# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:59:21 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: {4-[1-(3-chlorophenyl)cyclopropane-1-carbonyl]piperazin-1-yl}(thiophen-3-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(c1)C2(CC2)C(=O)N3CCN(CC3)C(=O)c4cscc4
#
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
 JYJ  JYJ  {4-[1-(3-chlorophenyl)cyclopropane-1-carbonyl]piperazin-1-yl}(thiophen-3-yl)methanone  ligand  44  25  .  2022-07-25  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_JYJ
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
 JYJ  C1   C   CH2   0  -0.456  -2.8886  -1.6008  -2.6718
 JYJ  C2   C   CT    0  -0.227  -2.1929  -0.9390  -1.5179
 JYJ  C3   C   C     0   0.560  -1.5137  -1.8651  -0.5323
 JYJ  C4   C   CH2   0  -0.321   0.3081  -2.1931   1.0570
 JYJ  C5   C   CH2   0  -0.321   1.7089  -2.5014   0.5506
 JYJ  C6   C   CH2   0  -0.315   1.6999  -0.4621  -0.7483
 JYJ  C10  C   CR15  0  -0.181   4.6735   1.3263   1.4677
 JYJ  C14  C   CR16  0  -0.316  -2.6941   1.5417  -1.3573
 JYJ  C17  C   CR6   0  -0.022  -4.3386   1.0932   0.8069
 JYJ  C18  C   CR16  0  -0.256  -3.6918   0.0255   0.2104
 JYJ  C7   C   CH2   0  -0.310   0.2894  -0.1634  -0.2490
 JYJ  C9   C   CR5   0  -0.005   4.2241   0.3296   0.5526
 JYJ  C11  C   CR15  0  -0.466   5.4769   2.2493   0.8774
 JYJ  C12  C   CR15  0  -0.502   4.7253   0.5180  -0.7037
 JYJ  C13  C   CR6   0   0.146  -2.8575   0.2440  -0.8859
 JYJ  C16  C   CR16  0  -0.229  -4.1862   2.3894   0.3379
 JYJ  C15  C   CR16  0  -0.245  -3.3571   2.6013  -0.7522
 JYJ  N    N   NT    0  -0.453  -0.4074  -1.3913   0.0800
 JYJ  C    C   CH2   0  -0.483  -1.6107  -0.8661  -2.9026
 JYJ  O    O   O     0  -0.482   3.7611  -1.4188   2.0324
 JYJ  N1   N   NT    0  -0.462   2.4183  -1.2775   0.2158
 JYJ  O1   O   O     0  -0.486  -1.9750  -2.9708  -0.2877
 JYJ  S    S   S2    0   0.243   5.7229   1.9012  -0.7833
 JYJ  H1   H   HCH2  0   0.263  -2.8838  -2.6818  -2.7144
 JYJ  H2   H   HCH2  0   0.265  -3.8062  -1.1405  -3.0140
 JYJ  H3   H   HCH2  0   0.276  -0.2315  -3.1162   1.2486
 JYJ  H4   H   HCH2  0   0.257   0.3683  -1.6365   1.9975
 JYJ  H5   H   HCH2  0   0.275   2.2650  -3.0590   1.2989
 JYJ  H6   H   HCH2  0   0.260   1.6455  -3.1186  -0.3504
 JYJ  H7   H   HCH2  0   0.254   1.6472  -0.9943  -1.7026
 JYJ  H8   H   HCH2  0   0.286   2.2135   0.4786  -0.9233
 JYJ  H10  H   HCR6  0   0.260  -2.0437   1.7366  -2.1993
 JYJ  H11  H   HCR6  0   0.274  -3.8452  -0.9771   0.5893
 JYJ  H12  H   HCH2  0   0.258   0.3430   0.4660   0.6447
 JYJ  H13  H   HCH2  0   0.290  -0.2368   0.4029  -1.0106
 JYJ  H14  H   HCR5  0   0.301   5.9382   3.1136   1.3292
 JYJ  H15  H   HCR5  0   0.309   4.5743  -0.0953  -1.5793
 JYJ  H16  H   HCR6  0   0.281  -4.7014   3.2140   0.8109
 JYJ  H17  H   HCR6  0   0.270  -3.2227   3.6057  -1.1310
 JYJ  H18  H   HCH2  0   0.269  -0.7154  -1.4472  -3.0905
 JYJ  H19  H   HCH2  0   0.268  -1.6373   0.0753  -3.4368
 JYJ  CL   CL  CL    0  -0.129  -5.3701   0.7994   2.1702
 JYJ  C8   C   C     0   0.531   3.4355  -0.8502   0.9988
 JYJ  H9   H   HCR5  0   0.272   4.3954   1.3557   2.5113

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
 JYJ  CL   C17  single    1.735  0.020  1.735
 JYJ  S    C12  aromatic  1.707  0.020  1.707
 JYJ  S    C11  aromatic  1.715  0.020  1.715
 JYJ  C17  C16  aromatic  1.387  0.020  1.387
 JYJ  C17  C18  aromatic  1.383  0.020  1.383
 JYJ  C12  C9   aromatic  1.366  0.020  1.366
 JYJ  C16  C15  aromatic  1.386  0.020  1.386
 JYJ  C18  C13  aromatic  1.395  0.020  1.395
 JYJ  C11  C10  aromatic  1.359  0.020  1.359
 JYJ  C4   N    single    1.452  0.020  1.452
 JYJ  C4   C5   single    1.521  0.020  1.521
 JYJ  C9   C10  aromatic  1.426  0.020  1.426
 JYJ  C9   C8   single    1.488  0.020  1.488
 JYJ  N    C7   single    1.450  0.020  1.450
 JYJ  N    C3   single    1.350  0.020  1.350
 JYJ  C7   C6   single    1.526  0.020  1.526
 JYJ  C15  C14  aromatic  1.389  0.020  1.389
 JYJ  C8   N1   single    1.353  0.020  1.353
 JYJ  C8   O    double    1.224  0.020  1.224
 JYJ  C5   N1   single    1.454  0.020  1.454
 JYJ  C13  C14  aromatic  1.390  0.020  1.390
 JYJ  C13  C2   single    1.497  0.020  1.497
 JYJ  O1   C3   double    1.223  0.020  1.223
 JYJ  C3   C2   single    1.513  0.020  1.513
 JYJ  N1   C6   single    1.453  0.020  1.453
 JYJ  C2   C    single    1.504  0.020  1.504
 JYJ  C2   C1   single    1.501  0.020  1.501
 JYJ  C    C1   single    1.492  0.020  1.492
 JYJ  C1   H1   single    0.970  0.020  1.090
 JYJ  C1   H2   single    0.970  0.020  1.090
 JYJ  C4   H3   single    0.970  0.020  1.090
 JYJ  C4   H4   single    0.970  0.020  1.090
 JYJ  C5   H5   single    0.970  0.020  1.090
 JYJ  C5   H6   single    0.970  0.020  1.090
 JYJ  C6   H7   single    0.970  0.020  1.090
 JYJ  C6   H8   single    0.970  0.020  1.090
 JYJ  C10  H9   single    0.930  0.020  1.080
 JYJ  C14  H10  single    0.930  0.020  1.080
 JYJ  C18  H11  single    0.930  0.020  1.080
 JYJ  C7   H12  single    0.970  0.020  1.090
 JYJ  C7   H13  single    0.970  0.020  1.090
 JYJ  C11  H14  single    0.930  0.020  1.080
 JYJ  C12  H15  single    0.930  0.020  1.080
 JYJ  C16  H16  single    0.930  0.020  1.080
 JYJ  C15  H17  single    0.930  0.020  1.080
 JYJ  C    H18  single    0.970  0.020  1.090
 JYJ  C    H19  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
 JYJ  H2   C1   H1   114.60  3.000
 JYJ  H2   C1   C    117.90  3.000
 JYJ  H1   C1   C    118.83  3.000
 JYJ  H2   C1   C2   116.64  3.000
 JYJ  H1   C1   C2   117.95  3.000
 JYJ  C    C1   C2    60.32  3.000
 JYJ  C    C2   C13  121.49  3.000
 JYJ  C    C2   C3   117.11  3.000
 JYJ  C13  C2   C3   114.07  3.000
 JYJ  C    C2   C1    59.54  3.000
 JYJ  C3   C2   C1   116.03  3.000
 JYJ  C13  C2   C1   117.86  3.000
 JYJ  O1   C3   N    122.39  3.000
 JYJ  O1   C3   C2   120.95  3.000
 JYJ  N    C3   C2   116.63  3.000
 JYJ  H4   C4   H3   107.94  3.000
 JYJ  H4   C4   N    108.93  3.000
 JYJ  H3   C4   N    110.06  3.000
 JYJ  H4   C4   C5   109.79  3.000
 JYJ  H3   C4   C5   110.12  3.000
 JYJ  N    C4   C5   109.98  3.000
 JYJ  H6   C5   H5   107.90  3.000
 JYJ  H6   C5   N1   108.27  3.000
 JYJ  H5   C5   N1   109.94  3.000
 JYJ  H6   C5   C4   109.58  3.000
 JYJ  H5   C5   C4   110.25  3.000
 JYJ  N1   C5   C4   110.82  3.000
 JYJ  H8   C6   H7   107.68  3.000
 JYJ  H8   C6   N1   111.06  3.000
 JYJ  H7   C6   N1   109.25  3.000
 JYJ  H8   C6   C7   108.69  3.000
 JYJ  H7   C6   C7   109.64  3.000
 JYJ  N1   C6   C7   110.48  3.000
 JYJ  H9   C10  C11  123.60  3.000
 JYJ  H9   C10  C9   123.91  3.000
 JYJ  C11  C10  C9   112.49  3.000
 JYJ  H10  C14  C15  119.26  3.000
 JYJ  H10  C14  C13  120.18  3.000
 JYJ  C15  C14  C13  120.55  3.000
 JYJ  CL   C17  C16  119.30  3.000
 JYJ  C16  C17  C18  121.61  3.000
 JYJ  CL   C17  C18  119.09  3.000
 JYJ  H11  C18  C13  120.32  3.000
 JYJ  H11  C18  C17  119.83  3.000
 JYJ  C13  C18  C17  119.84  3.000
 JYJ  H13  C7   H12  107.26  3.000
 JYJ  H13  C7   N    111.61  3.000
 JYJ  H12  C7   N    108.98  3.000
 JYJ  H13  C7   C6   108.71  3.000
 JYJ  H12  C7   C6   109.55  3.000
 JYJ  N    C7   C6   110.66  3.000
 JYJ  C12  C9   C8   125.44  3.000
 JYJ  C8   C9   C10  121.94  3.000
 JYJ  C12  C9   C10  112.23  3.000
 JYJ  H14  C11  S    120.46  3.000
 JYJ  H14  C11  C10  127.96  3.000
 JYJ  S    C11  C10  111.57  3.000
 JYJ  H15  C12  S    120.28  3.000
 JYJ  H15  C12  C9   128.05  3.000
 JYJ  S    C12  C9   111.66  3.000
 JYJ  C18  C13  C14  118.88  3.000
 JYJ  C14  C13  C2   122.84  3.000
 JYJ  C18  C13  C2   118.27  3.000
 JYJ  H16  C16  C15  120.84  3.000
 JYJ  H16  C16  C17  120.83  3.000
 JYJ  C15  C16  C17  118.34  3.000
 JYJ  H17  C15  C16  119.45  3.000
 JYJ  H17  C15  C14  119.77  3.000
 JYJ  C16  C15  C14  120.78  3.000
 JYJ  C7   N    C4   112.55  3.000
 JYJ  C7   N    C3   126.02  3.000
 JYJ  C4   N    C3   120.99  3.000
 JYJ  H19  C    H18  113.64  3.000
 JYJ  H19  C    C2   119.14  3.000
 JYJ  H18  C    C2   116.96  3.000
 JYJ  H19  C    C1   118.91  3.000
 JYJ  H18  C    C1   118.05  3.000
 JYJ  C2   C    C1    60.14  3.000
 JYJ  C8   N1   C6   125.35  3.000
 JYJ  C6   N1   C5   112.59  3.000
 JYJ  C8   N1   C5   119.96  3.000
 JYJ  C12  S    C11   92.04  3.000
 JYJ  N1   C8   O    122.83  3.000
 JYJ  O    C8   C9   118.74  3.000
 JYJ  N1   C8   C9   118.39  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
 JYJ  CONST_01  C12  S    C11  C10     0.00   0.0  0
 JYJ  CONST_02  S    C12  C9   C10     0.00   0.0  0
 JYJ  CONST_03  C17  C16  C15  C14     0.00   0.0  0
 JYJ  CONST_04  C17  C18  C13  C14     0.00   0.0  0
 JYJ  CONST_05  C15  C16  C17  C18     0.00   0.0  0
 JYJ  CONST_06  C15  C14  C13  C18     0.00   0.0  0
 JYJ  CONST_07  C11  S    C12  C9      0.00   0.0  0
 JYJ  CONST_08  S    C11  C10  C9      0.00   0.0  0
 JYJ  CONST_09  C12  C9   C10  C11     0.00   0.0  0
 JYJ  CONST_10  C16  C17  C18  C13     0.00   0.0  0
 JYJ  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 JYJ  CONST_12  C17  C18  C13  C2    180.00   0.0  0
 JYJ  CONST_13  C15  C14  C13  C2    180.00   0.0  0
 JYJ  CONST_14  S    C12  C9   C8    180.00   0.0  0
 JYJ  CONST_15  C11  C10  C9   C8    180.00   0.0  0
 JYJ  CONST_16  CL   C17  C18  C13   180.00   0.0  0
 JYJ  CONST_17  CL   C17  C16  C15   180.00   0.0  0
 JYJ  CONST_18  C4   N    C3   C2    180.00   0.0  0
 JYJ  CONST_19  C7   N    C3   C2      0.00   0.0  0
 JYJ  CONST_20  C9   C8   N1   C5    180.00   0.0  0
 JYJ  CONST_22  H11  C18  C13  C2      0.00   0.0  0
 JYJ  CONST_23  H10  C14  C13  C2      0.00   0.0  0
 JYJ  CONST_24  H15  C12  C9   C10   180.00   0.0  0
 JYJ  CONST_25  H16  C16  C15  C14   180.00   0.0  0
 JYJ  CONST_26  H17  C15  C16  C17   180.00   0.0  0
 JYJ  CONST_27  H14  C11  C10  C9    180.00   0.0  0
 JYJ  CONST_28  H9   C10  C9   C12   180.00   0.0  0
 JYJ  CONST_29  O1   C3   N    C4      0.00   0.0  0
 JYJ  CONST_30  O    C8   N1   C5      0.00   0.0  0
 JYJ  CONST_32  O1   C3   N    C7    180.00   0.0  0
 JYJ  Var_01    C18  C13  C2   C1     92.69  30.0  3
 JYJ  Var_02    C13  C2   C    C1   -105.99  30.0  1
 JYJ  Var_03    C6   C7   N    C4     56.37  30.0  1
 JYJ  Var_04    C6   N1   C5   C4    -55.83  30.0  1
 JYJ  Var_05    C7   N    C4   C5    -56.62  30.0  1
 JYJ  Var_06    C7   C6   N1   C5     55.00  30.0  1
 JYJ  Var_07    N1   C5   C4   N      55.25  30.0  1
 JYJ  Var_08    N1   C6   C7   N     -54.27  30.0  1
 JYJ  Var_09    N    C3   C2   C1    148.69  30.0  3
 JYJ  Var_10    N1   C8   C9   C10   140.70  30.0  2
 JYJ  Var_11    H1   C1   C    C2   -107.59  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
 JYJ  chir_01  C2  C3  C  C1  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
 JYJ  plan-1  C10  0.020
 JYJ  plan-1  C9   0.020
 JYJ  plan-1  C11  0.020
 JYJ  plan-1  C12  0.020
 JYJ  plan-1  S    0.020
 JYJ  plan-1  H14  0.020
 JYJ  plan-1  H15  0.020
 JYJ  plan-1  C8   0.020
 JYJ  plan-1  H9   0.020
 JYJ  plan-2  C2   0.020
 JYJ  plan-2  C3   0.020
 JYJ  plan-2  C4   0.020
 JYJ  plan-2  C7   0.020
 JYJ  plan-2  N    0.020
 JYJ  plan-2  O1   0.020
 JYJ  plan-3  C2   0.020
 JYJ  plan-3  C14  0.020
 JYJ  plan-3  C17  0.020
 JYJ  plan-3  C18  0.020
 JYJ  plan-3  C13  0.020
 JYJ  plan-3  C16  0.020
 JYJ  plan-3  C15  0.020
 JYJ  plan-3  H10  0.020
 JYJ  plan-3  H11  0.020
 JYJ  plan-3  H16  0.020
 JYJ  plan-3  H17  0.020
 JYJ  plan-3  CL   0.020
 JYJ  plan-4  C5   0.020
 JYJ  plan-4  C6   0.020
 JYJ  plan-4  C9   0.020
 JYJ  plan-4  O    0.020
 JYJ  plan-4  N1   0.020
 JYJ  plan-4  C8   0.020

