# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 16:06:14 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: dimethyl butanedioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CCC(=O)OC
#
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
 9HB  9HB  'dimethyl butanedioate    '  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_9HB
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
 9HB  C10  C  CH3   0  -0.425   4.2280   0.1448  -0.0075
 9HB  C01  C  CH3   0  -0.425  -4.2591  -0.1014  -0.0229
 9HB  O02  O  O2    0  -0.455  -2.9315  -0.6262   0.0001
 9HB  C03  C  C     0   0.609  -1.9285   0.2406  -0.0370
 9HB  O04  O  O     0  -0.452  -2.0838   1.4351  -0.0875
 9HB  C05  C  CH2   0  -0.583  -0.5984  -0.4636  -0.0099
 9HB  C06  C  CH2   0  -0.583   0.5672   0.5070  -0.0151
 9HB  C07  C  C     0   0.609   1.8974  -0.1968   0.0165
 9HB  O08  O  O     0  -0.452   2.0525  -1.3906   0.0822
 9HB  O09  O  O2    0  -0.455   2.9002   0.6693  -0.0346
 9HB  H1   H  HCH3  0   0.252   4.8893   1.0018  -0.0940
 9HB  H2   H  HCH3  0   0.239   4.4313  -0.3749   0.9287
 9HB  H3   H  HCH3  0   0.239   4.4069  -0.5344  -0.8407
 9HB  H4   H  HCH3  0   0.252  -4.9208  -0.9598   0.0445
 9HB  H5   H  HCH3  0   0.238  -4.4413   0.5620   0.8221
 9HB  H6   H  HCH3  0   0.239  -4.4588   0.4360  -0.9498
 9HB  H7   H  HCH2  0   0.288  -0.5685  -1.1082   0.8720
 9HB  H8   H  HCH2  0   0.289  -0.5510  -1.1353  -0.8711
 9HB  H9   H  HCH2  0   0.287   0.5388   1.1498  -0.8983
 9HB  H10  H  HCH2  0   0.289   0.5179   1.1803   0.8449

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
 9HB  C10  O09  single  1.428  0.020  1.428
 9HB  O08  C07  double  1.206  0.020  1.206
 9HB  O09  C07  single  1.326  0.020  1.326
 9HB  C07  C06  single  1.505  0.020  1.505
 9HB  C06  C05  single  1.517  0.020  1.517
 9HB  C05  C03  single  1.505  0.020  1.505
 9HB  C03  O02  single  1.326  0.020  1.326
 9HB  C03  O04  double  1.206  0.020  1.206
 9HB  O02  C01  single  1.428  0.020  1.428
 9HB  C10  H1   single  0.970  0.020  1.090
 9HB  C10  H2   single  0.970  0.020  1.090
 9HB  C10  H3   single  0.970  0.020  1.090
 9HB  C01  H4   single  0.970  0.020  1.090
 9HB  C01  H5   single  0.970  0.020  1.090
 9HB  C01  H6   single  0.970  0.020  1.090
 9HB  C05  H7   single  0.970  0.020  1.090
 9HB  C05  H8   single  0.970  0.020  1.090
 9HB  C06  H9   single  0.970  0.020  1.090
 9HB  C06  H10  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
 9HB  H3   C10  H2   109.21  3.000
 9HB  H3   C10  H1   109.33  3.000
 9HB  H2   C10  H1   109.34  3.000
 9HB  H3   C10  O09  111.53  3.000
 9HB  H2   C10  O09  111.40  3.000
 9HB  H1   C10  O09  105.95  3.000
 9HB  H6   C01  H5   109.19  3.000
 9HB  H6   C01  H4   109.33  3.000
 9HB  H5   C01  H4   109.34  3.000
 9HB  H6   C01  O02  111.43  3.000
 9HB  H5   C01  O02  111.52  3.000
 9HB  H4   C01  O02  105.97  3.000
 9HB  C03  O02  C01  117.55  3.000
 9HB  C05  C03  O04  125.32  3.000
 9HB  O04  C03  O02  123.46  3.000
 9HB  C05  C03  O02  111.22  3.000
 9HB  H8   C05  H7   105.80  3.000
 9HB  H8   C05  C06  110.93  3.000
 9HB  H7   C05  C06  111.05  3.000
 9HB  H8   C05  C03  108.15  3.000
 9HB  H7   C05  C03  108.34  3.000
 9HB  C06  C05  C03  112.31  3.000
 9HB  H10  C06  H9   105.80  3.000
 9HB  H10  C06  C07  108.14  3.000
 9HB  H9   C06  C07  108.36  3.000
 9HB  H10  C06  C05  110.90  3.000
 9HB  H9   C06  C05  111.05  3.000
 9HB  C07  C06  C05  112.32  3.000
 9HB  O09  C07  O08  123.47  3.000
 9HB  O09  C07  C06  111.23  3.000
 9HB  O08  C07  C06  125.30  3.000
 9HB  C07  O09  C10  117.56  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
 9HB  Var_01  O08  C07  O09  C10    -0.09  30.0  3
 9HB  Var_02  C05  C03  O02  C01  -179.85  30.0  2
 9HB  Var_03  C06  C05  C03  O02  -178.52  30.0  1
 9HB  Var_04  C07  C06  C05  C03   179.81  30.0  1
 9HB  Var_05  H4   C01  O02  C03  -178.32  30.0  3
 9HB  Var_06  H1   C10  O09  C07   177.99  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
 9HB  plan-1  C06  0.020
 9HB  plan-1  C07  0.020
 9HB  plan-1  O08  0.020
 9HB  plan-1  O09  0.020
 9HB  plan-2  O02  0.020
 9HB  plan-2  C03  0.020
 9HB  plan-2  O04  0.020
 9HB  plan-2  C05  0.020

