# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:13:36 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-(4-bromobenzyl)pyrrolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccc(CN2CCCC2)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
 HXY  HXY  1-(4-bromobenzyl)pyrrolidine  ligand  27  13  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HXY
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
 HXY  C    C   CR6   0  -0.126  -1.8045   0.2132  -0.0338
 HXY  N    N   NT    0  -0.424   3.2192   0.3603  -0.0322
 HXY  BR   BR  BR    0  -0.056  -3.6231  -0.0408   0.4172
 HXY  C1   C   CR16  0  -0.215  -0.9144   0.6507   0.9379
 HXY  C2   C   CR16  0  -0.278   0.4175   0.8328   0.5998
 HXY  C3   C   CR6   0   0.097   0.8737   0.5855  -0.6928
 HXY  C4   C   CH2   0  -0.323   2.3164   0.8245  -1.0544
 HXY  C5   C   CH2   0  -0.274   4.6012   0.7540  -0.2390
 HXY  C6   C   CH2   0  -0.464   5.3613  -0.0658   0.8025
 HXY  C7   C   CH2   0  -0.465   4.4867  -1.3227   1.0048
 HXY  C8   C   CH2   0  -0.273   3.2656  -1.0843   0.1126
 HXY  C9   C   CR16  0  -0.311  -0.0382   0.1412  -1.6425
 HXY  C10  C   CR16  0  -0.213  -1.3785  -0.0452  -1.3263
 HXY  H1   H   HCR6  0   0.276  -1.2459   0.8508   1.9482
 HXY  H2   H   HCR6  0   0.257   1.1168   1.1605   1.3585
 HXY  H4   H   HCH2  0   0.255   2.4710   1.9010  -1.1834
 HXY  H4A  H   HCH2  0   0.211   2.5301   0.3647  -2.0350
 HXY  H5   H   HCH2  0   0.191   4.9503   0.4969  -1.2539
 HXY  H5A  H   HCH2  0   0.234   4.7238   1.8320  -0.1156
 HXY  H6   H   HCH2  0   0.234   6.3702  -0.3038   0.4674
 HXY  H6A  H   HCH2  0   0.234   5.4527   0.4919   1.7349
 HXY  H7   H   HCH2  0   0.234   5.0031  -2.2412   0.7277
 HXY  H7A  H   HCH2  0   0.235   4.1912  -1.4248   2.0491
 HXY  H8   H   HCH2  0   0.235   2.3392  -1.4708   0.5413
 HXY  H8A  H   HCH2  0   0.193   3.4045  -1.5759  -0.8657
 HXY  H9   H   HCR6  0   0.260   0.2947  -0.0717  -2.6513
 HXY  H10  H   HCR6  0   0.277  -2.0672  -0.3931  -2.0848

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
 HXY  C    BR   single    1.891  0.020  1.891
 HXY  C    C1   aromatic  1.388  0.020  1.388
 HXY  C    C10  aromatic  1.385  0.020  1.385
 HXY  N    C4   single    1.441  0.020  1.441
 HXY  N    C5   single    1.452  0.020  1.452
 HXY  N    C8   single    1.453  0.020  1.453
 HXY  C1   C2   aromatic  1.386  0.020  1.386
 HXY  C2   C3   aromatic  1.393  0.020  1.393
 HXY  C3   C4   single    1.506  0.020  1.506
 HXY  C3   C9   aromatic  1.390  0.020  1.390
 HXY  C5   C6   single    1.528  0.020  1.528
 HXY  C6   C7   single    1.545  0.020  1.545
 HXY  C7   C8   single    1.531  0.020  1.531
 HXY  C9   C10  aromatic  1.390  0.020  1.390
 HXY  C1   H1   single    0.930  0.020  1.080
 HXY  C2   H2   single    0.930  0.020  1.080
 HXY  C4   H4   single    0.970  0.020  1.090
 HXY  C4   H4A  single    0.970  0.020  1.090
 HXY  C5   H5   single    0.970  0.020  1.090
 HXY  C5   H5A  single    0.970  0.020  1.090
 HXY  C6   H6   single    0.970  0.020  1.090
 HXY  C6   H6A  single    0.970  0.020  1.090
 HXY  C7   H7   single    0.970  0.020  1.090
 HXY  C7   H7A  single    0.970  0.020  1.090
 HXY  C8   H8   single    0.970  0.020  1.090
 HXY  C8   H8A  single    0.970  0.020  1.090
 HXY  C9   H9   single    0.930  0.020  1.080
 HXY  C10  H10  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
 HXY  C10  C    C1   120.97  3.000
 HXY  C10  C    BR   119.56  3.000
 HXY  C1   C    BR   119.47  3.000
 HXY  C8   N    C5   104.69  3.000
 HXY  C8   N    C4   114.28  3.000
 HXY  C5   N    C4   114.08  3.000
 HXY  H1   C1   C2   119.86  3.000
 HXY  H1   C1   C    121.02  3.000
 HXY  C2   C1   C    119.12  3.000
 HXY  H2   C2   C3   119.51  3.000
 HXY  H2   C2   C1   119.30  3.000
 HXY  C3   C2   C1   121.18  3.000
 HXY  C9   C3   C4   121.01  3.000
 HXY  C9   C3   C2   118.43  3.000
 HXY  C4   C3   C2   120.55  3.000
 HXY  H4A  C4   H4   106.11  3.000
 HXY  H4A  C4   C3   109.43  3.000
 HXY  H4   C4   C3   108.63  3.000
 HXY  H4A  C4   N    112.01  3.000
 HXY  H4   C4   N    108.17  3.000
 HXY  C3   C4   N    112.25  3.000
 HXY  H5A  C5   H5   107.36  3.000
 HXY  H5A  C5   C6   113.38  3.000
 HXY  H5   C5   C6   110.15  3.000
 HXY  H5A  C5   N    111.01  3.000
 HXY  H5   C5   N    111.65  3.000
 HXY  C6   C5   N    103.35  3.000
 HXY  H6A  C6   H6   107.29  3.000
 HXY  H6A  C6   C7   110.58  3.000
 HXY  H6   C6   C7   112.76  3.000
 HXY  H6A  C6   C5   110.50  3.000
 HXY  H6   C6   C5   111.61  3.000
 HXY  C7   C6   C5   104.13  3.000
 HXY  H7A  C7   H7   107.05  3.000
 HXY  H7A  C7   C8   110.90  3.000
 HXY  H7   C7   C8   111.17  3.000
 HXY  H7A  C7   C6   110.80  3.000
 HXY  H7   C7   C6   112.60  3.000
 HXY  C8   C7   C6   104.39  3.000
 HXY  H8A  C8   H8   107.29  3.000
 HXY  H8A  C8   C7   110.29  3.000
 HXY  H8   C8   C7   113.14  3.000
 HXY  H8A  C8   N    111.02  3.000
 HXY  H8   C8   N    111.36  3.000
 HXY  C7   C8   N    103.80  3.000
 HXY  H9   C9   C10  118.80  3.000
 HXY  H9   C9   C3   119.84  3.000
 HXY  C10  C9   C3   121.35  3.000
 HXY  H10  C10  C9   119.84  3.000
 HXY  H10  C10  C    121.22  3.000
 HXY  C9   C10  C    118.94  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
 HXY  CONST_01  C3   C2   C1   C      0.00   0.0  0
 HXY  CONST_02  C3   C9   C10  C      0.00   0.0  0
 HXY  CONST_03  C9   C10  C    C1     0.00   0.0  0
 HXY  CONST_04  C9   C3   C2   C1     0.00   0.0  0
 HXY  CONST_05  C10  C    C1   C2     0.00   0.0  0
 HXY  CONST_06  C10  C9   C3   C2     0.00   0.0  0
 HXY  CONST_07  C2   C1   C    BR   180.00   0.0  0
 HXY  CONST_08  C9   C10  C    BR   180.00   0.0  0
 HXY  CONST_09  C4   C3   C2   C1   180.00   0.0  0
 HXY  CONST_10  C10  C9   C3   C4   180.00   0.0  0
 HXY  CONST_11  H2   C2   C1   C    180.00   0.0  0
 HXY  CONST_12  H9   C9   C10  C    180.00   0.0  0
 HXY  CONST_13  H10  C10  C    C1   180.00   0.0  0
 HXY  CONST_14  H1   C1   C2   C3   180.00   0.0  0
 HXY  Var_01    C7   C6   C5   N     27.78  30.0  1
 HXY  Var_02    C6   C7   C8   N    -23.37  30.0  1
 HXY  Var_03    C7   C8   N    C5    42.34  30.0  1
 HXY  Var_04    C8   C7   C6   C5    -2.66  30.0  1
 HXY  Var_05    C8   N    C5   C6   -44.09  30.0  1
 HXY  Var_06    C2   C3   C4   N     42.41  30.0  2
 HXY  Var_07    C5   N    C4   C3  -170.91  30.0  1

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
 HXY  plan-1  C    0.020
 HXY  plan-1  BR   0.020
 HXY  plan-1  C1   0.020
 HXY  plan-1  C2   0.020
 HXY  plan-1  C3   0.020
 HXY  plan-1  C4   0.020
 HXY  plan-1  C9   0.020
 HXY  plan-1  C10  0.020
 HXY  plan-1  H1   0.020
 HXY  plan-1  H2   0.020
 HXY  plan-1  H9   0.020
 HXY  plan-1  H10  0.020

