# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 00:12:23 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 8-imidazol-1-yloctanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCCCn1ccnc1
#
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
 OIO  OIO  '8-imidazol-1-yloctanoic acid'  ligand  32  15  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OIO
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
 OIO  C1   C  CH2    0  -0.297  -3.0284   1.0190   0.0096
 OIO  C2   C  CH2    0  -0.427  -1.8272   0.0849  -0.0356
 OIO  C3   C  CH2    0  -0.422  -0.5145   0.8569  -0.0148
 OIO  C4   C  CH2    0  -0.411   0.7086  -0.0512  -0.0459
 OIO  C5   C  CH2    0  -0.410   2.0238   0.7171  -0.0165
 OIO  C6   C  CH2    0  -0.402   3.2499  -0.1886  -0.0364
 OIO  C7   C  CH2    0  -0.581   4.5554   0.5880   0.0098
 OIO  C8   C  C      0   0.409   5.8453  -0.2514   0.0059
 OIO  O9   O  O      0  -0.610   5.7423  -1.4821  -0.1648
 OIO  O10  O  OC    -1  -0.635   6.9102   0.3825   0.1687
 OIO  N11  N  NR5    0  -0.396  -4.2916   0.3069  -0.0016
 OIO  C12  C  CR15   0  -0.109  -4.9106  -0.2354  -1.0919
 OIO  C13  C  CR15   0  -0.220  -6.0218  -0.8657  -0.6082
 OIO  N14  N  N      0  -0.459  -6.0907  -0.7250   0.7488
 OIO  C15  C  CR15   0   0.093  -5.0359  -0.0209   1.0747
 OIO  H1   H  HCH2   0   0.261  -3.0008   1.6310   0.9120
 OIO  H1A  H  HCH2   0   0.260  -3.0130   1.7020  -0.8408
 OIO  H2   H  HCH2   0   0.229  -1.8715  -0.5986   0.8177
 OIO  H2A  H  HCH2   0   0.230  -1.8795  -0.5327  -0.9378
 OIO  H3   H  HCH2   0   0.216  -0.4797   1.5419  -0.8690
 OIO  H3A  H  HCH2   0   0.216  -0.4755   1.4859   0.8815
 OIO  H4   H  HCH2   0   0.209   0.6700  -0.7387   0.8064
 OIO  H4A  H  HCH2   0   0.209   0.6727  -0.6789  -0.9434
 OIO  H5   H  HCH2   0   0.203   2.0626   1.4032  -0.8705
 OIO  H5A  H  HCH2   0   0.203   2.0518   1.3499   0.8783
 OIO  H6   H  HCH2   0   0.200   3.1986  -0.8785   0.8117
 OIO  H6A  H  HCH2   0   0.201   3.2213  -0.8143  -0.9333
 OIO  H7   H  HCH2   0   0.218   4.6002   1.2775  -0.8427
 OIO  H7A  H  HCH2   0   0.213   4.5690   1.2354   0.8944
 OIO  H12  H  HCR5   0   0.286  -4.5207  -0.1223  -2.0900
 OIO  H13  H  HCR5   0   0.248  -6.7717  -1.4050  -1.1664
 OIO  H15  H  HCR5   0   0.277  -4.7614   0.2861   2.0733

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
 OIO  C2   C1   single    1.522  0.020  1.522
 OIO  C1   N11  single    1.450  0.020  1.450
 OIO  C1   H1   single    0.970  0.020  1.090
 OIO  C1   H1A  single    0.970  0.020  1.090
 OIO  C3   C2   single    1.523  0.020  1.523
 OIO  C2   H2   single    0.970  0.020  1.090
 OIO  C2   H2A  single    0.970  0.020  1.090
 OIO  C4   C3   single    1.524  0.020  1.524
 OIO  C3   H3   single    0.970  0.020  1.090
 OIO  C3   H3A  single    0.970  0.020  1.090
 OIO  C5   C4   single    1.523  0.020  1.523
 OIO  C4   H4   single    0.970  0.020  1.090
 OIO  C4   H4A  single    0.970  0.020  1.090
 OIO  C6   C5   single    1.524  0.020  1.524
 OIO  C5   H5   single    0.970  0.020  1.090
 OIO  C5   H5A  single    0.970  0.020  1.090
 OIO  C7   C6   single    1.520  0.020  1.520
 OIO  C6   H6   single    0.970  0.020  1.090
 OIO  C6   H6A  single    0.970  0.020  1.090
 OIO  C8   C7   single    1.539  0.020  1.539
 OIO  C7   H7   single    0.970  0.020  1.090
 OIO  C7   H7A  single    0.970  0.020  1.090
 OIO  O9   C8   deloc     1.247  0.020  1.247
 OIO  O10  C8   deloc     1.250  0.020  1.250
 OIO  N11  C15  aromatic  1.349  0.020  1.349
 OIO  N11  C12  aromatic  1.366  0.020  1.366
 OIO  C12  C13  aromatic  1.366  0.020  1.366
 OIO  C12  H12  single    0.930  0.020  1.080
 OIO  N14  C13  aromatic  1.366  0.020  1.366
 OIO  C13  H13  single    0.930  0.020  1.080
 OIO  C15  N14  aromatic  1.309  0.020  1.309
 OIO  C15  H15  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
 OIO  H1A  C1   H1   107.06  3.000
 OIO  H1A  C1   N11  108.29  3.000
 OIO  H1   C1   N11  107.70  3.000
 OIO  H1A  C1   C2   110.48  3.000
 OIO  H1   C1   C2   110.42  3.000
 OIO  N11  C1   C2   112.69  3.000
 OIO  H2A  C2   H2   106.76  3.000
 OIO  H2A  C2   C3   109.78  3.000
 OIO  H2   C2   C3   109.93  3.000
 OIO  H2A  C2   C1   109.45  3.000
 OIO  H2   C2   C1   109.16  3.000
 OIO  C3   C2   C1   111.63  3.000
 OIO  H3A  C3   H3   106.13  3.000
 OIO  H3A  C3   C4   109.28  3.000
 OIO  H3   C3   C4   109.35  3.000
 OIO  H3A  C3   C2   109.44  3.000
 OIO  H3   C3   C2   109.49  3.000
 OIO  C4   C3   C2   112.92  3.000
 OIO  H4A  C4   H4   106.06  3.000
 OIO  H4A  C4   C5   109.45  3.000
 OIO  H4   C4   C5   109.38  3.000
 OIO  H4A  C4   C3   109.38  3.000
 OIO  H4   C4   C3   109.26  3.000
 OIO  C5   C4   C3   113.08  3.000
 OIO  H5A  C5   H5   105.88  3.000
 OIO  H5A  C5   C6   109.46  3.000
 OIO  H5   C5   C6   109.47  3.000
 OIO  H5A  C5   C4   109.20  3.000
 OIO  H5   C5   C4   109.34  3.000
 OIO  C6   C5   C4   113.23  3.000
 OIO  H6A  C6   H6   105.87  3.000
 OIO  H6A  C6   C7   109.85  3.000
 OIO  H6   C6   C7   109.81  3.000
 OIO  H6A  C6   C5   109.24  3.000
 OIO  H6   C6   C5   109.06  3.000
 OIO  C7   C6   C5   112.76  3.000
 OIO  H7A  C7   H7   104.79  3.000
 OIO  H7A  C7   C8   108.28  3.000
 OIO  H7   C7   C8   107.85  3.000
 OIO  H7A  C7   C6   109.69  3.000
 OIO  H7   C7   C6   109.43  3.000
 OIO  C8   C7   C6   116.18  3.000
 OIO  O10  C8   O9   126.08  3.000
 OIO  O10  C8   C7   115.92  3.000
 OIO  O9   C8   C7   118.00  3.000
 OIO  C15  N11  C12  106.88  3.000
 OIO  C12  N11  C1   126.57  3.000
 OIO  C15  N11  C1   126.43  3.000
 OIO  H12  C12  C13  132.13  3.000
 OIO  H12  C12  N11  122.25  3.000
 OIO  C13  C12  N11  105.62  3.000
 OIO  H13  C13  N14  122.02  3.000
 OIO  H13  C13  C12  127.78  3.000
 OIO  N14  C13  C12  110.19  3.000
 OIO  C15  N14  C13  105.19  3.000
 OIO  H15  C15  N14  125.98  3.000
 OIO  H15  C15  N11  121.90  3.000
 OIO  N14  C15  N11  112.12  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
 OIO  CONST_01  C13  N14  C15  N11     0.00   0.0  0
 OIO  CONST_02  N14  C13  C12  N11     0.00   0.0  0
 OIO  CONST_03  N14  C15  N11  C12     0.00   0.0  0
 OIO  CONST_04  C15  N14  C13  C12     0.00   0.0  0
 OIO  CONST_05  C15  N11  C12  C13     0.00   0.0  0
 OIO  CONST_06  N14  C15  N11  C1    180.00   0.0  0
 OIO  CONST_07  C13  C12  N11  C1    180.00   0.0  0
 OIO  CONST_08  H13  C13  C12  N11   180.00   0.0  0
 OIO  CONST_09  H15  C15  N11  C12   180.00   0.0  0
 OIO  CONST_10  H12  C12  C13  N14   180.00   0.0  0
 OIO  Var_01    C15  N11  C1   C2     96.25  30.0  2
 OIO  Var_02    N11  C1   C2   C3   -179.67  30.0  3
 OIO  Var_03    C4   C3   C2   C1    179.46  30.0  1
 OIO  Var_04    C5   C4   C3   C2   -179.65  30.0  1
 OIO  Var_05    C6   C5   C4   C3    179.55  30.0  1
 OIO  Var_06    C7   C6   C5   C4   -179.32  30.0  2
 OIO  Var_07    C8   C7   C6   C5    179.47  30.0  1
 OIO  Var_08    O9   C8   C7   C6      6.83  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
 OIO  plan-1  C1   0.020
 OIO  plan-1  N11  0.020
 OIO  plan-1  C12  0.020
 OIO  plan-1  C13  0.020
 OIO  plan-1  N14  0.020
 OIO  plan-1  C15  0.020
 OIO  plan-1  H12  0.020
 OIO  plan-1  H13  0.020
 OIO  plan-1  H15  0.020
 OIO  plan-2  C7   0.020
 OIO  plan-2  C8   0.020
 OIO  plan-2  O9   0.020
 OIO  plan-2  O10  0.020

