# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 16:24:34 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 1-{4-[(3-methylphenyl)methyl]piperazin-1-yl}ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)Cc2cccc(C)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
 T2G  T2G  1-{4-[(3-methylphenyl)methyl]piperazin-1-yl}ethan-1-one  ligand  37  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_T2G
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
 T2G  N1   N  NT    0  -0.442  -3.0271  -0.1847   0.4682
 T2G  C4   C  CR16  0  -0.304   2.3033  -0.7344   0.9014
 T2G  C5   C  CR6   0   0.101   2.0587  -0.3413  -0.4121
 T2G  C6   C  CH2   0  -0.316   0.8159  -0.7966  -1.1343
 T2G  C7   C  CH2   0  -0.279  -1.4721  -1.4909  -0.8770
 T2G  C8   C  CH2   0  -0.315  -2.6434  -1.5321   0.0901
 T2G  C10  C  CH2   0  -0.272  -0.7567   0.5893   0.0483
 T2G  C13  C  CR16  0  -0.367   3.0012   0.4464  -1.0632
 T2G  N    N  NT    0  -0.422  -0.3613  -0.7631  -0.2939
 T2G  C1   C  CR6   0   0.116   4.1837   0.8443  -0.4413
 T2G  C11  C  C     0   0.513  -4.2545   0.3054   0.1892
 T2G  C12  C  CH3   0  -0.805  -4.5329   1.7423   0.5703
 T2G  C2   C  CR16  0  -0.317   4.4084   0.4379   0.8712
 T2G  C3   C  CR16  0  -0.227   3.4722  -0.3433   1.5368
 T2G  C9   C  CH2   0  -0.317  -1.9212   0.5696   1.0243
 T2G  H5   H  HCR6  0   0.242   1.5726  -1.3385   1.4244
 T2G  H7   H  HCH2  0   0.212   0.6895  -0.2029  -2.0551
 T2G  H6   H  HCH2  0   0.253   0.9616  -1.8313  -1.4606
 T2G  H9   H  HCH2  0   0.245  -1.1536  -2.5133  -1.0928
 T2G  H8   H  HCH2  0   0.199  -1.8051  -1.0441  -1.8294
 T2G  H11  H  HCH2  0   0.240  -2.3520  -2.0824   0.9903
 T2G  H10  H  HCH2  0   0.265  -3.4881  -2.0455  -0.3602
 T2G  H15  H  HCH2  0   0.250   0.0823   1.1086   0.5145
 T2G  H14  H  HCH2  0   0.201  -1.0473   1.1680  -0.8461
 T2G  H18  H  HCR6  0   0.239   2.8095   0.7622  -2.0837
 T2G  H1   H  HCH3  0   0.248   5.0052   2.7711  -0.9298
 T2G  H2   H  HCH3  0   0.243   6.1970   1.4842  -0.8666
 T2G  H    H  HCH3  0   0.242   5.0976   1.6037  -2.2400
 T2G  H20  H  HCH3  0   0.263  -3.8707   2.4374   0.0527
 T2G  H16  H  HCH3  0   0.268  -5.5579   1.9846   0.3027
 T2G  H17  H  HCH3  0   0.266  -4.4092   1.9097   1.6409
 T2G  H3   H  HCR6  0   0.244   5.3194   0.7356   1.3778
 T2G  H4   H  HCR6  0   0.249   3.6599  -0.6524   2.5574
 T2G  H13  H  HCH2  0   0.274  -2.2196   1.5865   1.2604
 T2G  H12  H  HCH2  0   0.244  -1.6035   0.0971   1.9589
 T2G  C    C  CH3   0  -0.723   5.1732   1.7166  -1.1588
 T2G  O    O  O     0  -0.510  -5.1224  -0.3780  -0.3417

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
 T2G  C1   C    single    1.502  0.020  1.502
 T2G  C2   C1   aromatic  1.392  0.020  1.392
 T2G  C3   C2   aromatic  1.389  0.020  1.389
 T2G  C4   C3   aromatic  1.387  0.020  1.387
 T2G  C5   C4   aromatic  1.393  0.020  1.393
 T2G  C6   C5   single    1.508  0.020  1.508
 T2G  N    C6   single    1.447  0.020  1.447
 T2G  C7   N    single    1.450  0.020  1.450
 T2G  C8   C7   single    1.520  0.020  1.520
 T2G  N1   C8   single    1.451  0.020  1.451
 T2G  N1   C9   single    1.450  0.020  1.450
 T2G  C9   C10  single    1.520  0.020  1.520
 T2G  C10  N    single    1.450  0.020  1.450
 T2G  C11  N1   single    1.351  0.020  1.351
 T2G  C11  O    double    1.226  0.020  1.226
 T2G  C12  C11  single    1.512  0.020  1.512
 T2G  C5   C13  aromatic  1.390  0.020  1.390
 T2G  C13  C1   aromatic  1.394  0.020  1.394
 T2G  C4   H5   single    0.930  0.020  1.080
 T2G  C6   H7   single    0.970  0.020  1.090
 T2G  C6   H6   single    0.970  0.020  1.090
 T2G  C7   H9   single    0.970  0.020  1.090
 T2G  C7   H8   single    0.970  0.020  1.090
 T2G  C8   H11  single    0.970  0.020  1.090
 T2G  C8   H10  single    0.970  0.020  1.090
 T2G  C10  H15  single    0.970  0.020  1.090
 T2G  C10  H14  single    0.970  0.020  1.090
 T2G  C13  H18  single    0.930  0.020  1.080
 T2G  C    H1   single    0.970  0.020  1.090
 T2G  C    H2   single    0.970  0.020  1.090
 T2G  C    H    single    0.970  0.020  1.090
 T2G  C12  H20  single    0.970  0.020  1.090
 T2G  C12  H16  single    0.970  0.020  1.090
 T2G  C12  H17  single    0.970  0.020  1.090
 T2G  C2   H3   single    0.930  0.020  1.080
 T2G  C3   H4   single    0.930  0.020  1.080
 T2G  C9   H13  single    0.970  0.020  1.090
 T2G  C9   H12  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
 T2G  C9   N1   C11  125.71  3.000
 T2G  C11  N1   C8   121.56  3.000
 T2G  C9   N1   C8   112.42  3.000
 T2G  H5   C4   C3   120.32  3.000
 T2G  H5   C4   C5   119.64  3.000
 T2G  C3   C4   C5   120.03  3.000
 T2G  C13  C5   C6   120.37  3.000
 T2G  C13  C5   C4   118.86  3.000
 T2G  C6   C5   C4   120.74  3.000
 T2G  H6   C6   H7   105.97  3.000
 T2G  H6   C6   N    107.66  3.000
 T2G  H7   C6   N    112.29  3.000
 T2G  H6   C6   C5   108.57  3.000
 T2G  H7   C6   C5   109.38  3.000
 T2G  N    C6   C5   112.67  3.000
 T2G  H8   C7   H9   107.25  3.000
 T2G  H8   C7   N    112.02  3.000
 T2G  H9   C7   N    109.01  3.000
 T2G  H8   C7   C8   109.13  3.000
 T2G  H9   C7   C8   108.97  3.000
 T2G  N    C7   C8   110.37  3.000
 T2G  H10  C8   H11  108.08  3.000
 T2G  H10  C8   C7   110.39  3.000
 T2G  H11  C8   C7   109.38  3.000
 T2G  H10  C8   N1   109.95  3.000
 T2G  H11  C8   N1   108.84  3.000
 T2G  C7   C8   N1   110.16  3.000
 T2G  H14  C10  H15  107.40  3.000
 T2G  H14  C10  C9   108.99  3.000
 T2G  H15  C10  C9   108.72  3.000
 T2G  H14  C10  N    111.68  3.000
 T2G  H15  C10  N    109.57  3.000
 T2G  C9   C10  N    110.39  3.000
 T2G  H18  C13  C1   119.10  3.000
 T2G  H18  C13  C5   119.04  3.000
 T2G  C1   C13  C5   121.86  3.000
 T2G  C10  N    C7   110.74  3.000
 T2G  C10  N    C6   112.37  3.000
 T2G  C7   N    C6   112.21  3.000
 T2G  C2   C1   C    120.91  3.000
 T2G  C2   C1   C13  118.31  3.000
 T2G  C    C1   C13  120.77  3.000
 T2G  C12  C11  O    120.57  3.000
 T2G  C12  C11  N1   117.38  3.000
 T2G  O    C11  N1   122.04  3.000
 T2G  H17  C12  H16  108.33  3.000
 T2G  H17  C12  H20  107.42  3.000
 T2G  H16  C12  H20  108.28  3.000
 T2G  H17  C12  C11  111.85  3.000
 T2G  H16  C12  C11  108.87  3.000
 T2G  H20  C12  C11  111.97  3.000
 T2G  H3   C2   C3   119.80  3.000
 T2G  H3   C2   C1   119.74  3.000
 T2G  C3   C2   C1   120.47  3.000
 T2G  H4   C3   C2   119.69  3.000
 T2G  H4   C3   C4   119.83  3.000
 T2G  C2   C3   C4   120.48  3.000
 T2G  H12  C9   H13  107.36  3.000
 T2G  H12  C9   C10  109.37  3.000
 T2G  H13  C9   C10  109.77  3.000
 T2G  H12  C9   N1   108.93  3.000
 T2G  H13  C9   N1   111.16  3.000
 T2G  C10  C9   N1   110.18  3.000
 T2G  H    C    H2   108.01  3.000
 T2G  H    C    H1   107.30  3.000
 T2G  H2   C    H1   107.12  3.000
 T2G  H    C    C1   111.60  3.000
 T2G  H2   C    C1   111.53  3.000
 T2G  H1   C    C1   111.06  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
 T2G  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 T2G  CONST_02  C1   C13  C5   C4      0.00   0.0  0
 T2G  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 T2G  CONST_04  C2   C1   C13  C5      0.00   0.0  0
 T2G  CONST_05  C3   C4   C5   C13     0.00   0.0  0
 T2G  CONST_06  C3   C2   C1   C13     0.00   0.0  0
 T2G  CONST_07  C    C1   C13  C5    180.00   0.0  0
 T2G  CONST_08  C3   C4   C5   C6    180.00   0.0  0
 T2G  CONST_09  C1   C13  C5   C6    180.00   0.0  0
 T2G  CONST_10  C3   C2   C1   C     180.00   0.0  0
 T2G  CONST_11  H3   C2   C3   C4    180.00   0.0  0
 T2G  CONST_12  H18  C13  C5   C4    180.00   0.0  0
 T2G  CONST_13  H4   C3   C4   C5    180.00   0.0  0
 T2G  CONST_14  H5   C4   C5   C13   180.00   0.0  0
 T2G  CONST_15  O    C11  N1   C8      0.00   0.0  0
 T2G  CONST_16  C12  C11  N1   C8    180.00   0.0  0
 T2G  CONST_17  C9   N1   C11  O     180.00   0.0  0
 T2G  CONST_18  C9   N1   C11  C12     0.00   0.0  0
 T2G  Var_01    N    C7   C8   N1     56.31  30.0  1
 T2G  Var_02    N    C10  C9   N1    -56.30  30.0  1
 T2G  Var_03    C9   C10  N    C7     58.46  30.0  1
 T2G  Var_04    C9   N1   C8   C7    -55.67  30.0  1
 T2G  Var_05    C10  N    C7   C8    -58.47  30.0  1
 T2G  Var_06    C10  C9   N1   C8     55.65  30.0  1
 T2G  Var_07    N    C6   C5   C4     41.34  30.0  3
 T2G  Var_08    C7   N    C6   C5   -166.22  30.0  1
 T2G  Var_09    H1   C    C1   C13    93.91  30.0  2
 T2G  Var_10    H20  C12  C11  N1     61.38  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
 T2G  plan-1  C4   0.020
 T2G  plan-1  C5   0.020
 T2G  plan-1  C6   0.020
 T2G  plan-1  C13  0.020
 T2G  plan-1  C1   0.020
 T2G  plan-1  C2   0.020
 T2G  plan-1  C3   0.020
 T2G  plan-1  H5   0.020
 T2G  plan-1  H18  0.020
 T2G  plan-1  H3   0.020
 T2G  plan-1  H4   0.020
 T2G  plan-1  C    0.020
 T2G  plan-2  N1   0.020
 T2G  plan-2  C8   0.020
 T2G  plan-2  C11  0.020
 T2G  plan-2  C12  0.020
 T2G  plan-2  C9   0.020
 T2G  plan-2  O    0.020

