# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 08:12:16 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (1S,2S)-N'-(chloroacetyl)-2-phenylcyclopropane-1-carbohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ClCC(=O)NNC(=O)[C@H]1C[C@@H]1c2ccccc2
#
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
 J4Y  J4Y  (1S,2S)-N'-(chloroacetyl)-2-phenylcyclopropane-1-carbohydrazide  ligand  30  17  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_J4Y
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
 J4Y  N1   N   NH1   0  -0.486   2.4350  -0.0543   0.6217
 J4Y  C4   C   CH1   0  -0.354  -2.2833   0.9426   0.5214
 J4Y  C5   C   CH2   0  -0.452  -2.0898   1.1327   1.9852
 J4Y  C6   C   CR6   0   0.229  -3.4196   0.1714  -0.0389
 J4Y  C7   C   CR16  0  -0.323  -3.8645   0.4569  -1.3284
 J4Y  C8   C   CR16  0  -0.240  -4.9224  -0.2451  -1.8908
 J4Y  C10  C   CR16  0  -0.236  -5.1180  -1.5439   0.1148
 J4Y  N    N   NH1   0  -0.515   1.1398  -0.3138   0.9324
 J4Y  C    C   C     0   0.611   0.2227   0.6878   0.9841
 J4Y  O    O   O     0  -0.471   0.5211   1.8578   0.8382
 J4Y  C1   C   C     0   0.554   2.8128   0.1516  -0.6623
 J4Y  C11  C   CR16  0  -0.351  -4.0626  -0.8400   0.6756
 J4Y  C2   C   CH2   0  -0.579   4.3029   0.4064  -0.7924
 J4Y  C3   C   CH1   0  -0.419  -1.1604   0.2195   1.2445
 J4Y  C9   C   CR16  0  -0.273  -5.5541  -1.2498  -1.1714
 J4Y  O1   O   O     0  -0.438   2.0583   0.0891  -1.6045
 J4Y  CL   CL  CL    0  -0.127   4.6444   1.3769  -2.2385
 J4Y  H1   H   HNH1  0   0.424   3.0690   0.1075   1.3897
 J4Y  H2   H   HCH1  0   0.275  -1.9546   1.7676  -0.1009
 J4Y  H3   H   HCH2  0   0.275  -1.6951   2.0834   2.3181
 J4Y  H4   H   HCH2  0   0.273  -2.7945   0.6706   2.6649
 J4Y  H5   H   HCR6  0   0.252  -3.3781   1.2377  -1.9010
 J4Y  H6   H   HCR6  0   0.256  -5.2511  -0.0056  -2.8939
 J4Y  H7   H   HCR6  0   0.256  -5.6033  -2.3235   0.6879
 J4Y  H8   H   HNH1  0   0.420   0.8604  -1.2822   0.9756
 J4Y  H9   H   HCR6  0   0.251  -3.7459  -1.0859   1.6826
 J4Y  H10  H   HCH2  0   0.311   4.7101   0.9246   0.0737
 J4Y  H11  H   HCH2  0   0.331   4.8202  -0.5478  -0.8940
 J4Y  H12  H   HCH1  0   0.291  -1.2948  -0.8470   1.3909
 J4Y  H13  H   HCR6  0   0.255  -6.3788  -1.7987  -1.6071

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
 J4Y  O1   C1   double    1.209  0.020  1.209
 J4Y  C2   CL   single    1.775  0.020  1.775
 J4Y  C2   C1   single    1.517  0.020  1.517
 J4Y  C1   N1   single    1.354  0.020  1.354
 J4Y  N1   N    single    1.357  0.020  1.357
 J4Y  N    C    single    1.359  0.020  1.359
 J4Y  C10  C11  aromatic  1.387  0.020  1.387
 J4Y  C10  C9   aromatic  1.390  0.020  1.390
 J4Y  C    O    double    1.216  0.020  1.216
 J4Y  C    C3   single    1.483  0.020  1.483
 J4Y  C11  C6   aromatic  1.395  0.020  1.395
 J4Y  C3   C4   single    1.519  0.020  1.519
 J4Y  C3   C5   single    1.499  0.020  1.499
 J4Y  C9   C8   aromatic  1.388  0.020  1.388
 J4Y  C6   C4   single    1.483  0.020  1.483
 J4Y  C6   C7   aromatic  1.394  0.020  1.394
 J4Y  C4   C5   single    1.489  0.020  1.489
 J4Y  C8   C7   aromatic  1.389  0.020  1.389
 J4Y  N1   H1   single    0.860  0.020  1.020
 J4Y  C4   H2   single    0.970  0.020  1.090
 J4Y  C5   H3   single    0.970  0.020  1.090
 J4Y  C5   H4   single    0.970  0.020  1.090
 J4Y  C7   H5   single    0.930  0.020  1.080
 J4Y  C8   H6   single    0.930  0.020  1.080
 J4Y  C10  H7   single    0.930  0.020  1.080
 J4Y  N    H8   single    0.860  0.020  1.020
 J4Y  C11  H9   single    0.930  0.020  1.080
 J4Y  C2   H10  single    0.970  0.020  1.090
 J4Y  C2   H11  single    0.970  0.020  1.090
 J4Y  C3   H12  single    0.970  0.020  1.090
 J4Y  C9   H13  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
 J4Y  H1   N1   C1   121.47  3.000
 J4Y  H1   N1   N    117.13  3.000
 J4Y  C1   N1   N    120.83  3.000
 J4Y  H2   C4   C3   114.29  3.000
 J4Y  H2   C4   C6   114.27  3.000
 J4Y  C3   C4   C6   119.91  3.000
 J4Y  H2   C4   C5   115.33  3.000
 J4Y  C6   C4   C5   122.51  3.000
 J4Y  C3   C4   C5    59.77  3.000
 J4Y  H4   C5   H3   114.79  3.000
 J4Y  H4   C5   C3   116.99  3.000
 J4Y  H3   C5   C3   117.47  3.000
 J4Y  H4   C5   C4   118.57  3.000
 J4Y  H3   C5   C4   117.53  3.000
 J4Y  C3   C5   C4    61.11  3.000
 J4Y  C11  C6   C7   118.37  3.000
 J4Y  C7   C6   C4   119.18  3.000
 J4Y  C11  C6   C4   122.45  3.000
 J4Y  H5   C7   C8   119.49  3.000
 J4Y  H5   C7   C6   119.55  3.000
 J4Y  C8   C7   C6   120.96  3.000
 J4Y  H6   C8   C9   120.16  3.000
 J4Y  H6   C8   C7   119.66  3.000
 J4Y  C9   C8   C7   120.18  3.000
 J4Y  H7   C10  C9   120.11  3.000
 J4Y  H7   C10  C11  119.51  3.000
 J4Y  C9   C10  C11  120.37  3.000
 J4Y  H8   N    C    121.26  3.000
 J4Y  H8   N    N1   117.24  3.000
 J4Y  C    N    N1   120.79  3.000
 J4Y  C3   C    O    123.61  3.000
 J4Y  C3   C    N    113.78  3.000
 J4Y  O    C    N    122.60  3.000
 J4Y  O1   C1   C2   123.70  3.000
 J4Y  C2   C1   N1   112.38  3.000
 J4Y  O1   C1   N1   123.86  3.000
 J4Y  H9   C11  C10  118.87  3.000
 J4Y  H9   C11  C6   120.37  3.000
 J4Y  C10  C11  C6   120.76  3.000
 J4Y  H11  C2   H10  108.26  3.000
 J4Y  H11  C2   CL   108.14  3.000
 J4Y  H10  C2   CL   108.43  3.000
 J4Y  H11  C2   C1   109.09  3.000
 J4Y  H10  C2   C1   112.28  3.000
 J4Y  CL   C2   C1   110.53  3.000
 J4Y  H12  C3   C    116.71  3.000
 J4Y  H12  C3   C5   117.10  3.000
 J4Y  C    C3   C5   118.20  3.000
 J4Y  H12  C3   C4   116.15  3.000
 J4Y  C5   C3   C4    59.12  3.000
 J4Y  C    C3   C4   117.10  3.000
 J4Y  H13  C9   C10  120.30  3.000
 J4Y  H13  C9   C8   120.35  3.000
 J4Y  C10  C9   C8   119.35  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
 J4Y  CONST_01  C9   C10  C11  C6     0.00   0.0  0
 J4Y  CONST_02  C9   C8   C7   C6     0.00   0.0  0
 J4Y  CONST_03  C10  C11  C6   C7     0.00   0.0  0
 J4Y  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 J4Y  CONST_05  C11  C10  C9   C8     0.00   0.0  0
 J4Y  CONST_06  C11  C6   C7   C8     0.00   0.0  0
 J4Y  CONST_07  C10  C11  C6   C4   180.00   0.0  0
 J4Y  CONST_08  C8   C7   C6   C4   180.00   0.0  0
 J4Y  CONST_09  H9   C11  C6   C4     0.00   0.0  0
 J4Y  CONST_10  H5   C7   C6   C4     0.00   0.0  0
 J4Y  CONST_11  H7   C10  C11  C6   180.00   0.0  0
 J4Y  CONST_12  H6   C8   C7   C6   180.00   0.0  0
 J4Y  CONST_13  H13  C9   C8   C7   180.00   0.0  0
 J4Y  CONST_14  C3   C    N    N1   180.00   0.0  0
 J4Y  CONST_15  H8   N    C    C3     0.00   0.0  0
 J4Y  CONST_16  O    C    N    N1     0.00   0.0  0
 J4Y  CONST_17  O1   C1   N1   N      0.00   0.0  0
 J4Y  CONST_18  C2   C1   N1   N    180.00   0.0  0
 J4Y  CONST_19  H1   N1   C1   C2     0.00   0.0  0
 J4Y  Var_01    C6   C4   C3   C5  -112.48  30.0  1
 J4Y  Var_02    C11  C6   C4   C5   -26.05  30.0  2
 J4Y  Var_03    C    C3   C5   C4   106.35  30.0  1
 J4Y  Var_04    N    C    C3   C4  -142.70  30.0  1
 J4Y  Var_05    CL   C2   C1   N1  -153.64  30.0  1
 J4Y  Var_06    C1   N1   N    C    -78.26  30.0  1

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
 J4Y  chir_01  C4  C3  C6  C5  both
 J4Y  chir_02  C3  C   C4  C5  both

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
 J4Y  plan-1  C4   0.020
 J4Y  plan-1  C6   0.020
 J4Y  plan-1  C7   0.020
 J4Y  plan-1  C8   0.020
 J4Y  plan-1  C10  0.020
 J4Y  plan-1  C11  0.020
 J4Y  plan-1  C9   0.020
 J4Y  plan-1  H5   0.020
 J4Y  plan-1  H6   0.020
 J4Y  plan-1  H7   0.020
 J4Y  plan-1  H9   0.020
 J4Y  plan-1  H13  0.020
 J4Y  plan-2  N1   0.020
 J4Y  plan-2  N    0.020
 J4Y  plan-2  C1   0.020
 J4Y  plan-2  C2   0.020
 J4Y  plan-2  O1   0.020
 J4Y  plan-2  H1   0.020
 J4Y  plan-3  N1   0.020
 J4Y  plan-3  N    0.020
 J4Y  plan-3  C    0.020
 J4Y  plan-3  O    0.020
 J4Y  plan-3  C3   0.020
 J4Y  plan-3  H8   0.020

