# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 18:50:29 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 2-nonyl-4,6-bis(oxidanyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCc1cc(O)cc(O)c1C(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
 8I6  8I6  "2-nonyl-4,6-bis(oxidanyl)benzoic acid"  ligand  43  20  .  2022-09-16  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8I6
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
 8I6  C10   C  CR6    0   0.149   9.0252   5.1855  13.3873
 8I6  C15   C  CR6    0   0.390   9.1853   4.1590  11.1950
 8I6  C17   C  CR6    0  -0.386   9.8155   4.8411  12.2731
 8I6  C01   C  CH3    0  -0.659  12.6277  14.9236  18.2045
 8I6  C02   C  CH2    0  -0.417  11.9772  14.1944  17.0371
 8I6  C03   C  CH2    0  -0.404  11.7687  12.7097  17.3076
 8I6  C04   C  CH2    0  -0.409  11.1232  11.9668  16.1445
 8I6  C05   C  CH2    0  -0.409  10.9532  10.4757  16.4061
 8I6  C06   C  CH2    0  -0.410  10.3144   9.7245  15.2446
 8I6  C07   C  CH2    0  -0.415  10.2085   8.2247  15.4900
 8I6  C08   C  CH2    0  -0.405   9.5970   7.4628  14.3216
 8I6  C09   C  CH2    0  -0.491   9.5336   5.9564  14.5800
 8I6  C11   C  CR16   0  -0.497   7.6748   4.8537  13.4137
 8I6  C12   C  CR6    0   0.390   7.0777   4.1802  12.3497
 8I6  C14   C  CR16   0  -0.469   7.8282   3.8349  11.2404
 8I6  C18   C  C      0   0.489  11.2926   5.1262  12.1554
 8I6  O13   O  OH1    0  -0.633   5.7731   3.8423  12.3558
 8I6  O16   O  OH1    0  -0.660   9.8708   3.8129  10.1168
 8I6  O19   O  O      0  -0.638  11.8381   4.7577  11.0565
 8I6  O20   O  OC    -1  -0.532  11.9190   5.6738  13.0649
 8I6  H013  H  HCH3   0   0.224  12.7721  15.9824  17.9863
 8I6  H012  H  HCH3   0   0.214  12.0146  14.8532  19.1049
 8I6  H011  H  HCH3   0   0.214  13.6053  14.4983  18.4391
 8I6  H022  H  HCH2   0   0.209  12.5946  14.3139  16.1415
 8I6  H021  H  HCH2   0   0.209  11.0145  14.6600  16.8045
 8I6  H032  H  HCH2   0   0.204  11.1511  12.5882  18.2043
 8I6  H031  H  HCH2   0   0.204  12.7337  12.2461  17.5411
 8I6  H041  H  HCH2   0   0.204  11.7306  12.1079  15.2438
 8I6  H042  H  HCH2   0   0.205  10.1475  12.4137  15.9241
 8I6  H052  H  HCH2   0   0.205  10.3494  10.3308  17.3085
 8I6  H051  H  HCH2   0   0.204  11.9322  10.0347  16.6244
 8I6  H061  H  HCH2   0   0.204  10.9003   9.8994  14.3357
 8I6  H062  H  HCH2   0   0.205   9.3187  10.1362  15.0470
 8I6  H072  H  HCH2   0   0.205   9.6200   8.0424  16.3960
 8I6  H071  H  HCH2   0   0.206  11.2075   7.8227  15.6917
 8I6  H081  H  HCH2   0   0.217  10.1831   7.6536  13.4204
 8I6  H082  H  HCH2   0   0.206   8.5883   7.8399  14.1231
 8I6  H092  H  HCH2   0   0.222   8.8552   5.7786  15.4191
 8I6  H091  H  HCH2   0   0.235  10.5166   5.6042  14.8814
 8I6  H111  H  HCR6   0   0.246   7.0796   5.1257  14.2796
 8I6  H141  H  HCR6   0   0.245   7.3736   3.3120  10.4074
 8I6  H131  H  HOH1   0   0.470   5.3577   4.1308  13.1764
 8I6  H161  H  HOH1   0   0.457  10.8406   4.1680  10.3377

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
 8I6  O16  C15   single    1.324  0.020  1.324
 8I6  C14  C15   aromatic  1.396  0.020  1.396
 8I6  C14  C12   aromatic  1.383  0.020  1.383
 8I6  C15  C17   aromatic  1.423  0.020  1.423
 8I6  O19  C18   deloc     1.281  0.020  1.281
 8I6  O13  C12   single    1.348  0.020  1.348
 8I6  C12  C11   aromatic  1.394  0.020  1.394
 8I6  C17  C18   single    1.509  0.020  1.509
 8I6  C17  C10   aromatic  1.409  0.020  1.409
 8I6  C18  O20   deloc     1.233  0.020  1.233
 8I6  C11  C10   aromatic  1.391  0.020  1.391
 8I6  C10  C09   single    1.508  0.020  1.508
 8I6  C08  C09   single    1.530  0.020  1.530
 8I6  C08  C07   single    1.523  0.020  1.523
 8I6  C06  C07   single    1.523  0.020  1.523
 8I6  C06  C05   single    1.524  0.020  1.524
 8I6  C04  C05   single    1.523  0.020  1.523
 8I6  C04  C03   single    1.524  0.020  1.524
 8I6  C02  C03   single    1.524  0.020  1.524
 8I6  C02  C01   single    1.522  0.020  1.522
 8I6  C01  H013  single    0.970  0.020  1.090
 8I6  C01  H012  single    0.970  0.020  1.090
 8I6  C01  H011  single    0.970  0.020  1.090
 8I6  C02  H022  single    0.970  0.020  1.090
 8I6  C02  H021  single    0.970  0.020  1.090
 8I6  C03  H032  single    0.970  0.020  1.090
 8I6  C03  H031  single    0.970  0.020  1.090
 8I6  C04  H041  single    0.970  0.020  1.090
 8I6  C04  H042  single    0.970  0.020  1.090
 8I6  C05  H052  single    0.970  0.020  1.090
 8I6  C05  H051  single    0.970  0.020  1.090
 8I6  C06  H061  single    0.970  0.020  1.090
 8I6  C06  H062  single    0.970  0.020  1.090
 8I6  C07  H072  single    0.970  0.020  1.090
 8I6  C07  H071  single    0.970  0.020  1.090
 8I6  C08  H081  single    0.970  0.020  1.090
 8I6  C08  H082  single    0.970  0.020  1.090
 8I6  C09  H092  single    0.970  0.020  1.090
 8I6  C09  H091  single    0.970  0.020  1.090
 8I6  C11  H111  single    0.930  0.020  1.080
 8I6  C14  H141  single    0.930  0.020  1.080
 8I6  O13  H131  single    0.850  0.020  0.980
 8I6  O16  H161  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
 8I6  C11   C10  C09   115.73  3.000
 8I6  C09   C10  C17   124.14  3.000
 8I6  C11   C10  C17   120.09  3.000
 8I6  O16   C15  C14   117.98  3.000
 8I6  C14   C15  C17   121.14  3.000
 8I6  O16   C15  C17   120.87  3.000
 8I6  C18   C17  C15   117.71  3.000
 8I6  C18   C17  C10   124.37  3.000
 8I6  C15   C17  C10   117.91  3.000
 8I6  H011  C01  H012  107.50  3.000
 8I6  H011  C01  H013  107.62  3.000
 8I6  H012  C01  H013  107.58  3.000
 8I6  H011  C01  C02   111.15  3.000
 8I6  H012  C01  C02   111.20  3.000
 8I6  H013  C01  C02   111.60  3.000
 8I6  H021  C02  H022  106.02  3.000
 8I6  H021  C02  C03   109.39  3.000
 8I6  H022  C02  C03   109.20  3.000
 8I6  H021  C02  C01   109.58  3.000
 8I6  H022  C02  C01   109.52  3.000
 8I6  C03   C02  C01   112.90  3.000
 8I6  H031  C03  H032  105.97  3.000
 8I6  H031  C03  C04   109.24  3.000
 8I6  H032  C03  C04   109.38  3.000
 8I6  H031  C03  C02   109.24  3.000
 8I6  H032  C03  C02   109.30  3.000
 8I6  C04   C03  C02   113.43  3.000
 8I6  H042  C04  H041  106.02  3.000
 8I6  H042  C04  C05   109.54  3.000
 8I6  H041  C04  C05   109.21  3.000
 8I6  H042  C04  C03   109.39  3.000
 8I6  H041  C04  C03   109.26  3.000
 8I6  C05   C04  C03   113.17  3.000
 8I6  H051  C05  H052  105.97  3.000
 8I6  H051  C05  C06   109.15  3.000
 8I6  H052  C05  C06   109.37  3.000
 8I6  H051  C05  C04   109.18  3.000
 8I6  H052  C05  C04   109.42  3.000
 8I6  C06   C05  C04   113.49  3.000
 8I6  H062  C06  H061  106.05  3.000
 8I6  H062  C06  C07   109.63  3.000
 8I6  H061  C06  C07   109.15  3.000
 8I6  H062  C06  C05   109.47  3.000
 8I6  H061  C06  C05   109.24  3.000
 8I6  C07   C06  C05   113.07  3.000
 8I6  H071  C07  H072  106.05  3.000
 8I6  H071  C07  C08   108.89  3.000
 8I6  H072  C07  C08   109.60  3.000
 8I6  H071  C07  C06   109.12  3.000
 8I6  H072  C07  C06   109.54  3.000
 8I6  C08   C07  C06   113.39  3.000
 8I6  H082  C08  H081  106.53  3.000
 8I6  H082  C08  C09   109.37  3.000
 8I6  H081  C08  C09   109.49  3.000
 8I6  H082  C08  C07   109.68  3.000
 8I6  H081  C08  C07   109.28  3.000
 8I6  C09   C08  C07   112.32  3.000
 8I6  H091  C09  H092  107.19  3.000
 8I6  H091  C09  C08   109.18  3.000
 8I6  H092  C09  C08   108.38  3.000
 8I6  H091  C09  C10   111.01  3.000
 8I6  H092  C09  C10   108.33  3.000
 8I6  C08   C09  C10   112.57  3.000
 8I6  H111  C11  C12   119.68  3.000
 8I6  H111  C11  C10   119.20  3.000
 8I6  C12   C11  C10   121.12  3.000
 8I6  O13   C12  C14   117.79  3.000
 8I6  O13   C12  C11   122.18  3.000
 8I6  C14   C12  C11   120.03  3.000
 8I6  H141  C14  C12   120.62  3.000
 8I6  H141  C14  C15   119.67  3.000
 8I6  C12   C14  C15   119.71  3.000
 8I6  O20   C18  O19   122.97  3.000
 8I6  O20   C18  C17   121.59  3.000
 8I6  O19   C18  C17   115.43  3.000
 8I6  H131  O13  C12   110.24  3.000
 8I6  H161  O16  C15   102.55  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
 8I6  CONST_01  C14   C15  C17  C10     0.00   0.0  0
 8I6  CONST_02  C14   C12  C11  C10     0.00   0.0  0
 8I6  CONST_03  C11   C12  C14  C15     0.00   0.0  0
 8I6  CONST_04  C11   C10  C17  C15     0.00   0.0  0
 8I6  CONST_05  C12   C14  C15  C17     0.00   0.0  0
 8I6  CONST_06  C12   C11  C10  C17     0.00   0.0  0
 8I6  CONST_07  O16   C15  C17  C10   180.00   0.0  0
 8I6  CONST_08  O13   C12  C11  C10   180.00   0.0  0
 8I6  CONST_09  O13   C12  C14  C15   180.00   0.0  0
 8I6  CONST_10  C09   C10  C17  C15   180.00   0.0  0
 8I6  CONST_11  C12   C11  C10  C09   180.00   0.0  0
 8I6  CONST_12  C18   C17  C10  C11   180.00   0.0  0
 8I6  CONST_13  O16   C15  C14  C12   180.00   0.0  0
 8I6  CONST_14  C18   C17  C15  C14   180.00   0.0  0
 8I6  CONST_15  H141  C14  C15  C17   180.00   0.0  0
 8I6  CONST_16  H111  C11  C10  C17   180.00   0.0  0
 8I6  CONST_17  H141  C14  C12  C11   180.00   0.0  0
 8I6  CONST_18  H111  C11  C12  C14   180.00   0.0  0
 8I6  Var_01    O19   C18  C17  C10  -178.90  30.0  2
 8I6  Var_02    O20   C18  C17  C10     1.30  30.0  2
 8I6  Var_03    O19   C18  C17  C15     2.19  30.0  2
 8I6  Var_04    O20   C18  C17  C15  -177.61  30.0  2
 8I6  Var_05    C08   C09  C10  C17    80.10  30.0  2
 8I6  Var_06    C11   C10  C09  C08   -97.71  30.0  3
 8I6  Var_07    H092  C09  C10  C17  -160.07  30.0  2
 8I6  Var_08    H091  C09  C10  C17   -42.63  30.0  2
 8I6  Var_09    H092  C09  C10  C11    22.11  30.0  2
 8I6  Var_10    H091  C09  C10  C11   139.55  30.0  2
 8I6  Var_11    C07   C08  C09  C10  -175.70  30.0  2
 8I6  Var_12    H081  C08  C09  C10   -54.10  30.0  2
 8I6  Var_13    H082  C08  C09  C10    62.29  30.0  2
 8I6  Var_14    C04   C03  C02  C01  -179.78  30.0  3
 8I6  Var_15    C05   C04  C03  C02   178.38  30.0  1
 8I6  Var_16    C06   C05  C04  C03  -179.72  30.0  3
 8I6  Var_17    C07   C06  C05  C04   177.31  30.0  1
 8I6  Var_18    C08   C07  C06  C05  -178.82  30.0  3
 8I6  Var_19    C09   C08  C07  C06   178.60  30.0  2
 8I6  Var_20    H032  C03  C02  C01    57.88  30.0  3
 8I6  Var_21    H031  C03  C02  C01   -57.65  30.0  3
 8I6  Var_22    H041  C04  C03  C02    56.47  30.0  1
 8I6  Var_23    H042  C04  C03  C02   -59.18  30.0  1
 8I6  Var_24    H052  C05  C04  C03    57.83  30.0  3
 8I6  Var_25    H051  C05  C04  C03   -57.73  30.0  3
 8I6  Var_26    H013  C01  C02  C03   179.67  30.0  3
 8I6  Var_27    H012  C01  C02  C03   -60.20  30.0  3
 8I6  Var_28    H011  C01  C02  C03    59.52  30.0  3
 8I6  Var_29    H061  C06  C05  C04    55.56  30.0  1
 8I6  Var_30    H062  C06  C05  C04   -60.16  30.0  1
 8I6  Var_31    H022  C02  C03  C04   -57.68  30.0  1
 8I6  Var_32    H021  C02  C03  C04    57.93  30.0  1
 8I6  Var_33    H072  C07  C06  C05    58.41  30.0  3
 8I6  Var_34    H071  C07  C06  C05   -57.27  30.0  3
 8I6  Var_35    H032  C03  C04  C05   -59.32  30.0  3
 8I6  Var_36    H031  C03  C04  C05    56.26  30.0  3
 8I6  Var_37    H081  C08  C07  C06    56.88  30.0  2
 8I6  Var_38    H082  C08  C07  C06   -59.56  30.0  2
 8I6  Var_39    H041  C04  C05  C06   -57.77  30.0  1
 8I6  Var_40    H042  C04  C05  C06    57.93  30.0  1
 8I6  Var_41    H092  C09  C08  C07    64.50  30.0  3
 8I6  Var_42    H091  C09  C08  C07   -51.95  30.0  3
 8I6  Var_43    H052  C05  C06  C07   -60.21  30.0  3
 8I6  Var_44    H051  C05  C06  C07    55.30  30.0  3
 8I6  Var_45    H061  C06  C07  C08   -57.01  30.0  1
 8I6  Var_46    H062  C06  C07  C08    58.74  30.0  1
 8I6  Var_47    H072  C07  C08  C09   -58.67  30.0  3
 8I6  Var_48    H071  C07  C08  C09    56.92  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
 8I6  plan-1  C10   0.020
 8I6  plan-1  C15   0.020
 8I6  plan-1  C17   0.020
 8I6  plan-1  C09   0.020
 8I6  plan-1  C11   0.020
 8I6  plan-1  C12   0.020
 8I6  plan-1  C14   0.020
 8I6  plan-1  C18   0.020
 8I6  plan-1  O13   0.020
 8I6  plan-1  O16   0.020
 8I6  plan-1  H111  0.020
 8I6  plan-1  H141  0.020
 8I6  plan-2  C17   0.020
 8I6  plan-2  C18   0.020
 8I6  plan-2  O19   0.020
 8I6  plan-2  O20   0.020

