# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 02:44:42 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-(4-bromophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CC(CC(C)(C)N1)NC(=O)C(=O)Nc2ccc(Br)cc2
#
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
 0LY  0LY  N-(4-bromophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide  ligand  47  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0LY
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
 0LY  C2   C   CR6   0  -0.126   5.2297  -0.2787   0.0827
 0LY  C7   C   CR16  0  -0.215   4.6337  -1.3400   0.7487
 0LY  C6   C   CR16  0  -0.339   3.2556  -1.3870   0.8491
 0LY  C5   C   CR6   0   0.388   2.4585  -0.3856   0.2922
 0LY  N8   N   NH1   0  -0.735   1.0787  -0.5194   0.4519
 0LY  C9   C   C     0   0.438   0.0900   0.2409  -0.0431
 0LY  O23  O   O     0  -0.447   0.2099   1.2259  -0.7469
 0LY  C10  C   C     0   0.460  -1.2939  -0.2771   0.3884
 0LY  O22  O   O     0  -0.479  -1.3986  -1.2587   1.1101
 0LY  N11  N   NH1   0  -0.632  -2.2920   0.4506  -0.0926
 0LY  C12  C   CH1   0  -0.065  -3.6964   0.1749   0.1578
 0LY  C17  C   CH2   0  -0.428  -4.4865   1.4696   0.0334
 0LY  C16  C   CT    0   0.059  -5.9926   1.2524   0.2552
 0LY  C21  C   CH3   0  -0.660  -6.7374   2.5058  -0.2040
 0LY  C20  C   CH3   0  -0.645  -6.2896   1.0581   1.7462
 0LY  N15  N   NH1   0  -0.589  -6.5131   0.1400  -0.5481
 0LY  C14  C   CT    0   0.058  -5.7469  -1.1099  -0.6264
 0LY  C19  C   CH3   0  -0.643  -5.9810  -1.9847   0.6082
 0LY  C18  C   CH3   0  -0.658  -6.2811  -1.8714  -1.8387
 0LY  C13  C   CH2   0  -0.402  -4.2437  -0.8546  -0.8263
 0LY  C4   C   CR16  0  -0.305   3.0710   0.6758  -0.3736
 0LY  C3   C   CR16  0  -0.216   4.4541   0.7242  -0.4748
 0LY  BR   BR  BR    0  -0.046   7.1097  -0.2025  -0.0620
 0LY  H1   H   HCR6  0   0.285   5.2248  -2.1316   1.1887
 0LY  H2   H   HCR6  0   0.286   2.7948  -2.2196   1.3661
 0LY  H3   H   HNH1  0   0.425   0.7677  -1.3076   1.0063
 0LY  H4   H   HNH1  0   0.408  -2.0574   1.2217  -0.7014
 0LY  H5   H   HCH1  0   0.247  -3.7672  -0.2091   1.1789
 0LY  H6   H   HCH2  0   0.243  -4.1070   2.2180   0.7355
 0LY  H7   H   HCH2  0   0.227  -4.3303   1.8718  -0.9755
 0LY  H8   H   HCH3  0   0.230  -6.3747   3.3868   0.3271
 0LY  H9   H   HCH3  0   0.226  -6.5936   2.6791  -1.2736
 0LY  H10  H   HCH3  0   0.233  -7.8084   2.4135  -0.0161
 0LY  H11  H   HCH3  0   0.228  -7.3354   0.7851   1.8910
 0LY  H12  H   HCH3  0   0.226  -5.6790   0.2891   2.2168
 0LY  H13  H   HCH3  0   0.226  -6.1018   1.9872   2.2868
 0LY  H14  H   HNH1  0   0.337  -6.6184   0.4847  -1.4961
 0LY  H16  H   HCH3  0   0.224  -5.5652  -2.9805   0.4437
 0LY  H17  H   HCH3  0   0.226  -5.5201  -1.5945   1.5133
 0LY  H18  H   HCH3  0   0.227  -7.0491  -2.0919   0.8000
 0LY  H19  H   HCH3  0   0.226  -6.1631  -1.2890  -2.7561
 0LY  H20  H   HCH3  0   0.229  -5.7455  -2.8118  -1.9732
 0LY  H21  H   HCH3  0   0.232  -7.3413  -2.1019  -1.7182
 0LY  H22  H   HCH2  0   0.222  -4.0735  -0.4793  -1.8420
 0LY  H23  H   HCH2  0   0.237  -3.6867  -1.7917  -0.7402
 0LY  H24  H   HCR6  0   0.293   2.4940   1.4711  -0.8154
 0LY  H25  H   HCR6  0   0.284   4.9099   1.5570  -0.9929

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
 0LY  C19  C14  single    1.531  0.020  1.531
 0LY  C14  C18  single    1.528  0.020  1.528
 0LY  C14  N15  single    1.468  0.020  1.468
 0LY  C14  C13  single    1.538  0.020  1.538
 0LY  N15  C16  single    1.468  0.020  1.468
 0LY  C13  C12  single    1.526  0.020  1.526
 0LY  C16  C20  single    1.533  0.020  1.533
 0LY  C16  C21  single    1.529  0.020  1.529
 0LY  C16  C17  single    1.538  0.020  1.538
 0LY  C12  C17  single    1.522  0.020  1.522
 0LY  C12  N11  single    1.453  0.020  1.453
 0LY  O22  C10  double    1.223  0.020  1.223
 0LY  N11  C10  single    1.326  0.020  1.326
 0LY  C10  C9   single    1.539  0.020  1.539
 0LY  C9   N8   single    1.342  0.020  1.342
 0LY  C9   O23  double    1.217  0.020  1.217
 0LY  N8   C5   single    1.395  0.020  1.395
 0LY  C4   C5   aromatic  1.395  0.020  1.395
 0LY  C4   C3   aromatic  1.388  0.020  1.388
 0LY  C5   C6   aromatic  1.396  0.020  1.396
 0LY  C3   C2   aromatic  1.385  0.020  1.385
 0LY  C6   C7   aromatic  1.383  0.020  1.383
 0LY  C2   C7   aromatic  1.388  0.020  1.388
 0LY  C2   BR   single    1.887  0.020  1.887
 0LY  C7   H1   single    0.930  0.020  1.080
 0LY  C6   H2   single    0.930  0.020  1.080
 0LY  N8   H3   single    0.860  0.020  1.020
 0LY  N11  H4   single    0.860  0.020  1.020
 0LY  C12  H5   single    0.970  0.020  1.090
 0LY  C17  H6   single    0.970  0.020  1.090
 0LY  C17  H7   single    0.970  0.020  1.090
 0LY  C21  H8   single    0.970  0.020  1.090
 0LY  C21  H9   single    0.970  0.020  1.090
 0LY  C21  H10  single    0.970  0.020  1.090
 0LY  C20  H11  single    0.970  0.020  1.090
 0LY  C20  H12  single    0.970  0.020  1.090
 0LY  C20  H13  single    0.970  0.020  1.090
 0LY  N15  H14  single    0.890  0.020  1.040
 0LY  C19  H16  single    0.970  0.020  1.090
 0LY  C19  H17  single    0.970  0.020  1.090
 0LY  C19  H18  single    0.970  0.020  1.090
 0LY  C18  H19  single    0.970  0.020  1.090
 0LY  C18  H20  single    0.970  0.020  1.090
 0LY  C18  H21  single    0.970  0.020  1.090
 0LY  C13  H22  single    0.970  0.020  1.090
 0LY  C13  H23  single    0.970  0.020  1.090
 0LY  C4   H24  single    0.930  0.020  1.080
 0LY  C3   H25  single    0.930  0.020  1.080

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
 0LY  BR   C2   C3   119.86  3.000
 0LY  BR   C2   C7   119.71  3.000
 0LY  C3   C2   C7   120.43  3.000
 0LY  H1   C7   C6   119.36  3.000
 0LY  H1   C7   C2   121.36  3.000
 0LY  C6   C7   C2   119.28  3.000
 0LY  H2   C6   C5   119.93  3.000
 0LY  H2   C6   C7   119.01  3.000
 0LY  C5   C6   C7   121.06  3.000
 0LY  C4   C5   N8   124.19  3.000
 0LY  C4   C5   C6   119.06  3.000
 0LY  N8   C5   C6   116.76  3.000
 0LY  H3   N8   C9   114.62  3.000
 0LY  H3   N8   C5   116.17  3.000
 0LY  C9   N8   C5   129.20  3.000
 0LY  C10  C9   O23  121.55  3.000
 0LY  O23  C9   N8   126.83  3.000
 0LY  C10  C9   N8   111.62  3.000
 0LY  N11  C10  O22  126.18  3.000
 0LY  N11  C10  C9   112.98  3.000
 0LY  O22  C10  C9   120.83  3.000
 0LY  H4   N11  C12  118.24  3.000
 0LY  H4   N11  C10  117.58  3.000
 0LY  C12  N11  C10  124.13  3.000
 0LY  H5   C12  C13  110.01  3.000
 0LY  H5   C12  C17  109.97  3.000
 0LY  C13  C12  C17  109.58  3.000
 0LY  H5   C12  N11  106.87  3.000
 0LY  C17  C12  N11  109.04  3.000
 0LY  C13  C12  N11  111.32  3.000
 0LY  H7   C17  H6   106.86  3.000
 0LY  H7   C17  C16  108.89  3.000
 0LY  H6   C17  C16  110.11  3.000
 0LY  H7   C17  C12  108.24  3.000
 0LY  H6   C17  C12  110.45  3.000
 0LY  C16  C17  C12  112.12  3.000
 0LY  N15  C16  C20  111.57  3.000
 0LY  C20  C16  C21  107.57  3.000
 0LY  N15  C16  C21  106.52  3.000
 0LY  C21  C16  C17  108.54  3.000
 0LY  C20  C16  C17  110.36  3.000
 0LY  N15  C16  C17  112.06  3.000
 0LY  H10  C21  H9   108.12  3.000
 0LY  H10  C21  H8   108.10  3.000
 0LY  H9   C21  H8   107.73  3.000
 0LY  H10  C21  C16  110.92  3.000
 0LY  H9   C21  C16  111.09  3.000
 0LY  H8   C21  C16  110.73  3.000
 0LY  H13  C20  H12  106.90  3.000
 0LY  H13  C20  H11  108.20  3.000
 0LY  H12  C20  H11  107.67  3.000
 0LY  H13  C20  C16  109.92  3.000
 0LY  H12  C20  C16  113.67  3.000
 0LY  H11  C20  C16  110.29  3.000
 0LY  H14  N15  C14  107.08  3.000
 0LY  H14  N15  C16  106.91  3.000
 0LY  C14  N15  C16  119.30  3.000
 0LY  C13  C14  C18  108.74  3.000
 0LY  C13  C14  C19  110.44  3.000
 0LY  C18  C14  C19  107.55  3.000
 0LY  C13  C14  N15  112.07  3.000
 0LY  C18  C14  N15  106.50  3.000
 0LY  C19  C14  N15  111.32  3.000
 0LY  H18  C19  H17  107.69  3.000
 0LY  H18  C19  H16  108.05  3.000
 0LY  H17  C19  H16  106.92  3.000
 0LY  H18  C19  C14  110.36  3.000
 0LY  H17  C19  C14  113.65  3.000
 0LY  H16  C19  C14  109.96  3.000
 0LY  H21  C18  H20  107.97  3.000
 0LY  H21  C18  H19  108.06  3.000
 0LY  H20  C18  H19  107.63  3.000
 0LY  H21  C18  C14  110.93  3.000
 0LY  H20  C18  C14  110.85  3.000
 0LY  H19  C18  C14  111.26  3.000
 0LY  H23  C13  H22  106.70  3.000
 0LY  H23  C13  C14  110.20  3.000
 0LY  H22  C13  C14  109.21  3.000
 0LY  H23  C13  C12  110.16  3.000
 0LY  H22  C13  C12  108.11  3.000
 0LY  C14  C13  C12  112.26  3.000
 0LY  H24  C4   C3   118.57  3.000
 0LY  H24  C4   C5   121.49  3.000
 0LY  C3   C4   C5   119.94  3.000
 0LY  H25  C3   C4   118.80  3.000
 0LY  H25  C3   C2   120.96  3.000
 0LY  C4   C3   C2   120.24  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
 0LY  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 0LY  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 0LY  CONST_03  C4   C5   C6   C7      0.00   0.0  0
 0LY  CONST_04  C4   C3   C2   C7      0.00   0.0  0
 0LY  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 0LY  CONST_06  C3   C2   C7   C6      0.00   0.0  0
 0LY  CONST_07  N8   C5   C6   C7    180.00   0.0  0
 0LY  CONST_08  BR   C2   C7   C6    180.00   0.0  0
 0LY  CONST_09  C3   C4   C5   N8    180.00   0.0  0
 0LY  CONST_10  BR   C2   C3   C4    180.00   0.0  0
 0LY  CONST_11  H24  C4   C3   C2    180.00   0.0  0
 0LY  CONST_12  H2   C6   C7   C2    180.00   0.0  0
 0LY  CONST_13  H25  C3   C2   C7    180.00   0.0  0
 0LY  CONST_14  H1   C7   C6   C5    180.00   0.0  0
 0LY  CONST_15  C9   N8   C5   C6    180.00   0.0  0
 0LY  CONST_16  C4   C5   N8   C9      0.00   0.0  0
 0LY  CONST_17  H3   N8   C5   C6      0.00   0.0  0
 0LY  CONST_18  C10  C9   N8   C5    180.00   0.0  0
 0LY  CONST_19  O23  C9   N8   C5      0.00   0.0  0
 0LY  CONST_20  C12  N11  C10  C9    180.00   0.0  0
 0LY  CONST_21  C12  N11  C10  O22     0.00   0.0  0
 0LY  CONST_22  N11  C10  C9   N8    180.00   0.0  0
 0LY  CONST_23  N11  C10  C9   O23     0.00   0.0  0
 0LY  CONST_24  H4   N11  C10  C9      0.00   0.0  0
 0LY  Var_01    N15  C14  C13  C12    48.89  30.0  1
 0LY  Var_02    N15  C16  C17  C12   -49.52  30.0  1
 0LY  Var_03    C14  N15  C16  C17    43.90  30.0  1
 0LY  Var_04    C13  C14  N15  C16   -43.60  30.0  1
 0LY  Var_05    H11  C20  C16  C17  -173.18  30.0  3
 0LY  Var_06    H8   C21  C16  C17   -57.06  30.0  3
 0LY  Var_07    H16  C19  C14  N15   168.94  30.0  3
 0LY  Var_08    H19  C18  C14  N15    59.35  30.0  3

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
 0LY  chir_01  C12  C13  C17  N11  positiv

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
 0LY  plan-1  C2   0.020
 0LY  plan-1  C7   0.020
 0LY  plan-1  C6   0.020
 0LY  plan-1  C5   0.020
 0LY  plan-1  N8   0.020
 0LY  plan-1  C4   0.020
 0LY  plan-1  C3   0.020
 0LY  plan-1  BR   0.020
 0LY  plan-1  H1   0.020
 0LY  plan-1  H2   0.020
 0LY  plan-1  H24  0.020
 0LY  plan-1  H25  0.020
 0LY  plan-2  C5   0.020
 0LY  plan-2  N8   0.020
 0LY  plan-2  C9   0.020
 0LY  plan-2  O23  0.020
 0LY  plan-2  C10  0.020
 0LY  plan-2  O22  0.020
 0LY  plan-2  N11  0.020
 0LY  plan-2  C12  0.020
 0LY  plan-2  H3   0.020
 0LY  plan-2  H4   0.020

