# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 19:07:28 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (2~{R})-2-methyloctanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[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
 C9T  C9T  '(2~{R})-2-methyloctanoic acid'  ligand  28  11  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C9T
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
 C9T  C1   C  CH3    0  -0.662   5.7072  -0.1345  -0.1514
 C9T  C2   C  CH2    0  -0.418   4.4044   0.6180   0.0822
 C9T  C3   C  CH2    0  -0.404   3.1718  -0.2583  -0.1022
 C9T  C4   C  CH2    0  -0.407   1.8600   0.4819   0.1290
 C9T  C5   C  CH2    0  -0.417   0.6312  -0.3897  -0.1001
 C9T  C6   C  CH2    0  -0.388  -0.6802   0.3381   0.1824
 C9T  C7   C  CH1    0  -0.364  -1.9272  -0.4265  -0.2533
 C9T  C7B  C  CH3    0  -0.662  -2.0707  -1.7676   0.4688
 C9T  C    C  C      0   0.420  -3.2347   0.3818  -0.0894
 C9T  O    O  O      0  -0.606  -3.1838   1.4685   0.5217
 C9T  H11  H  HCH3   0   0.215   5.8176  -0.9625   0.5513
 C9T  H13  H  HCH3   0   0.215   5.7441  -0.5527  -1.1592
 C9T  H12  H  HCH3   0   0.225   6.5744   0.5166  -0.0333
 C9T  H21  H  HCH2   0   0.209   4.4004   1.0409   1.0918
 C9T  H22  H  HCH2   0   0.209   4.3487   1.4702  -0.6025
 C9T  H32  H  HCH2   0   0.204   3.1762  -0.6796  -1.1138
 C9T  H31  H  HCH2   0   0.204   3.2293  -1.1131   0.5810
 C9T  H41  H  HCH2   0   0.203   1.8427   0.8779   1.1506
 C9T  H42  H  HCH2   0   0.203   1.8153   1.3532  -0.5341
 C9T  H52  H  HCH2   0   0.199   0.6342  -0.7492  -1.1358
 C9T  H51  H  HCH2   0   0.207   0.7073  -1.2823   0.5283
 C9T  H61  H  HCH2   0   0.194  -0.7429   0.5671   1.2513
 C9T  H62  H  HCH2   0   0.201  -0.6599   1.3047  -0.3296
 C9T  H7   H  HCH1   0   0.202  -1.8261  -0.6468  -1.3248
 C9T  HB2  H  HCH3   0   0.222  -2.9511  -2.3049   0.1178
 C9T  HB1  H  HCH3   0   0.219  -1.2071  -2.4147   0.3101
 C9T  HB3  H  HCH3   0   0.207  -2.1771  -1.6228   1.5473
 C9T  O1   O  OC    -1  -0.629  -4.2621  -0.1325  -0.5817

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
 C9T  C2   C1   single  1.523  0.020  1.523
 C9T  C2   C3   single  1.524  0.020  1.524
 C9T  C6   C5   single  1.526  0.020  1.526
 C9T  C6   C7   single  1.526  0.020  1.526
 C9T  C    O    deloc   1.248  0.020  1.248
 C9T  C    C7   single  1.546  0.020  1.546
 C9T  C7   C7B  single  1.530  0.020  1.530
 C9T  C5   C4   single  1.524  0.020  1.524
 C9T  C4   C3   single  1.524  0.020  1.524
 C9T  C1   H11  single  0.970  0.020  1.090
 C9T  C1   H13  single  0.970  0.020  1.090
 C9T  C1   H12  single  0.970  0.020  1.090
 C9T  C2   H21  single  0.970  0.020  1.090
 C9T  C2   H22  single  0.970  0.020  1.090
 C9T  C3   H32  single  0.970  0.020  1.090
 C9T  C3   H31  single  0.970  0.020  1.090
 C9T  C4   H41  single  0.970  0.020  1.090
 C9T  C4   H42  single  0.970  0.020  1.090
 C9T  C5   H52  single  0.970  0.020  1.090
 C9T  C5   H51  single  0.970  0.020  1.090
 C9T  C6   H61  single  0.970  0.020  1.090
 C9T  C6   H62  single  0.970  0.020  1.090
 C9T  C7   H7   single  0.970  0.020  1.090
 C9T  C7B  HB2  single  0.970  0.020  1.090
 C9T  C7B  HB1  single  0.970  0.020  1.090
 C9T  C7B  HB3  single  0.970  0.020  1.090
 C9T  C    O1   deloc   1.250  0.020  1.250

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
 C9T  H12  C1   H13  107.57  3.000
 C9T  H12  C1   H11  107.62  3.000
 C9T  H13  C1   H11  107.48  3.000
 C9T  H12  C1   C2   111.63  3.000
 C9T  H13  C1   C2   111.09  3.000
 C9T  H11  C1   C2   111.26  3.000
 C9T  H22  C2   H21  106.02  3.000
 C9T  H22  C2   C3   109.32  3.000
 C9T  H21  C2   C3   109.32  3.000
 C9T  H22  C2   C1   109.41  3.000
 C9T  H21  C2   C1   109.61  3.000
 C9T  C3   C2   C1   112.92  3.000
 C9T  H31  C3   H32  105.99  3.000
 C9T  H31  C3   C4   109.24  3.000
 C9T  H32  C3   C4   109.28  3.000
 C9T  H31  C3   C2   109.31  3.000
 C9T  H32  C3   C2   109.24  3.000
 C9T  C4   C3   C2   113.50  3.000
 C9T  H42  C4   H41  106.03  3.000
 C9T  H42  C4   C5   109.32  3.000
 C9T  H41  C4   C5   109.52  3.000
 C9T  H42  C4   C3   109.25  3.000
 C9T  H41  C4   C3   109.30  3.000
 C9T  C5   C4   C3   113.17  3.000
 C9T  H51  C5   H52  105.95  3.000
 C9T  H51  C5   C6   110.03  3.000
 C9T  H52  C5   C6   109.49  3.000
 C9T  H51  C5   C4   108.91  3.000
 C9T  H52  C5   C4   109.11  3.000
 C9T  C6   C5   C4   113.10  3.000
 C9T  H62  C6   H61  105.85  3.000
 C9T  H62  C6   C7   108.92  3.000
 C9T  H61  C6   C7   109.68  3.000
 C9T  H62  C6   C5   108.59  3.000
 C9T  H61  C6   C5   109.25  3.000
 C9T  C7   C6   C5   114.22  3.000
 C9T  H7   C7   C    106.63  3.000
 C9T  H7   C7   C7B  107.05  3.000
 C9T  C    C7   C7B  109.21  3.000
 C9T  H7   C7   C6   107.68  3.000
 C9T  C7B  C7   C6   112.40  3.000
 C9T  C    C7   C6   113.50  3.000
 C9T  HB3  C7B  HB1  107.41  3.000
 C9T  HB3  C7B  HB2  107.73  3.000
 C9T  HB1  C7B  HB2  107.48  3.000
 C9T  HB3  C7B  C7   111.01  3.000
 C9T  HB1  C7B  C7   112.16  3.000
 C9T  HB2  C7B  C7   110.86  3.000
 C9T  O1   C    O    125.79  3.000
 C9T  O1   C    C7   115.99  3.000
 C9T  O    C    C7   118.22  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
 C9T  Var_01  C4   C3  C2  C1  179.99  30.0  3
 C9T  Var_02  C5   C4  C3  C2  178.19  30.0  1
 C9T  Var_03  C6   C5  C4  C3  177.85  30.0  1
 C9T  Var_04  C7   C6  C5  C4  170.49  30.0  1
 C9T  Var_05  H11  C1  C2  C3  -60.88  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
 C9T  chir_01  C7  C6  C  C7B  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
 C9T  plan-1  C7  0.020
 C9T  plan-1  C   0.020
 C9T  plan-1  O   0.020
 C9T  plan-1  O1  0.020

