# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:44:07 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-(piperidin-1-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1)N2CCCCC2
#
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
 JLA  JLA  '4-(piperidin-1-yl)benzoic acid'  ligand  30  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JLA
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
 JLA  C13   C  CH2   0  -0.443  -4.6599  -0.0001  -0.1797
 JLA  C15   C  CH2   0  -0.305  -2.4922   1.2841  -0.0888
 JLA  O01   O  O     0  -0.456   4.5727   1.0911  -0.0157
 JLA  O03   O  OH1   0  -0.602   4.4776  -1.1179   0.2653
 JLA  C04   C  CR6   0  -0.121   2.4496   0.0310   0.0537
 JLA  C05   C  CR16  0  -0.246   1.7195  -1.1536   0.1914
 JLA  C06   C  CR16  0  -0.331   0.3436  -1.1533   0.1383
 JLA  C07   C  CR6   0   0.399  -0.3866   0.0382  -0.0542
 JLA  C08   C  CR16  0  -0.355   0.3587   1.2249  -0.1959
 JLA  C09   C  CR16  0  -0.242   1.7375   1.2136  -0.1385
 JLA  N10   N  NT    0  -0.510  -1.7603   0.0288  -0.0699
 JLA  C11   C  CH2   0  -0.302  -2.4652  -1.0656  -0.7302
 JLA  C12   C  CH2   0  -0.438  -3.8468  -1.2856  -0.1384
 JLA  C14   C  CH2   0  -0.434  -3.8844   1.1149   0.5060
 JLA  H132  H  HCH2  0   0.216  -4.8554   0.2755  -1.2214
 JLA  H131  H  HCH2  0   0.237  -5.6321  -0.1420   0.2963
 JLA  H152  H  HCH2  0   0.254  -1.9541   2.0234   0.5023
 JLA  H151  H  HCH2  0   0.218  -2.5697   1.6784  -1.1130
 JLA  H1    H  HOH1  0   0.483   5.4411  -1.0255   0.2818
 JLA  H051  H  HCR6  0   0.261   2.2233  -2.0963   0.3574
 JLA  H061  H  HCR6  0   0.268  -0.1713  -2.0928   0.2822
 JLA  H081  H  HCR6  0   0.271  -0.1346   2.1679  -0.3823
 JLA  H091  H  HCR6  0   0.260   2.2696   2.1474  -0.2672
 JLA  H112  H  HCH2  0   0.223  -2.5608  -0.8395  -1.8024
 JLA  H111  H  HCH2  0   0.258  -1.8868  -1.9824  -0.6562
 JLA  H122  H  HCH2  0   0.223  -3.7479  -1.6318   0.8947
 JLA  H121  H  HCH2  0   0.238  -4.3424  -2.0808  -0.6989
 JLA  H141  H  HCH2  0   0.238  -4.4134   2.0668   0.4251
 JLA  H142  H  HCH2  0   0.222  -3.7888   0.8932   1.5730
 JLA  C02   C  C     0   0.518   3.9179   0.0776   0.0954

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
 JLA  C14  C13   single    1.521  0.020  1.521
 JLA  C14  C15   single    1.523  0.020  1.523
 JLA  C13  C12   single    1.522  0.020  1.522
 JLA  C15  N10   single    1.453  0.020  1.453
 JLA  C06  C05   aromatic  1.377  0.020  1.377
 JLA  C06  C07   aromatic  1.411  0.020  1.411
 JLA  N10  C07   single    1.374  0.020  1.374
 JLA  N10  C11   single    1.460  0.020  1.460
 JLA  C12  C11   single    1.519  0.020  1.519
 JLA  C05  C04   aromatic  1.398  0.020  1.398
 JLA  C07  C08   aromatic  1.408  0.020  1.408
 JLA  O01  C02   double    1.212  0.020  1.212
 JLA  C04  C02   single    1.470  0.020  1.470
 JLA  C04  C09   aromatic  1.394  0.020  1.394
 JLA  C08  C09   aromatic  1.380  0.020  1.380
 JLA  C02  O03   single    1.331  0.020  1.331
 JLA  C13  H132  single    0.970  0.020  1.090
 JLA  C13  H131  single    0.970  0.020  1.090
 JLA  C15  H152  single    0.970  0.020  1.090
 JLA  C15  H151  single    0.970  0.020  1.090
 JLA  O03  H1    single    0.850  0.020  0.980
 JLA  C05  H051  single    0.930  0.020  1.080
 JLA  C06  H061  single    0.930  0.020  1.080
 JLA  C08  H081  single    0.930  0.020  1.080
 JLA  C09  H091  single    0.930  0.020  1.080
 JLA  C11  H112  single    0.970  0.020  1.090
 JLA  C11  H111  single    0.970  0.020  1.090
 JLA  C12  H122  single    0.970  0.020  1.090
 JLA  C12  H121  single    0.970  0.020  1.090
 JLA  C14  H141  single    0.970  0.020  1.090
 JLA  C14  H142  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
 JLA  H131  C13  H132  106.76  3.000
 JLA  H131  C13  C14   110.65  3.000
 JLA  H132  C13  C14   109.58  3.000
 JLA  H131  C13  C12   110.75  3.000
 JLA  H132  C13  C12   109.50  3.000
 JLA  C14   C13  C12   109.55  3.000
 JLA  H151  C15  H152  107.27  3.000
 JLA  H151  C15  C14   109.80  3.000
 JLA  H152  C15  C14   108.36  3.000
 JLA  H151  C15  N10   110.93  3.000
 JLA  H152  C15  N10   109.31  3.000
 JLA  C14   C15  N10   111.06  3.000
 JLA  H1    O03  C02   109.58  3.000
 JLA  C09   C04  C05   117.75  3.000
 JLA  C09   C04  C02   119.17  3.000
 JLA  C05   C04  C02   123.07  3.000
 JLA  H051  C05  C06   118.14  3.000
 JLA  H051  C05  C04   120.67  3.000
 JLA  C06   C05  C04   121.18  3.000
 JLA  H061  C06  C07   120.38  3.000
 JLA  H061  C06  C05   118.08  3.000
 JLA  C07   C06  C05   121.51  3.000
 JLA  N10   C07  C08   122.26  3.000
 JLA  C08   C07  C06   116.84  3.000
 JLA  N10   C07  C06   120.89  3.000
 JLA  H081  C08  C09   118.06  3.000
 JLA  H081  C08  C07   120.74  3.000
 JLA  C09   C08  C07   121.17  3.000
 JLA  H091  C09  C08   118.63  3.000
 JLA  H091  C09  C04   119.82  3.000
 JLA  C08   C09  C04   121.54  3.000
 JLA  C11   N10  C07   119.55  3.000
 JLA  C11   N10  C15   113.49  3.000
 JLA  C07   N10  C15   119.85  3.000
 JLA  H111  C11  H112  106.62  3.000
 JLA  H111  C11  C12   109.60  3.000
 JLA  H112  C11  C12   109.30  3.000
 JLA  H111  C11  N10   110.17  3.000
 JLA  H112  C11  N10   109.20  3.000
 JLA  C12   C11  N10   111.81  3.000
 JLA  H121  C12  H122  107.18  3.000
 JLA  H121  C12  C11   108.56  3.000
 JLA  H122  C12  C11   109.36  3.000
 JLA  H121  C12  C13   111.02  3.000
 JLA  H122  C12  C13   109.96  3.000
 JLA  C11   C12  C13   110.67  3.000
 JLA  H142  C14  H141  106.94  3.000
 JLA  H142  C14  C15   108.86  3.000
 JLA  H141  C14  C15   108.48  3.000
 JLA  H142  C14  C13   109.61  3.000
 JLA  H141  C14  C13   111.01  3.000
 JLA  C15   C14  C13   111.79  3.000
 JLA  C04   C02  O03   113.29  3.000
 JLA  O03   C02  O01   122.40  3.000
 JLA  C04   C02  O01   124.32  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
 JLA  CONST_01  C07   C06  C05  C04     0.00   0.0  0
 JLA  CONST_02  C07   C08  C09  C04     0.00   0.0  0
 JLA  CONST_03  C08   C07  C06  C05     0.00   0.0  0
 JLA  CONST_04  C08   C09  C04  C05     0.00   0.0  0
 JLA  CONST_05  C09   C04  C05  C06     0.00   0.0  0
 JLA  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 JLA  CONST_07  N10   C07  C06  C05   180.00   0.0  0
 JLA  CONST_08  N10   C07  C08  C09   180.00   0.0  0
 JLA  CONST_09  C06   C05  C04  C02   180.00   0.0  0
 JLA  CONST_10  C08   C09  C04  C02   180.00   0.0  0
 JLA  CONST_11  H061  C06  C05  C04   180.00   0.0  0
 JLA  CONST_12  H081  C08  C09  C04   180.00   0.0  0
 JLA  CONST_13  H091  C09  C04  C05   180.00   0.0  0
 JLA  CONST_14  H051  C05  C06  C07   180.00   0.0  0
 JLA  CONST_15  H1    O03  C02  C04   180.00   0.0  0
 JLA  Var_01    N10   C15  C14  C13   -54.44  30.0  1
 JLA  Var_02    N10   C11  C12  C13    55.32  30.0  1
 JLA  Var_03    C12   C13  C14  C15    54.50  30.0  1
 JLA  Var_04    C06   C07  N10  C15   171.73  30.0  2
 JLA  Var_05    C12   C11  N10  C15   -56.01  30.0  1
 JLA  Var_06    C14   C15  N10  C07  -154.63  30.0  1
 JLA  Var_07    C14   C13  C12  C11   -54.48  30.0  1
 JLA  Var_08    C05   C04  C02  O01  -179.68  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
 JLA  plan-1  C04   0.020
 JLA  plan-1  C05   0.020
 JLA  plan-1  C06   0.020
 JLA  plan-1  C07   0.020
 JLA  plan-1  C08   0.020
 JLA  plan-1  C09   0.020
 JLA  plan-1  N10   0.020
 JLA  plan-1  H051  0.020
 JLA  plan-1  H061  0.020
 JLA  plan-1  H081  0.020
 JLA  plan-1  H091  0.020
 JLA  plan-1  C02   0.020
 JLA  plan-2  O01   0.020
 JLA  plan-2  O03   0.020
 JLA  plan-2  C04   0.020
 JLA  plan-2  H1    0.020
 JLA  plan-2  C02   0.020

