# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 01:57:21 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-[(piperidin-1-yl)methyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(CN2CCCCC2)c1
#
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
 RK4  RK4  '3-[(piperidin-1-yl)methyl]benzoic acid'  ligand  32  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RK4
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
 RK4  C13  C  CH2    0  -0.427  68.6551  77.7707  26.4042
 RK4  C15  C  CH2    0  -0.289  66.4014  78.3240  27.4084
 RK4  O01  O  O      0  -0.587  62.4379  78.8720  30.4879
 RK4  O03  O  OC    -1  -0.589  62.6215  80.1191  32.3279
 RK4  C04  C  CR6    0  -0.083  64.0717  80.5799  30.5214
 RK4  C05  C  CR16   0  -0.308  64.7401  81.5805  31.2243
 RK4  C06  C  CR16   0  -0.234  65.7595  82.3041  30.6229
 RK4  C07  C  CR16   0  -0.313  66.1241  82.0372  29.3094
 RK4  C08  C  CR6    0   0.141  65.4765  81.0391  28.5852
 RK4  C09  C  CH2    0  -0.398  65.8928  80.7120  27.1678
 RK4  N10  N  NT     0  -0.406  66.8600  79.6419  27.0192
 RK4  C11  C  CH2    0  -0.260  68.1718  79.9484  27.5642
 RK4  C12  C  CH2    0  -0.477  69.0852  78.7165  27.5156
 RK4  C14  C  CH2    0  -0.427  67.2361  77.2607  26.6809
 RK4  C16  C  CR16   0  -0.348  64.4540  80.3264  29.2071
 RK4  H1   H  HCH2   0   0.216  68.6864  78.2963  25.4469
 RK4  H2   H  HCH2   0   0.226  69.3500  76.9329  26.3201
 RK4  H3   H  HCH2   0   0.194  66.4482  78.1694  28.4980
 RK4  H4   H  HCH2   0   0.234  65.3490  78.2219  27.1353
 RK4  H6   H  HCR6   0   0.236  64.4543  81.7953  32.2455
 RK4  H7   H  HCR6   0   0.241  66.2694  83.0833  31.1761
 RK4  H8   H  HCR6   0   0.244  66.9126  82.6167  28.8418
 RK4  H9   H  HCH2   0   0.237  66.3143  81.6078  26.7003
 RK4  H10  H  HCH2   0   0.241  65.0069  80.4403  26.5868
 RK4  H12  H  HCH2   0   0.215  68.6023  80.7609  26.9691
 RK4  H13  H  HCH2   0   0.200  68.1220  80.3137  28.6015
 RK4  H14  H  HCH2   0   0.221  69.0466  78.1825  28.4695
 RK4  H15  H  HCH2   0   0.237  70.1210  79.0358  27.3878
 RK4  H16  H  HCH2   0   0.222  66.7525  76.9848  25.7416
 RK4  H17  H  HCH2   0   0.216  67.2715  76.3552  27.2913
 RK4  H18  H  HCR6   0   0.234  63.9295  79.5583  28.6511
 RK4  C02  C  C      0   0.392  62.9408  79.7850  31.1710

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
 RK4  C13  C12  single    1.521  0.020  1.521
 RK4  C13  C14  single    1.533  0.020  1.533
 RK4  C11  N10  single    1.453  0.020  1.453
 RK4  C11  C12  single    1.534  0.020  1.534
 RK4  N10  C09  single    1.450  0.020  1.450
 RK4  N10  C15  single    1.449  0.020  1.449
 RK4  C14  C15  single    1.535  0.020  1.535
 RK4  C09  C08  single    1.513  0.020  1.513
 RK4  C08  C16  aromatic  1.393  0.020  1.393
 RK4  C08  C07  aromatic  1.393  0.020  1.393
 RK4  C16  C04  aromatic  1.392  0.020  1.392
 RK4  C07  C06  aromatic  1.389  0.020  1.389
 RK4  O01  C02  deloc     1.246  0.020  1.246
 RK4  C04  C02  single    1.527  0.020  1.527
 RK4  C04  C05  aromatic  1.394  0.020  1.394
 RK4  C02  O03  deloc     1.246  0.020  1.246
 RK4  C06  C05  aromatic  1.387  0.020  1.387
 RK4  C13  H1   single    0.970  0.020  1.090
 RK4  C13  H2   single    0.970  0.020  1.090
 RK4  C15  H3   single    0.970  0.020  1.090
 RK4  C15  H4   single    0.970  0.020  1.090
 RK4  C05  H6   single    0.930  0.020  1.080
 RK4  C06  H7   single    0.930  0.020  1.080
 RK4  C07  H8   single    0.930  0.020  1.080
 RK4  C09  H9   single    0.970  0.020  1.090
 RK4  C09  H10  single    0.970  0.020  1.090
 RK4  C11  H12  single    0.970  0.020  1.090
 RK4  C11  H13  single    0.970  0.020  1.090
 RK4  C12  H14  single    0.970  0.020  1.090
 RK4  C12  H15  single    0.970  0.020  1.090
 RK4  C14  H16  single    0.970  0.020  1.090
 RK4  C14  H17  single    0.970  0.020  1.090
 RK4  C16  H18  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
 RK4  H2   C13  H1   106.47  3.000
 RK4  H2   C13  C14  110.36  3.000
 RK4  H1   C13  C14  110.17  3.000
 RK4  H2   C13  C12  110.69  3.000
 RK4  H1   C13  C12  109.44  3.000
 RK4  C14  C13  C12  109.67  3.000
 RK4  H4   C15  H3   105.97  3.000
 RK4  H4   C15  C14  109.92  3.000
 RK4  H3   C15  C14  110.40  3.000
 RK4  H4   C15  N10  108.84  3.000
 RK4  H3   C15  N10  112.33  3.000
 RK4  C14  C15  N10  109.31  3.000
 RK4  C16  C04  C05  118.38  3.000
 RK4  C05  C04  C02  120.95  3.000
 RK4  C16  C04  C02  120.67  3.000
 RK4  H6   C05  C06  119.98  3.000
 RK4  H6   C05  C04  119.47  3.000
 RK4  C06  C05  C04  120.54  3.000
 RK4  H7   C06  C07  119.84  3.000
 RK4  H7   C06  C05  119.98  3.000
 RK4  C07  C06  C05  120.18  3.000
 RK4  H8   C07  C08  119.79  3.000
 RK4  H8   C07  C06  119.73  3.000
 RK4  C08  C07  C06  120.48  3.000
 RK4  C16  C08  C09  120.64  3.000
 RK4  C16  C08  C07  118.41  3.000
 RK4  C09  C08  C07  120.93  3.000
 RK4  H10  C09  H9   106.75  3.000
 RK4  H10  C09  N10  107.61  3.000
 RK4  H9   C09  N10  107.65  3.000
 RK4  H10  C09  C08  109.18  3.000
 RK4  H9   C09  C08  109.22  3.000
 RK4  N10  C09  C08  116.04  3.000
 RK4  C11  N10  C09  114.08  3.000
 RK4  C09  N10  C15  115.64  3.000
 RK4  C11  N10  C15  112.14  3.000
 RK4  H13  C11  H12  106.47  3.000
 RK4  H13  C11  C12  108.85  3.000
 RK4  H12  C11  C12  110.15  3.000
 RK4  H13  C11  N10  112.49  3.000
 RK4  H12  C11  N10  107.91  3.000
 RK4  C12  C11  N10  110.87  3.000
 RK4  H15  C12  H14  106.17  3.000
 RK4  H15  C12  C11  109.50  3.000
 RK4  H14  C12  C11  110.08  3.000
 RK4  H15  C12  C13  111.39  3.000
 RK4  H14  C12  C13  108.88  3.000
 RK4  C11  C12  C13  110.73  3.000
 RK4  H17  C14  H16  106.59  3.000
 RK4  H17  C14  C15  109.08  3.000
 RK4  H16  C14  C15  109.99  3.000
 RK4  H17  C14  C13  110.27  3.000
 RK4  H16  C14  C13  109.80  3.000
 RK4  C15  C14  C13  111.00  3.000
 RK4  H18  C16  C08  119.27  3.000
 RK4  H18  C16  C04  118.72  3.000
 RK4  C08  C16  C04  122.00  3.000
 RK4  C04  C02  O03  116.44  3.000
 RK4  O03  C02  O01  127.02  3.000
 RK4  C04  C02  O01  116.55  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
 RK4  CONST_01  C07  C08  C16  C04    0.00   0.0  0
 RK4  CONST_02  C07  C06  C05  C04    0.00   0.0  0
 RK4  CONST_03  C08  C16  C04  C05    0.00   0.0  0
 RK4  CONST_04  C08  C07  C06  C05    0.00   0.0  0
 RK4  CONST_05  C16  C08  C07  C06    0.00   0.0  0
 RK4  CONST_06  C16  C04  C05  C06    0.00   0.0  0
 RK4  CONST_07  C08  C16  C04  C02  180.00   0.0  0
 RK4  CONST_08  C06  C05  C04  C02  180.00   0.0  0
 RK4  CONST_09  C09  C08  C16  C04  180.00   0.0  0
 RK4  CONST_10  C09  C08  C07  C06  180.00   0.0  0
 RK4  CONST_11  H7   C06  C05  C04  180.00   0.0  0
 RK4  CONST_12  H18  C16  C04  C05  180.00   0.0  0
 RK4  CONST_13  H8   C07  C06  C05  180.00   0.0  0
 RK4  CONST_14  H6   C05  C06  C07  180.00   0.0  0
 RK4  Var_01    N10  C11  C12  C13   25.87  30.0  1
 RK4  Var_02    N10  C15  C14  C13   30.05  30.0  1
 RK4  Var_03    C12  C11  N10  C15   39.51  30.0  1
 RK4  Var_04    C12  C13  C14  C15   32.22  30.0  1
 RK4  Var_05    C14  C15  N10  C11  -70.51  30.0  1
 RK4  Var_06    C14  C13  C12  C11  -62.34  30.0  1
 RK4  Var_07    C08  C09  N10  C15   65.79  30.0  3
 RK4  Var_08    N10  C09  C08  C07   93.45  30.0  2
 RK4  Var_09    C16  C04  C02  O01    3.34  30.0  2

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
 RK4  plan-1  C04  0.020
 RK4  plan-1  C05  0.020
 RK4  plan-1  C06  0.020
 RK4  plan-1  C07  0.020
 RK4  plan-1  C08  0.020
 RK4  plan-1  C09  0.020
 RK4  plan-1  C16  0.020
 RK4  plan-1  H6   0.020
 RK4  plan-1  H7   0.020
 RK4  plan-1  H8   0.020
 RK4  plan-1  H18  0.020
 RK4  plan-1  C02  0.020
 RK4  plan-2  O01  0.020
 RK4  plan-2  O03  0.020
 RK4  plan-2  C04  0.020
 RK4  plan-2  C02  0.020

