# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:21:15 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  31  12  .  2021-08-23  2021-08-23  
;
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  -4.7877   1.3265   0.5602
 T55  CAE   C  CH1    0  -0.231  -4.5097   0.0839  -0.2797
 T55  CAG   C  CH2    0  -0.392  -3.1583  -0.5522   0.0512
 T55  CAH   C  CH2    0  -0.419  -1.9446   0.3394  -0.1848
 T55  CAI   C  CH2    0  -0.407  -0.6254  -0.3983   0.0118
 T55  CAJ   C  CH2    0  -0.408   0.5997   0.4852  -0.1869
 T55  CAK   C  CH2    0  -0.401   1.9155  -0.2612  -0.0010
 T55  CAL   C  CH2    0  -0.580   3.1327   0.6271  -0.1974
 T55  CAF   C  CH3    0  -0.650  -5.6303  -0.9380  -0.1110
 T55  C     C  C      0   0.409   4.5034  -0.0501  -0.0201
 T55  O     O  O      0  -0.610   4.5243  -1.2363   0.3637
 T55  OXT   O  OC    -1  -0.635   5.5009   0.6603  -0.2707
 T55  HAL1  H  HCH2   0   0.213   3.1011   1.0845  -1.1933
 T55  HAL2  H  HCH2   0   0.216   3.0856   1.4729   0.4999
 T55  HAK1  H  HCH2   0   0.200   1.9388  -0.7054   0.9984
 T55  HAK2  H  HCH2   0   0.199   1.9532  -1.1008  -0.7022
 T55  HAJ1  H  HCH2   0   0.201   0.5688   0.9279  -1.1893
 T55  HAJ2  H  HCH2   0   0.201   0.5570   1.3268   0.5142
 T55  HAI1  H  HCH2   0   0.203  -0.5999  -0.8323   1.0179
 T55  HAI2  H  HCH2   0   0.204  -0.5785  -1.2447  -0.6826
 T55  HAH1  H  HCH2   0   0.204  -1.9830   0.7470  -1.2017
 T55  HAH2  H  HCH2   0   0.210  -1.9716   1.2018   0.4885
 T55  HAG1  H  HCH2   0   0.201  -3.1668  -0.8866   1.0959
 T55  HAG2  H  HCH2   0   0.209  -3.0483  -1.4600  -0.5530
 T55  HAE   H  HCH1   0   0.207  -4.4860   0.3869  -1.3338
 T55  HAD1  H  HCH3   0   0.223  -5.7635   1.7527   0.3192
 T55  HAD2  H  HCH3   0   0.210  -4.7877   1.0840   1.6262
 T55  HAD3  H  HCH3   0   0.227  -4.0436   2.1070   0.3983
 T55  HAF1  H  HCH3   0   0.222  -6.5975  -0.5234  -0.4004
 T55  HAF2  H  HCH3   0   0.221  -5.4540  -1.8262  -0.7208
 T55  HAF3  H  HCH3   0   0.210  -5.7091  -1.2626   0.9296

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     deloc   1.250  0.020  1.250
 T55  CAL  C     single  1.539  0.020  1.539
 T55  CAL  CAK   single  1.520  0.020  1.520
 T55  C    O     deloc   1.247  0.020  1.247
 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  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  107.66  3.000
 T55  HAD3  CAD  HAD1  107.32  3.000
 T55  HAD2  CAD  HAD1  107.57  3.000
 T55  HAD3  CAD  CAE   112.15  3.000
 T55  HAD2  CAD  CAE   110.87  3.000
 T55  HAD1  CAD  CAE   111.06  3.000
 T55  HAE   CAE  CAF   107.88  3.000
 T55  HAE   CAE  CAG   107.68  3.000
 T55  CAF   CAE  CAG   110.26  3.000
 T55  HAE   CAE  CAD   107.94  3.000
 T55  CAF   CAE  CAD   110.54  3.000
 T55  CAG   CAE  CAD   112.38  3.000
 T55  HAG2  CAG  HAG1  105.86  3.000
 T55  HAG2  CAG  CAH   108.61  3.000
 T55  HAG1  CAG  CAH   109.38  3.000
 T55  HAG2  CAG  CAE   108.29  3.000
 T55  HAG1  CAG  CAE   109.02  3.000
 T55  CAH   CAG  CAE   115.25  3.000
 T55  HAH2  CAH  HAH1  106.07  3.000
 T55  HAH2  CAH  CAI   108.87  3.000
 T55  HAH1  CAH  CAI   109.26  3.000
 T55  HAH2  CAH  CAG   110.25  3.000
 T55  HAH1  CAH  CAG   109.46  3.000
 T55  CAI   CAH  CAG   112.71  3.000
 T55  HAI2  CAI  HAI1  105.95  3.000
 T55  HAI2  CAI  CAJ   109.33  3.000
 T55  HAI1  CAI  CAJ   109.31  3.000
 T55  HAI2  CAI  CAH   109.21  3.000
 T55  HAI1  CAI  CAH   109.28  3.000
 T55  CAJ   CAI  CAH   113.48  3.000
 T55  HAJ2  CAJ  HAJ1  105.89  3.000
 T55  HAJ2  CAJ  CAK   109.37  3.000
 T55  HAJ1  CAJ  CAK   109.49  3.000
 T55  HAJ2  CAJ  CAI   109.30  3.000
 T55  HAJ1  CAJ  CAI   109.32  3.000
 T55  CAK   CAJ  CAI   113.22  3.000
 T55  HAK2  CAK  HAK1  105.85  3.000
 T55  HAK2  CAK  CAL   109.76  3.000
 T55  HAK1  CAK  CAL   109.78  3.000
 T55  HAK2  CAK  CAJ   109.10  3.000
 T55  HAK1  CAK  CAJ   109.19  3.000
 T55  CAL   CAK  CAJ   112.92  3.000
 T55  HAL2  CAL  HAL1  104.74  3.000
 T55  HAL2  CAL  C     107.71  3.000
 T55  HAL1  CAL  C     108.30  3.000
 T55  HAL2  CAL  CAK   109.51  3.000
 T55  HAL1  CAL  CAK   109.76  3.000
 T55  C     CAL  CAK   116.18  3.000
 T55  HAF3  CAF  HAF2  107.57  3.000
 T55  HAF3  CAF  HAF1  107.54  3.000
 T55  HAF2  CAF  HAF1  107.70  3.000
 T55  HAF3  CAF  CAE   110.93  3.000
 T55  HAF2  CAF  CAE   111.38  3.000
 T55  HAF1  CAF  CAE   111.53  3.000
 T55  OXT   C    O     126.08  3.000
 T55  O     C    CAL   117.97  3.000
 T55  OXT   C    CAL   115.95  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  Var_01  CAH   CAG  CAE  CAD   -60.76  30.0  1
 T55  Var_02  CAI   CAH  CAG  CAE  -173.53  30.0  1
 T55  Var_03  CAJ   CAI  CAH  CAG  -178.61  30.0  1
 T55  Var_04  CAK   CAJ  CAI  CAH  -179.49  30.0  1
 T55  Var_05  CAL   CAK  CAJ  CAI  -179.86  30.0  1
 T55  Var_06  C     CAL  CAK  CAJ   179.72  30.0  1
 T55  Var_07  OXT   C    CAL  CAK   175.34  30.0  3
 T55  Var_08  HAF1  CAF  CAE  CAD    58.60  30.0  3
 T55  Var_09  HAD1  CAD  CAE  CAG  -179.02  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

