# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:32:44 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-[3-(4-chloro-3,5-dimethylphenoxy)benzyl]-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Oc2cccc(Cn3ccnc3)c2)cc(C)c1Cl
#
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
 NEE  NEE  1-[3-(4-chloro-3,5-dimethylphenoxy)benzyl]-1H-imidazole  ligand  39  22  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NEE
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
 NEE  CAA  C   CH3   0  -0.722   3.7315   1.9861  -1.3538
 NEE  CAP  C   CR6   0   0.209   3.2779   0.7859  -0.5803
 NEE  CAJ  C   CR16  0  -0.419   1.9228   0.5903  -0.3291
 NEE  CAU  C   CR6   0  -0.206   4.1770  -0.1621  -0.0982
 NEE  CL1  CL  CL    0  -0.132   5.8746   0.0680  -0.3988
 NEE  CAQ  C   CR6   0   0.205   3.7706  -1.2895   0.6140
 NEE  CAB  C   CH3   0  -0.723   4.7503  -2.3048   1.1174
 NEE  CAK  C   CR16  0  -0.427   2.4117  -1.4493   0.8540
 NEE  CAT  C   CR6   0   0.403   1.4957  -0.5180   0.3871
 NEE  OAO  O   O2    0  -0.513   0.1816  -0.7850   0.6314
 NEE  CAS  C   CR6   0   0.338  -0.7314   0.2357   0.6508
 NEE  CAL  C   CR16  0  -0.352  -1.8165   0.1502  -0.2022
 NEE  CAG  C   CR16  0  -0.312  -0.6023   1.2970   1.5413
 NEE  CAD  C   CR16  0  -0.236  -1.5811   2.2754   1.5628
 NEE  CAF  C   CR16  0  -0.312  -2.6806   2.1951   0.7146
 NEE  CAR  C   CR6   0   0.118  -2.8041   1.1320  -0.1683
 NEE  CAM  C   CH2   0  -0.394  -3.9910   1.0296  -1.0900
 NEE  NAV  N   NR5   0  -0.394  -4.7639  -0.1708  -0.8452
 NEE  CAH  C   CR15  0  -0.097  -5.4312  -0.4837   0.3057
 NEE  CAE  C   CR15  0  -0.217  -5.9903  -1.7087   0.0804
 NEE  NAN  N   N     0  -0.457  -5.6774  -2.1487  -1.1748
 NEE  CAI  C   CR15  0   0.097  -4.9406  -1.2027  -1.6977
 NEE  H1   H   HCH3  0   0.253   4.3898   2.6184  -0.7561
 NEE  H2   H   HCH3  0   0.252   4.2875   1.6996  -2.2472
 NEE  H3   H   HCH3  0   0.253   2.8804   2.5880  -1.6667
 NEE  H4   H   HCR6  0   0.278   1.2132   1.3141  -0.7096
 NEE  H5   H   HCH3  0   0.253   5.4802  -1.8552   1.7916
 NEE  H6   H   HCH3  0   0.253   4.2384  -3.1001   1.6553
 NEE  H7   H   HCH3  0   0.253   5.3092  -2.7578   0.2975
 NEE  H8   H   HCR6  0   0.269   2.0638  -2.3144   1.4051
 NEE  H9   H   HCR6  0   0.267  -1.8897  -0.6847  -0.8899
 NEE  H10  H   HCR6  0   0.281   0.2462   1.3529   2.2114
 NEE  H11  H   HCR6  0   0.267  -1.4933   3.1027   2.2543
 NEE  H12  H   HCR6  0   0.261  -3.4442   2.9619   0.7490
 NEE  H13  H   HCH2  0   0.288  -4.6362   1.9013  -0.9784
 NEE  H14  H   HCH2  0   0.290  -3.6654   1.0003  -2.1305
 NEE  H15  H   HCR5  0   0.290  -5.4499   0.1737   1.1591
 NEE  H16  H   HCR5  0   0.251  -6.6013  -2.2898   0.7539
 NEE  H17  H   HCR5  0   0.282  -4.5109  -1.2041  -2.6886

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
 NEE  CL1  CAU  single    1.739  0.020  1.739
 NEE  CAA  CAP  single    1.498  0.020  1.498
 NEE  CAU  CAP  aromatic  1.393  0.020  1.393
 NEE  CAU  CAQ  aromatic  1.394  0.020  1.394
 NEE  CAP  CAJ  aromatic  1.392  0.020  1.392
 NEE  CAB  CAQ  single    1.498  0.020  1.498
 NEE  CAQ  CAK  aromatic  1.389  0.020  1.389
 NEE  CAI  NAN  aromatic  1.308  0.020  1.308
 NEE  CAI  NAV  aromatic  1.350  0.020  1.350
 NEE  CAJ  CAT  aromatic  1.387  0.020  1.387
 NEE  NAN  CAE  aromatic  1.366  0.020  1.366
 NEE  CAK  CAT  aromatic  1.387  0.020  1.387
 NEE  CAT  OAO  single    1.363  0.020  1.363
 NEE  NAV  CAM  single    1.449  0.020  1.449
 NEE  NAV  CAH  aromatic  1.367  0.020  1.367
 NEE  OAO  CAS  single    1.370  0.020  1.370
 NEE  CAL  CAS  aromatic  1.383  0.020  1.383
 NEE  CAL  CAR  aromatic  1.393  0.020  1.393
 NEE  CAM  CAR  single    1.506  0.020  1.506
 NEE  CAE  CAH  aromatic  1.365  0.020  1.365
 NEE  CAS  CAG  aromatic  1.391  0.020  1.391
 NEE  CAR  CAF  aromatic  1.387  0.020  1.387
 NEE  CAG  CAD  aromatic  1.384  0.020  1.384
 NEE  CAF  CAD  aromatic  1.391  0.020  1.391
 NEE  CAA  H1   single    0.970  0.020  1.090
 NEE  CAA  H2   single    0.970  0.020  1.090
 NEE  CAA  H3   single    0.970  0.020  1.090
 NEE  CAJ  H4   single    0.930  0.020  1.080
 NEE  CAB  H5   single    0.970  0.020  1.090
 NEE  CAB  H6   single    0.970  0.020  1.090
 NEE  CAB  H7   single    0.970  0.020  1.090
 NEE  CAK  H8   single    0.930  0.020  1.080
 NEE  CAL  H9   single    0.930  0.020  1.080
 NEE  CAG  H10  single    0.930  0.020  1.080
 NEE  CAD  H11  single    0.930  0.020  1.080
 NEE  CAF  H12  single    0.930  0.020  1.080
 NEE  CAM  H13  single    0.970  0.020  1.090
 NEE  CAM  H14  single    0.970  0.020  1.090
 NEE  CAH  H15  single    0.930  0.020  1.080
 NEE  CAE  H16  single    0.930  0.020  1.080
 NEE  CAI  H17  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
 NEE  H3   CAA  H2   107.96  3.000
 NEE  H3   CAA  H1   107.99  3.000
 NEE  H2   CAA  H1   107.07  3.000
 NEE  H3   CAA  CAP  110.77  3.000
 NEE  H2   CAA  CAP  111.51  3.000
 NEE  H1   CAA  CAP  111.35  3.000
 NEE  CAU  CAP  CAJ  118.06  3.000
 NEE  CAJ  CAP  CAA  120.03  3.000
 NEE  CAU  CAP  CAA  121.91  3.000
 NEE  H4   CAJ  CAT  120.92  3.000
 NEE  H4   CAJ  CAP  118.73  3.000
 NEE  CAT  CAJ  CAP  120.35  3.000
 NEE  CAQ  CAU  CL1  118.67  3.000
 NEE  CAQ  CAU  CAP  122.63  3.000
 NEE  CL1  CAU  CAP  118.70  3.000
 NEE  CAK  CAQ  CAB  120.25  3.000
 NEE  CAK  CAQ  CAU  117.80  3.000
 NEE  CAB  CAQ  CAU  121.95  3.000
 NEE  H7   CAB  H6   108.00  3.000
 NEE  H7   CAB  H5   107.03  3.000
 NEE  H6   CAB  H5   108.10  3.000
 NEE  H7   CAB  CAQ  111.34  3.000
 NEE  H6   CAB  CAQ  110.72  3.000
 NEE  H5   CAB  CAQ  111.48  3.000
 NEE  H8   CAK  CAT  119.69  3.000
 NEE  H8   CAK  CAQ  119.61  3.000
 NEE  CAT  CAK  CAQ  120.70  3.000
 NEE  OAO  CAT  CAK  116.41  3.000
 NEE  OAO  CAT  CAJ  123.09  3.000
 NEE  CAK  CAT  CAJ  120.46  3.000
 NEE  CAS  OAO  CAT  119.95  3.000
 NEE  CAG  CAS  CAL  120.98  3.000
 NEE  CAG  CAS  OAO  121.05  3.000
 NEE  CAL  CAS  OAO  117.92  3.000
 NEE  H9   CAL  CAR  120.68  3.000
 NEE  H9   CAL  CAS  119.47  3.000
 NEE  CAR  CAL  CAS  119.85  3.000
 NEE  H10  CAG  CAD  120.54  3.000
 NEE  H10  CAG  CAS  120.55  3.000
 NEE  CAD  CAG  CAS  118.91  3.000
 NEE  H11  CAD  CAF  119.88  3.000
 NEE  H11  CAD  CAG  119.54  3.000
 NEE  CAF  CAD  CAG  120.57  3.000
 NEE  H12  CAF  CAR  120.01  3.000
 NEE  H12  CAF  CAD  119.81  3.000
 NEE  CAR  CAF  CAD  120.18  3.000
 NEE  CAM  CAR  CAF  120.77  3.000
 NEE  CAF  CAR  CAL  119.50  3.000
 NEE  CAM  CAR  CAL  119.73  3.000
 NEE  H14  CAM  H13  107.21  3.000
 NEE  H14  CAM  NAV  107.35  3.000
 NEE  H13  CAM  NAV  109.24  3.000
 NEE  H14  CAM  CAR  110.51  3.000
 NEE  H13  CAM  CAR  110.45  3.000
 NEE  NAV  CAM  CAR  111.92  3.000
 NEE  CAI  NAV  CAH  107.03  3.000
 NEE  CAH  NAV  CAM  126.34  3.000
 NEE  CAI  NAV  CAM  126.62  3.000
 NEE  H15  CAH  CAE  132.15  3.000
 NEE  H15  CAH  NAV  122.40  3.000
 NEE  CAE  CAH  NAV  105.45  3.000
 NEE  H16  CAE  NAN  121.97  3.000
 NEE  H16  CAE  CAH  127.74  3.000
 NEE  NAN  CAE  CAH  110.29  3.000
 NEE  CAI  NAN  CAE  105.26  3.000
 NEE  H17  CAI  NAN  126.14  3.000
 NEE  H17  CAI  NAV  121.89  3.000
 NEE  NAN  CAI  NAV  111.96  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
 NEE  CONST_01  CAK  CAQ  CAU  CAP     0.00   0.0  0
 NEE  CONST_02  CAK  CAT  CAJ  CAP     0.00   0.0  0
 NEE  CONST_03  CAQ  CAU  CAP  CAJ     0.00   0.0  0
 NEE  CONST_04  CAQ  CAK  CAT  CAJ     0.00   0.0  0
 NEE  CONST_05  CAT  CAJ  CAP  CAU     0.00   0.0  0
 NEE  CONST_06  CAT  CAK  CAQ  CAU     0.00   0.0  0
 NEE  CONST_07  CAF  CAR  CAL  CAS     0.00   0.0  0
 NEE  CONST_08  CAF  CAD  CAG  CAS     0.00   0.0  0
 NEE  CONST_09  CAD  CAG  CAS  CAL     0.00   0.0  0
 NEE  CONST_10  CAD  CAF  CAR  CAL     0.00   0.0  0
 NEE  CONST_11  CAR  CAL  CAS  CAG     0.00   0.0  0
 NEE  CONST_12  CAR  CAF  CAD  CAG     0.00   0.0  0
 NEE  CONST_13  CAE  NAN  CAI  NAV     0.00   0.0  0
 NEE  CONST_14  NAN  CAE  CAH  NAV     0.00   0.0  0
 NEE  CONST_15  NAN  CAI  NAV  CAH     0.00   0.0  0
 NEE  CONST_16  CAI  NAN  CAE  CAH     0.00   0.0  0
 NEE  CONST_17  CAI  NAV  CAH  CAE     0.00   0.0  0
 NEE  CONST_18  CAQ  CAU  CAP  CAA   180.00   0.0  0
 NEE  CONST_19  CAT  CAJ  CAP  CAA   180.00   0.0  0
 NEE  CONST_20  CAB  CAQ  CAU  CAP   180.00   0.0  0
 NEE  CONST_21  OAO  CAT  CAJ  CAP   180.00   0.0  0
 NEE  CONST_22  CL1  CAU  CAP  CAJ   180.00   0.0  0
 NEE  CONST_23  CAK  CAQ  CAU  CL1   180.00   0.0  0
 NEE  CONST_24  OAO  CAT  CAK  CAQ   180.00   0.0  0
 NEE  CONST_25  CAT  CAK  CAQ  CAB   180.00   0.0  0
 NEE  CONST_26  CAR  CAL  CAS  OAO   180.00   0.0  0
 NEE  CONST_27  CAD  CAG  CAS  OAO   180.00   0.0  0
 NEE  CONST_28  CAM  CAR  CAL  CAS   180.00   0.0  0
 NEE  CONST_29  CAM  CAR  CAF  CAD   180.00   0.0  0
 NEE  CONST_30  NAN  CAI  NAV  CAM   180.00   0.0  0
 NEE  CONST_31  CAE  CAH  NAV  CAM   180.00   0.0  0
 NEE  CONST_32  H8   CAK  CAT  CAJ   180.00   0.0  0
 NEE  CONST_33  H4   CAJ  CAP  CAU   180.00   0.0  0
 NEE  CONST_34  H11  CAD  CAG  CAS   180.00   0.0  0
 NEE  CONST_35  H10  CAG  CAS  CAL   180.00   0.0  0
 NEE  CONST_36  H12  CAF  CAR  CAL   180.00   0.0  0
 NEE  CONST_37  H9   CAL  CAS  CAG   180.00   0.0  0
 NEE  CONST_38  H16  CAE  CAH  NAV   180.00   0.0  0
 NEE  CONST_39  H17  CAI  NAV  CAH   180.00   0.0  0
 NEE  CONST_40  H15  CAH  CAE  NAN   180.00   0.0  0
 NEE  Var_01    CAL  CAS  OAO  CAT   123.66  30.0  2
 NEE  Var_02    NAV  CAM  CAR  CAL    61.30  30.0  2
 NEE  Var_03    CAI  NAV  CAM  CAR  -115.35  30.0  2
 NEE  Var_04    H1   CAA  CAP  CAJ   118.74  30.0  2
 NEE  Var_05    H5   CAB  CAQ  CAU    59.02  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
 NEE  plan-1  CAM  0.020
 NEE  plan-1  NAV  0.020
 NEE  plan-1  CAH  0.020
 NEE  plan-1  CAE  0.020
 NEE  plan-1  NAN  0.020
 NEE  plan-1  CAI  0.020
 NEE  plan-1  H15  0.020
 NEE  plan-1  H16  0.020
 NEE  plan-1  H17  0.020
 NEE  plan-2  CAA  0.020
 NEE  plan-2  CAP  0.020
 NEE  plan-2  CAJ  0.020
 NEE  plan-2  CAU  0.020
 NEE  plan-2  CL1  0.020
 NEE  plan-2  CAQ  0.020
 NEE  plan-2  CAB  0.020
 NEE  plan-2  CAK  0.020
 NEE  plan-2  CAT  0.020
 NEE  plan-2  OAO  0.020
 NEE  plan-2  H4   0.020
 NEE  plan-2  H8   0.020
 NEE  plan-3  OAO  0.020
 NEE  plan-3  CAS  0.020
 NEE  plan-3  CAL  0.020
 NEE  plan-3  CAG  0.020
 NEE  plan-3  CAD  0.020
 NEE  plan-3  CAF  0.020
 NEE  plan-3  CAR  0.020
 NEE  plan-3  CAM  0.020
 NEE  plan-3  H9   0.020
 NEE  plan-3  H10  0.020
 NEE  plan-3  H11  0.020
 NEE  plan-3  H12  0.020

