# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:58:05 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: (2Z)-4,6-dioxooct-2-enedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC(=O)CC(=O)\C=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
 M8O  M8O  '(2Z)-4,6-dioxooct-2-enedioic acid'  ligand  22  14  .  2021-08-14  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M8O
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
 M8O  C1   C  C1    0  -0.405  18.8424  44.8147  -3.2348
 M8O  O1   O  OH1   0  -0.452  17.2657  43.2388   0.7115
 M8O  C2   C  C     0   0.490  17.3561  41.9966   0.2597
 M8O  O2   O  OH1   0  -0.580  19.8673  45.6050  -1.2982
 M8O  C3   C  C     0   0.526  19.4338  44.5230  -1.9202
 M8O  O3   O  O     0  -0.386  18.1882  41.2056   0.6199
 M8O  C4   C  CH2   0  -0.711  16.2837  41.7065  -0.7652
 M8O  O4   O  O     0  -0.461  19.5065  43.4044  -1.4591
 M8O  C5   C  C     0   0.398  16.6507  42.3094  -2.1099
 M8O  O5   O  O     0  -0.256  16.1125  43.3010  -2.5331
 M8O  C6   C  CH2   0  -0.690  17.6737  41.5518  -2.9120
 M8O  O6   O  O     0  -0.515  19.6130  41.8269  -4.2338
 M8O  C7   C  C1    0  -0.208  18.4253  43.8142  -4.0032
 M8O  C50  C  C     0   0.444  18.6611  42.3636  -3.7196
 M8O  H1   H  H     0   0.348  18.7265  45.8440  -3.5471
 M8O  HO1  H  HOH1  0   0.484  17.9786  43.4167   1.3436
 M8O  HO2  H  HOH1  0   0.477  20.2510  45.3701  -0.4396
 M8O  H4   H  HCH2  0   0.285  16.1889  40.6254  -0.8707
 M8O  H4A  H  HCH2  0   0.255  15.3308  42.1215  -0.4371
 M8O  H6   H  HCH2  0   0.320  18.2287  40.8409  -2.2987
 M8O  H6A  H  HCH2  0   0.301  17.1072  40.9416  -3.6289
 M8O  H7   H  H     0   0.334  17.9633  44.0276  -4.9614

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
 M8O  C7   C1   double  1.329  0.020  1.329
 M8O  C1   C3   single  1.471  0.020  1.471
 M8O  C1   H1   single  0.930  0.020  1.080
 M8O  C2   O1   single  1.325  0.020  1.325
 M8O  O1   HO1  single  0.850  0.020  0.980
 M8O  C4   C2   single  1.512  0.020  1.512
 M8O  O3   C2   double  1.203  0.020  1.203
 M8O  C3   O2   single  1.321  0.020  1.321
 M8O  O2   HO2  single  0.850  0.020  0.980
 M8O  C3   O4   double  1.212  0.020  1.212
 M8O  C5   C4   single  1.519  0.020  1.519
 M8O  C4   H4   single  0.970  0.020  1.090
 M8O  C4   H4A  single  0.970  0.020  1.090
 M8O  C6   C5   single  1.505  0.020  1.505
 M8O  O5   C5   double  1.205  0.020  1.205
 M8O  C50  C6   single  1.512  0.020  1.512
 M8O  C6   H6   single  0.970  0.020  1.090
 M8O  C6   H6A  single  0.970  0.020  1.090
 M8O  O6   C50  double  1.208  0.020  1.208
 M8O  C7   C50  single  1.497  0.020  1.497
 M8O  C7   H7   single  0.930  0.020  1.080

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
 M8O  H1   C1   C7   121.05  3.000
 M8O  H1   C1   C3   119.33  3.000
 M8O  C7   C1   C3   119.59  3.000
 M8O  HO1  O1   C2   110.14  3.000
 M8O  C4   C2   O3   124.57  3.000
 M8O  O3   C2   O1   124.16  3.000
 M8O  C4   C2   O1   111.27  3.000
 M8O  HO2  O2   C3   110.39  3.000
 M8O  O4   C3   O2   123.85  3.000
 M8O  O4   C3   C1   123.18  3.000
 M8O  O2   C3   C1   112.97  3.000
 M8O  H4A  C4   H4   109.31  3.000
 M8O  H4A  C4   C5   109.07  3.000
 M8O  H4   C4   C5   109.21  3.000
 M8O  H4A  C4   C2   110.06  3.000
 M8O  H4   C4   C2   108.52  3.000
 M8O  C5   C4   C2   110.66  3.000
 M8O  C6   C5   O5   122.07  3.000
 M8O  O5   C5   C4   121.98  3.000
 M8O  C6   C5   C4   115.87  3.000
 M8O  H6A  C6   H6   105.51  3.000
 M8O  H6A  C6   C50  106.63  3.000
 M8O  H6   C6   C50  108.54  3.000
 M8O  H6A  C6   C5   106.08  3.000
 M8O  H6   C6   C5   111.99  3.000
 M8O  C50  C6   C5   117.28  3.000
 M8O  H7   C7   C50  115.15  3.000
 M8O  H7   C7   C1   119.76  3.000
 M8O  C50  C7   C1   124.81  3.000
 M8O  C7   C50  O6   118.30  3.000
 M8O  C7   C50  C6   121.25  3.000
 M8O  O6   C50  C6   120.23  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
 M8O  CONST_01  HO2  O2   C3  C1  180.00   0.0  0
 M8O  CONST_02  HO1  O1   C2  O3    0.00   0.0  0
 M8O  Var_01    C50  C7   C1  C3   -8.17   0.0  2
 M8O  Var_02    C6   C50  C7  C1   90.35  30.0  2
 M8O  Var_03    C5   C4   C2  O1   77.97  30.0  2
 M8O  Var_04    C6   C5   C4  C2   77.78  30.0  1
 M8O  Var_05    C7   C1   C3  O2  176.61  30.0  2

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
 M8O  plan-1  C4   0.020
 M8O  plan-1  C5   0.020
 M8O  plan-1  O5   0.020
 M8O  plan-1  C6   0.020
 M8O  plan-2  C6   0.020
 M8O  plan-2  O6   0.020
 M8O  plan-2  C7   0.020
 M8O  plan-2  C50  0.020
 M8O  plan-3  O1   0.020
 M8O  plan-3  C2   0.020
 M8O  plan-3  O3   0.020
 M8O  plan-3  C4   0.020
 M8O  plan-3  HO1  0.020
 M8O  plan-4  C1   0.020
 M8O  plan-4  O2   0.020
 M8O  plan-4  C3   0.020
 M8O  plan-4  O4   0.020
 M8O  plan-4  HO2  0.020
 M8O  plan-5  C1   0.020
 M8O  plan-5  C3   0.020
 M8O  plan-5  C7   0.020
 M8O  plan-5  C50  0.020
 M8O  plan-5  H1   0.020
 M8O  plan-5  H7   0.020

