# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:01:59 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 1-{4-[(naphthalen-1-yl)methyl]piperazin-1-yl}ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)Cc2cccc3ccccc23
#
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
 T4V  T4V  1-{4-[(naphthalen-1-yl)methyl]piperazin-1-yl}ethan-1-one  ligand  40  20  .  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_T4V
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
 T4V  N1   N  NT    0  -0.414  -0.6967  -0.0328   0.8465
 T4V  C4   C  CH2   0  -0.379   0.3531   0.4786   1.7069
 T4V  C5   C  CR6   0   0.103   1.5938   0.8611   0.9441
 T4V  C6   C  CR16  0  -0.329   2.0138   2.1665   0.9386
 T4V  C7   C  CR16  0  -0.245   3.1764   2.5691   0.2502
 T4V  C8   C  CR16  0  -0.333   3.9206   1.6490  -0.4308
 T4V  C10  C  CR16  0  -0.313   4.3013  -0.6779  -1.1413
 T4V  C13  C  CR16  0  -0.320   1.9925  -1.4849   0.1958
 T4V  C15  C  CH2   0  -0.267  -1.2053   0.9639  -0.0717
 T4V  N    N  NT    0  -0.446  -3.2696  -0.3184  -0.2968
 T4V  C    C  CH3   0  -0.806  -4.9943   0.9661  -1.4623
 T4V  O    O  O     0  -0.511  -5.4378  -0.6567   0.2241
 T4V  C1   C  C     0   0.515  -4.5898  -0.0706  -0.4391
 T4V  C11  C  CR16  0  -0.260   3.9290  -1.9935  -1.1522
 T4V  C12  C  CR16  0  -0.254   2.7620  -2.3983  -0.4738
 T4V  C14  C  CR66  0   0.080   2.3536  -0.1154   0.2343
 T4V  C16  C  CH2   0  -0.310  -2.2047   0.3385  -1.0297
 T4V  C2   C  CH2   0  -0.308  -2.7798  -1.2844   0.6683
 T4V  C3   C  CH2   0  -0.281  -1.7773  -0.6314   1.6034
 T4V  C9   C  CR66  0   0.110   3.5311   0.2885  -0.4518
 T4V  H6   H  HCH2  0   0.230   0.0158   1.3496   2.2921
 T4V  H7   H  HCH2  0   0.252   0.5933  -0.3026   2.4352
 T4V  H8   H  HCR6  0   0.252   1.4390   2.9103   1.4778
 T4V  H9   H  HCR6  0   0.256   3.4730   3.6096   0.2664
 T4V  H10  H  HCR6  0   0.254   4.8188   1.9472  -0.9580
 T4V  H11  H  HCR6  0   0.254   5.1977  -0.3577  -1.6590
 T4V  H14  H  HCR6  0   0.256   1.0855  -1.8101   0.6837
 T4V  H16  H  HCH2  0   0.196  -1.6851   1.8040   0.4610
 T4V  H15  H  HCH2  0   0.250  -0.3815   1.3807  -0.6536
 T4V  H    H  HCH3  0   0.264  -4.5953   1.9513  -1.2187
 T4V  H20  H  HCH3  0   0.265  -4.6444   0.7099  -2.4626
 T4V  H1   H  HCH3  0   0.268  -6.0787   1.0334  -1.4851
 T4V  H12  H  HCR6  0   0.256   4.5259  -2.7249  -1.6814
 T4V  H13  H  HCR6  0   0.255   2.4692  -3.4403  -0.4882
 T4V  H18  H  HCH2  0   0.272  -2.6021   1.1044  -1.6887
 T4V  H17  H  HCH2  0   0.242  -1.6901  -0.3990  -1.6542
 T4V  H3   H  HCH2  0   0.263  -3.6132  -1.6921   1.2330
 T4V  H2   H  HCH2  0   0.238  -2.2950  -2.1097   0.1364
 T4V  H5   H  HCH2  0   0.243  -1.3650  -1.3940   2.2680
 T4V  H4   H  HCH2  0   0.201  -2.2991   0.1073   2.2364

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
 T4V  C1   C    single    1.512  0.020  1.512
 T4V  O    C1   double    1.226  0.020  1.226
 T4V  C1   N    single    1.351  0.020  1.351
 T4V  N    C2   single    1.451  0.020  1.451
 T4V  C3   C2   single    1.519  0.020  1.519
 T4V  N1   C3   single    1.449  0.020  1.449
 T4V  N1   C4   single    1.450  0.020  1.450
 T4V  C4   C5   single    1.506  0.020  1.506
 T4V  C5   C6   aromatic  1.371  0.020  1.371
 T4V  C7   C6   aromatic  1.410  0.020  1.410
 T4V  C8   C7   aromatic  1.365  0.020  1.365
 T4V  C9   C8   aromatic  1.415  0.020  1.415
 T4V  C10  C9   aromatic  1.415  0.020  1.415
 T4V  C11  C10  aromatic  1.367  0.020  1.367
 T4V  C12  C11  aromatic  1.409  0.020  1.409
 T4V  C13  C12  aromatic  1.369  0.020  1.369
 T4V  C14  C13  aromatic  1.417  0.020  1.417
 T4V  C5   C14  aromatic  1.426  0.020  1.426
 T4V  C14  C9   aromatic  1.421  0.020  1.421
 T4V  C15  N1   single    1.447  0.020  1.447
 T4V  C16  C15  single    1.519  0.020  1.519
 T4V  N    C16  single    1.450  0.020  1.450
 T4V  C4   H6   single    0.970  0.020  1.090
 T4V  C4   H7   single    0.970  0.020  1.090
 T4V  C6   H8   single    0.930  0.020  1.080
 T4V  C7   H9   single    0.930  0.020  1.080
 T4V  C8   H10  single    0.930  0.020  1.080
 T4V  C10  H11  single    0.930  0.020  1.080
 T4V  C13  H14  single    0.930  0.020  1.080
 T4V  C15  H16  single    0.970  0.020  1.090
 T4V  C15  H15  single    0.970  0.020  1.090
 T4V  C    H    single    0.970  0.020  1.090
 T4V  C    H20  single    0.970  0.020  1.090
 T4V  C    H1   single    0.970  0.020  1.090
 T4V  C11  H12  single    0.930  0.020  1.080
 T4V  C12  H13  single    0.930  0.020  1.080
 T4V  C16  H18  single    0.970  0.020  1.090
 T4V  C16  H17  single    0.970  0.020  1.090
 T4V  C2   H3   single    0.970  0.020  1.090
 T4V  C2   H2   single    0.970  0.020  1.090
 T4V  C3   H5   single    0.970  0.020  1.090
 T4V  C3   H4   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
 T4V  C3   N1   C15  110.72  3.000
 T4V  C15  N1   C4   112.82  3.000
 T4V  C3   N1   C4   112.06  3.000
 T4V  H7   C4   H6   106.13  3.000
 T4V  H7   C4   C5   109.72  3.000
 T4V  H6   C4   C5   108.68  3.000
 T4V  H7   C4   N1   107.57  3.000
 T4V  H6   C4   N1   111.85  3.000
 T4V  C5   C4   N1   112.67  3.000
 T4V  C14  C5   C6   119.12  3.000
 T4V  C14  C5   C4   121.13  3.000
 T4V  C6   C5   C4   119.75  3.000
 T4V  H8   C6   C7   118.97  3.000
 T4V  H8   C6   C5   119.28  3.000
 T4V  C7   C6   C5   121.76  3.000
 T4V  H9   C7   C8   120.40  3.000
 T4V  H9   C7   C6   119.56  3.000
 T4V  C8   C7   C6   120.04  3.000
 T4V  H10  C8   C9   119.05  3.000
 T4V  H10  C8   C7   120.61  3.000
 T4V  C9   C8   C7   120.34  3.000
 T4V  H11  C10  C9   118.77  3.000
 T4V  H11  C10  C11  120.39  3.000
 T4V  C9   C10  C11  120.85  3.000
 T4V  H14  C13  C14  119.52  3.000
 T4V  H14  C13  C12  119.48  3.000
 T4V  C14  C13  C12  120.99  3.000
 T4V  H15  C15  H16  107.13  3.000
 T4V  H15  C15  C16  108.52  3.000
 T4V  H16  C15  C16  109.36  3.000
 T4V  H15  C15  N1   109.63  3.000
 T4V  H16  C15  N1   111.75  3.000
 T4V  C16  C15  N1   110.35  3.000
 T4V  C2   N    C16  112.95  3.000
 T4V  C16  N    C1   125.55  3.000
 T4V  C2   N    C1   121.48  3.000
 T4V  H1   C    H20  108.39  3.000
 T4V  H1   C    H    108.29  3.000
 T4V  H20  C    H    107.45  3.000
 T4V  H1   C    C1   108.88  3.000
 T4V  H20  C    C1   111.96  3.000
 T4V  H    C    C1   111.74  3.000
 T4V  O    C1   C    120.60  3.000
 T4V  O    C1   N    122.10  3.000
 T4V  C    C1   N    117.30  3.000
 T4V  H12  C11  C12  119.87  3.000
 T4V  H12  C11  C10  120.26  3.000
 T4V  C12  C11  C10  119.87  3.000
 T4V  H13  C12  C11  119.61  3.000
 T4V  H13  C12  C13  119.78  3.000
 T4V  C11  C12  C13  120.61  3.000
 T4V  C9   C14  C13  118.21  3.000
 T4V  C9   C14  C5   119.14  3.000
 T4V  C13  C14  C5   122.65  3.000
 T4V  H17  C16  H18  107.52  3.000
 T4V  H17  C16  N    109.16  3.000
 T4V  H18  C16  N    110.95  3.000
 T4V  H17  C16  C15  109.14  3.000
 T4V  H18  C16  C15  109.46  3.000
 T4V  N    C16  C15  110.54  3.000
 T4V  H2   C2   H3   108.02  3.000
 T4V  H2   C2   C3   109.32  3.000
 T4V  H3   C2   C3   110.35  3.000
 T4V  H2   C2   N    109.16  3.000
 T4V  H3   C2   N    109.68  3.000
 T4V  C3   C2   N    110.26  3.000
 T4V  H4   C3   H5   107.26  3.000
 T4V  H4   C3   C2   109.20  3.000
 T4V  H5   C3   C2   108.88  3.000
 T4V  H4   C3   N1   112.06  3.000
 T4V  H5   C3   N1   108.95  3.000
 T4V  C2   C3   N1   110.39  3.000
 T4V  C14  C9   C10  119.47  3.000
 T4V  C14  C9   C8   119.60  3.000
 T4V  C10  C9   C8   120.92  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
 T4V  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 T4V  CONST_02  C12  C13  C14  C5   180.00   0.0  0
 T4V  CONST_03  C8   C9   C14  C5     0.00   0.0  0
 T4V  CONST_04  C10  C9   C14  C5   180.00   0.0  0
 T4V  CONST_05  C13  C14  C5   C6   180.00   0.0  0
 T4V  CONST_06  C9   C14  C5   C6     0.00   0.0  0
 T4V  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 T4V  CONST_08  C14  C5   C6   C7     0.00   0.0  0
 T4V  CONST_09  C10  C9   C8   C7   180.00   0.0  0
 T4V  CONST_10  C14  C9   C8   C7     0.00   0.0  0
 T4V  CONST_11  C11  C10  C9   C8   180.00   0.0  0
 T4V  CONST_12  C13  C14  C9   C8   180.00   0.0  0
 T4V  CONST_13  C13  C14  C9   C10    0.00   0.0  0
 T4V  CONST_14  C13  C12  C11  C10    0.00   0.0  0
 T4V  CONST_15  C14  C9   C10  C11    0.00   0.0  0
 T4V  CONST_16  C14  C13  C12  C11    0.00   0.0  0
 T4V  CONST_17  C9   C10  C11  C12    0.00   0.0  0
 T4V  CONST_18  C9   C14  C13  C12    0.00   0.0  0
 T4V  CONST_19  C7   C6   C5   C4   180.00   0.0  0
 T4V  CONST_20  C13  C14  C5   C4     0.00   0.0  0
 T4V  CONST_21  C9   C14  C5   C4   180.00   0.0  0
 T4V  CONST_22  H9   C7   C6   C5   180.00   0.0  0
 T4V  CONST_23  H14  C13  C14  C5     0.00   0.0  0
 T4V  CONST_24  H10  C8   C7   C6   180.00   0.0  0
 T4V  CONST_25  H8   C6   C7   C8   180.00   0.0  0
 T4V  CONST_26  H11  C10  C9   C8     0.00   0.0  0
 T4V  CONST_27  H13  C12  C11  C10  180.00   0.0  0
 T4V  CONST_28  H12  C11  C12  C13  180.00   0.0  0
 T4V  CONST_29  C2   N    C1   C    180.00   0.0  0
 T4V  CONST_30  C16  N    C1   C      0.00   0.0  0
 T4V  CONST_31  C2   N    C1   O      0.00   0.0  0
 T4V  CONST_32  C16  N    C1   O    180.00   0.0  0
 T4V  Var_01    N    C2   C3   N1   -56.02  30.0  1
 T4V  Var_02    N    C16  C15  N1    55.56  30.0  1
 T4V  Var_03    C2   C3   N1   C15   59.13  30.0  1
 T4V  Var_04    C2   N    C16  C15  -54.21  30.0  1
 T4V  Var_05    C3   N1   C15  C16  -58.79  30.0  1
 T4V  Var_06    C3   C2   N    C16   54.36  30.0  1
 T4V  Var_07    C6   C5   C4   N1   117.00  30.0  2
 T4V  Var_08    H    C    C1   N    -62.17  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
 T4V  plan-1  C4   0.020
 T4V  plan-1  C5   0.020
 T4V  plan-1  C6   0.020
 T4V  plan-1  C7   0.020
 T4V  plan-1  C8   0.020
 T4V  plan-1  C10  0.020
 T4V  plan-1  C13  0.020
 T4V  plan-1  C11  0.020
 T4V  plan-1  C12  0.020
 T4V  plan-1  C14  0.020
 T4V  plan-1  C9   0.020
 T4V  plan-1  H8   0.020
 T4V  plan-1  H9   0.020
 T4V  plan-1  H10  0.020
 T4V  plan-1  H11  0.020
 T4V  plan-1  H14  0.020
 T4V  plan-1  H12  0.020
 T4V  plan-1  H13  0.020
 T4V  plan-2  N    0.020
 T4V  plan-2  C    0.020
 T4V  plan-2  O    0.020
 T4V  plan-2  C1   0.020
 T4V  plan-2  C16  0.020
 T4V  plan-2  C2   0.020

