# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 21:42:19 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2~{S})-2-methylpentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CCC(O)=O)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
 9ON  9ON  '(2~{S})-2-methylpentanedioic acid'  ligand  20  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9ON
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
 9ON  O12  O  O     0  -0.441   2.3797  -1.4180  -0.4677
 9ON  C7   C  C     0   0.566   2.3624  -0.3496   0.0920
 9ON  O10  O  OH1   0  -0.596   3.4437   0.1895   0.6466
 9ON  C4   C  CH1   0  -0.382   1.1520   0.5461   0.2257
 9ON  C5   C  CH3   0  -0.667   1.3166   1.7456  -0.7168
 9ON  C3   C  CH2   0  -0.411  -0.1300  -0.2422  -0.0321
 9ON  C2   C  CH2   0  -0.591  -1.3774   0.5827   0.2424
 9ON  C1   C  C     0   0.557  -2.6497  -0.2062   0.1014
 9ON  O8   O  OH1   0  -0.597  -3.7203   0.5337   0.3754
 9ON  O9   O  O     0  -0.444  -2.7195  -1.3658  -0.2220
 9ON  H1   H  HOH1  0   0.479   4.2092  -0.3878   0.5063
 9ON  H2   H  HCH1  0   0.271   1.1383   0.9243   1.2537
 9ON  H3   H  HCH3  0   0.249   0.4871   2.4408  -0.5999
 9ON  H4   H  HCH3  0   0.249   2.2311   2.2992  -0.5102
 9ON  H5   H  HCH3  0   0.234   1.3384   1.4229  -1.7589
 9ON  H6   H  HCH2  0   0.237  -0.1416  -0.6010  -1.0634
 9ON  H7   H  HCH2  0   0.246  -0.1398  -1.1263   0.6085
 9ON  H8   H  HCH2  0   0.279  -1.3491   1.0080   1.2509
 9ON  H9   H  HCH2  0   0.283  -1.4480   1.4393  -0.4334
 9ON  H10  H  HOH1  0   0.479  -4.5233   0.0010   0.2770

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
 9ON  O12  C7   double  1.206  0.020  1.206
 9ON  C4   C7   single  1.512  0.020  1.512
 9ON  C4   C5   single  1.534  0.020  1.534
 9ON  C4   C3   single  1.527  0.020  1.527
 9ON  C7   O10  single  1.329  0.020  1.329
 9ON  C2   C3   single  1.520  0.020  1.520
 9ON  C2   C1   single  1.504  0.020  1.504
 9ON  O9   C1   double  1.206  0.020  1.206
 9ON  C1   O8   single  1.330  0.020  1.330
 9ON  O10  H1   single  0.850  0.020  0.980
 9ON  C4   H2   single  0.970  0.020  1.090
 9ON  C5   H3   single  0.970  0.020  1.090
 9ON  C5   H4   single  0.970  0.020  1.090
 9ON  C5   H5   single  0.970  0.020  1.090
 9ON  C3   H6   single  0.970  0.020  1.090
 9ON  C3   H7   single  0.970  0.020  1.090
 9ON  C2   H8   single  0.970  0.020  1.090
 9ON  C2   H9   single  0.970  0.020  1.090
 9ON  O8   H10  single  0.850  0.020  0.980

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
 9ON  C4   C7   O10  111.97  3.000
 9ON  O10  C7   O12  122.76  3.000
 9ON  C4   C7   O12  125.26  3.000
 9ON  H1   O10  C7   109.91  3.000
 9ON  H2   C4   C3   109.03  3.000
 9ON  H2   C4   C5   107.93  3.000
 9ON  C3   C4   C5   112.95  3.000
 9ON  H2   C4   C7   107.32  3.000
 9ON  C3   C4   C7   110.58  3.000
 9ON  C5   C4   C7   108.84  3.000
 9ON  H5   C5   H4   108.35  3.000
 9ON  H5   C5   H3   107.86  3.000
 9ON  H4   C5   H3   107.16  3.000
 9ON  H5   C5   C4   110.95  3.000
 9ON  H4   C5   C4   111.78  3.000
 9ON  H3   C5   C4   110.58  3.000
 9ON  H7   C3   H6   106.74  3.000
 9ON  H7   C3   C2   109.03  3.000
 9ON  H6   C3   C2   109.88  3.000
 9ON  H7   C3   C4   109.05  3.000
 9ON  H6   C3   C4   109.75  3.000
 9ON  C2   C3   C4   112.22  3.000
 9ON  H9   C2   H8   105.47  3.000
 9ON  H9   C2   C1   107.36  3.000
 9ON  H8   C2   C1   108.18  3.000
 9ON  H9   C2   C3   111.50  3.000
 9ON  H8   C2   C3   110.85  3.000
 9ON  C1   C2   C3   113.11  3.000
 9ON  O9   C1   O8   122.93  3.000
 9ON  O8   C1   C2   111.71  3.000
 9ON  O9   C1   C2   125.36  3.000
 9ON  H10  O8   C1   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
 9ON  CONST_01  H1   O10  C7  O12     0.00   0.0  0
 9ON  CONST_02  H10  O8   C1  C2    180.00   0.0  0
 9ON  Var_01    C1   C2   C3  C4   -175.39  30.0  1
 9ON  Var_02    O9   C1   C2  C3     -1.55  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
 9ON  chir_01  C4  C7  C5  C3  negativ

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
 9ON  plan-1  O12  0.020
 9ON  plan-1  C7   0.020
 9ON  plan-1  O10  0.020
 9ON  plan-1  C4   0.020
 9ON  plan-1  H1   0.020
 9ON  plan-2  C2   0.020
 9ON  plan-2  C1   0.020
 9ON  plan-2  O8   0.020
 9ON  plan-2  O9   0.020
 9ON  plan-2  H10  0.020

