# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:22:45 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  29  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  -0.441  -4.6577   0.0278  -0.2531
 JLA  C15   C  CH2    0  -0.302  -2.4817   1.2537   0.0703
 JLA  O01   O  O      0  -0.601   4.5435   1.0860  -0.0143
 JLA  O03   O  OC    -1  -0.601   4.5297  -1.1146   0.3272
 JLA  C04   C  C      0  -0.128   2.4568  -0.0058   0.1296
 JLA  C05   C  C1     0  -0.280   1.7217  -1.1718   0.3456
 JLA  C06   C  C1     0  -0.320   0.3400  -1.1726   0.3319
 JLA  C07   C  C      0   0.352  -0.3863   0.0048   0.0873
 JLA  C08   C  C1     0  -0.350   0.3512   1.1744  -0.1359
 JLA  C09   C  C1     0  -0.281   1.7391   1.1607  -0.1049
 JLA  N10   N  NT     0  -0.507  -1.7798  -0.0156   0.1085
 JLA  C11   C  CH2    0  -0.298  -2.4401  -1.0469  -0.6861
 JLA  C12   C  CH2    0  -0.438  -3.8691  -1.2739  -0.2220
 JLA  C14   C  CH2    0  -0.433  -3.9196   1.0927   0.5457
 JLA  H132  H  HCH2   0   0.213  -4.7739   0.3601  -1.2904
 JLA  H131  H  HCH2   0   0.233  -5.6646  -0.1205   0.1427
 JLA  H152  H  HCH2   0   0.246  -1.9718   1.9631   0.7232
 JLA  H151  H  HCH2   0   0.203  -2.4775   1.6867  -0.9432
 JLA  H051  H  H      0   0.236   2.2439  -2.0986   0.5460
 JLA  H061  H  H      0   0.250  -0.1841  -2.0972   0.5396
 JLA  H081  H  H      0   0.257  -0.1499   2.1080  -0.3536
 JLA  H091  H  H      0   0.237   2.2741   2.0844  -0.2853
 JLA  H112  H  HCH2   0   0.208  -2.4440  -0.7566  -1.7491
 JLA  H111  H  HCH2   0   0.251  -1.8810  -1.9777  -0.6189
 JLA  H122  H  HCH2   0   0.218  -3.8562  -1.6747   0.7959
 JLA  H121  H  HCH2   0   0.234  -4.3339  -2.0290  -0.8596
 JLA  H141  H  HCH2   0   0.234  -4.4244   2.0581   0.4702
 JLA  H142  H  HCH2   0   0.218  -3.9136   0.8171   1.6046
 JLA  C02   C  C      0   0.387   3.9733  -0.0118   0.1494

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    1.522  0.020  1.522
 JLA  C14  C15   single    1.523  0.020  1.523
 JLA  C13  C12   single    1.522  0.020  1.522
 JLA  C15  N10   single    1.451  0.020  1.451
 JLA  C06  C05   aromatic  1.382  0.020  1.382
 JLA  C06  C07   aromatic  1.405  0.020  1.405
 JLA  N10  C07   single    1.394  0.020  1.394
 JLA  N10  C11   single    1.460  0.020  1.460
 JLA  C12  C11   single    1.520  0.020  1.520
 JLA  C05  C04   aromatic  1.395  0.020  1.395
 JLA  C07  C08   aromatic  1.401  0.020  1.401
 JLA  O01  C02   deloc     1.248  0.020  1.248
 JLA  C04  C02   single    1.517  0.020  1.517
 JLA  C04  C09   aromatic  1.390  0.020  1.390
 JLA  C08  C09   aromatic  1.388  0.020  1.388
 JLA  C02  O03   deloc     1.248  0.020  1.248
 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  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  106.65  3.000
 JLA  H131  C13  C14   110.60  3.000
 JLA  H132  C13  C14   109.65  3.000
 JLA  H131  C13  C12   110.74  3.000
 JLA  H132  C13  C12   109.49  3.000
 JLA  C14   C13  C12   109.66  3.000
 JLA  H151  C15  H152  107.05  3.000
 JLA  H151  C15  C14   109.40  3.000
 JLA  H152  C15  C14   108.86  3.000
 JLA  H151  C15  N10   111.47  3.000
 JLA  H152  C15  N10   109.10  3.000
 JLA  C14   C15  N10   110.86  3.000
 JLA  C09   C04  C05   117.10  3.000
 JLA  C09   C04  C02   121.47  3.000
 JLA  C05   C04  C02   121.44  3.000
 JLA  H051  C05  C06   118.93  3.000
 JLA  H051  C05  C04   119.33  3.000
 JLA  C06   C05  C04   121.72  3.000
 JLA  H061  C06  C07   119.92  3.000
 JLA  H061  C06  C05   118.85  3.000
 JLA  C07   C06  C05   121.21  3.000
 JLA  N10   C07  C08   122.76  3.000
 JLA  C08   C07  C06   117.09  3.000
 JLA  N10   C07  C06   120.13  3.000
 JLA  H081  C08  C09   118.44  3.000
 JLA  H081  C08  C07   120.58  3.000
 JLA  C09   C08  C07   120.97  3.000
 JLA  H091  C09  C08   118.81  3.000
 JLA  H091  C09  C04   119.28  3.000
 JLA  C08   C09  C04   121.90  3.000
 JLA  C11   N10  C07   117.02  3.000
 JLA  C11   N10  C15   112.63  3.000
 JLA  C07   N10  C15   118.06  3.000
 JLA  H111  C11  H112  106.67  3.000
 JLA  H111  C11  C12   109.67  3.000
 JLA  H112  C11  C12   109.31  3.000
 JLA  H111  C11  N10   109.77  3.000
 JLA  H112  C11  N10   109.91  3.000
 JLA  C12   C11  N10   111.39  3.000
 JLA  H121  C12  H122  107.15  3.000
 JLA  H121  C12  C11   108.98  3.000
 JLA  H122  C12  C11   109.14  3.000
 JLA  H121  C12  C13   111.03  3.000
 JLA  H122  C12  C13   109.78  3.000
 JLA  C11   C12  C13   110.68  3.000
 JLA  H142  C14  H141  106.98  3.000
 JLA  H142  C14  C15   108.88  3.000
 JLA  H141  C14  C15   108.75  3.000
 JLA  H142  C14  C13   109.53  3.000
 JLA  H141  C14  C13   110.98  3.000
 JLA  C15   C14  C13   111.59  3.000
 JLA  C04   C02  O03   116.82  3.000
 JLA  O03   C02  O01   126.33  3.000
 JLA  C04   C02  O01   116.85  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
 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  Var_01    N10   C15  C14  C13   -55.30  30.0  1
 JLA  Var_02    N10   C11  C12  C13    55.98  30.0  1
 JLA  Var_03    C12   C13  C14  C15    53.89  30.0  1
 JLA  Var_04    C06   C07  N10  C15   170.04  30.0  2
 JLA  Var_05    C12   C11  N10  C15   -57.91  30.0  1
 JLA  Var_06    C14   C15  N10  C07  -161.66  30.0  1
 JLA  Var_07    C14   C13  C12  C11   -53.91  30.0  1
 JLA  Var_08    C05   C04  C02  O01  -177.92  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
 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  C02   0.020

