# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:27:15 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 1-(biphenyl-3-yl)-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1ccc(cc1)c2cccc(c2)n3ccnc3
#
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
 53O  53O  1-(biphenyl-3-yl)-1H-imidazole  ligand  29  17  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_53O
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
 53O  CAK  C  CR15  0  -0.115   3.8484   0.2930  -0.6736
 53O  CAD  C  CR15  0  -0.214   4.7085  -0.7603  -0.5923
 53O  NAO  N  N     0  -0.445   4.1212  -1.8050   0.0676
 53O  CAL  C  CR15  0   0.088   2.9229  -1.3944   0.3761
 53O  NBC  N  NR5   0  -0.529   2.6988  -0.1247  -0.0506
 53O  CAY  C  CR6   0   0.388   1.5144   0.6197   0.1286
 53O  CAN  C  CR16  0  -0.374   0.2850  -0.0069  -0.0203
 53O  CAI  C  CR16  0  -0.309   1.5852   1.9708   0.4430
 53O  CAC  C  CR16  0  -0.233   0.4093   2.6870   0.6030
 53O  CAH  C  CR16  0  -0.315  -0.8221   2.0638   0.4730
 53O  CAX  C  CR6   0   0.104  -0.8989   0.7053   0.1648
 53O  CAW  C  CR6   0   0.085  -2.2047   0.0297   0.0239
 53O  CAM  C  CR16  0  -0.306  -2.3832  -1.2772   0.4805
 53O  CAG  C  CR16  0  -0.308  -3.2884   0.6843  -0.5643
 53O  CAB  C  CR16  0  -0.239  -4.5154   0.0502  -0.6916
 53O  CAF  C  CR16  0  -0.264  -4.6814  -1.2501  -0.2330
 53O  CAV  C  CR16  0  -0.240  -3.6103  -1.9116   0.3530
 53O  H1   H  HCR5  0   0.300   3.9379   1.2645  -1.1295
 53O  H2   H  HCR5  0   0.258   5.7142  -0.8210  -0.9783
 53O  H3   H  HCR5  0   0.289   2.1799  -1.9548   0.9234
 53O  H4   H  HCR6  0   0.279   0.2472  -1.0477  -0.3169
 53O  H5   H  HCR6  0   0.281   2.5427   2.4565   0.5783
 53O  H6   H  HCR6  0   0.269   0.4560   3.7384   0.8529
 53O  H7   H  HCR6  0   0.261  -1.7275   2.6348   0.6325
 53O  H8   H  HCR6  0   0.255  -1.5645  -1.7981   0.9614
 53O  H9   H  HCR6  0   0.256  -3.1693   1.6910  -0.9454
 53O  H10  H  HCR6  0   0.259  -5.3420   0.5717  -1.1564
 53O  H11  H  HCR6  0   0.259  -5.6394  -1.7439  -0.3312
 53O  H12  H  HCR6  0   0.259  -3.7323  -2.9223   0.7203

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
 53O  CAD  NAO  aromatic  1.368  0.020  1.368
 53O  CAD  CAK  aromatic  1.362  0.020  1.362
 53O  NAO  CAL  aromatic  1.304  0.020  1.304
 53O  CAK  NBC  aromatic  1.373  0.020  1.373
 53O  CAL  NBC  aromatic  1.358  0.020  1.358
 53O  NBC  CAY  single    1.410  0.020  1.410
 53O  CAV  CAM  aromatic  1.387  0.020  1.387
 53O  CAV  CAF  aromatic  1.389  0.020  1.389
 53O  CAM  CAW  aromatic  1.396  0.020  1.396
 53O  CAN  CAY  aromatic  1.388  0.020  1.388
 53O  CAN  CAX  aromatic  1.394  0.020  1.394
 53O  CAY  CAI  aromatic  1.389  0.020  1.389
 53O  CAF  CAB  aromatic  1.389  0.020  1.389
 53O  CAW  CAX  single    1.477  0.020  1.477
 53O  CAW  CAG  aromatic  1.396  0.020  1.396
 53O  CAX  CAH  aromatic  1.395  0.020  1.395
 53O  CAI  CAC  aromatic  1.386  0.020  1.386
 53O  CAB  CAG  aromatic  1.387  0.020  1.387
 53O  CAH  CAC  aromatic  1.386  0.020  1.386
 53O  CAK  H1   single    0.930  0.020  1.080
 53O  CAD  H2   single    0.930  0.020  1.080
 53O  CAL  H3   single    0.930  0.020  1.080
 53O  CAN  H4   single    0.930  0.020  1.080
 53O  CAI  H5   single    0.930  0.020  1.080
 53O  CAC  H6   single    0.930  0.020  1.080
 53O  CAH  H7   single    0.930  0.020  1.080
 53O  CAM  H8   single    0.930  0.020  1.080
 53O  CAG  H9   single    0.930  0.020  1.080
 53O  CAB  H10  single    0.930  0.020  1.080
 53O  CAF  H11  single    0.930  0.020  1.080
 53O  CAV  H12  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
 53O  H1   CAK  NBC  122.43  3.000
 53O  H1   CAK  CAD  132.09  3.000
 53O  NBC  CAK  CAD  105.45  3.000
 53O  H2   CAD  NAO  121.99  3.000
 53O  H2   CAD  CAK  127.64  3.000
 53O  NAO  CAD  CAK  110.37  3.000
 53O  CAL  NAO  CAD  105.56  3.000
 53O  H3   CAL  NBC  122.07  3.000
 53O  H3   CAL  NAO  126.09  3.000
 53O  NBC  CAL  NAO  111.83  3.000
 53O  CAY  NBC  CAL  126.31  3.000
 53O  CAY  NBC  CAK  126.89  3.000
 53O  CAL  NBC  CAK  106.79  3.000
 53O  CAI  CAY  CAN  120.57  3.000
 53O  CAI  CAY  NBC  119.96  3.000
 53O  CAN  CAY  NBC  119.47  3.000
 53O  H4   CAN  CAX  119.85  3.000
 53O  H4   CAN  CAY  119.62  3.000
 53O  CAX  CAN  CAY  120.49  3.000
 53O  H5   CAI  CAC  120.28  3.000
 53O  H5   CAI  CAY  120.67  3.000
 53O  CAC  CAI  CAY  119.04  3.000
 53O  H6   CAC  CAH  119.80  3.000
 53O  H6   CAC  CAI  119.49  3.000
 53O  CAH  CAC  CAI  120.70  3.000
 53O  H7   CAH  CAX  120.02  3.000
 53O  H7   CAH  CAC  119.48  3.000
 53O  CAX  CAH  CAC  120.49  3.000
 53O  CAW  CAX  CAH  121.01  3.000
 53O  CAH  CAX  CAN  118.69  3.000
 53O  CAW  CAX  CAN  120.30  3.000
 53O  CAG  CAW  CAM  118.53  3.000
 53O  CAG  CAW  CAX  120.80  3.000
 53O  CAM  CAW  CAX  120.67  3.000
 53O  H8   CAM  CAV  119.31  3.000
 53O  H8   CAM  CAW  119.93  3.000
 53O  CAV  CAM  CAW  120.75  3.000
 53O  H9   CAG  CAB  119.34  3.000
 53O  H9   CAG  CAW  119.92  3.000
 53O  CAB  CAG  CAW  120.73  3.000
 53O  H10  CAB  CAF  120.11  3.000
 53O  H10  CAB  CAG  119.66  3.000
 53O  CAF  CAB  CAG  120.23  3.000
 53O  H11  CAF  CAV  120.25  3.000
 53O  H11  CAF  CAB  120.20  3.000
 53O  CAV  CAF  CAB  119.55  3.000
 53O  H12  CAV  CAF  120.07  3.000
 53O  H12  CAV  CAM  119.71  3.000
 53O  CAF  CAV  CAM  120.21  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
 53O  CONST_01  CAL  NAO  CAD  CAK    0.00  0.0  0
 53O  CONST_02  NAO  CAL  NBC  CAK    0.00  0.0  0
 53O  CONST_05  NBC  CAL  NAO  CAD    0.00  0.0  0
 53O  CONST_06  CAL  NBC  CAK  CAD    0.00  0.0  0
 53O  CONST_07  CAY  NBC  CAK  CAD  180.00  0.0  0
 53O  CONST_08  NBC  CAK  CAD  NAO    0.00  0.0  0
 53O  CONST_09  CAY  NBC  CAL  NAO  180.00  0.0  0
 53O  CONST_12  CAX  CAN  CAY  NBC  180.00  0.0  0
 53O  CONST_13  CAC  CAI  CAY  NBC  180.00  0.0  0
 53O  CONST_14  CAW  CAX  CAN  CAY  180.00  0.0  0
 53O  CONST_15  CAH  CAX  CAN  CAY    0.00  0.0  0
 53O  CONST_16  CAH  CAC  CAI  CAY    0.00  0.0  0
 53O  CONST_17  CAC  CAI  CAY  CAN    0.00  0.0  0
 53O  CONST_20  CAC  CAH  CAX  CAN    0.00  0.0  0
 53O  CONST_21  CAX  CAN  CAY  CAI    0.00  0.0  0
 53O  CONST_22  CAX  CAH  CAC  CAI    0.00  0.0  0
 53O  CONST_23  CAW  CAX  CAH  CAC  180.00  0.0  0
 53O  CONST_26  CAV  CAM  CAW  CAX  180.00  0.0  0
 53O  CONST_27  CAB  CAG  CAW  CAX  180.00  0.0  0
 53O  CONST_28  CAF  CAV  CAM  CAW    0.00  0.0  0
 53O  CONST_29  CAF  CAB  CAG  CAW    0.00  0.0  0
 53O  CONST_30  CAB  CAF  CAV  CAM    0.00  0.0  0
 53O  CONST_31  CAB  CAG  CAW  CAM    0.00  0.0  0
 53O  CONST_32  CAV  CAM  CAW  CAG    0.00  0.0  0
 53O  CONST_33  CAV  CAF  CAB  CAG    0.00  0.0  0
 53O  CONST_34  H3   CAL  NBC  CAK  180.00  0.0  0
 53O  CONST_35  H1   CAK  CAD  NAO  180.00  0.0  0
 53O  CONST_36  H2   CAD  NAO  CAL  180.00  0.0  0
 53O  CONST_37  H4   CAN  CAY  NBC    0.00  0.0  0
 53O  CONST_38  H5   CAI  CAY  NBC    0.00  0.0  0
 53O  CONST_39  H6   CAC  CAI  CAY  180.00  0.0  0
 53O  CONST_40  H7   CAH  CAX  CAN  180.00  0.0  0
 53O  CONST_41  H8   CAM  CAW  CAX    0.00  0.0  0
 53O  CONST_42  H9   CAG  CAW  CAX    0.00  0.0  0
 53O  CONST_43  H12  CAV  CAM  CAW  180.00  0.0  0
 53O  CONST_44  H10  CAB  CAG  CAW  180.00  0.0  0
 53O  CONST_45  H11  CAF  CAV  CAM  180.00  0.0  0

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
 53O  plan-1  CAK  0.020
 53O  plan-1  CAD  0.020
 53O  plan-1  NAO  0.020
 53O  plan-1  CAL  0.020
 53O  plan-1  NBC  0.020
 53O  plan-1  CAY  0.020
 53O  plan-1  H1   0.020
 53O  plan-1  H2   0.020
 53O  plan-1  H3   0.020
 53O  plan-2  NBC  0.020
 53O  plan-2  CAY  0.020
 53O  plan-2  CAN  0.020
 53O  plan-2  CAI  0.020
 53O  plan-2  CAC  0.020
 53O  plan-2  CAH  0.020
 53O  plan-2  CAX  0.020
 53O  plan-2  CAW  0.020
 53O  plan-2  H4   0.020
 53O  plan-2  H5   0.020
 53O  plan-2  H6   0.020
 53O  plan-2  H7   0.020
 53O  plan-3  CAX  0.020
 53O  plan-3  CAW  0.020
 53O  plan-3  CAM  0.020
 53O  plan-3  CAG  0.020
 53O  plan-3  CAB  0.020
 53O  plan-3  CAF  0.020
 53O  plan-3  CAV  0.020
 53O  plan-3  H8   0.020
 53O  plan-3  H9   0.020
 53O  plan-3  H10  0.020
 53O  plan-3  H11  0.020
 53O  plan-3  H12  0.020

