# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 03:53:08 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 2-phenyl-1H-imidazole-4,5-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]c(nc1C(O)=O)c2ccccc2
#
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
 4F8  4F8  '2-phenyl-1H-imidazole-4,5-dicarboxylic acid'  ligand  25  17  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4F8
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
 4F8  N4C  N  N     0  -0.440  -0.0525  -1.1186  -0.0600
 4F8  C5C  C  CR5   0   0.035  -1.3443  -0.7205  -0.0457
 4F8  C6C  C  CR5   0   0.223  -1.4153   0.6590   0.0149
 4F8  C7C  C  C     0   0.473  -2.5234   1.6169   0.1215
 4F8  O8C  O  O     0  -0.411  -3.6695   1.3237   0.3359
 4F8  O9C  O  OH1   0  -0.602  -2.0841   2.8604  -0.0331
 4F8  C1D  C  CR6   0   0.026   2.1354   0.0089  -0.0073
 4F8  C2D  C  CR16  0  -0.285   2.8380  -1.1953   0.0591
 4F8  C3D  C  CR16  0  -0.237   4.2228  -1.1966   0.0641
 4F8  C4D  C  CR16  0  -0.255   4.9237   0.0016   0.0030
 4F8  C5D  C  CR16  0  -0.237   4.2303   1.2025  -0.0645
 4F8  C6D  C  CR16  0  -0.300   2.8440   1.2085  -0.0708
 4F8  C7D  C  CR5   0   0.502   0.6755  -0.0250  -0.0118
 4F8  O    O  O     0  -0.421  -3.5720  -1.4380  -0.4592
 4F8  O2   O  OH1   0  -0.586  -2.0131  -2.9299   0.1184
 4F8  N3   N  NR15  0  -0.670  -0.1151   1.0651   0.0337
 4F8  C6   C  C     0   0.453  -2.4384  -1.7051  -0.1518
 4F8  H3   H  HNR5  0   0.438   0.1867   2.0264   0.1047
 4F8  H9C  H  HOH1  0   0.498  -2.8105   3.4920   0.0821
 4F8  H2D  H  HCR6  0   0.261   2.2941  -2.1291   0.1095
 4F8  H6D  H  HCR6  0   0.249   2.3308   2.1600  -0.1328
 4F8  H3D  H  HCR6  0   0.265   4.7572  -2.1358   0.1178
 4F8  H4D  H  HCR6  0   0.265   6.0056  -0.0008   0.0066
 4F8  H5D  H  HCR6  0   0.267   4.7686   2.1394  -0.1158
 4F8  H2   H  HOH1  0   0.489  -2.7442  -3.5574   0.0135

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
 4F8  N4C  C5C  aromatic  1.352  0.020  1.352
 4F8  N4C  C7D  aromatic  1.315  0.020  1.315
 4F8  C5C  C6C  aromatic  1.383  0.020  1.383
 4F8  C5C  C6   single    1.476  0.020  1.476
 4F8  C6C  C7C  single    1.469  0.020  1.469
 4F8  C6C  N3   aromatic  1.362  0.020  1.362
 4F8  C7C  O8C  double    1.202  0.020  1.202
 4F8  C7C  O9C  single    1.328  0.020  1.328
 4F8  C1D  C2D  aromatic  1.396  0.020  1.396
 4F8  C1D  C6D  aromatic  1.395  0.020  1.395
 4F8  C1D  C7D  single    1.460  0.020  1.460
 4F8  C2D  C3D  aromatic  1.385  0.020  1.385
 4F8  C3D  C4D  aromatic  1.390  0.020  1.390
 4F8  C4D  C5D  aromatic  1.388  0.020  1.388
 4F8  C5D  C6D  aromatic  1.386  0.020  1.386
 4F8  C7D  N3   aromatic  1.347  0.020  1.347
 4F8  O    C6   double    1.204  0.020  1.204
 4F8  O2   C6   single    1.324  0.020  1.324
 4F8  N3   H3   single    0.860  0.020  1.020
 4F8  O9C  H9C  single    0.850  0.020  0.980
 4F8  C2D  H2D  single    0.930  0.020  1.080
 4F8  C6D  H6D  single    0.930  0.020  1.080
 4F8  C3D  H3D  single    0.930  0.020  1.080
 4F8  C4D  H4D  single    0.930  0.020  1.080
 4F8  C5D  H5D  single    0.930  0.020  1.080
 4F8  O2   H2   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
 4F8  C7D  N4C  C5C  106.49  3.000
 4F8  C6   C5C  C6C  129.11  3.000
 4F8  C6   C5C  N4C  120.75  3.000
 4F8  C6C  C5C  N4C  110.08  3.000
 4F8  N3   C6C  C7C  121.65  3.000
 4F8  N3   C6C  C5C  104.42  3.000
 4F8  C7C  C6C  C5C  133.84  3.000
 4F8  O9C  C7C  O8C  124.36  3.000
 4F8  O9C  C7C  C6C  110.66  3.000
 4F8  O8C  C7C  C6C  124.97  3.000
 4F8  H9C  O9C  C7C  110.39  3.000
 4F8  C7D  C1D  C6D  121.85  3.000
 4F8  C7D  C1D  C2D  118.90  3.000
 4F8  C6D  C1D  C2D  119.24  3.000
 4F8  H2D  C2D  C3D  120.12  3.000
 4F8  H2D  C2D  C1D  119.60  3.000
 4F8  C3D  C2D  C1D  120.29  3.000
 4F8  H3D  C3D  C4D  120.10  3.000
 4F8  H3D  C3D  C2D  119.67  3.000
 4F8  C4D  C3D  C2D  120.23  3.000
 4F8  H4D  C4D  C5D  120.10  3.000
 4F8  H4D  C4D  C3D  120.16  3.000
 4F8  C5D  C4D  C3D  119.74  3.000
 4F8  H5D  C5D  C6D  119.58  3.000
 4F8  H5D  C5D  C4D  120.19  3.000
 4F8  C6D  C5D  C4D  120.23  3.000
 4F8  H6D  C6D  C5D  118.56  3.000
 4F8  H6D  C6D  C1D  121.17  3.000
 4F8  C5D  C6D  C1D  120.27  3.000
 4F8  N3   C7D  C1D  124.59  3.000
 4F8  N3   C7D  N4C  110.44  3.000
 4F8  C1D  C7D  N4C  124.97  3.000
 4F8  H2   O2   C6   109.54  3.000
 4F8  H3   N3   C7D  126.66  3.000
 4F8  H3   N3   C6C  124.74  3.000
 4F8  C7D  N3   C6C  108.56  3.000
 4F8  O2   C6   O    124.01  3.000
 4F8  O2   C6   C5C  111.36  3.000
 4F8  O    C6   C5C  124.62  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
 4F8  CONST_01  N3   C6C  C5C  N4C     0.00   0.0  0
 4F8  CONST_02  C2D  C1D  C7D  N4C     0.00   0.0  0
 4F8  CONST_03  C6D  C1D  C7D  N4C   180.00   0.0  0
 4F8  CONST_04  C6C  N3   C7D  N4C     0.00   0.0  0
 4F8  CONST_05  C1D  C7D  N4C  C5C   180.00   0.0  0
 4F8  CONST_06  N3   C7D  N4C  C5C     0.00   0.0  0
 4F8  CONST_07  C7D  N3   C6C  C5C     0.00   0.0  0
 4F8  CONST_08  C7D  N4C  C5C  C6C     0.00   0.0  0
 4F8  CONST_09  C1D  C7D  N3   C6C   180.00   0.0  0
 4F8  CONST_10  C4D  C3D  C2D  C1D     0.00   0.0  0
 4F8  CONST_11  C4D  C5D  C6D  C1D     0.00   0.0  0
 4F8  CONST_12  C5D  C6D  C1D  C2D     0.00   0.0  0
 4F8  CONST_13  N3   C7D  C1D  C2D   180.00   0.0  0
 4F8  CONST_14  C5D  C4D  C3D  C2D     0.00   0.0  0
 4F8  CONST_15  C6D  C1D  C2D  C3D     0.00   0.0  0
 4F8  CONST_16  C7D  C1D  C2D  C3D   180.00   0.0  0
 4F8  CONST_17  C6D  C5D  C4D  C3D     0.00   0.0  0
 4F8  CONST_18  C7D  C1D  C6D  C5D   180.00   0.0  0
 4F8  CONST_19  N3   C7D  C1D  C6D     0.00   0.0  0
 4F8  CONST_20  C7C  C6C  C5C  N4C   180.00   0.0  0
 4F8  CONST_21  C7D  N3   C6C  C7C   180.00   0.0  0
 4F8  CONST_22  C6   C5C  N4C  C7D   180.00   0.0  0
 4F8  CONST_23  C6   C5C  C6C  N3    180.00   0.0  0
 4F8  CONST_24  H3   N3   C7D  N4C   180.00   0.0  0
 4F8  CONST_25  H3D  C3D  C2D  C1D   180.00   0.0  0
 4F8  CONST_26  H5D  C5D  C6D  C1D   180.00   0.0  0
 4F8  CONST_27  H6D  C6D  C1D  C2D   180.00   0.0  0
 4F8  CONST_28  H4D  C4D  C3D  C2D   180.00   0.0  0
 4F8  CONST_29  H2D  C2D  C3D  C4D   180.00   0.0  0
 4F8  CONST_30  H2   O2   C6   C5C   180.00   0.0  0
 4F8  CONST_31  H9C  O9C  C7C  C6C   180.00   0.0  0
 4F8  Var_01    O    C6   C5C  N4C  -161.69  30.0  2
 4F8  Var_02    O8C  C7C  C6C  C5C     9.12  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
 4F8  plan-1  N4C  0.020
 4F8  plan-1  C5C  0.020
 4F8  plan-1  C6C  0.020
 4F8  plan-1  C7C  0.020
 4F8  plan-1  C1D  0.020
 4F8  plan-1  C7D  0.020
 4F8  plan-1  N3   0.020
 4F8  plan-1  C6   0.020
 4F8  plan-1  H3   0.020
 4F8  plan-2  C1D  0.020
 4F8  plan-2  C2D  0.020
 4F8  plan-2  C3D  0.020
 4F8  plan-2  C4D  0.020
 4F8  plan-2  C5D  0.020
 4F8  plan-2  C6D  0.020
 4F8  plan-2  C7D  0.020
 4F8  plan-2  H2D  0.020
 4F8  plan-2  H6D  0.020
 4F8  plan-2  H3D  0.020
 4F8  plan-2  H4D  0.020
 4F8  plan-2  H5D  0.020
 4F8  plan-3  C6C  0.020
 4F8  plan-3  C7C  0.020
 4F8  plan-3  O8C  0.020
 4F8  plan-3  O9C  0.020
 4F8  plan-3  H9C  0.020
 4F8  plan-4  C5C  0.020
 4F8  plan-4  O    0.020
 4F8  plan-4  O2   0.020
 4F8  plan-4  C6   0.020
 4F8  plan-4  H2   0.020

