridine  ligand  28  17  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N1Y
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
 N1Y  CL   CL  CL     0  -0.102  -4.9373  -0.5368   0.6186
 N1Y  C1   C   CR6    0   0.158  -3.3763  -0.1049  -0.0040
 N1Y  N1   N   N      0  -0.386  -3.2702   1.0803  -0.5481
 N1Y  C2   C   CR16   0  -0.094  -2.0817   1.4316  -1.0314
 N1Y  C3   C   CR6    0   0.037  -0.9623   0.6146  -0.9934
 N1Y  C4   C   CH2    0  -0.431   0.3551   1.0949  -1.5454
 N1Y  N2   N   NT     0  -0.501   1.3487   1.3061  -0.5209
 N1Y  C5   C   CR16   0  -0.169  -1.1101  -0.6410  -0.4073
 N1Y  C6   C   CR16   0  -0.258  -2.3374  -1.0193   0.1022
 N1Y  C7   C   C      0   0.665   2.2411   0.4008  -0.0701
 N1Y  C8   C   C1     0  -0.283   2.5001  -0.8075  -0.7194
 N1Y  N3   N   NH1    0  -0.661   2.8009   0.8587   1.0530
 N1Y  C9   C   CH2    0  -0.294   2.4393   2.2437   1.2954
 N1Y  C10  C   CH2    0  -0.306   1.1736   2.3725   0.4556
 N1Y  N4   N   N      1   0.395   3.4586  -1.6914  -0.3036
 N1Y  O1   O   O      0  -0.502   4.1378  -1.4624   0.7040
 N1Y  O2   O   O     -1  -0.489   3.6244  -2.7217  -0.9551
 N1Y  H1   H   HCR6   0   0.277  -2.0219   2.4194  -1.4759
 N1Y  H2   H   HCH2   0   0.296   0.7423   0.4010  -2.2912
 N1Y  H3   H   HCH2   0   0.296   0.2088   2.0426  -2.0668
 N1Y  H4   H   HCR6   0   0.285  -0.2768  -1.3302  -0.3482
 N1Y  H5   H   HCR6   0   0.297  -2.4839  -1.9868   0.5604
 N1Y  H6   H   H      0   0.286   1.9727  -1.0909  -1.6134
 N1Y  H8   H   HCH2   0   0.272   2.2616   2.4279   2.3524
 N1Y  H9   H   HCH2   0   0.275   1.0877   3.3393  -0.0385
 N1Y  H7   H   HNH1   0   0.419   3.6389   0.4327   1.4133
 N1Y  H10  H   HCH2   0   0.262   3.2269   2.9174   0.9494
 N1Y  H11  H   HCH2   0   0.259   0.2723   2.2079   1.0545

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
 N1Y  CL   C1   single    1.735  0.020  1.735
 N1Y  C6   C1   aromatic  1.388  0.020  1.388
 N1Y  C6   C5   aromatic  1.382  0.020  1.382
 N1Y  C1   N1   aromatic  1.308  0.020  1.308
 N1Y  C5   C3   aromatic  1.394  0.020  1.394
 N1Y  N1   C2   aromatic  1.330  0.020  1.330
 N1Y  C2   C3   aromatic  1.386  0.020  1.386
 N1Y  C3   C4   single    1.507  0.020  1.507
 N1Y  C4   N2   single    1.443  0.020  1.443
 N1Y  N2   C7   single    1.349  0.020  1.349
 N1Y  N2   C10  single    1.457  0.020  1.457
 N1Y  O2   N4   single    1.230  0.020  1.230
 N1Y  C8   C7   double    1.396  0.020  1.396
 N1Y  C8   N4   single    1.369  0.020  1.369
 N1Y  C7   N3   single    1.336  0.020  1.336
 N1Y  N4   O1   double    1.237  0.020  1.237
 N1Y  C10  C9   single    1.524  0.020  1.524
 N1Y  N3   C9   single    1.452  0.020  1.452
 N1Y  C2   H1   single    0.930  0.020  1.080
 N1Y  C4   H2   single    0.970  0.020  1.090
 N1Y  C4   H3   single    0.970  0.020  1.090
 N1Y  C5   H4   single    0.930  0.020  1.080
 N1Y  C6   H5   single    0.930  0.020  1.080
 N1Y  C8   H6   single    0.930  0.020  1.080
 N1Y  C9   H8   single    0.970  0.020  1.090
 N1Y  C10  H9   single    0.970  0.020  1.090
 N1Y  N3   H7   single    0.890  0.020  1.040
 N1Y  C9   H10  single    0.970  0.020  1.090
 N1Y  C10  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
 N1Y  C6   C1   N1   124.60  3.000
 N1Y  N1   C1   CL   116.59  3.000
 N1Y  C6   C1   CL   118.81  3.000
 N1Y  C2   N1   C1   117.57  3.000
 N1Y  H1   C2   C3   120.22  3.000
 N1Y  H1   C2   N1   116.01  3.000
 N1Y  C3   C2   N1   123.77  3.000
 N1Y  C5   C3   C4   122.28  3.000
 N1Y  C4   C3   C2   120.53  3.000
 N1Y  C5   C3   C2   117.18  3.000
 N1Y  H3   C4   H2   105.88  3.000
 N1Y  H3   C4   N2   107.72  3.000
 N1Y  H2   C4   N2   109.54  3.000
 N1Y  H3   C4   C3   109.55  3.000
 N1Y  H2   C4   C3   111.00  3.000
 N1Y  N2   C4   C3   112.86  3.000
 N1Y  C10  N2   C7   110.30  3.000
 N1Y  C10  N2   C4   120.03  3.000
 N1Y  C7   N2   C4   126.49  3.000
 N1Y  H4   C5   C6   119.28  3.000
 N1Y  H4   C5   C3   120.98  3.000
 N1Y  C6   C5   C3   119.74  3.000
 N1Y  H5   C6   C5   121.47  3.000
 N1Y  H5   C6   C1   121.39  3.000
 N1Y  C5   C6   C1   117.14  3.000
 N1Y  N3   C7   C8   127.59  3.000
 N1Y  N3   C7   N2   109.16  3.000
 N1Y  C8   C7   N2   123.25  3.000
 N1Y  H6   C8   N4   115.19  3.000
 N1Y  H6   C8   C7   121.57  3.000
 N1Y  N4   C8   C7   123.21  3.000
 N1Y  H7   N3   C9   123.45  3.000
 N1Y  H7   N3   C7   120.31  3.000
 N1Y  C9   N3   C7   111.29  3.000
 N1Y  H10  C9   H8   108.73  3.000
 N1Y  H10  C9   C10  111.84  3.000
 N1Y  H8   C9   C10  112.68  3.000
 N1Y  H10  C9   N3   110.84  3.000
 N1Y  H8   C9   N3   111.38  3.000
 N1Y  C10  C9   N3   101.27  3.000
 N1Y  H11  C10  H9   108.46  3.000
 N1Y  H11  C10  C9   111.69  3.000
 N1Y  H9   C10  C9   112.98  3.000
 N1Y  H11  C10  N2   110.84  3.000
 N1Y  H9   C10  N2   110.81  3.000
 N1Y  C9   C10  N2   101.99  3.000
 N1Y  O2   N4   O1   120.83  3.000
 N1Y  O1   N4   C8   120.84  3.000
 N1Y  O2   N4   C8   118.32  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
 N1Y  CONST_01  C3   C5   C6   C1     0.00   0.0  0
 N1Y  CONST_02  C3   C2   N1   C1     0.00   0.0  0
 N1Y  CONST_03  C5   C6   C1   N1     0.00   0.0  0
 N1Y  CONST_04  C5   C3   C2   N1     0.00   0.0  0
 N1Y  CONST_05  C6   C1   N1   C2     0.00   0.0  0
 N1Y  CONST_06  C6   C5   C3   C2     0.00   0.0  0
 N1Y  CONST_07  C9   N3   C7   N2     0.00   0.0  0
 N1Y  CONST_11  C10  N2   C7   N3     0.00   0.0  0
 N1Y  CONST_12  C5   C6   C1   CL   180.00   0.0  0
 N1Y  CONST_13  C2   N1   C1   CL   180.00   0.0  0
 N1Y  CONST_14  C4   C3   C2   N1   180.00   0.0  0
 N1Y  CONST_15  C6   C5   C3   C4   180.00   0.0  0
 N1Y  CONST_16  N3   C7   N2   C4   180.00   0.0  0
 N1Y  CONST_17  C9   C10  N2   C4   180.00   0.0  0
 N1Y  CONST_18  C10  N2   C7   C8   180.00   0.0  0
 N1Y  CONST_19  C9   N3   C7   C8   180.00   0.0  0
 N1Y  CONST_20  H4   C5   C6   C1   180.00   0.0  0
 N1Y  CONST_21  H1   C2   N1   C1   180.00   0.0  0
 N1Y  CONST_22  H5   C6   C1   N1   180.00   0.0  0
 N1Y  CONST_23  H7   N3   C7   N2   180.00   0.0  0
 N1Y  CONST_24  C8   C7   N2   C4     0.00   0.0  0
 N1Y  Var_01    N2   C4   C3   C2   111.58  30.0  2
 N1Y  Var_02    C7   N2   C4   C3    90.85  30.0  3
 N1Y  Var_03    H8   C9   C10  N2  -142.40  30.0  1
 N1Y  Var_04    H9   C10  N2   C7   140.49  30.0  1
 N1Y  Var_05    N4   C8   C7   N2   176.21  30.0  2
 N1Y  Var_06    O2   N4   C8   C7  -178.95  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
 N1Y  plan-1  CL   0.020
 N1Y  plan-1  C1   0.020
 N1Y  plan-1  N1   0.020
 N1Y  plan-1  C2   0.020
 N1Y  plan-1  C3   0.020
 N1Y  plan-1  C4   0.020
 N1Y  plan-1  C5   0.020
 N1Y  plan-1  C6   0.020
 N1Y  plan-1  H1   0.020
 N1Y  plan-1  H4   0.020
 N1Y  plan-1  H5   0.020
 N1Y  plan-2  C4   0.020
 N1Y  plan-2  N2   0.020
 N1Y  plan-2  C7   0.020
 N1Y  plan-2  C8   0.020
 N1Y  plan-2  N3   0.020
 N1Y  plan-2  C9   0.020
 N1Y  plan-2  C10  0.020
 N1Y  plan-2  H7   0.020
 N1Y  plan-3  C8   0.020
 N1Y  plan-3  N4   0.020
 N1Y  plan-3  O1   0.020
 N1Y  plan-3  O2   0.020

