# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:37:34 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (2S)-2,4-dimethylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](C)C(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
 7GA  7GA  '(2S)-2,4-dimethylpentanoic acid'  ligand  23  9  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7GA
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
 7GA  CA    C  CH1   0  -0.391  -0.5466  -0.3924   0.0292
 7GA  C     C  C     0   0.568  -1.8461   0.3766  -0.0288
 7GA  O     O  O     0  -0.444  -2.0094   1.4329  -0.5888
 7GA  C8    C  CH2   0  -0.389   0.6439   0.5301  -0.2266
 7GA  C9    C  CH1   0  -0.244   2.0186  -0.1351  -0.1240
 7GA  C10   C  CH3   0  -0.649   3.1041   0.8864  -0.4500
 7GA  C11   C  CH3   0  -0.661   2.2679  -0.7543   1.2477
 7GA  C6    C  CH3   0  -0.665  -0.6183  -1.5514  -0.9733
 7GA  OXT   O  OH1   0  -0.597  -2.8325  -0.2642   0.5934
 7GA  HA    H  HCH1  0   0.267  -0.4736  -0.8189   1.0338
 7GA  H81C  H  HCH2  0   0.226   0.5442   0.9737  -1.2218
 7GA  H82C  H  HCH2  0   0.224   0.6127   1.3620   0.4860
 7GA  H61C  H  HCH3  0   0.246  -1.4847  -2.1884  -0.7991
 7GA  H62C  H  HCH3  0   0.232  -0.6704  -1.1777  -1.9973
 7GA  H63C  H  HCH3  0   0.247   0.2669  -2.1805  -0.8933
 7GA  HXT   H  HOH1  0   0.477  -3.6594   0.2318   0.4988
 7GA  H9    H  HCH1  0   0.221   2.0810  -0.9309  -0.8736
 7GA  H101  H  HCH3  0   0.226   4.0929   0.4244  -0.4502
 7GA  H102  H  HCH3  0   0.224   2.9475   1.3365  -1.4319
 7GA  H103  H  HCH3  0   0.213   3.1172   1.6934   0.2870
 7GA  H111  H  HCH3  0   0.227   1.5784  -1.5701   1.4687
 7GA  H112  H  HCH3  0   0.228   3.2787  -1.1611   1.3116
 7GA  H113  H  HCH3  0   0.215   2.1626  -0.0056   2.0369

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
 7GA  CA   C     single  1.511  0.020  1.511
 7GA  CA   C8    single  1.528  0.020  1.528
 7GA  CA   C6    single  1.534  0.020  1.534
 7GA  C    O     double  1.207  0.020  1.207
 7GA  C    OXT   single  1.331  0.020  1.331
 7GA  C8   C9    single  1.531  0.020  1.531
 7GA  C9   C10   single  1.526  0.020  1.526
 7GA  C9   C11   single  1.525  0.020  1.525
 7GA  CA   HA    single  0.970  0.020  1.090
 7GA  C8   H81C  single  0.970  0.020  1.090
 7GA  C8   H82C  single  0.970  0.020  1.090
 7GA  C6   H61C  single  0.970  0.020  1.090
 7GA  C6   H62C  single  0.970  0.020  1.090
 7GA  C6   H63C  single  0.970  0.020  1.090
 7GA  OXT  HXT   single  0.850  0.020  0.980
 7GA  C9   H9    single  0.970  0.020  1.090
 7GA  C10  H101  single  0.970  0.020  1.090
 7GA  C10  H102  single  0.970  0.020  1.090
 7GA  C10  H103  single  0.970  0.020  1.090
 7GA  C11  H111  single  0.970  0.020  1.090
 7GA  C11  H112  single  0.970  0.020  1.090
 7GA  C11  H113  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
 7GA  HA    CA   C6    107.98  3.000
 7GA  HA    CA   C8    109.71  3.000
 7GA  C6    CA   C8    112.53  3.000
 7GA  HA    CA   C     106.92  3.000
 7GA  C6    CA   C     108.61  3.000
 7GA  C8    CA   C     110.88  3.000
 7GA  OXT   C    O     122.56  3.000
 7GA  OXT   C    CA    111.99  3.000
 7GA  O     C    CA    125.43  3.000
 7GA  H82C  C8   H81C  106.33  3.000
 7GA  H82C  C8   C9    108.17  3.000
 7GA  H81C  C8   C9    108.61  3.000
 7GA  H82C  C8   CA    109.11  3.000
 7GA  H81C  C8   CA    109.03  3.000
 7GA  C9    C8   CA    115.23  3.000
 7GA  H9    C9   C11   108.13  3.000
 7GA  H9    C9   C10   107.44  3.000
 7GA  C11   C9   C10   110.34  3.000
 7GA  H9    C9   C8    108.73  3.000
 7GA  C11   C9   C8    112.55  3.000
 7GA  C10   C9   C8    109.49  3.000
 7GA  H103  C10  H102  107.69  3.000
 7GA  H103  C10  H101  107.57  3.000
 7GA  H102  C10  H101  107.72  3.000
 7GA  H103  C10  C9    111.02  3.000
 7GA  H102  C10  C9    111.48  3.000
 7GA  H101  C10  C9    111.17  3.000
 7GA  H113  C11  H112  107.60  3.000
 7GA  H113  C11  H111  107.76  3.000
 7GA  H112  C11  H111  107.14  3.000
 7GA  H113  C11  C9    110.82  3.000
 7GA  H112  C11  C9    110.81  3.000
 7GA  H111  C11  C9    112.49  3.000
 7GA  H63C  C6   H62C  107.80  3.000
 7GA  H63C  C6   H61C  107.27  3.000
 7GA  H62C  C6   H61C  108.20  3.000
 7GA  H63C  C6   CA    110.51  3.000
 7GA  H62C  C6   CA    110.90  3.000
 7GA  H61C  C6   CA    111.99  3.000
 7GA  HXT   OXT  C     109.91  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
 7GA  CONST_01  HXT   OXT  C   CA   180.00   0.0  0
 7GA  Var_01    C10   C9   C8  CA   178.01  30.0  3
 7GA  Var_02    H101  C10  C9  C8  -176.21  30.0  3
 7GA  Var_03    H111  C11  C9  C8    63.87  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 7GA  chir_01  CA  C  C8  C6  positiv

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
 7GA  plan-1  CA   0.020
 7GA  plan-1  C    0.020
 7GA  plan-1  O    0.020
 7GA  plan-1  OXT  0.020
 7GA  plan-1  HXT  0.020

