# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:54:43 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-(2-aminoethyl)-2-(3-chloro-4-{[4-(1-methylethyl)benzyl]oxy}phenyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1ccc(COc2ccc(CC(=O)NCCN)cc2Cl)cc1
#
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
 TF3  TF3  N-(2-aminoethyl)-2-(3-chloro-4-{[4-(1-methylethyl)benzyl]oxy}phenyl)acetamide  ligand  50  25  .  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_TF3
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
 TF3  C1    C   CR6   0   0.449  -0.0228  -0.1363  -0.7717
 TF3  C2    C   CR6   0  -0.146  -0.7167   0.9985  -0.3407
 TF3  C3    C   CR16  0  -0.383  -0.7382  -1.1134  -1.4583
 TF3  O1    O   O2    0  -0.450   1.2863  -0.1907  -0.4901
 TF3  C4    C   CR16  0  -0.242  -2.0694   1.1491  -0.5778
 TF3  CL1   CL  CL    0  -0.115   0.1495   2.2365   0.5028
 TF3  C5    C   CR16  0  -0.283  -2.0981  -0.9583  -1.6928
 TF3  C6    C   CH2   0  -0.274   2.0300  -1.3252  -0.9275
 TF3  C7    C   CR6   0   0.111  -2.7829   0.1683  -1.2607
 TF3  C8    C   CR6   0   0.083   3.4456  -1.1230  -0.4858
 TF3  C9    C   CH2   0  -0.677  -4.2589   0.3246  -1.4807
 TF3  C10   C   CR16  0  -0.278   3.9126  -1.6938   0.6911
 TF3  C11   C   CR16  0  -0.271   4.3119  -0.3227  -1.2267
 TF3  C12   C   C     0   0.556  -5.0630  -0.3348  -0.3703
 TF3  C13   C   CR16  0  -0.320   5.2161  -1.4722   1.1168
 TF3  C14   C   CR16  0  -0.300   5.6105  -0.1011  -0.7988
 TF3  N1    N   NH1   0  -0.627  -6.1069   0.3790   0.0760
 TF3  O2    O   O     0  -0.491  -4.7684  -1.4399   0.0607
 TF3  C15   C   CR6   0   0.167   6.0860  -0.6724   0.3827
 TF3  C16   C   CH2   0  -0.295  -7.0488  -0.1069   1.0590
 TF3  C17   C   CH1   0  -0.328   7.4981  -0.4261   0.8579
 TF3  C18   C   CH2   0  -0.284  -8.2007  -0.8869   0.4349
 TF3  C19   C   CH3   0  -0.644   8.5323  -0.8915  -0.1670
 TF3  C20   C   CH3   0  -0.644   7.7098   1.0446   1.2167
 TF3  N2    N   NH2   0  -0.801  -9.1201  -1.3164   1.4756
 TF3  H3    H   HCR6  0   0.291  -0.2463  -2.0056  -1.8205
 TF3  H4    H   HCR6  0   0.272  -2.5711   2.0423  -0.2272
 TF3  H5    H   HCR6  0   0.258  -2.6241  -1.7352  -2.2327
 TF3  H6C1  H   HCH2  0   0.244   1.9700  -1.4143  -2.0168
 TF3  H6C2  H   HCH2  0   0.246   1.6166  -2.2406  -0.4920
 TF3  H9C1  H   HCH2  0   0.275  -4.5213   1.3788  -1.5853
 TF3  H9C2  H   HCH2  0   0.294  -4.5531  -0.1623  -2.4147
 TF3  H10   H   HCR6  0   0.252   3.2564  -2.3222   1.2817
 TF3  H11   H   HCR6  0   0.251   3.9708   0.1288  -2.1511
 TF3  H13   H   HCR6  0   0.249   5.5595  -1.9290   2.0377
 TF3  H14   H   HCR6  0   0.248   6.2607   0.5267  -1.3967
 TF3  H1    H   HNH1  0   0.403  -6.2970   1.2723  -0.3474
 TF3  H161  H   HCH2  0   0.239  -6.5176  -0.7321   1.7784
 TF3  H162  H   HCH2  0   0.247  -7.4426   0.7509   1.6048
 TF3  H17   H   HCH1  0   0.240   7.6440  -1.0164   1.7678
 TF3  H181  H   HCH2  0   0.222  -8.7386  -0.2306  -0.2532
 TF3  H182  H   HCH2  0   0.202  -7.7901  -1.7085  -0.1678
 TF3  H191  H   HCH3  0   0.231   9.5412  -0.7809   0.2338
 TF3  H192  H   HCH3  0   0.231   8.3901  -1.9400  -0.4313
 TF3  H193  H   HCH3  0   0.219   8.4809  -0.3036  -1.0858
 TF3  H201  H   HCH3  0   0.221   7.5887   1.6860   0.3418
 TF3  H202  H   HCH3  0   0.231   7.0018   1.3771   1.9766
 TF3  H203  H   HCH3  0   0.230   8.7174   1.2030   1.6048
 TF3  H2N1  H   HNH2  0   0.352  -9.9419  -1.7272   1.0528
 TF3  H2N2  H   HNH2  0   0.342  -8.6940  -2.0570   2.0193

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
 TF3  C1   C2    aromatic  1.398  0.020  1.398
 TF3  C1   C3    aromatic  1.392  0.020  1.392
 TF3  C1   O1    single    1.340  0.020  1.340
 TF3  C2   C4    aromatic  1.382  0.020  1.382
 TF3  C2   CL1   single    1.730  0.020  1.730
 TF3  C3   C5    aromatic  1.389  0.020  1.389
 TF3  C3   H3    single    0.930  0.020  1.080
 TF3  O1   C6    single    1.425  0.020  1.425
 TF3  C4   C7    aromatic  1.392  0.020  1.392
 TF3  C4   H4    single    0.930  0.020  1.080
 TF3  C5   C7    aromatic  1.387  0.020  1.387
 TF3  C5   H5    single    0.930  0.020  1.080
 TF3  C6   C8    single    1.497  0.020  1.497
 TF3  C6   H6C1  single    0.970  0.020  1.090
 TF3  C6   H6C2  single    0.970  0.020  1.090
 TF3  C7   C9    single    1.500  0.020  1.500
 TF3  C8   C10   aromatic  1.389  0.020  1.389
 TF3  C8   C11   aromatic  1.393  0.020  1.393
 TF3  C9   C12   single    1.521  0.020  1.521
 TF3  C9   H9C1  single    0.970  0.020  1.090
 TF3  C9   H9C2  single    0.970  0.020  1.090
 TF3  C10  C13   aromatic  1.389  0.020  1.389
 TF3  C10  H10   single    0.930  0.020  1.080
 TF3  C11  C14   aromatic  1.385  0.020  1.385
 TF3  C11  H11   single    0.930  0.020  1.080
 TF3  C12  N1    single    1.341  0.020  1.341
 TF3  C12  O2    double    1.222  0.020  1.222
 TF3  C13  C15   aromatic  1.391  0.020  1.391
 TF3  C13  H13   single    0.930  0.020  1.080
 TF3  C14  C15   aromatic  1.396  0.020  1.396
 TF3  C14  H14   single    0.930  0.020  1.080
 TF3  N1   C16   single    1.446  0.020  1.446
 TF3  N1   H1    single    0.860  0.020  1.020
 TF3  C15  C17   single    1.510  0.020  1.510
 TF3  C16  C18   single    1.525  0.020  1.525
 TF3  C16  H161  single    0.970  0.020  1.090
 TF3  C16  H162  single    0.970  0.020  1.090
 TF3  C17  C19   single    1.529  0.020  1.529
 TF3  C17  C20   single    1.529  0.020  1.529
 TF3  C17  H17   single    0.970  0.020  1.090
 TF3  C18  N2    single    1.454  0.020  1.454
 TF3  C18  H181  single    0.970  0.020  1.090
 TF3  C18  H182  single    0.970  0.020  1.090
 TF3  C19  H191  single    0.970  0.020  1.090
 TF3  C19  H192  single    0.970  0.020  1.090
 TF3  C19  H193  single    0.970  0.020  1.090
 TF3  C20  H201  single    0.970  0.020  1.090
 TF3  C20  H202  single    0.970  0.020  1.090
 TF3  C20  H203  single    0.970  0.020  1.090
 TF3  N2   H2N1  single    0.890  0.020  1.040
 TF3  N2   H2N2  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
 TF3  O1    C1   C3    125.25  3.000
 TF3  O1    C1   C2    116.93  3.000
 TF3  C3    C1   C2    117.82  3.000
 TF3  CL1   C2   C4    119.72  3.000
 TF3  CL1   C2   C1    118.85  3.000
 TF3  C4    C2   C1    121.43  3.000
 TF3  H3    C3   C5    118.76  3.000
 TF3  H3    C3   C1    120.70  3.000
 TF3  C5    C3   C1    120.54  3.000
 TF3  C6    O1   C1    118.52  3.000
 TF3  H4    C4   C7    120.17  3.000
 TF3  H4    C4   C2    119.21  3.000
 TF3  C7    C4   C2    120.62  3.000
 TF3  H5    C5   C7    119.89  3.000
 TF3  H5    C5   C3    118.68  3.000
 TF3  C7    C5   C3    121.43  3.000
 TF3  H6C2  C6   H6C1  107.88  3.000
 TF3  H6C2  C6   C8    110.66  3.000
 TF3  H6C1  C6   C8    110.89  3.000
 TF3  H6C2  C6   O1    110.27  3.000
 TF3  H6C1  C6   O1    109.97  3.000
 TF3  C8    C6   O1    107.19  3.000
 TF3  C9    C7   C5    121.63  3.000
 TF3  C9    C7   C4    120.18  3.000
 TF3  C5    C7   C4    118.16  3.000
 TF3  C11   C8   C10   118.54  3.000
 TF3  C11   C8   C6    120.60  3.000
 TF3  C10   C8   C6    120.83  3.000
 TF3  H9C2  C9   H9C1  106.47  3.000
 TF3  H9C2  C9   C12   106.75  3.000
 TF3  H9C1  C9   C12   111.20  3.000
 TF3  H9C2  C9   C7    110.08  3.000
 TF3  H9C1  C9   C7    110.56  3.000
 TF3  C12   C9   C7    111.57  3.000
 TF3  H10   C10  C13   119.58  3.000
 TF3  H10   C10  C8    119.77  3.000
 TF3  C13   C10  C8    120.64  3.000
 TF3  H11   C11  C14   119.47  3.000
 TF3  H11   C11  C8    119.82  3.000
 TF3  C14   C11  C8    120.71  3.000
 TF3  O2    C12  N1    123.47  3.000
 TF3  O2    C12  C9    121.46  3.000
 TF3  N1    C12  C9    115.06  3.000
 TF3  H13   C13  C15   119.51  3.000
 TF3  H13   C13  C10   119.38  3.000
 TF3  C15   C13  C10   121.12  3.000
 TF3  H14   C14  C15   119.99  3.000
 TF3  H14   C14  C11   118.99  3.000
 TF3  C15   C14  C11   121.02  3.000
 TF3  H1    N1   C16   117.47  3.000
 TF3  H1    N1   C12   118.64  3.000
 TF3  C16   N1   C12   123.68  3.000
 TF3  C17   C15  C14   121.20  3.000
 TF3  C17   C15  C13   120.82  3.000
 TF3  C14   C15  C13   117.97  3.000
 TF3  H162  C16  H161  107.25  3.000
 TF3  H162  C16  C18   109.54  3.000
 TF3  H161  C16  C18   110.15  3.000
 TF3  H162  C16  N1    108.14  3.000
 TF3  H161  C16  N1    108.89  3.000
 TF3  C18   C16  N1    112.70  3.000
 TF3  H17   C17  C20   107.78  3.000
 TF3  H17   C17  C19   107.64  3.000
 TF3  C20   C17  C19   110.89  3.000
 TF3  H17   C17  C15   107.36  3.000
 TF3  C20   C17  C15   111.12  3.000
 TF3  C19   C17  C15   111.84  3.000
 TF3  H182  C18  H181  106.72  3.000
 TF3  H182  C18  N2    114.09  3.000
 TF3  H181  C18  N2    108.48  3.000
 TF3  H182  C18  C16   108.96  3.000
 TF3  H181  C18  C16   108.81  3.000
 TF3  N2    C18  C16   109.63  3.000
 TF3  H193  C19  H192  107.91  3.000
 TF3  H193  C19  H191  107.34  3.000
 TF3  H192  C19  H191  107.88  3.000
 TF3  H193  C19  C17   111.62  3.000
 TF3  H192  C19  C17   111.53  3.000
 TF3  H191  C19  C17   110.39  3.000
 TF3  H203  C20  H202  107.90  3.000
 TF3  H203  C20  H201  107.59  3.000
 TF3  H202  C20  H201  107.90  3.000
 TF3  H203  C20  C17   110.55  3.000
 TF3  H202  C20  C17   111.53  3.000
 TF3  H201  C20  C17   111.21  3.000
 TF3  H2N2  N2   H2N1  105.63  3.000
 TF3  H2N2  N2   C18   109.53  3.000
 TF3  H2N1  N2   C18   109.55  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
 TF3  CONST_01  C7    C4   C2   C1      0.00   0.0  0
 TF3  CONST_02  C7    C5   C3   C1      0.00   0.0  0
 TF3  CONST_03  C5    C3   C1   C2      0.00   0.0  0
 TF3  CONST_04  C5    C7   C4   C2      0.00   0.0  0
 TF3  CONST_05  C4    C2   C1   C3      0.00   0.0  0
 TF3  CONST_06  C4    C7   C5   C3      0.00   0.0  0
 TF3  CONST_07  C15   C13  C10  C8      0.00   0.0  0
 TF3  CONST_08  C15   C14  C11  C8      0.00   0.0  0
 TF3  CONST_09  C14   C11  C8   C10     0.00   0.0  0
 TF3  CONST_10  C14   C15  C13  C10     0.00   0.0  0
 TF3  CONST_11  C13   C10  C8   C11     0.00   0.0  0
 TF3  CONST_12  C13   C15  C14  C11     0.00   0.0  0
 TF3  CONST_13  C9    C7   C4   C2    180.00   0.0  0
 TF3  CONST_14  CL1   C2   C1   C3    180.00   0.0  0
 TF3  CONST_15  C9    C7   C5   C3    180.00   0.0  0
 TF3  CONST_16  C4    C2   C1   O1    180.00   0.0  0
 TF3  CONST_17  C5    C3   C1   O1    180.00   0.0  0
 TF3  CONST_18  C7    C4   C2   CL1   180.00   0.0  0
 TF3  CONST_19  C13   C10  C8   C6    180.00   0.0  0
 TF3  CONST_20  C14   C11  C8   C6    180.00   0.0  0
 TF3  CONST_21  C17   C15  C13  C10   180.00   0.0  0
 TF3  CONST_22  C17   C15  C14  C11   180.00   0.0  0
 TF3  CONST_23  H4    C4   C2   C1    180.00   0.0  0
 TF3  CONST_24  H5    C5   C3   C1    180.00   0.0  0
 TF3  CONST_25  H3    C3   C1   C2    180.00   0.0  0
 TF3  CONST_26  H13   C13  C10  C8    180.00   0.0  0
 TF3  CONST_27  H14   C14  C11  C8    180.00   0.0  0
 TF3  CONST_28  H11   C11  C8   C10   180.00   0.0  0
 TF3  CONST_29  H10   C10  C8   C11   180.00   0.0  0
 TF3  CONST_30  C16   N1   C12  C9    180.00   0.0  0
 TF3  CONST_31  C16   N1   C12  O2      0.00   0.0  0
 TF3  CONST_32  H1    N1   C12  C9      0.00   0.0  0
 TF3  Var_01    C8    C6   O1   C1    179.86  30.0  3
 TF3  Var_02    C10   C8   C6   O1     96.37  30.0  2
 TF3  Var_03    C12   C9   C7   C4    -92.38  30.0  2
 TF3  Var_04    C19   C17  C15  C13   121.06  30.0  2
 TF3  Var_05    N1    C12  C9   C7    137.06  30.0  3
 TF3  Var_06    H191  C19  C17  C15  -175.22  30.0  3
 TF3  Var_07    H201  C20  C17  C15   -63.32  30.0  3
 TF3  Var_08    C18   C16  N1   C12   -87.43  30.0  3
 TF3  Var_09    N2    C18  C16  N1   -178.71  30.0  3
 TF3  Var_10    H2N1  N2   C18  C16   172.68  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
 TF3  plan-1  C1   0.020
 TF3  plan-1  C2   0.020
 TF3  plan-1  C3   0.020
 TF3  plan-1  O1   0.020
 TF3  plan-1  C4   0.020
 TF3  plan-1  CL1  0.020
 TF3  plan-1  C5   0.020
 TF3  plan-1  C7   0.020
 TF3  plan-1  C9   0.020
 TF3  plan-1  H3   0.020
 TF3  plan-1  H4   0.020
 TF3  plan-1  H5   0.020
 TF3  plan-2  C6   0.020
 TF3  plan-2  C8   0.020
 TF3  plan-2  C10  0.020
 TF3  plan-2  C11  0.020
 TF3  plan-2  C13  0.020
 TF3  plan-2  C14  0.020
 TF3  plan-2  C15  0.020
 TF3  plan-2  C17  0.020
 TF3  plan-2  H10  0.020
 TF3  plan-2  H11  0.020
 TF3  plan-2  H13  0.020
 TF3  plan-2  H14  0.020
 TF3  plan-3  C9   0.020
 TF3  plan-3  C12  0.020
 TF3  plan-3  N1   0.020
 TF3  plan-3  O2   0.020
 TF3  plan-3  C16  0.020
 TF3  plan-3  H1   0.020

