# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 18:25:36 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-amino-4-chloro-N-(1-{[(2E)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(Cl)ccc1C(=O)NC2(CCCCC2)C(=O)NCC=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
 3Y2  3Y2  2-amino-4-chloro-N-(1-{[(2E)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide  ligand  44  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3Y2
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
 3Y2  C1   C   C1    0  -0.019  -3.6558   3.4495   0.9322
 3Y2  C2   C   CH2   0  -0.359  -2.6149   3.0447  -0.0718
 3Y2  C4   C   C     0   0.604  -2.6934   0.6145  -0.3809
 3Y2  C6   C   CT    0  -0.023  -2.0914  -0.7315   0.0616
 3Y2  C7   C   CH2   0  -0.460  -2.6666  -1.0651   1.4528
 3Y2  C8   C   CH2   0  -0.445  -2.2350  -2.4420   1.9519
 3Y2  C9   C   CH2   0  -0.428  -2.5747  -3.5373   0.9492
 3Y2  C10  C   CH2   0  -0.440  -2.0140  -3.2153  -0.4310
 3Y2  C11  C   CH2   0  -0.420  -2.4828  -1.8490  -0.9157
 3Y2  N3   N   NH1   0  -0.631  -2.1343   1.7053   0.1680
 3Y2  N1   N   N     0  -0.544  -3.5923   4.5571   1.5343
 3Y2  O5   O   O     0  -0.484  -3.6612   0.6723  -1.1230
 3Y2  N12  N   NH1   0  -0.682  -0.6468  -0.6222   0.1947
 3Y2  O14  O   O     0  -0.488  -0.2804   0.1305  -1.8929
 3Y2  C15  C   CR6   0  -0.102   1.6236  -0.3577  -0.5500
 3Y2  C16  C   CR6   0   0.325   2.5292   0.5512  -1.1461
 3Y2  C17  C   CR16  0  -0.290   3.8973   0.4085  -0.8579
 3Y2  C18  C   CR6   0  -0.032   4.3372  -0.6105  -0.0425
 3Y2  C19  C   CR16  0  -0.245   3.4661  -1.5309   0.5259
 3Y2  C20  C   CR16  0  -0.300   2.1191  -1.3797   0.2594
 3Y2  N21  N   NH2   0  -0.862   2.1233   1.5877  -1.9271
 3Y2  CL2  CL  CL    0  -0.123   6.0348  -0.7545   0.2701
 3Y2  H1   H   H     0   0.228  -4.4564   2.7204   1.0875
 3Y2  H2   H   HCH2  0   0.269  -3.0426   3.0971  -1.0750
 3Y2  H3   H   HCH2  0   0.269  -1.7780   3.7408  -0.0330
 3Y2  H4   H   HCH2  0   0.255  -2.3835  -0.2931   2.1736
 3Y2  H5   H   HCH2  0   0.254  -3.7568  -1.0363   1.3770
 3Y2  H6   H   HCH2  0   0.216  -1.1604  -2.4571   2.1609
 3Y2  H7   H   HCH2  0   0.246  -2.7228  -2.6377   2.9091
 3Y2  H8   H   HCH2  0   0.233  -2.1936  -4.4983   1.3015
 3Y2  H9   H   HCH2  0   0.215  -3.6629  -3.6398   0.8822
 3Y2  H10  H   HCH2  0   0.217  -0.9200  -3.2557  -0.4048
 3Y2  H11  H   HCH2  0   0.236  -2.3282  -3.9747  -1.1504
 3Y2  H12  H   HCH2  0   0.234  -3.5710  -1.8576  -1.0047
 3Y2  H13  H   HCH2  0   0.249  -2.0935  -1.6395  -1.9120
 3Y2  H14  H   HNH1  0   0.402  -1.3534   1.5990   0.7948
 3Y2  H15  H   H     0   0.347  -4.3841   4.6671   2.1620
 3Y2  H16  H   HNH1  0   0.410  -0.2377  -0.8021   1.0975
 3Y2  H17  H   HCR6  0   0.284   4.6045   1.1032  -1.2930
 3Y2  H18  H   HCR6  0   0.277   3.8244  -2.3407   1.1445
 3Y2  H19  H   HCR6  0   0.263   1.4374  -2.1083   0.6812
 3Y2  H20  H   HNH2  0   0.398   1.2315   1.5043  -2.3852
 3Y2  H21  H   HNH2  0   0.390   2.8297   2.0643  -2.4618
 3Y2  C13  C   C     0   0.559   0.1655  -0.2599  -0.8189

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
 3Y2  N1   C1   double    1.262  0.020  1.262
 3Y2  C1   C2   single    1.502  0.020  1.502
 3Y2  C2   N3   single    1.443  0.020  1.443
 3Y2  N3   C4   single    1.343  0.020  1.343
 3Y2  C4   O5   double    1.221  0.020  1.221
 3Y2  C4   C6   single    1.539  0.020  1.539
 3Y2  C11  C6   single    1.535  0.020  1.535
 3Y2  C11  C10  single    1.524  0.020  1.524
 3Y2  C6   C7   single    1.542  0.020  1.542
 3Y2  C6   N12  single    1.455  0.020  1.455
 3Y2  C7   C8   single    1.527  0.020  1.527
 3Y2  O14  C13  double    1.227  0.020  1.227
 3Y2  C9   C10  single    1.524  0.020  1.524
 3Y2  C9   C8   single    1.523  0.020  1.523
 3Y2  N12  C13  single    1.348  0.020  1.348
 3Y2  C13  C15  single    1.486  0.020  1.486
 3Y2  N21  C16  single    1.360  0.020  1.360
 3Y2  C15  C16  aromatic  1.415  0.020  1.415
 3Y2  C15  C20  aromatic  1.395  0.020  1.395
 3Y2  C16  C17  aromatic  1.405  0.020  1.405
 3Y2  C20  C19  aromatic  1.381  0.020  1.381
 3Y2  C17  C18  aromatic  1.377  0.020  1.377
 3Y2  C19  C18  aromatic  1.389  0.020  1.389
 3Y2  C18  CL2  single    1.732  0.020  1.732
 3Y2  C1   H1   single    0.930  0.020  1.080
 3Y2  C2   H2   single    0.970  0.020  1.090
 3Y2  C2   H3   single    0.970  0.020  1.090
 3Y2  C7   H4   single    0.970  0.020  1.090
 3Y2  C7   H5   single    0.970  0.020  1.090
 3Y2  C8   H6   single    0.970  0.020  1.090
 3Y2  C8   H7   single    0.970  0.020  1.090
 3Y2  C9   H8   single    0.970  0.020  1.090
 3Y2  C9   H9   single    0.970  0.020  1.090
 3Y2  C10  H10  single    0.970  0.020  1.090
 3Y2  C10  H11  single    0.970  0.020  1.090
 3Y2  C11  H12  single    0.970  0.020  1.090
 3Y2  C11  H13  single    0.970  0.020  1.090
 3Y2  N3   H14  single    0.860  0.020  1.020
 3Y2  N1   H15  single    0.890  0.020  1.040
 3Y2  N12  H16  single    0.860  0.020  1.020
 3Y2  C17  H17  single    0.930  0.020  1.080
 3Y2  C19  H18  single    0.930  0.020  1.080
 3Y2  C20  H19  single    0.930  0.020  1.080
 3Y2  N21  H20  single    0.890  0.020  1.040
 3Y2  N21  H21  single    0.890  0.020  1.040

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
 3Y2  H1   C1   N1   123.64  3.000
 3Y2  H1   C1   C2   114.99  3.000
 3Y2  N1   C1   C2   121.37  3.000
 3Y2  H3   C2   H2   107.64  3.000
 3Y2  H3   C2   N3   109.36  3.000
 3Y2  H2   C2   N3   109.12  3.000
 3Y2  H3   C2   C1   109.66  3.000
 3Y2  H2   C2   C1   109.26  3.000
 3Y2  N3   C2   C1   111.71  3.000
 3Y2  O5   C4   N3   122.68  3.000
 3Y2  O5   C4   C6   121.74  3.000
 3Y2  N3   C4   C6   115.46  3.000
 3Y2  N12  C6   C11  111.48  3.000
 3Y2  N12  C6   C7   107.70  3.000
 3Y2  C11  C6   C7   108.76  3.000
 3Y2  N12  C6   C4   110.43  3.000
 3Y2  C7   C6   C4   107.61  3.000
 3Y2  C11  C6   C4   110.72  3.000
 3Y2  H5   C7   H4   106.58  3.000
 3Y2  H5   C7   C8   109.17  3.000
 3Y2  H4   C7   C8   110.36  3.000
 3Y2  H5   C7   C6   107.68  3.000
 3Y2  H4   C7   C6   110.21  3.000
 3Y2  C8   C7   C6   112.62  3.000
 3Y2  H7   C8   H6   105.58  3.000
 3Y2  H7   C8   C9   110.40  3.000
 3Y2  H6   C8   C9   109.55  3.000
 3Y2  H7   C8   C7   108.78  3.000
 3Y2  H6   C8   C7   110.63  3.000
 3Y2  C9   C8   C7   111.73  3.000
 3Y2  H9   C9   H8   106.50  3.000
 3Y2  H9   C9   C10  109.26  3.000
 3Y2  H8   C9   C10  110.46  3.000
 3Y2  H9   C9   C8   109.22  3.000
 3Y2  H8   C9   C8   110.03  3.000
 3Y2  C10  C9   C8   111.23  3.000
 3Y2  H11  C10  H10  106.11  3.000
 3Y2  H11  C10  C11  108.99  3.000
 3Y2  H10  C10  C11  110.37  3.000
 3Y2  H11  C10  C9   110.10  3.000
 3Y2  H10  C10  C9   109.76  3.000
 3Y2  C11  C10  C9   111.37  3.000
 3Y2  H13  C11  H12  106.44  3.000
 3Y2  H13  C11  C10  110.69  3.000
 3Y2  H12  C11  C10  109.00  3.000
 3Y2  H13  C11  C6   110.54  3.000
 3Y2  H12  C11  C6   108.16  3.000
 3Y2  C10  C11  C6   111.82  3.000
 3Y2  H14  N3   C4   119.44  3.000
 3Y2  H14  N3   C2   117.36  3.000
 3Y2  C4   N3   C2   123.19  3.000
 3Y2  H15  N1   C1   110.51  3.000
 3Y2  H16  N12  C13  118.48  3.000
 3Y2  H16  N12  C6   118.16  3.000
 3Y2  C13  N12  C6   123.33  3.000
 3Y2  C20  C15  C16  119.20  3.000
 3Y2  C20  C15  C13  120.12  3.000
 3Y2  C16  C15  C13  120.64  3.000
 3Y2  N21  C16  C17  119.06  3.000
 3Y2  C17  C16  C15  118.13  3.000
 3Y2  N21  C16  C15  122.72  3.000
 3Y2  H17  C17  C18  120.27  3.000
 3Y2  H17  C17  C16  119.23  3.000
 3Y2  C18  C17  C16  120.49  3.000
 3Y2  CL2  C18  C19  119.06  3.000
 3Y2  CL2  C18  C17  118.78  3.000
 3Y2  C19  C18  C17  122.16  3.000
 3Y2  H18  C19  C20  121.06  3.000
 3Y2  H18  C19  C18  121.55  3.000
 3Y2  C20  C19  C18  117.39  3.000
 3Y2  H19  C20  C19  117.70  3.000
 3Y2  H19  C20  C15  119.68  3.000
 3Y2  C19  C20  C15  122.59  3.000
 3Y2  H21  N21  H20  114.82  3.000
 3Y2  H21  N21  C16  117.18  3.000
 3Y2  H20  N21  C16  117.58  3.000
 3Y2  C15  C13  O14  122.41  3.000
 3Y2  C15  C13  N12  115.94  3.000
 3Y2  O14  C13  N12  121.65  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
 3Y2  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 3Y2  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 3Y2  CONST_03  C19  C20  C15  C16     0.00   0.0  0
 3Y2  CONST_04  C19  C18  C17  C16     0.00   0.0  0
 3Y2  CONST_05  C20  C15  C16  C17     0.00   0.0  0
 3Y2  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 3Y2  CONST_07  C17  C16  C15  C13   180.00   0.0  0
 3Y2  CONST_08  C19  C20  C15  C13   180.00   0.0  0
 3Y2  CONST_09  CL2  C18  C17  C16   180.00   0.0  0
 3Y2  CONST_10  N21  C16  C17  C18   180.00   0.0  0
 3Y2  CONST_11  N21  C16  C15  C20   180.00   0.0  0
 3Y2  CONST_12  CL2  C18  C19  C20   180.00   0.0  0
 3Y2  CONST_13  H17  C17  C16  C15   180.00   0.0  0
 3Y2  CONST_14  H18  C19  C20  C15   180.00   0.0  0
 3Y2  CONST_15  H19  C20  C15  C16   180.00   0.0  0
 3Y2  CONST_16  C15  C13  N12  C6    180.00   0.0  0
 3Y2  CONST_18  H21  N21  C16  C15   180.00   0.0  0
 3Y2  CONST_19  C6   C4   N3   C2    180.00   0.0  0
 3Y2  CONST_20  O14  C13  N12  C6      0.00   0.0  0
 3Y2  CONST_21  H14  N3   C4   C6      0.00   0.0  0
 3Y2  CONST_22  H16  N12  C13  C15     0.00   0.0  0
 3Y2  CONST_23  O5   C4   N3   C2      0.00   0.0  0
 3Y2  Var_01    C9   C10  C11  C6     57.52  30.0  1
 3Y2  Var_02    C9   C8   C7   C6    -54.54  30.0  1
 3Y2  Var_03    C10  C9   C8   C7     53.37  30.0  1
 3Y2  Var_04    C11  C10  C9   C8    -54.94  30.0  1
 3Y2  Var_05    C16  C15  C13  N12  -147.42  30.0  2
 3Y2  Var_06    C4   N3   C2   C1     90.08  30.0  3
 3Y2  Var_07    N1   C1   C2   N3    131.53  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
 3Y2  chir_01  C6  C11  C7  N12  negativ

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
 3Y2  plan-1  C15  0.020
 3Y2  plan-1  C16  0.020
 3Y2  plan-1  C17  0.020
 3Y2  plan-1  C18  0.020
 3Y2  plan-1  C19  0.020
 3Y2  plan-1  C20  0.020
 3Y2  plan-1  N21  0.020
 3Y2  plan-1  CL2  0.020
 3Y2  plan-1  H17  0.020
 3Y2  plan-1  H18  0.020
 3Y2  plan-1  H19  0.020
 3Y2  plan-1  C13  0.020
 3Y2  plan-2  C6   0.020
 3Y2  plan-2  N12  0.020
 3Y2  plan-2  O14  0.020
 3Y2  plan-2  C15  0.020
 3Y2  plan-2  H16  0.020
 3Y2  plan-2  C13  0.020
 3Y2  plan-3  C16  0.020
 3Y2  plan-3  N21  0.020
 3Y2  plan-3  H20  0.020
 3Y2  plan-3  H21  0.020
 3Y2  plan-4  C2   0.020
 3Y2  plan-4  C4   0.020
 3Y2  plan-4  C6   0.020
 3Y2  plan-4  N3   0.020
 3Y2  plan-4  O5   0.020
 3Y2  plan-4  H14  0.020
 3Y2  plan-5  C1   0.020
 3Y2  plan-5  C2   0.020
 3Y2  plan-5  N1   0.020
 3Y2  plan-5  H1   0.020
 3Y2  plan-5  H15  0.020

