# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 08:46:48 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: hexadecanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCCCCCCCCCCC(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
 RF8  RF8  'hexadecanedioic acid     '  ligand  48  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RF8
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
 RF8  O01   O  O      0  -0.622  -16.0259  -14.2755   5.1066
 RF8  C02   C  C      0   0.403  -15.7780  -13.6073   6.1324
 RF8  O03   O  OC    -1  -0.609  -16.6125  -13.1651   6.9486
 RF8  C04   C  CH2    0  -0.566  -14.2881  -13.3412   6.4274
 RF8  C05   C  CH2    0  -0.402  -13.9862  -12.1227   7.2867
 RF8  C06   C  CH2    0  -0.403  -12.4962  -11.9342   7.5406
 RF8  C07   C  CH2    0  -0.414  -12.1744  -10.7151   8.3963
 RF8  C08   C  CH2    0  -0.418  -10.6778  -10.5311   8.6194
 RF8  C09   C  CH2    0  -0.418  -10.3115   -9.4067   9.5827
 RF8  C10   C  CH2    0  -0.416  -10.7284   -8.0147   9.1230
 RF8  C11   C  CH2    0  -0.405  -10.2121   -6.9125  10.0395
 RF8  C12   C  CH2    0  -0.439  -10.6360   -5.5177   9.5995
 RF8  C13   C  CH2    0  -0.426  -10.0291   -4.4153  10.4625
 RF8  C14   C  CH2    0  -0.426  -10.3205   -2.9859   9.9941
 RF8  C15   C  CH2    0  -0.425   -9.3534   -2.3811   8.9730
 RF8  C16   C  CH2    0  -0.431   -9.2814   -3.0744   7.6077
 RF8  C17   C  CH2    0  -0.561   -8.2104   -4.1585   7.5021
 RF8  C18   C  C      0   0.398   -8.3099   -5.0339   6.2371
 RF8  O19   O  OC    -1  -0.611   -9.4471   -5.4675   5.9453
 RF8  O20   O  O      0  -0.614   -7.2528   -5.2667   5.6168
 RF8  H041  H  HCH2   0   0.213  -13.8847  -14.2339   6.9240
 RF8  H042  H  HCH2   0   0.199  -13.7425  -13.2706   5.4811
 RF8  H051  H  HCH2   0   0.196  -14.3837  -11.2228   6.8050
 RF8  H052  H  HCH2   0   0.198  -14.5079  -12.2066   8.2435
 RF8  H061  H  HCH2   0   0.200  -12.0940  -12.8308   8.0262
 RF8  H062  H  HCH2   0   0.200  -11.9698  -11.8513   6.5828
 RF8  H071  H  HCH2   0   0.209  -12.5969   -9.8241   7.9213
 RF8  H072  H  HCH2   0   0.201  -12.6776  -10.8090   9.3656
 RF8  H081  H  HCH2   0   0.211  -10.2615  -11.4694   9.0006
 RF8  H082  H  HCH2   0   0.204  -10.1886  -10.3558   7.6546
 RF8  H091  H  HCH2   0   0.204  -10.7551   -9.6110  10.5637
 RF8  H092  H  HCH2   0   0.212   -9.2273   -9.4161   9.7358
 RF8  H102  H  HCH2   0   0.210  -11.8191   -7.9485   9.0605
 RF8  H101  H  HCH2   0   0.201  -10.3552   -7.8393   8.1070
 RF8  H111  H  HCH2   0   0.203  -10.5530   -7.0949  11.0650
 RF8  H112  H  HCH2   0   0.202   -9.1175   -6.9623  10.0724
 RF8  H122  H  HCH2   0   0.208  -11.7283   -5.4386   9.6381
 RF8  H121  H  HCH2   0   0.226  -10.3640   -5.3838   8.5506
 RF8  H132  H  HCH2   0   0.205   -8.9454   -4.5594  10.5374
 RF8  H131  H  HCH2   0   0.214  -10.4104   -4.5396  11.4813
 RF8  H142  H  HCH2   0   0.216  -10.3195   -2.3278  10.8678
 RF8  H141  H  HCH2   0   0.205  -11.3396   -2.9399   9.5936
 RF8  H152  H  HCH2   0   0.204   -8.3514   -2.3339   9.4143
 RF8  H151  H  HCH2   0   0.215   -9.6552   -1.3400   8.8254
 RF8  H162  H  HCH2   0   0.212   -9.0782   -2.3233   6.8380
 RF8  H161  H  HCH2   0   0.210  -10.2598   -3.4909   7.3600
 RF8  H172  H  HCH2   0   0.224   -8.2750   -4.8246   8.3692
 RF8  H171  H  HCH2   0   0.201   -7.2229   -3.6923   7.5616

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
 RF8  O01  C02   deloc   1.249  0.020  1.249
 RF8  C02  O03   deloc   1.248  0.020  1.248
 RF8  C02  C04   single  1.542  0.020  1.542
 RF8  O20  C18   deloc   1.248  0.020  1.248
 RF8  C04  C05   single  1.521  0.020  1.521
 RF8  C18  C17   single  1.542  0.020  1.542
 RF8  C18  O19   deloc   1.252  0.020  1.252
 RF8  C17  C16   single  1.528  0.020  1.528
 RF8  C05  C06   single  1.523  0.020  1.523
 RF8  C16  C15   single  1.533  0.020  1.533
 RF8  C06  C07   single  1.524  0.020  1.524
 RF8  C15  C14   single  1.531  0.020  1.531
 RF8  C07  C08   single  1.524  0.020  1.524
 RF8  C14  C13   single  1.532  0.020  1.532
 RF8  C08  C09   single  1.525  0.020  1.525
 RF8  C10  C11   single  1.524  0.020  1.524
 RF8  C10  C09   single  1.524  0.020  1.524
 RF8  C12  C13   single  1.526  0.020  1.526
 RF8  C12  C11   single  1.523  0.020  1.523
 RF8  C04  H041  single  0.970  0.020  1.090
 RF8  C04  H042  single  0.970  0.020  1.090
 RF8  C05  H051  single  0.970  0.020  1.090
 RF8  C05  H052  single  0.970  0.020  1.090
 RF8  C06  H061  single  0.970  0.020  1.090
 RF8  C06  H062  single  0.970  0.020  1.090
 RF8  C07  H071  single  0.970  0.020  1.090
 RF8  C07  H072  single  0.970  0.020  1.090
 RF8  C08  H081  single  0.970  0.020  1.090
 RF8  C08  H082  single  0.970  0.020  1.090
 RF8  C09  H091  single  0.970  0.020  1.090
 RF8  C09  H092  single  0.970  0.020  1.090
 RF8  C10  H102  single  0.970  0.020  1.090
 RF8  C10  H101  single  0.970  0.020  1.090
 RF8  C11  H111  single  0.970  0.020  1.090
 RF8  C11  H112  single  0.970  0.020  1.090
 RF8  C12  H122  single  0.970  0.020  1.090
 RF8  C12  H121  single  0.970  0.020  1.090
 RF8  C13  H132  single  0.970  0.020  1.090
 RF8  C13  H131  single  0.970  0.020  1.090
 RF8  C14  H142  single  0.970  0.020  1.090
 RF8  C14  H141  single  0.970  0.020  1.090
 RF8  C15  H152  single  0.970  0.020  1.090
 RF8  C15  H151  single  0.970  0.020  1.090
 RF8  C16  H162  single  0.970  0.020  1.090
 RF8  C16  H161  single  0.970  0.020  1.090
 RF8  C17  H172  single  0.970  0.020  1.090
 RF8  C17  H171  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
 RF8  C04   C02  O03   117.37  3.000
 RF8  C04   C02  O01   116.18  3.000
 RF8  O03   C02  O01   126.43  3.000
 RF8  H042  C04  H041  105.08  3.000
 RF8  H042  C04  C05   109.74  3.000
 RF8  H041  C04  C05   108.83  3.000
 RF8  H042  C04  C02   109.11  3.000
 RF8  H041  C04  C02   107.53  3.000
 RF8  C05   C04  C02   115.98  3.000
 RF8  H052  C05  H051  105.95  3.000
 RF8  H052  C05  C06   109.30  3.000
 RF8  H051  C05  C06   109.07  3.000
 RF8  H052  C05  C04   109.76  3.000
 RF8  H051  C05  C04   109.73  3.000
 RF8  C06   C05  C04   112.80  3.000
 RF8  H062  C06  H061  105.82  3.000
 RF8  H062  C06  C07   109.20  3.000
 RF8  H061  C06  C07   109.16  3.000
 RF8  H062  C06  C05   109.48  3.000
 RF8  H061  C06  C05   109.36  3.000
 RF8  C07   C06  C05   113.53  3.000
 RF8  H072  C07  H071  106.04  3.000
 RF8  H072  C07  C08   109.36  3.000
 RF8  H071  C07  C08   110.14  3.000
 RF8  H072  C07  C06   109.34  3.000
 RF8  H071  C07  C06   109.03  3.000
 RF8  C08   C07  C06   112.71  3.000
 RF8  H082  C08  H081  105.89  3.000
 RF8  H082  C08  C09   109.32  3.000
 RF8  H081  C08  C09   108.69  3.000
 RF8  H082  C08  C07   109.19  3.000
 RF8  H081  C08  C07   108.72  3.000
 RF8  C09   C08  C07   114.66  3.000
 RF8  H092  C09  H091  105.91  3.000
 RF8  H092  C09  C10   108.71  3.000
 RF8  H091  C09  C10   109.24  3.000
 RF8  H092  C09  C08   108.65  3.000
 RF8  H091  C09  C08   109.31  3.000
 RF8  C10   C09  C08   114.65  3.000
 RF8  H101  C10  H102  106.05  3.000
 RF8  H101  C10  C11   109.05  3.000
 RF8  H102  C10  C11   109.17  3.000
 RF8  H101  C10  C09   109.41  3.000
 RF8  H102  C10  C09   110.18  3.000
 RF8  C11   C10  C09   112.75  3.000
 RF8  H112  C11  H111  105.96  3.000
 RF8  H112  C11  C12   109.16  3.000
 RF8  H111  C11  C12   109.65  3.000
 RF8  H112  C11  C10   108.88  3.000
 RF8  H111  C11  C10   109.69  3.000
 RF8  C12   C11  C10   113.23  3.000
 RF8  H121  C12  H122  105.86  3.000
 RF8  H121  C12  C13   110.84  3.000
 RF8  H122  C12  C13   108.93  3.000
 RF8  H121  C12  C11   108.70  3.000
 RF8  H122  C12  C11   109.48  3.000
 RF8  C13   C12  C11   112.80  3.000
 RF8  H131  C13  H132  105.42  3.000
 RF8  H131  C13  C14   108.91  3.000
 RF8  H132  C13  C14   109.37  3.000
 RF8  H131  C13  C12   107.80  3.000
 RF8  H132  C13  C12   109.70  3.000
 RF8  C14   C13  C12   115.17  3.000
 RF8  H141  C14  H142  105.52  3.000
 RF8  H141  C14  C15   109.09  3.000
 RF8  H142  C14  C15   107.12  3.000
 RF8  H141  C14  C13   109.13  3.000
 RF8  H142  C14  C13   108.48  3.000
 RF8  C15   C14  C13   116.89  3.000
 RF8  H151  C15  H152  105.40  3.000
 RF8  H151  C15  C16   108.86  3.000
 RF8  H152  C15  C16   109.58  3.000
 RF8  H151  C15  C14   106.96  3.000
 RF8  H152  C15  C14   109.03  3.000
 RF8  C16   C15  C14   116.42  3.000
 RF8  H161  C16  H162  105.57  3.000
 RF8  H161  C16  C17   109.99  3.000
 RF8  H162  C16  C17   107.95  3.000
 RF8  H161  C16  C15   109.42  3.000
 RF8  H162  C16  C15   108.95  3.000
 RF8  C17   C16  C15   114.55  3.000
 RF8  H171  C17  H172  105.63  3.000
 RF8  H171  C17  C18   110.18  3.000
 RF8  H172  C17  C18   107.49  3.000
 RF8  H171  C17  C16   109.07  3.000
 RF8  H172  C17  C16   109.60  3.000
 RF8  C18   C17  C16   114.49  3.000
 RF8  O20   C18  O19   126.11  3.000
 RF8  O19   C18  C17   116.54  3.000
 RF8  O20   C18  C17   117.34  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
 RF8  Var_01  C05  C04  C02  O01   156.26  30.0  3
 RF8  Var_02  C06  C05  C04  C02   179.59  30.0  3
 RF8  Var_03  C07  C06  C05  C04   179.81  30.0  3
 RF8  Var_04  C08  C07  C06  C05  -179.05  30.0  3
 RF8  Var_05  C09  C08  C07  C06  -174.21  30.0  3
 RF8  Var_06  C10  C09  C08  C07   -62.88  30.0  3
 RF8  Var_07  C11  C10  C09  C08  -173.82  30.0  2
 RF8  Var_08  C12  C11  C10  C09  -179.32  30.0  3
 RF8  Var_09  C13  C12  C11  C10  -175.73  30.0  1
 RF8  Var_10  C14  C13  C12  C11   174.89  30.0  3
 RF8  Var_11  C15  C14  C13  C12   -87.66  30.0  1
 RF8  Var_12  C16  C15  C14  C13    63.22  30.0  1
 RF8  Var_13  C17  C16  C15  C14   -91.67  30.0  1
 RF8  Var_14  C18  C17  C16  C15   168.95  30.0  1
 RF8  Var_15  O20  C18  C17  C16   134.89  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
 RF8  plan-1  O01  0.020
 RF8  plan-1  C02  0.020
 RF8  plan-1  O03  0.020
 RF8  plan-1  C04  0.020
 RF8  plan-2  C17  0.020
 RF8  plan-2  C18  0.020
 RF8  plan-2  O19  0.020
 RF8  plan-2  O20  0.020

