# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:32:38 2021
#   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  33  16  .  2022-03-23  2022-11-17
;
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  -0.429  68.6672  77.7840  26.4382
 RK4  C15  C  CH2   0  -0.293  66.4113  78.3235  27.4469
 RK4  O01  O  O     0  -0.440  62.2309  78.9942  30.3871
 RK4  O03  O  OH1   0  -0.594  62.5392  80.1656  32.2571
 RK4  C04  C  CR6   0  -0.067  63.9852  80.5991  30.4612
 RK4  C05  C  CR16  0  -0.277  64.6643  81.5596  31.2101
 RK4  C06  C  CR16  0  -0.231  65.7178  82.2539  30.6373
 RK4  C07  C  CR16  0  -0.294  66.0990  81.9926  29.3282
 RK4  C08  C  CR6   0   0.146  65.4394  81.0284  28.5685
 RK4  C09  C  CH2   0  -0.406  65.8831  80.7023  27.1588
 RK4  N10  N  NT    0  -0.405  66.8599  79.6402  27.0397
 RK4  C11  C  CH2   0  -0.266  68.1657  79.9662  27.5864
 RK4  C12  C  CH2   0  -0.477  69.0994  78.7494  27.5318
 RK4  C14  C  CH2   0  -0.429  67.2593  77.2567  26.7386
 RK4  C16  C  CR16  0  -0.312  64.3793  80.3436  29.1499
 RK4  H1   H  HCH2  0   0.217  68.6794  78.2954  25.4727
 RK4  H2   H  HCH2  0   0.228  69.3731  76.9552  26.3582
 RK4  H3   H  HCH2  0   0.199  66.4546  78.1896  28.5394
 RK4  H4   H  HCH2  0   0.234  65.3606  78.2054  27.1724
 RK4  H5   H  HOH1  0   0.487  61.7854  79.6415  32.5662
 RK4  H6   H  HCR6  0   0.267  64.3782  81.7759  32.2298
 RK4  H7   H  HCR6  0   0.264  66.2404  83.0059  31.2133
 RK4  H8   H  HCR6  0   0.263  66.9147  82.5552  28.8885
 RK4  H9   H  HCH2  0   0.247  66.3048  81.6010  26.6985
 RK4  H10  H  HCH2  0   0.251  65.0081  80.4230  26.5652
 RK4  H12  H  HCH2  0   0.221  68.5809  80.7900  26.9967
 RK4  H13  H  HCH2  0   0.202  68.1108  80.3217  28.6269
 RK4  H14  H  HCH2  0   0.223  69.0887  78.2252  28.4917
 RK4  H15  H  HCH2  0   0.240  70.1265  79.0864  27.3811
 RK4  H16  H  HCH2  0   0.225  66.7737  76.9519  25.8095
 RK4  H17  H  HCH2  0   0.218  67.3145  76.3658  27.3690
 RK4  H18  H  HCR6  0   0.258  63.8425  79.6056  28.5660
 RK4  C02  C  C     0   0.532  62.8378  79.8341  31.0086

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    1.535  0.020  1.535
 RK4  N10  C09  single    1.448  0.020  1.448
 RK4  N10  C15  single    1.449  0.020  1.449
 RK4  C14  C15  single    1.536  0.020  1.536
 RK4  C09  C08  single    1.513  0.020  1.513
 RK4  C08  C16  aromatic  1.390  0.020  1.390
 RK4  C08  C07  aromatic  1.394  0.020  1.394
 RK4  C16  C04  aromatic  1.393  0.020  1.393
 RK4  C07  C06  aromatic  1.388  0.020  1.388
 RK4  O01  C02  double    1.208  0.020  1.208
 RK4  C04  C02  single    1.484  0.020  1.484
 RK4  C04  C05  aromatic  1.394  0.020  1.394
 RK4  C02  O03  single    1.326  0.020  1.326
 RK4  C06  C05  aromatic  1.386  0.020  1.386
 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  O03  H5   single    0.850  0.020  0.980
 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   106.46  3.000
 RK4  H2   C13  C14  110.31  3.000
 RK4  H1   C13  C14  110.14  3.000
 RK4  H2   C13  C12  110.53  3.000
 RK4  H1   C13  C12  109.57  3.000
 RK4  C14  C13  C12  109.77  3.000
 RK4  H4   C15  H3   105.90  3.000
 RK4  H4   C15  C14  109.89  3.000
 RK4  H3   C15  C14  110.57  3.000
 RK4  H4   C15  N10  108.98  3.000
 RK4  H3   C15  N10  112.14  3.000
 RK4  C14  C15  N10  109.30  3.000
 RK4  H5   O03  C02  109.90  3.000
 RK4  C16  C04  C05  119.62  3.000
 RK4  C05  C04  C02  122.25  3.000
 RK4  C16  C04  C02  118.14  3.000
 RK4  H6   C05  C06  119.40  3.000
 RK4  H6   C05  C04  121.04  3.000
 RK4  C06  C05  C04  119.56  3.000
 RK4  H7   C06  C07  120.01  3.000
 RK4  H7   C06  C05  119.70  3.000
 RK4  C07  C06  C05  120.28  3.000
 RK4  H8   C07  C08  119.61  3.000
 RK4  H8   C07  C06  119.43  3.000
 RK4  C08  C07  C06  120.95  3.000
 RK4  C16  C08  C09  120.48  3.000
 RK4  C16  C08  C07  118.29  3.000
 RK4  C09  C08  C07  121.21  3.000
 RK4  H10  C09  H9   106.84  3.000
 RK4  H10  C09  N10  107.92  3.000
 RK4  H9   C09  N10  107.93  3.000
 RK4  H10  C09  C08  109.03  3.000
 RK4  H9   C09  C08  109.14  3.000
 RK4  N10  C09  C08  115.63  3.000
 RK4  C11  N10  C09  114.25  3.000
 RK4  C09  N10  C15  115.75  3.000
 RK4  C11  N10  C15  112.11  3.000
 RK4  H13  C11  H12  106.56  3.000
 RK4  H13  C11  C12  108.67  3.000
 RK4  H12  C11  C12  110.28  3.000
 RK4  H13  C11  N10  112.54  3.000
 RK4  H12  C11  N10  107.88  3.000
 RK4  C12  C11  N10  110.82  3.000
 RK4  H15  C12  H14  106.16  3.000
 RK4  H15  C12  C11  109.43  3.000
 RK4  H14  C12  C11  110.04  3.000
 RK4  H15  C12  C13  111.35  3.000
 RK4  H14  C12  C13  108.90  3.000
 RK4  C11  C12  C13  110.85  3.000
 RK4  H17  C14  H16  106.60  3.000
 RK4  H17  C14  C15  109.16  3.000
 RK4  H16  C14  C15  109.92  3.000
 RK4  H17  C14  C13  110.31  3.000
 RK4  H16  C14  C13  109.74  3.000
 RK4  C15  C14  C13  111.01  3.000
 RK4  H18  C16  C08  119.22  3.000
 RK4  H18  C16  C04  119.48  3.000
 RK4  C08  C16  C04  121.29  3.000
 RK4  C04  C02  O03  113.13  3.000
 RK4  O03  C02  O01  123.02  3.000
 RK4  C04  C02  O01  123.85  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  CONST_15  H5   O03  C02  C04  180.00   0.0  0
 RK4  Var_01    N10  C11  C12  C13   24.50  30.0  1
 RK4  Var_02    N10  C15  C14  C13   29.05  30.0  1
 RK4  Var_03    C12  C11  N10  C15   40.78  30.0  1
 RK4  Var_04    C12  C13  C14  C15   33.01  30.0  1
 RK4  Var_05    C14  C15  N10  C11  -70.55  30.0  1
 RK4  Var_06    C14  C13  C12  C11  -61.97  30.0  1
 RK4  Var_07    C08  C09  N10  C15   64.89  30.0  3
 RK4  Var_08    N10  C09  C08  C07   90.67  30.0  3
 RK4  Var_09    C16  C04  C02  O01    0.61  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  H5   0.020
 RK4  plan-2  C02  0.020

