# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:24:09 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: nonanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCCCC(O)=O
#
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
 AZ1  AZ1  'nonanedioic acid         '  ligand  29  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AZ1
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
 AZ1  C1   C  C     0   0.549   0.1509   0.0300   5.0631
 AZ1  C2   C  CH2   0  -0.580  -0.6380   0.0292   3.7835
 AZ1  C3   C  CH2   0  -0.418   0.2208   0.0079   2.5298
 AZ1  C4   C  CH2   0  -0.415  -0.6266   0.0091   1.2635
 AZ1  C5   C  CH2   0  -0.413   0.2119  -0.0103  -0.0081
 AZ1  C6   C  CH2   0  -0.415  -0.6302  -0.0091  -1.2773
 AZ1  C7   C  CH2   0  -0.418   0.2133  -0.0291  -2.5463
 AZ1  C8   C  CH2   0  -0.580  -0.6505  -0.0280  -3.7967
 AZ1  C9   C  C     0   0.550   0.1317  -0.0524  -5.0801
 AZ1  O1   O  OH1   0  -0.599  -0.6413   0.0281   6.1323
 AZ1  O2   O  O     0  -0.446   1.3544   0.0335   5.1405
 AZ1  O3   O  O     0  -0.446   1.3344  -0.0834  -5.1644
 AZ1  O4   O  OH1   0  -0.599  -0.6661  -0.0369  -6.1452
 AZ1  H21  H  HCH2  0   0.275  -1.2893   0.9097   3.7873
 AZ1  H22  H  HCH2  0   0.275  -1.3145  -0.8315   3.8006
 AZ1  H31  H  HCH2  0   0.225   0.8638  -0.8765   2.5355
 AZ1  H32  H  HCH2  0   0.225   0.8869   0.8748   2.5212
 AZ1  H41  H  HCH2  0   0.213  -1.2748   0.8925   1.2579
 AZ1  H42  H  HCH2  0   0.213  -1.2959  -0.8583   1.2706
 AZ1  H51  H  HCH2  0   0.211   0.8597  -0.8940  -0.0026
 AZ1  H52  H  HCH2  0   0.211   0.8813   0.8570  -0.0152
 AZ1  H61  H  HCH2  0   0.213  -1.2782   0.8743  -1.2830
 AZ1  H62  H  HCH2  0   0.213  -1.2995  -0.8764  -1.2696
 AZ1  H71  H  HCH2  0   0.225   0.8572  -0.9127  -2.5402
 AZ1  H72  H  HCH2  0   0.225   0.8783   0.8388  -2.5533
 AZ1  H81  H  HCH2  0   0.275  -1.3027   0.8515  -3.8125
 AZ1  H82  H  HCH2  0   0.275  -1.3264  -0.8896  -3.7964
 AZ1  HO1  H  HOH1  0   0.478  -0.1065   0.0304   6.9401
 AZ1  HO4  H  HOH1  0   0.478  -0.1356  -0.0554  -6.9555

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
 AZ1  C1  C2   single  1.503  0.020  1.503
 AZ1  C1  O1   single  1.331  0.020  1.331
 AZ1  C1  O2   double  1.206  0.020  1.206
 AZ1  C2  C3   single  1.520  0.020  1.520
 AZ1  C2  H21  single  0.970  0.020  1.090
 AZ1  C2  H22  single  0.970  0.020  1.090
 AZ1  C3  C4   single  1.524  0.020  1.524
 AZ1  C3  H31  single  0.970  0.020  1.090
 AZ1  C3  H32  single  0.970  0.020  1.090
 AZ1  C4  C5   single  1.523  0.020  1.523
 AZ1  C4  H41  single  0.970  0.020  1.090
 AZ1  C4  H42  single  0.970  0.020  1.090
 AZ1  C5  C6   single  1.523  0.020  1.523
 AZ1  C5  H51  single  0.970  0.020  1.090
 AZ1  C5  H52  single  0.970  0.020  1.090
 AZ1  C6  C7   single  1.524  0.020  1.524
 AZ1  C6  H61  single  0.970  0.020  1.090
 AZ1  C6  H62  single  0.970  0.020  1.090
 AZ1  C7  C8   single  1.520  0.020  1.520
 AZ1  C7  H71  single  0.970  0.020  1.090
 AZ1  C7  H72  single  0.970  0.020  1.090
 AZ1  C8  C9   single  1.503  0.020  1.503
 AZ1  C8  H81  single  0.970  0.020  1.090
 AZ1  C8  H82  single  0.970  0.020  1.090
 AZ1  C9  O3   double  1.206  0.020  1.206
 AZ1  C9  O4   single  1.331  0.020  1.331
 AZ1  O1  HO1  single  0.850  0.020  0.980
 AZ1  O4  HO4  single  0.850  0.020  0.980

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
 AZ1  O2   C1  O1   122.85  3.000
 AZ1  O2   C1  C2   125.33  3.000
 AZ1  O1   C1  C2   111.81  3.000
 AZ1  H22  C2  H21  105.34  3.000
 AZ1  H22  C2  C3   110.55  3.000
 AZ1  H21  C2  C3   110.50  3.000
 AZ1  H22  C2  C1   108.14  3.000
 AZ1  H21  C2  C1   107.98  3.000
 AZ1  C3   C2  C1   113.93  3.000
 AZ1  H32  C3  H31  106.44  3.000
 AZ1  H32  C3  C4   109.37  3.000
 AZ1  H31  C3  C4   109.39  3.000
 AZ1  H32  C3  C2   109.86  3.000
 AZ1  H31  C3  C2   109.84  3.000
 AZ1  C4   C3  C2   111.79  3.000
 AZ1  H42  C4  H41  106.08  3.000
 AZ1  H42  C4  C5   109.36  3.000
 AZ1  H41  C4  C5   109.37  3.000
 AZ1  H42  C4  C3   109.50  3.000
 AZ1  H41  C4  C3   109.50  3.000
 AZ1  C5   C4  C3   112.80  3.000
 AZ1  H52  C5  H51  106.10  3.000
 AZ1  H52  C5  C6   109.37  3.000
 AZ1  H51  C5  C6   109.37  3.000
 AZ1  H52  C5  C4   109.37  3.000
 AZ1  H51  C5  C4   109.36  3.000
 AZ1  C6   C5  C4   113.03  3.000
 AZ1  H62  C6  H61  106.08  3.000
 AZ1  H62  C6  C7   109.49  3.000
 AZ1  H61  C6  C7   109.49  3.000
 AZ1  H62  C6  C5   109.35  3.000
 AZ1  H61  C6  C5   109.39  3.000
 AZ1  C7   C6  C5   112.82  3.000
 AZ1  H72  C7  H71  106.46  3.000
 AZ1  H72  C7  C8   109.86  3.000
 AZ1  H71  C7  C8   109.87  3.000
 AZ1  H72  C7  C6   109.37  3.000
 AZ1  H71  C7  C6   109.39  3.000
 AZ1  C8   C7  C6   111.75  3.000
 AZ1  H82  C8  H81  105.33  3.000
 AZ1  H82  C8  C9   107.98  3.000
 AZ1  H81  C8  C9   108.10  3.000
 AZ1  H82  C8  C7   110.48  3.000
 AZ1  H81  C8  C7   110.54  3.000
 AZ1  C9   C8  C7   114.00  3.000
 AZ1  O4   C9  O3   122.83  3.000
 AZ1  O4   C9  C8   111.79  3.000
 AZ1  O3   C9  C8   125.38  3.000
 AZ1  HO1  O1  C1   109.96  3.000
 AZ1  HO4  O4  C9   109.94  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
 AZ1  CONST_01  HO1  O1  C1  C2   180.00   0.0  0
 AZ1  CONST_02  HO4  O4  C9  C8   180.00   0.0  0
 AZ1  Var_01    C4   C3  C2  C1  -179.96  30.0  3
 AZ1  Var_02    C5   C4  C3  C2   179.93  30.0  3
 AZ1  Var_03    O1   C1  C2  C3  -179.03  30.0  2
 AZ1  Var_04    C6   C5  C4  C3  -180.00  30.0  3
 AZ1  Var_05    C7   C6  C5  C4  -179.98  30.0  3
 AZ1  Var_06    C8   C7  C6  C5   179.98  30.0  3
 AZ1  Var_07    C9   C8  C7  C6  -179.79  30.0  3
 AZ1  Var_08    O3   C9  C8  C7     0.68  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
 AZ1  plan-1  C1   0.020
 AZ1  plan-1  C2   0.020
 AZ1  plan-1  O1   0.020
 AZ1  plan-1  O2   0.020
 AZ1  plan-1  HO1  0.020
 AZ1  plan-2  C8   0.020
 AZ1  plan-2  C9   0.020
 AZ1  plan-2  O3   0.020
 AZ1  plan-2  O4   0.020
 AZ1  plan-2  HO4  0.020

