# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:03:59 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 1-{4-[(3-chlorophenyl)methyl]piperazin-1-yl}ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)Cc2cccc(Cl)c2
#
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
 T47  T47  1-{4-[(3-chlorophenyl)methyl]piperazin-1-yl}ethan-1-one  ligand  34  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T47
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
 T47  N1   N   NT    0  -0.423  -0.7538  -0.8968  -0.3326
 T47  C4   C   CH2   0  -0.314   0.3958  -1.0463  -1.1943
 T47  C5   C   CR6   0   0.078   1.6951  -0.8616  -0.4505
 T47  C6   C   CR16  0  -0.274   1.8561  -1.3625   0.8391
 T47  C7   C   CR16  0  -0.245   3.0679  -1.2269   1.4982
 T47  C8   C   CR16  0  -0.233   4.1425  -0.5936   0.8867
 T47  C10  C   CR16  0  -0.274   2.7637  -0.2193  -1.0650
 T47  N    N   NT    0  -0.443  -3.2952  -0.0243   0.5553
 T47  C    C   CH3   0  -0.805  -5.6143   0.0141  -0.2239
 T47  O    O   O     0  -0.510  -4.4948   1.8744   0.7564
 T47  C1   C   C     0   0.514  -4.4230   0.7037   0.4007
 T47  C11  C   CH2   0  -0.280  -0.9581   0.4766   0.0854
 T47  C12  C   CH2   0  -0.310  -2.0842   0.5591   1.1010
 T47  C2   C   CH2   0  -0.318  -3.0993  -1.3860   0.0989
 T47  C3   C   CH2   0  -0.273  -1.9642  -1.4442  -0.9112
 T47  C9   C   CR6   0  -0.021   3.9718  -0.0975  -0.3947
 T47  CL1  CL  CL    0  -0.134   5.2957   0.7050  -1.1807
 T47  H6   H   HCH2  0   0.261   0.3769  -2.0593  -1.6087
 T47  H7   H   HCH2  0   0.219   0.3691  -0.3619  -2.0582
 T47  H8   H   HCR6  0   0.253   1.0217  -1.8496   1.3262
 T47  H9   H   HCR6  0   0.265   3.1864  -1.6170   2.5006
 T47  H10  H   HCR6  0   0.277   5.0881  -0.4883   1.4007
 T47  H11  H   HCR6  0   0.272   2.6516   0.1861  -2.0631
 T47  H    H   HCH3  0   0.265  -5.9108  -0.8739   0.3349
 T47  H17  H   HCH3  0   0.268  -6.4530   0.7050  -0.2405
 T47  H1   H   HCH3  0   0.264  -5.4102  -0.2975  -1.2490
 T47  H12  H   HCH2  0   0.248  -0.0438   0.8579   0.5442
 T47  H13  H   HCH2  0   0.204  -1.1907   1.1326  -0.7712
 T47  H14  H   HCH2  0   0.264  -2.2667   1.5926   1.3805
 T47  H15  H   HCH2  0   0.241  -1.7996   0.0092   2.0036
 T47  H2   H   HCH2  0   0.244  -2.8489  -2.0166   0.9578
 T47  H3   H   HCH2  0   0.275  -4.0057  -1.7865  -0.3450
 T47  H4   H   HCH2  0   0.200  -2.2684  -0.9087  -1.8266
 T47  H5   H   HCH2  0   0.247  -1.7904  -2.4868  -1.1861

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
 T47  C1   C    single    1.512  0.020  1.512
 T47  C1   O    double    1.226  0.020  1.226
 T47  N    C1   single    1.351  0.020  1.351
 T47  C2   N    single    1.449  0.020  1.449
 T47  C3   C2   single    1.521  0.020  1.521
 T47  N1   C3   single    1.449  0.020  1.449
 T47  C4   N1   single    1.444  0.020  1.444
 T47  C5   C4   single    1.509  0.020  1.509
 T47  C6   C5   aromatic  1.393  0.020  1.393
 T47  C7   C6   aromatic  1.386  0.020  1.386
 T47  C8   C7   aromatic  1.389  0.020  1.389
 T47  C9   C8   aromatic  1.385  0.020  1.385
 T47  CL1  C9   single    1.736  0.020  1.736
 T47  C9   C10  aromatic  1.387  0.020  1.387
 T47  C10  C5   aromatic  1.390  0.020  1.390
 T47  N1   C11  single    1.450  0.020  1.450
 T47  C11  C12  single    1.519  0.020  1.519
 T47  C12  N    single    1.451  0.020  1.451
 T47  C4   H6   single    0.970  0.020  1.090
 T47  C4   H7   single    0.970  0.020  1.090
 T47  C6   H8   single    0.930  0.020  1.080
 T47  C7   H9   single    0.930  0.020  1.080
 T47  C8   H10  single    0.930  0.020  1.080
 T47  C10  H11  single    0.930  0.020  1.080
 T47  C    H    single    0.970  0.020  1.090
 T47  C    H17  single    0.970  0.020  1.090
 T47  C    H1   single    0.970  0.020  1.090
 T47  C11  H12  single    0.970  0.020  1.090
 T47  C11  H13  single    0.970  0.020  1.090
 T47  C12  H14  single    0.970  0.020  1.090
 T47  C12  H15  single    0.970  0.020  1.090
 T47  C2   H2   single    0.970  0.020  1.090
 T47  C2   H3   single    0.970  0.020  1.090
 T47  C3   H4   single    0.970  0.020  1.090
 T47  C3   H5   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
 T47  C3   N1   C11  110.81  3.000
 T47  C11  N1   C4   112.47  3.000
 T47  C3   N1   C4   112.80  3.000
 T47  H7   C4   H6   106.10  3.000
 T47  H7   C4   C5   109.34  3.000
 T47  H6   C4   C5   108.36  3.000
 T47  H7   C4   N1   112.57  3.000
 T47  H6   C4   N1   107.93  3.000
 T47  C5   C4   N1   112.25  3.000
 T47  C10  C5   C6   119.13  3.000
 T47  C10  C5   C4   120.05  3.000
 T47  C6   C5   C4   120.80  3.000
 T47  H8   C6   C7   120.28  3.000
 T47  H8   C6   C5   119.32  3.000
 T47  C7   C6   C5   120.40  3.000
 T47  H9   C7   C8   119.17  3.000
 T47  H9   C7   C6   120.06  3.000
 T47  C8   C7   C6   120.77  3.000
 T47  H10  C8   C9   120.85  3.000
 T47  H10  C8   C7   120.77  3.000
 T47  C9   C8   C7   118.38  3.000
 T47  H11  C10  C9   120.17  3.000
 T47  H11  C10  C5   120.06  3.000
 T47  C9   C10  C5   119.77  3.000
 T47  C2   N    C12  112.55  3.000
 T47  C12  N    C1   121.54  3.000
 T47  C2   N    C1   125.66  3.000
 T47  H1   C    H17  108.16  3.000
 T47  H1   C    H    107.45  3.000
 T47  H17  C    H    108.40  3.000
 T47  H1   C    C1   111.80  3.000
 T47  H17  C    C1   108.94  3.000
 T47  H    C    C1   111.97  3.000
 T47  O    C1   C    120.64  3.000
 T47  O    C1   N    122.02  3.000
 T47  C    C1   N    117.34  3.000
 T47  H13  C11  H12  107.16  3.000
 T47  H13  C11  C12  109.30  3.000
 T47  H12  C11  C12  108.72  3.000
 T47  H13  C11  N1   111.64  3.000
 T47  H12  C11  N1   109.51  3.000
 T47  C12  C11  N1   110.41  3.000
 T47  H15  C12  H14  108.03  3.000
 T47  H15  C12  C11  109.35  3.000
 T47  H14  C12  C11  110.38  3.000
 T47  H15  C12  N    108.98  3.000
 T47  H14  C12  N    109.83  3.000
 T47  C11  C12  N    110.22  3.000
 T47  H3   C2   H2   107.41  3.000
 T47  H3   C2   C3   109.72  3.000
 T47  H2   C2   C3   109.18  3.000
 T47  H3   C2   N    111.25  3.000
 T47  H2   C2   N    108.96  3.000
 T47  C3   C2   N    110.24  3.000
 T47  H5   C3   H4   107.36  3.000
 T47  H5   C3   C2   108.82  3.000
 T47  H4   C3   C2   109.07  3.000
 T47  H5   C3   N1   109.16  3.000
 T47  H4   C3   N1   112.23  3.000
 T47  C2   C3   N1   110.12  3.000
 T47  CL1  C9   C10  119.08  3.000
 T47  C10  C9   C8   121.55  3.000
 T47  CL1  C9   C8   119.38  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
 T47  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 T47  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 T47  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 T47  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 T47  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 T47  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 T47  CONST_07  C7   C6   C5   C4   180.00   0.0  0
 T47  CONST_08  C9   C10  C5   C4   180.00   0.0  0
 T47  CONST_09  CL1  C9   C10  C5   180.00   0.0  0
 T47  CONST_10  CL1  C9   C8   C7   180.00   0.0  0
 T47  CONST_11  H9   C7   C6   C5   180.00   0.0  0
 T47  CONST_12  H11  C10  C5   C6   180.00   0.0  0
 T47  CONST_13  H10  C8   C7   C6   180.00   0.0  0
 T47  CONST_14  H8   C6   C7   C8   180.00   0.0  0
 T47  CONST_15  C2   N    C1   C      0.00   0.0  0
 T47  CONST_16  C12  N    C1   C    180.00   0.0  0
 T47  CONST_17  C2   N    C1   O    180.00   0.0  0
 T47  CONST_18  C12  N    C1   O      0.00   0.0  0
 T47  Var_01    N    C2   C3   N1    56.46  30.0  1
 T47  Var_02    N    C12  C11  N1   -55.97  30.0  1
 T47  Var_03    C2   C3   N1   C11  -58.77  30.0  1
 T47  Var_04    C2   N    C12  C11   55.22  30.0  1
 T47  Var_05    C3   N1   C11  C12   58.65  30.0  1
 T47  Var_06    C3   C2   N    C12  -55.52  30.0  1
 T47  Var_07    C6   C5   C4   N1    39.10  30.0  2
 T47  Var_08    H    C    C1   N     57.53  30.0  3

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
 T47  plan-1  C4   0.020
 T47  plan-1  C5   0.020
 T47  plan-1  C6   0.020
 T47  plan-1  C7   0.020
 T47  plan-1  C8   0.020
 T47  plan-1  C10  0.020
 T47  plan-1  C9   0.020
 T47  plan-1  CL1  0.020
 T47  plan-1  H8   0.020
 T47  plan-1  H9   0.020
 T47  plan-1  H10  0.020
 T47  plan-1  H11  0.020
 T47  plan-2  N    0.020
 T47  plan-2  C    0.020
 T47  plan-2  O    0.020
 T47  plan-2  C1   0.020
 T47  plan-2  C12  0.020
 T47  plan-2  C2   0.020

