# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 08:30:41 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 8-methylnonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCCCCCC(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
 T55  T55  '8-methylnonanoic acid    '  ligand  32  12  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T55
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
 T55  CAD   C  CH3   0  -0.657  -4.7883   1.3163   0.5846
 T55  CAE   C  CH1   0  -0.231  -4.5044   0.0949  -0.2840
 T55  CAG   C  CH2   0  -0.393  -3.1586  -0.5533   0.0461
 T55  CAH   C  CH2   0  -0.420  -1.9396   0.3369  -0.1662
 T55  CAI   C  CH2   0  -0.409  -0.6257  -0.4082   0.0361
 T55  CAJ   C  CH2   0  -0.414   0.6014   0.4727  -0.1578
 T55  CAK   C  CH2   0  -0.417   1.9095  -0.2842   0.0351
 T55  CAL   C  CH2   0  -0.579   3.1182   0.6155  -0.1623
 T55  CAF   C  CH3   0  -0.650  -5.6294  -0.9278  -0.1537
 T55  C     C  C     0   0.549   4.4361  -0.0841   0.0191
 T55  O     O  O     0  -0.446   4.5763  -1.2287   0.3722
 T55  OXT   O  OH1   0  -0.599   5.4633   0.7175  -0.2530
 T55  HXT   H  HOH1  0   0.478   6.2967   0.2412  -0.1232
 T55  HAL1  H  HCH2  0   0.273   3.1034   1.0682  -1.1587
 T55  HAL2  H  HCH2  0   0.276   3.0892   1.4571   0.5382
 T55  HAK1  H  HCH2  0   0.224   1.9317  -0.7224   1.0364
 T55  HAK2  H  HCH2  0   0.224   1.9516  -1.1198  -0.6690
 T55  HAJ1  H  HCH2  0   0.212   0.5784   0.9117  -1.1612
 T55  HAJ2  H  HCH2  0   0.212   0.5611   1.3144   0.5423
 T55  HAI1  H  HCH2  0   0.208  -0.6062  -0.8426   1.0423
 T55  HAI2  H  HCH2  0   0.208  -0.5788  -1.2536  -0.6591
 T55  HAH1  H  HCH2  0   0.206  -1.9663   0.7557  -1.1787
 T55  HAH2  H  HCH2  0   0.212  -1.9704   1.1917   0.5164
 T55  HAG1  H  HCH2  0   0.202  -3.1766  -0.9055   1.0851
 T55  HAG2  H  HCH2  0   0.210  -3.0477  -1.4506  -0.5733
 T55  HAE   H  HCH1  0   0.207  -4.4681   0.4239  -1.3298
 T55  HAD1  H  HCH3  0   0.223  -5.7602   1.7514   0.3438
 T55  HAD2  H  HCH3  0   0.210  -4.8014   1.0454   1.6436
 T55  HAD3  H  HCH3  0   0.227  -4.0400   2.0984   0.4521
 T55  HAF1  H  HCH3  0   0.223  -6.5922  -0.5032  -0.4430
 T55  HAF2  H  HCH3  0   0.221  -5.4484  -1.8003  -0.7843
 T55  HAF3  H  HCH3  0   0.211  -5.7209  -1.2790   0.8772

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
 T55  OXT  C     single  1.331  0.020  1.331
 T55  CAL  C     single  1.503  0.020  1.503
 T55  CAL  CAK   single  1.520  0.020  1.520
 T55  C    O     double  1.206  0.020  1.206
 T55  CAK  CAJ   single  1.524  0.020  1.524
 T55  CAJ  CAI   single  1.523  0.020  1.523
 T55  CAI  CAH   single  1.524  0.020  1.524
 T55  CAH  CAG   single  1.524  0.020  1.524
 T55  CAG  CAE   single  1.530  0.020  1.530
 T55  CAE  CAD   single  1.525  0.020  1.525
 T55  CAE  CAF   single  1.526  0.020  1.526
 T55  OXT  HXT   single  0.850  0.020  0.980
 T55  CAL  HAL1  single  0.970  0.020  1.090
 T55  CAL  HAL2  single  0.970  0.020  1.090
 T55  CAK  HAK1  single  0.970  0.020  1.090
 T55  CAK  HAK2  single  0.970  0.020  1.090
 T55  CAJ  HAJ1  single  0.970  0.020  1.090
 T55  CAJ  HAJ2  single  0.970  0.020  1.090
 T55  CAI  HAI1  single  0.970  0.020  1.090
 T55  CAI  HAI2  single  0.970  0.020  1.090
 T55  CAH  HAH1  single  0.970  0.020  1.090
 T55  CAH  HAH2  single  0.970  0.020  1.090
 T55  CAG  HAG1  single  0.970  0.020  1.090
 T55  CAG  HAG2  single  0.970  0.020  1.090
 T55  CAE  HAE   single  0.970  0.020  1.090
 T55  CAD  HAD1  single  0.970  0.020  1.090
 T55  CAD  HAD2  single  0.970  0.020  1.090
 T55  CAD  HAD3  single  0.970  0.020  1.090
 T55  CAF  HAF1  single  0.970  0.020  1.090
 T55  CAF  HAF2  single  0.970  0.020  1.090
 T55  CAF  HAF3  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
 T55  HAD3  CAD  HAD2  107.68  3.000
 T55  HAD3  CAD  HAD1  107.35  3.000
 T55  HAD2  CAD  HAD1  107.56  3.000
 T55  HAD3  CAD  CAE   112.17  3.000
 T55  HAD2  CAD  CAE   110.82  3.000
 T55  HAD1  CAD  CAE   111.05  3.000
 T55  HAE   CAE  CAF   107.86  3.000
 T55  HAE   CAE  CAG   107.68  3.000
 T55  CAF   CAE  CAG   110.25  3.000
 T55  HAE   CAE  CAD   107.99  3.000
 T55  CAF   CAE  CAD   110.53  3.000
 T55  CAG   CAE  CAD   112.34  3.000
 T55  HAG2  CAG  HAG1  105.91  3.000
 T55  HAG2  CAG  CAH   108.58  3.000
 T55  HAG1  CAG  CAH   109.42  3.000
 T55  HAG2  CAG  CAE   108.29  3.000
 T55  HAG1  CAG  CAE   109.02  3.000
 T55  CAH   CAG  CAE   115.21  3.000
 T55  HAH2  CAH  HAH1  106.09  3.000
 T55  HAH2  CAH  CAI   108.87  3.000
 T55  HAH1  CAH  CAI   109.29  3.000
 T55  HAH2  CAH  CAG   110.29  3.000
 T55  HAH1  CAH  CAG   109.41  3.000
 T55  CAI   CAH  CAG   112.67  3.000
 T55  HAI2  CAI  HAI1  106.02  3.000
 T55  HAI2  CAI  CAJ   109.33  3.000
 T55  HAI1  CAI  CAJ   109.38  3.000
 T55  HAI2  CAI  CAH   109.27  3.000
 T55  HAI1  CAI  CAH   109.33  3.000
 T55  CAJ   CAI  CAH   113.26  3.000
 T55  HAJ2  CAJ  HAJ1  106.06  3.000
 T55  HAJ2  CAJ  CAK   109.41  3.000
 T55  HAJ1  CAJ  CAK   109.46  3.000
 T55  HAJ2  CAJ  CAI   109.47  3.000
 T55  HAJ1  CAJ  CAI   109.37  3.000
 T55  CAK   CAJ  CAI   112.85  3.000
 T55  HAK2  CAK  HAK1  106.42  3.000
 T55  HAK2  CAK  CAL   109.76  3.000
 T55  HAK1  CAK  CAL   109.89  3.000
 T55  HAK2  CAK  CAJ   109.34  3.000
 T55  HAK1  CAK  CAJ   109.43  3.000
 T55  CAL   CAK  CAJ   111.86  3.000
 T55  HAL2  CAL  HAL1  105.31  3.000
 T55  HAL2  CAL  C     107.68  3.000
 T55  HAL1  CAL  C     108.31  3.000
 T55  HAL2  CAL  CAK   110.53  3.000
 T55  HAL1  CAL  CAK   110.63  3.000
 T55  C     CAL  CAK   113.96  3.000
 T55  HAF3  CAF  HAF2  107.58  3.000
 T55  HAF3  CAF  HAF1  107.53  3.000
 T55  HAF2  CAF  HAF1  107.71  3.000
 T55  HAF3  CAF  CAE   110.95  3.000
 T55  HAF2  CAF  CAE   111.35  3.000
 T55  HAF1  CAF  CAE   111.53  3.000
 T55  OXT   C    O     122.80  3.000
 T55  O     C    CAL   125.38  3.000
 T55  OXT   C    CAL   111.82  3.000
 T55  HXT   OXT  C     109.90  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
 T55  CONST_01  HXT   OXT  C    CAL   180.00   0.0  0
 T55  Var_01    CAH   CAG  CAE  CAD   -61.34  30.0  1
 T55  Var_02    CAI   CAH  CAG  CAE  -173.89  30.0  1
 T55  Var_03    CAJ   CAI  CAH  CAG  -179.37  30.0  1
 T55  Var_04    CAK   CAJ  CAI  CAH  -179.52  30.0  1
 T55  Var_05    CAL   CAK  CAJ  CAI  -179.95  30.0  1
 T55  Var_06    C     CAL  CAK  CAJ   179.93  30.0  1
 T55  Var_07    OXT   C    CAL  CAK   175.68  30.0  3
 T55  Var_08    HAF1  CAF  CAE  CAD    58.62  30.0  3
 T55  Var_09    HAD1  CAD  CAE  CAG  -179.01  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
 T55  plan-1  CAL  0.020
 T55  plan-1  C    0.020
 T55  plan-1  O    0.020
 T55  plan-1  OXT  0.020
 T55  plan-1  HXT  0.020

