# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 20:33:48 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-[(piperidin-1-yl)methyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(CN2CCCCC2)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
 VU1  VU1  "4-[(piperidin-1-yl)methyl]benzoic acid"  ligand  32  16  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VU1
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
 VU1  C10  C  CH2    0  -0.436   2.1251  -15.9130   -1.9294
 VU1  C11  C  CH2    0  -0.438   2.0548  -14.4053   -1.7218
 VU1  C12  C  CH2    0  -0.435   1.5996  -13.7305   -3.0099
 VU1  C13  C  CH2    0  -0.275   0.3001  -14.3429   -3.5098
 VU1  OH   O  O      0  -0.589  -0.7644  -15.1417  -10.6659
 VU1  C01  C  CR6    0  -0.108  -1.4104  -15.1884   -8.3939
 VU1  C02  C  CR16   0  -0.276  -2.3961  -14.9895   -7.4327
 VU1  C03  C  CR16   0  -0.301  -2.1909  -15.3565   -6.1084
 VU1  C04  C  CR6    0   0.091  -0.9899  -15.9261   -5.7030
 VU1  C05  C  CR16   0  -0.279   0.0054  -16.1157   -6.6606
 VU1  C06  C  CR16   0  -0.279  -0.2064  -15.7617   -7.9834
 VU1  C09  C  CH2    0  -0.277   0.8036  -16.4422   -2.4656
 VU1  N01  N  NT     0  -0.412   0.4337  -15.7769   -3.7039
 VU1  H1   H  HCH2   0   0.228   2.3682  -16.4252   -0.9958
 VU1  H2   H  HCH2   0   0.213   2.9207  -16.1496   -2.6422
 VU1  H3   H  HCH2   0   0.229   3.0196  -14.0108   -1.3962
 VU1  H4   H  HCH2   0   0.209   1.3371  -14.1836   -0.9247
 VU1  H5   H  HCH2   0   0.214   2.3687  -13.8516   -3.7784
 VU1  H6   H  HCH2   0   0.228   1.4611  -12.6574   -2.8617
 VU1  H7   H  HCH2   0   0.237   0.0164  -13.8810   -4.4580
 VU1  H8   H  HCH2   0   0.182  -0.5099  -14.1175   -2.7919
 VU1  H10  H  HCR6   0   0.235  -3.3376  -14.5409   -7.7212
 VU1  H11  H  HCR6   0   0.238  -2.9767  -15.1926   -5.3792
 VU1  H12  H  HCR6   0   0.233   0.9525  -16.5510   -6.3638
 VU1  H13  H  HCR6   0   0.235   0.5763  -15.9301   -8.7117
 VU1  H14  H  HCH2   0   0.207  -1.6640  -16.1134   -3.6781
 VU1  H15  H  HCH2   0   0.244  -0.6616  -17.4411   -4.2452
 VU1  H16  H  HCH2   0   0.182   0.0243  -16.3131   -1.6926
 VU1  H17  H  HCH2   0   0.231   0.8807  -17.5154   -2.6581
 VU1  O1   O  OC    -1  -0.589  -2.6873  -14.1635  -10.0966
 VU1  C07  C  CH2    0  -0.329  -0.7674  -16.3521   -4.2755
 VU1  CH   C  C      0   0.388  -1.6407  -14.7941   -9.8507

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
 VU1  OH   CH   deloc     1.246  0.020  1.246
 VU1  CH   C01  single    1.527  0.020  1.527
 VU1  C01  C06  aromatic  1.395  0.020  1.395
 VU1  C01  C02  aromatic  1.391  0.020  1.391
 VU1  C06  C05  aromatic  1.386  0.020  1.386
 VU1  C02  C03  aromatic  1.389  0.020  1.389
 VU1  C05  C04  aromatic  1.394  0.020  1.394
 VU1  C03  C04  aromatic  1.390  0.020  1.390
 VU1  C04  C07  single    1.506  0.020  1.506
 VU1  C07  N01  single    1.449  0.020  1.449
 VU1  N01  C13  single    1.453  0.020  1.453
 VU1  N01  C09  single    1.454  0.020  1.454
 VU1  C13  C12  single    1.521  0.020  1.521
 VU1  C12  C11  single    1.524  0.020  1.524
 VU1  C09  C10  single    1.521  0.020  1.521
 VU1  C10  C11  single    1.524  0.020  1.524
 VU1  C10  H1   single    0.970  0.020  1.090
 VU1  C10  H2   single    0.970  0.020  1.090
 VU1  C11  H3   single    0.970  0.020  1.090
 VU1  C11  H4   single    0.970  0.020  1.090
 VU1  C12  H5   single    0.970  0.020  1.090
 VU1  C12  H6   single    0.970  0.020  1.090
 VU1  C13  H7   single    0.970  0.020  1.090
 VU1  C13  H8   single    0.970  0.020  1.090
 VU1  CH   O1   deloc     1.246  0.020  1.246
 VU1  C02  H10  single    0.930  0.020  1.080
 VU1  C03  H11  single    0.930  0.020  1.080
 VU1  C05  H12  single    0.930  0.020  1.080
 VU1  C06  H13  single    0.930  0.020  1.080
 VU1  C07  H14  single    0.970  0.020  1.090
 VU1  C07  H15  single    0.970  0.020  1.090
 VU1  C09  H16  single    0.970  0.020  1.090
 VU1  C09  H17  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
 VU1  H2   C10  H1   107.08  3.000
 VU1  H2   C10  C09  109.08  3.000
 VU1  H1   C10  C09  109.36  3.000
 VU1  H2   C10  C11  109.65  3.000
 VU1  H1   C10  C11  110.97  3.000
 VU1  C09  C10  C11  110.62  3.000
 VU1  H4   C11  H3   106.79  3.000
 VU1  H4   C11  C12  109.26  3.000
 VU1  H3   C11  C12  110.85  3.000
 VU1  H4   C11  C10  109.25  3.000
 VU1  H3   C11  C10  110.94  3.000
 VU1  C12  C11  C10  109.69  3.000
 VU1  H6   C12  H5   107.06  3.000
 VU1  H6   C12  C13  109.38  3.000
 VU1  H5   C12  C13  108.97  3.000
 VU1  H6   C12  C11  111.00  3.000
 VU1  H5   C12  C11  109.56  3.000
 VU1  C13  C12  C11  110.78  3.000
 VU1  H8   C13  H7   106.69  3.000
 VU1  H8   C13  N01  110.81  3.000
 VU1  H7   C13  N01  108.98  3.000
 VU1  H8   C13  C12  109.29  3.000
 VU1  H7   C13  C12  109.69  3.000
 VU1  N01  C13  C12  111.26  3.000
 VU1  C06  C01  C02  117.83  3.000
 VU1  C02  C01  CH   121.03  3.000
 VU1  C06  C01  CH   121.14  3.000
 VU1  H10  C02  C03  119.48  3.000
 VU1  H10  C02  C01  119.44  3.000
 VU1  C03  C02  C01  121.08  3.000
 VU1  H11  C03  C04  119.47  3.000
 VU1  H11  C03  C02  119.60  3.000
 VU1  C04  C03  C02  120.92  3.000
 VU1  C07  C04  C05  120.47  3.000
 VU1  C07  C04  C03  121.33  3.000
 VU1  C05  C04  C03  118.19  3.000
 VU1  H12  C05  C06  119.84  3.000
 VU1  H12  C05  C04  119.37  3.000
 VU1  C06  C05  C04  120.79  3.000
 VU1  H13  C06  C05  119.48  3.000
 VU1  H13  C06  C01  119.34  3.000
 VU1  C05  C06  C01  121.18  3.000
 VU1  H17  C09  H16  106.71  3.000
 VU1  H17  C09  N01  108.50  3.000
 VU1  H16  C09  N01  111.28  3.000
 VU1  H17  C09  C10  110.02  3.000
 VU1  H16  C09  C10  108.99  3.000
 VU1  N01  C09  C10  111.23  3.000
 VU1  C09  N01  C07  111.42  3.000
 VU1  C09  N01  C13  111.18  3.000
 VU1  C07  N01  C13  111.60  3.000
 VU1  H15  C07  H14  106.18  3.000
 VU1  H15  C07  N01  107.69  3.000
 VU1  H14  C07  N01  111.97  3.000
 VU1  H15  C07  C04  108.78  3.000
 VU1  H14  C07  C04  109.38  3.000
 VU1  N01  C07  C04  112.58  3.000
 VU1  O1   CH   C01  116.46  3.000
 VU1  O1   CH   OH   127.05  3.000
 VU1  C01  CH   OH   116.49  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
 VU1  CONST_01  C04  C05  C06  C01     0.00   0.0  0
 VU1  CONST_02  C04  C03  C02  C01     0.00   0.0  0
 VU1  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 VU1  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 VU1  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 VU1  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 VU1  CONST_07  C05  C06  C01  CH    180.00   0.0  0
 VU1  CONST_08  C03  C02  C01  CH    180.00   0.0  0
 VU1  CONST_09  C07  C04  C03  C02   180.00   0.0  0
 VU1  CONST_10  C07  C04  C05  C06   180.00   0.0  0
 VU1  CONST_11  H12  C05  C06  C01   180.00   0.0  0
 VU1  CONST_12  H11  C03  C02  C01   180.00   0.0  0
 VU1  CONST_13  H13  C06  C01  C02   180.00   0.0  0
 VU1  CONST_14  H12  C05  C04  C03   180.00   0.0  0
 VU1  CONST_15  H13  C06  C05  C04   180.00   0.0  0
 VU1  CONST_16  H10  C02  C03  C04   180.00   0.0  0
 VU1  CONST_17  H11  C03  C04  C05   180.00   0.0  0
 VU1  CONST_18  H10  C02  C01  C06   180.00   0.0  0
 VU1  Var_01    C13  N01  C09  C10   -59.49  30.0  1
 VU1  Var_02    C13  C12  C11  C10    53.53  30.0  1
 VU1  Var_03    N01  C13  C12  C11   -56.56  30.0  1
 VU1  Var_04    N01  C09  C10  C11    56.92  30.0  1
 VU1  Var_05    C09  N01  C13  C12    59.27  30.0  1
 VU1  Var_06    C09  C10  C11  C12   -53.67  30.0  1
 VU1  Var_07    C07  N01  C09  C10   175.34  30.0  1
 VU1  Var_08    C07  N01  C13  C12  -175.66  30.0  1
 VU1  Var_09    C04  C07  N01  C13    69.02  30.0  1
 VU1  Var_10    N01  C07  C04  C03  -126.49  30.0  2
 VU1  Var_11    C09  N01  C07  C04  -166.04  30.0  3
 VU1  Var_12    N01  C07  C04  C05    54.55  30.0  2
 VU1  Var_13    H5   C12  C11  C10   -66.72  30.0  1
 VU1  Var_14    H6   C12  C11  C10   175.25  30.0  1
 VU1  Var_15    H7   C13  C12  C11  -177.22  30.0  1
 VU1  Var_16    H8   C13  C12  C11    66.13  30.0  1
 VU1  Var_17    H16  C09  C10  C11   -66.14  30.0  1
 VU1  Var_18    H17  C09  C10  C11   177.18  30.0  1
 VU1  Var_19    H1   C10  C11  C12  -175.24  30.0  1
 VU1  Var_20    H2   C10  C11  C12    66.68  30.0  1
 VU1  Var_21    H16  C09  N01  C13    62.25  30.0  1
 VU1  Var_22    H17  C09  N01  C13   179.36  30.0  1
 VU1  Var_23    H3   C11  C12  C13   176.38  30.0  1
 VU1  Var_24    H4   C11  C12  C13   -66.20  30.0  1
 VU1  Var_25    H7   C13  N01  C09  -179.66  30.0  1
 VU1  Var_26    H8   C13  N01  C09   -62.54  30.0  1
 VU1  Var_27    H3   C11  C10  C09  -176.47  30.0  1
 VU1  Var_28    H4   C11  C10  C09    66.07  30.0  1
 VU1  Var_29    H5   C12  C13  N01    64.05  30.0  1
 VU1  Var_30    H6   C12  C13  N01  -179.22  30.0  1
 VU1  Var_31    H1   C10  C09  N01   179.44  30.0  1
 VU1  Var_32    H2   C10  C09  N01   -63.76  30.0  1
 VU1  Var_33    C06  C01  CH   OH      7.52  30.0  2
 VU1  Var_34    C02  C01  CH   OH   -172.37  30.0  2
 VU1  Var_35    O1   CH   C01  C02     7.38  30.0  2
 VU1  Var_36    O1   CH   C01  C06  -172.73  30.0  2
 VU1  Var_37    H14  C07  N01  C13   -54.71  30.0  1
 VU1  Var_38    H15  C07  N01  C13  -171.08  30.0  1
 VU1  Var_39    H14  C07  C04  C03    -1.33  30.0  2
 VU1  Var_40    H15  C07  C04  C03   114.24  30.0  2
 VU1  Var_41    H14  C07  C04  C05   179.71  30.0  2
 VU1  Var_42    H15  C07  C04  C05   -64.72  30.0  2
 VU1  Var_43    H7   C13  N01  C07   -54.58  30.0  1
 VU1  Var_44    H8   C13  N01  C07    62.53  30.0  1
 VU1  Var_45    H16  C09  N01  C07   -62.92  30.0  1
 VU1  Var_46    H17  C09  N01  C07    54.19  30.0  1
 VU1  Var_47    H14  C07  N01  C09    70.22  30.0  1
 VU1  Var_48    H15  C07  N01  C09   -46.14  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
 VU1  plan-1  C01  0.020
 VU1  plan-1  C02  0.020
 VU1  plan-1  C03  0.020
 VU1  plan-1  C04  0.020
 VU1  plan-1  C05  0.020
 VU1  plan-1  C06  0.020
 VU1  plan-1  H10  0.020
 VU1  plan-1  H11  0.020
 VU1  plan-1  H12  0.020
 VU1  plan-1  H13  0.020
 VU1  plan-1  C07  0.020
 VU1  plan-1  CH   0.020
 VU1  plan-2  OH   0.020
 VU1  plan-2  C01  0.020
 VU1  plan-2  O1   0.020
 VU1  plan-2  CH   0.020

