# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 01:42:36 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  33  15  .  2021-08-19  2021-08-19  
;
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  -0.298  -3.0097   1.0349   0.0260
 OIO  C2    C  CH2   0  -0.428  -1.8161   0.0903  -0.0026
 OIO  C3    C  CH2   0  -0.423  -0.4973   0.8520   0.0122
 OIO  C4    C  CH2   0  -0.414   0.7167  -0.0683  -0.0061
 OIO  C5    C  CH2   0  -0.415   2.0368   0.6913  -0.0083
 OIO  C6    C  CH2   0  -0.418   3.2486  -0.2322  -0.0169
 OIO  C7    C  CH2   0  -0.580   4.5532   0.5473  -0.0288
 OIO  C8    C  C     0   0.550   5.7807  -0.3202  -0.0426
 OIO  O9    O  O     0  -0.446   5.7832  -1.5262  -0.0296
 OIO  O10   O  OH1   0  -0.599   6.8974   0.4032  -0.0716
 OIO  N11   N  NR5   0  -0.396  -4.2782   0.3329   0.0025
 OIO  C12   C  CR15  0  -0.109  -4.8998  -0.1886  -1.0964
 OIO  C13   C  CR15  0  -0.220  -6.0156  -0.8188  -0.6233
 OIO  N14   N  N     0  -0.458  -6.0847  -0.6983   0.7355
 OIO  C15   C  CR15  0   0.093  -5.0254  -0.0067   1.0732
 OIO  H1    H  HCH2  0   0.262  -2.9870   1.6510   0.9258
 OIO  H1A   H  HCH2  0   0.261  -2.9792   1.7138  -0.8271
 OIO  H2    H  HCH2  0   0.230  -1.8691  -0.5825   0.8586
 OIO  H2A   H  HCH2  0   0.231  -1.8707  -0.5371  -0.8978
 OIO  H3    H  HCH2  0   0.218  -0.4547   1.5250  -0.8510
 OIO  H3A   H  HCH2  0   0.218  -0.4543   1.4918   0.9004
 OIO  H4    H  HCH2  0   0.213   0.6804  -0.7350   0.8624
 OIO  H4A   H  HCH2  0   0.213   0.6681  -0.7155  -0.8886
 OIO  H5    H  HCH2  0   0.214   2.0741   1.3512  -0.8821
 OIO  H5A   H  HCH2  0   0.214   2.0820   1.3461   0.8689
 OIO  H6    H  HCH2  0   0.225   3.2133  -0.8849   0.8596
 OIO  H6A   H  HCH2  0   0.225   3.1994  -0.8861  -0.8917
 OIO  H7    H  HCH2  0   0.275   4.5964   1.2103  -0.8992
 OIO  H7A   H  HCH2  0   0.276   4.6148   1.2080   0.8422
 OIO  HO10  H  HOH1  0   0.478   7.6695  -0.1819  -0.0793
 OIO  H12   H  HCR5  0   0.286  -4.5084  -0.0630  -2.0924
 OIO  H13   H  HCR5  0   0.248  -6.7692  -1.3438  -1.1900
 OIO  H15   H  HCR5  0   0.277  -4.7497   0.2832   2.0766

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    1.503  0.020  1.503
 OIO  C7   H7    single    0.970  0.020  1.090
 OIO  C7   H7A   single    0.970  0.020  1.090
 OIO  O9   C8    double    1.206  0.020  1.206
 OIO  O10  C8    single    1.331  0.020  1.331
 OIO  O10  HO10  single    0.850  0.020  0.980
 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   107.04  3.000
 OIO  H1A   C1   N11  108.25  3.000
 OIO  H1    C1   N11  107.76  3.000
 OIO  H1A   C1   C2   110.46  3.000
 OIO  H1    C1   C2   110.47  3.000
 OIO  N11   C1   C2   112.66  3.000
 OIO  H2A   C2   H2   106.79  3.000
 OIO  H2A   C2   C3   109.74  3.000
 OIO  H2    C2   C3   109.98  3.000
 OIO  H2A   C2   C1   109.39  3.000
 OIO  H2    C2   C1   109.19  3.000
 OIO  C3    C2   C1   111.62  3.000
 OIO  H3A   C3   H3   106.17  3.000
 OIO  H3A   C3   C4   109.35  3.000
 OIO  H3    C3   C4   109.31  3.000
 OIO  H3A   C3   C2   109.51  3.000
 OIO  H3    C3   C2   109.47  3.000
 OIO  C4    C3   C2   112.82  3.000
 OIO  H4A   C4   H4   106.12  3.000
 OIO  H4A   C4   C5   109.38  3.000
 OIO  H4    C4   C5   109.48  3.000
 OIO  H4A   C4   C3   109.34  3.000
 OIO  H4    C4   C3   109.37  3.000
 OIO  C5    C4   C3   112.92  3.000
 OIO  H5A   C5   H5   106.10  3.000
 OIO  H5A   C5   C6   109.51  3.000
 OIO  H5    C5   C6   109.48  3.000
 OIO  H5A   C5   C4   109.43  3.000
 OIO  H5    C5   C4   109.33  3.000
 OIO  C6    C5   C4   112.77  3.000
 OIO  H6A   C6   H6   106.44  3.000
 OIO  H6A   C6   C7   109.82  3.000
 OIO  H6    C6   C7   109.89  3.000
 OIO  H6A   C6   C5   109.34  3.000
 OIO  H6    C6   C5   109.37  3.000
 OIO  C7    C6   C5   111.83  3.000
 OIO  H7A   C7   H7   105.35  3.000
 OIO  H7A   C7   C8   108.03  3.000
 OIO  H7    C7   C8   108.05  3.000
 OIO  H7A   C7   C6   110.58  3.000
 OIO  H7    C7   C6   110.53  3.000
 OIO  C8    C7   C6   113.89  3.000
 OIO  O10   C8   O9   122.82  3.000
 OIO  O10   C8   C7   111.82  3.000
 OIO  O9    C8   C7   125.36  3.000
 OIO  HO10  O10  C8   109.92  3.000
 OIO  C15   N11  C12  106.88  3.000
 OIO  C12   N11  C1   126.58  3.000
 OIO  C15   N11  C1   126.41  3.000
 OIO  H12   C12  C13  132.12  3.000
 OIO  H12   C12  N11  122.27  3.000
 OIO  C13   C12  N11  105.62  3.000
 OIO  H13   C13  N14  122.01  3.000
 OIO  H13   C13  C12  127.80  3.000
 OIO  N14   C13  C12  110.19  3.000
 OIO  C15   N14  C13  105.21  3.000
 OIO  H15   C15  N14  126.00  3.000
 OIO  H15   C15  N11  121.89  3.000
 OIO  N14   C15  N11  112.11  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  CONST_11  HO10  O10  C8   C7    180.00   0.0  0
 OIO  Var_01    C15   N11  C1   C2     94.97  30.0  2
 OIO  Var_02    N11   C1   C2   C3    179.57  30.0  3
 OIO  Var_03    C4    C3   C2   C1    179.60  30.0  2
 OIO  Var_04    C5    C4   C3   C2    179.30  30.0  2
 OIO  Var_05    C6    C5   C4   C3    179.60  30.0  1
 OIO  Var_06    C7    C6   C5   C4    179.60  30.0  1
 OIO  Var_07    C8    C7   C6   C5   -179.79  30.0  1
 OIO  Var_08    O9    C8   C7   C6     -0.87  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
 OIO  plan-2  HO10  0.020

