# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:13:38 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 1-(biphenyl-4-ylmethyl)-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(n1ccnc1)c2ccc(cc2)c3ccccc3
#
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
 PB2  PB2  1-(biphenyl-4-ylmethyl)-1H-imidazole  ligand  32  18  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PB2
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
 PB2  CDB   C  CR16  0  -0.309  -3.3751  -1.1536   0.5856
 PB2  CDC   C  CR16  0  -0.240  -4.7155  -1.1906   0.9411
 PB2  CDD   C  CR16  0  -0.266  -5.5261  -0.0833   0.7284
 PB2  CDE   C  CR16  0  -0.240  -4.9848   1.0607   0.1565
 PB2  CDF   C  CR16  0  -0.310  -3.6442   1.0976  -0.1984
 PB2  CDA   C  CR6   0   0.087  -2.8191  -0.0087   0.0114
 PB2  CCD   C  CR6   0   0.077  -1.3929   0.0253  -0.3697
 PB2  CCE   C  CR16  0  -0.296  -0.6258   1.1777  -0.1829
 PB2  CCF   C  CR16  0  -0.270   0.7116   1.2062  -0.5395
 PB2  CCC   C  CR16  0  -0.295  -0.7761  -1.0923  -0.9309
 PB2  CCB   C  CR16  0  -0.284   0.5633  -1.0601  -1.2907
 PB2  CCA   C  CR6   0   0.118   1.3228   0.0873  -1.0980
 PB2  CAA   C  CH2   0  -0.414   2.7852   0.1117  -1.4514
 PB2  NAB   N  NR5   0  -0.389   3.6261  -0.0144  -0.2747
 PB2  CAF   C  CR15  0  -0.100   3.7219  -1.1057   0.5417
 PB2  CAE   C  CR15  0  -0.216   4.5868  -0.7429   1.5343
 PB2  NAD   N  N     0  -0.457   5.0145   0.5406   1.3440
 PB2  CAC   C  CR15  0   0.097   4.4155   0.9447   0.2531
 PB2  HDB   H  HCR6  0   0.255  -2.7501  -2.0177   0.7751
 PB2  HDC   H  HCR6  0   0.258  -5.1245  -2.0848   1.3930
 PB2  HDD   H  HCR6  0   0.258  -6.5719  -0.1109   1.0053
 PB2  HDE   H  HCR6  0   0.258  -5.6105   1.9257  -0.0222
 PB2  HDF   H  HCR6  0   0.255  -3.2442   1.9896  -0.6647
 PB2  HCE   H  HCR6  0   0.257  -1.0720   2.0581   0.2623
 PB2  HCF   H  HCR6  0   0.255   1.2856   2.1111  -0.3761
 PB2  HCC   H  HCR6  0   0.257  -1.3501  -1.9928  -1.1105
 PB2  HCB   H  HCR6  0   0.259   1.0168  -1.9392  -1.7328
 PB2  HAA   H  HCH2  0   0.287   3.0251  -0.6952  -2.1443
 PB2  HAAA  H  HCH2  0   0.288   3.0527   1.0486  -1.9391
 PB2  HAF   H  HCR5  0   0.289   3.1814  -2.0184   0.3518
 PB2  HAE   H  HCR5  0   0.251   4.9241  -1.3389   2.3684
 PB2  HAC   H  HCR5  0   0.281   4.5181   1.9167  -0.2068

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
 PB2  CDB  CDC   aromatic  1.387  0.020  1.387
 PB2  CDB  CDA   aromatic  1.396  0.020  1.396
 PB2  CDC  CDD   aromatic  1.389  0.020  1.389
 PB2  CDD  CDE   aromatic  1.389  0.020  1.389
 PB2  CDE  CDF   aromatic  1.387  0.020  1.387
 PB2  CDF  CDA   aromatic  1.396  0.020  1.396
 PB2  CDA  CCD   single    1.477  0.020  1.477
 PB2  CCD  CCE   aromatic  1.397  0.020  1.397
 PB2  CCD  CCC   aromatic  1.394  0.020  1.394
 PB2  CCE  CCF   aromatic  1.384  0.020  1.384
 PB2  CCF  CCA   aromatic  1.392  0.020  1.392
 PB2  CCC  CCB   aromatic  1.387  0.020  1.387
 PB2  CCB  CCA   aromatic  1.389  0.020  1.389
 PB2  CCA  CAA   single    1.505  0.020  1.505
 PB2  CAA  NAB   single    1.452  0.020  1.452
 PB2  NAB  CAF   aromatic  1.366  0.020  1.366
 PB2  NAB  CAC   aromatic  1.350  0.020  1.350
 PB2  CAF  CAE   aromatic  1.366  0.020  1.366
 PB2  CAE  NAD   aromatic  1.366  0.020  1.366
 PB2  NAD  CAC   aromatic  1.309  0.020  1.309
 PB2  CDB  HDB   single    0.930  0.020  1.080
 PB2  CDC  HDC   single    0.930  0.020  1.080
 PB2  CDD  HDD   single    0.930  0.020  1.080
 PB2  CDE  HDE   single    0.930  0.020  1.080
 PB2  CDF  HDF   single    0.930  0.020  1.080
 PB2  CCE  HCE   single    0.930  0.020  1.080
 PB2  CCF  HCF   single    0.930  0.020  1.080
 PB2  CCC  HCC   single    0.930  0.020  1.080
 PB2  CCB  HCB   single    0.930  0.020  1.080
 PB2  CAA  HAA   single    0.970  0.020  1.090
 PB2  CAA  HAAA  single    0.970  0.020  1.090
 PB2  CAF  HAF   single    0.930  0.020  1.080
 PB2  CAE  HAE   single    0.930  0.020  1.080
 PB2  CAC  HAC   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
 PB2  HDB   CDB  CDA  119.76  3.000
 PB2  HDB   CDB  CDC  119.43  3.000
 PB2  CDA   CDB  CDC  120.80  3.000
 PB2  HDC   CDC  CDD  120.14  3.000
 PB2  HDC   CDC  CDB  119.62  3.000
 PB2  CDD   CDC  CDB  120.23  3.000
 PB2  HDD   CDD  CDE  120.20  3.000
 PB2  HDD   CDD  CDC  120.30  3.000
 PB2  CDE   CDD  CDC  119.50  3.000
 PB2  HDE   CDE  CDF  119.68  3.000
 PB2  HDE   CDE  CDD  120.06  3.000
 PB2  CDF   CDE  CDD  120.26  3.000
 PB2  HDF   CDF  CDA  119.94  3.000
 PB2  HDF   CDF  CDE  119.27  3.000
 PB2  CDA   CDF  CDE  120.77  3.000
 PB2  CCD   CDA  CDF  120.92  3.000
 PB2  CCD   CDA  CDB  120.64  3.000
 PB2  CDF   CDA  CDB  118.45  3.000
 PB2  CCC   CCD  CCE  118.17  3.000
 PB2  CCC   CCD  CDA  120.84  3.000
 PB2  CCE   CCD  CDA  120.99  3.000
 PB2  HCE   CCE  CCF  119.16  3.000
 PB2  HCE   CCE  CCD  119.97  3.000
 PB2  CCF   CCE  CCD  120.86  3.000
 PB2  HCF   CCF  CCA  119.93  3.000
 PB2  HCF   CCF  CCE  119.33  3.000
 PB2  CCA   CCF  CCE  120.73  3.000
 PB2  HCC   CCC  CCB  119.22  3.000
 PB2  HCC   CCC  CCD  119.92  3.000
 PB2  CCB   CCC  CCD  120.85  3.000
 PB2  HCB   CCB  CCA  119.86  3.000
 PB2  HCB   CCB  CCC  119.41  3.000
 PB2  CCA   CCB  CCC  120.73  3.000
 PB2  CAA   CCA  CCB  120.80  3.000
 PB2  CAA   CCA  CCF  120.53  3.000
 PB2  CCB   CCA  CCF  118.65  3.000
 PB2  HAAA  CAA  HAA  107.33  3.000
 PB2  HAAA  CAA  NAB  107.17  3.000
 PB2  HAA   CAA  NAB  108.87  3.000
 PB2  HAAA  CAA  CCA  110.96  3.000
 PB2  HAA   CAA  CCA  110.56  3.000
 PB2  NAB   CAA  CCA  111.79  3.000
 PB2  CAC   NAB  CAF  107.03  3.000
 PB2  CAC   NAB  CAA  126.45  3.000
 PB2  CAF   NAB  CAA  126.46  3.000
 PB2  HAF   CAF  CAE  132.12  3.000
 PB2  HAF   CAF  NAB  122.42  3.000
 PB2  CAE   CAF  NAB  105.46  3.000
 PB2  HAE   CAE  NAD  121.92  3.000
 PB2  HAE   CAE  CAF  127.80  3.000
 PB2  NAD   CAE  CAF  110.28  3.000
 PB2  CAC   NAD  CAE  105.25  3.000
 PB2  HAC   CAC  NAD  126.11  3.000
 PB2  HAC   CAC  NAB  121.90  3.000
 PB2  NAD   CAC  NAB  111.98  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
 PB2  CONST_01  CDE  CDD  CDC  CDB    0.00   0.0  0
 PB2  CONST_02  CDE  CDF  CDA  CDB    0.00   0.0  0
 PB2  CONST_05  CDF  CDA  CDB  CDC    0.00   0.0  0
 PB2  CONST_06  CCD  CDA  CDB  CDC  180.00   0.0  0
 PB2  CONST_07  CDF  CDE  CDD  CDC    0.00   0.0  0
 PB2  CONST_08  CDA  CDB  CDC  CDD    0.00   0.0  0
 PB2  CONST_09  CDA  CDF  CDE  CDD    0.00   0.0  0
 PB2  CONST_10  CCD  CDA  CDF  CDE  180.00   0.0  0
 PB2  CONST_13  CCF  CCE  CCD  CDA  180.00   0.0  0
 PB2  CONST_14  CCB  CCC  CCD  CDA  180.00   0.0  0
 PB2  CONST_15  CCA  CCF  CCE  CCD    0.00   0.0  0
 PB2  CONST_16  CCA  CCB  CCC  CCD    0.00   0.0  0
 PB2  CONST_17  CCB  CCC  CCD  CCE    0.00   0.0  0
 PB2  CONST_18  CCB  CCA  CCF  CCE    0.00   0.0  0
 PB2  CONST_19  CCC  CCD  CCE  CCF    0.00   0.0  0
 PB2  CONST_20  CCC  CCB  CCA  CCF    0.00   0.0  0
 PB2  CONST_21  NAD  CAE  CAF  NAB    0.00   0.0  0
 PB2  CONST_22  CAE  NAD  CAC  NAB    0.00   0.0  0
 PB2  CONST_23  NAD  CAC  NAB  CAF    0.00   0.0  0
 PB2  CONST_24  CAC  NAD  CAE  CAF    0.00   0.0  0
 PB2  CONST_25  CAC  NAB  CAF  CAE    0.00   0.0  0
 PB2  CONST_26  CAA  CCA  CCF  CCE  180.00   0.0  0
 PB2  CONST_27  CAA  CCA  CCB  CCC  180.00   0.0  0
 PB2  CONST_28  CAE  CAF  NAB  CAA  180.00   0.0  0
 PB2  CONST_29  NAD  CAC  NAB  CAA  180.00   0.0  0
 PB2  CONST_30  HDD  CDD  CDC  CDB  180.00   0.0  0
 PB2  CONST_31  HDF  CDF  CDA  CDB  180.00   0.0  0
 PB2  CONST_32  HDE  CDE  CDD  CDC  180.00   0.0  0
 PB2  CONST_33  HDB  CDB  CDC  CDD  180.00   0.0  0
 PB2  CONST_34  HDC  CDC  CDD  CDE  180.00   0.0  0
 PB2  CONST_35  HCE  CCE  CCD  CDA    0.00   0.0  0
 PB2  CONST_36  HCC  CCC  CCD  CDA    0.00   0.0  0
 PB2  CONST_37  HCF  CCF  CCE  CCD  180.00   0.0  0
 PB2  CONST_38  HCB  CCB  CCC  CCD  180.00   0.0  0
 PB2  CONST_39  HAE  CAE  CAF  NAB  180.00   0.0  0
 PB2  CONST_40  HAC  CAC  NAB  CAF  180.00   0.0  0
 PB2  CONST_41  HAF  CAF  CAE  NAD  180.00   0.0  0
 PB2  Var_01    NAB  CAA  CCA  CCF   76.29  30.0  2
 PB2  Var_02    CAF  NAB  CAA  CCA   65.83  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
 PB2  plan-1  CAA  0.020
 PB2  plan-1  NAB  0.020
 PB2  plan-1  CAF  0.020
 PB2  plan-1  CAE  0.020
 PB2  plan-1  NAD  0.020
 PB2  plan-1  CAC  0.020
 PB2  plan-1  HAF  0.020
 PB2  plan-1  HAE  0.020
 PB2  plan-1  HAC  0.020
 PB2  plan-2  CDB  0.020
 PB2  plan-2  CDC  0.020
 PB2  plan-2  CDD  0.020
 PB2  plan-2  CDE  0.020
 PB2  plan-2  CDF  0.020
 PB2  plan-2  CDA  0.020
 PB2  plan-2  CCD  0.020
 PB2  plan-2  HDB  0.020
 PB2  plan-2  HDC  0.020
 PB2  plan-2  HDD  0.020
 PB2  plan-2  HDE  0.020
 PB2  plan-2  HDF  0.020
 PB2  plan-3  CDA  0.020
 PB2  plan-3  CCD  0.020
 PB2  plan-3  CCE  0.020
 PB2  plan-3  CCF  0.020
 PB2  plan-3  CCC  0.020
 PB2  plan-3  CCB  0.020
 PB2  plan-3  CCA  0.020
 PB2  plan-3  CAA  0.020
 PB2  plan-3  HCE  0.020
 PB2  plan-3  HCF  0.020
 PB2  plan-3  HCC  0.020
 PB2  plan-3  HCB  0.020

