# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 00:52:56 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 1-(4-chlorobenzyl)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(C)c1c2ccc3n(Cc4ccc(Cl)cc4)cnc3c2
#
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
 2LK  2LK  1-(4-chlorobenzyl)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1H-benzimidazole  ligand  40  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2LK
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
 2LK  CAU  C   CH3   0  -0.759   4.7429   0.1368   2.2857
 2LK  CAN  C   CR5   0   0.416   4.6641   0.6589   0.9028
 2LK  OAM  O   O     0  -0.347   5.6751   1.4143   0.4662
 2LK  NAL  N   N     0  -0.183   5.4466   1.7974  -0.8244
 2LK  CAK  C   CR5   0   0.251   4.3074   1.2721  -1.1671
 2LK  CAV  C   CH3   0  -0.748   3.7364   1.4970  -2.5215
 2LK  CAJ  C   CR5   0  -0.184   3.7446   0.5240  -0.0896
 2LK  CAD  C   CR6   0   0.026   2.4647  -0.1908  -0.0601
 2LK  CAC  C   CR16  0  -0.377   2.1415  -1.0889  -1.0690
 2LK  CAE  C   CR16  0  -0.335   1.5585   0.0456   0.9940
 2LK  CAF  C   CR16  0  -0.274   0.3367  -0.5955   1.0726
 2LK  CAA  C   CR56  0   0.341   0.0320  -1.4882   0.0523
 2LK  CAB  C   CR56  0   0.142   0.9121  -1.7395  -1.0121
 2LK  NAI  N   N     0  -0.471   0.3607  -2.6623  -1.8706
 2LK  CAH  C   CR15  0   0.105  -0.7959  -2.9482  -1.3472
 2LK  NAG  N   NR5   0  -0.506  -1.0577  -2.2834  -0.1920
 2LK  CAX  C   CH2   0  -0.393  -2.2628  -2.3655   0.6026
 2LK  CAQ  C   CR6   0   0.116  -3.0232  -1.0642   0.6214
 2LK  CAP  C   CR16  0  -0.283  -3.3593  -0.4213  -0.5664
 2LK  CAO  C   CR16  0  -0.196  -4.0632   0.7715  -0.5552
 2LK  CAT  C   CR6   0  -0.052  -4.4350   1.3246   0.6618
 2LK  CL   CL  CL    0  -0.127  -5.3125   2.8190   0.6847
 2LK  CAS  C   CR16  0  -0.196  -4.1131   0.7046   1.8570
 2LK  CAR  C   CR16  0  -0.312  -3.4051  -0.4893   1.8262
 2LK  H1   H   HCH3  0   0.272   5.7118  -0.3261   2.4751
 2LK  H2   H   HCH3  0   0.271   4.6052   0.9321   3.0199
 2LK  H3   H   HCH3  0   0.263   3.9697  -0.6106   2.4499
 2LK  H4   H   HCH3  0   0.260   3.8050   0.5973  -3.1332
 2LK  H5   H   HCH3  0   0.257   2.6824   1.7643  -2.4543
 2LK  H6   H   HCH3  0   0.263   4.2672   2.2945  -3.0377
 2LK  H7   H   HCR6  0   0.251   2.8322  -1.2917  -1.8779
 2LK  H8   H   HCR6  0   0.257   1.8191   0.7664   1.7586
 2LK  H9   H   HCR6  0   0.272  -0.3459  -0.3946   1.8875
 2LK  H10  H   HCR5  0   0.295  -1.5112  -3.6465  -1.7586
 2LK  H11  H   HCH2  0   0.297  -2.8757  -3.1615   0.1772
 2LK  H12  H   HCH2  0   0.288  -2.0063  -2.6697   1.6189
 2LK  H13  H   HCR6  0   0.266  -3.0726  -0.8476  -1.5204
 2LK  H14  H   HCR6  0   0.282  -4.3180   1.2626  -1.4844
 2LK  H15  H   HCR6  0   0.283  -4.3989   1.1446   2.8024
 2LK  H16  H   HCR6  0   0.270  -3.1475  -0.9702   2.7621

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
 2LK  OAM  NAL  aromatic  1.365  0.020  1.365
 2LK  OAM  CAN  aromatic  1.335  0.020  1.335
 2LK  NAL  CAK  aromatic  1.300  0.020  1.300
 2LK  CAN  CAU  single    1.480  0.020  1.480
 2LK  CAN  CAJ  aromatic  1.360  0.020  1.360
 2LK  CAK  CAJ  aromatic  1.427  0.020  1.427
 2LK  CAK  CAV  single    1.487  0.020  1.487
 2LK  CAJ  CAD  single    1.466  0.020  1.466
 2LK  CAD  CAE  aromatic  1.410  0.020  1.410
 2LK  CAD  CAC  aromatic  1.389  0.020  1.389
 2LK  CAE  CAF  aromatic  1.382  0.020  1.382
 2LK  CAC  CAB  aromatic  1.392  0.020  1.392
 2LK  CAF  CAA  aromatic  1.390  0.020  1.390
 2LK  CAB  CAA  aromatic  1.404  0.020  1.404
 2LK  CAB  NAI  aromatic  1.376  0.020  1.376
 2LK  CAA  NAG  aromatic  1.371  0.020  1.371
 2LK  NAI  CAH  aromatic  1.301  0.020  1.301
 2LK  NAG  CAH  aromatic  1.358  0.020  1.358
 2LK  NAG  CAX  single    1.446  0.020  1.446
 2LK  CAR  CAS  aromatic  1.388  0.020  1.388
 2LK  CAR  CAQ  aromatic  1.389  0.020  1.389
 2LK  CAS  CAT  aromatic  1.384  0.020  1.384
 2LK  CAX  CAQ  single    1.507  0.020  1.507
 2LK  CAQ  CAP  aromatic  1.392  0.020  1.392
 2LK  CAT  CL   single    1.733  0.020  1.733
 2LK  CAT  CAO  aromatic  1.388  0.020  1.388
 2LK  CAP  CAO  aromatic  1.385  0.020  1.385
 2LK  CAU  H1   single    0.970  0.020  1.090
 2LK  CAU  H2   single    0.970  0.020  1.090
 2LK  CAU  H3   single    0.970  0.020  1.090
 2LK  CAV  H4   single    0.970  0.020  1.090
 2LK  CAV  H5   single    0.970  0.020  1.090
 2LK  CAV  H6   single    0.970  0.020  1.090
 2LK  CAC  H7   single    0.930  0.020  1.080
 2LK  CAE  H8   single    0.930  0.020  1.080
 2LK  CAF  H9   single    0.930  0.020  1.080
 2LK  CAH  H10  single    0.930  0.020  1.080
 2LK  CAX  H11  single    0.970  0.020  1.090
 2LK  CAX  H12  single    0.970  0.020  1.090
 2LK  CAP  H13  single    0.930  0.020  1.080
 2LK  CAO  H14  single    0.930  0.020  1.080
 2LK  CAS  H15  single    0.930  0.020  1.080
 2LK  CAR  H16  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
 2LK  H3   CAU  H2   108.03  3.000
 2LK  H3   CAU  H1   108.29  3.000
 2LK  H2   CAU  H1   107.74  3.000
 2LK  H3   CAU  CAN  110.21  3.000
 2LK  H2   CAU  CAN  111.39  3.000
 2LK  H1   CAU  CAN  111.06  3.000
 2LK  CAJ  CAN  OAM  109.24  3.000
 2LK  CAJ  CAN  CAU  133.07  3.000
 2LK  OAM  CAN  CAU  117.69  3.000
 2LK  NAL  OAM  CAN  109.94  3.000
 2LK  CAK  NAL  OAM  106.40  3.000
 2LK  CAJ  CAK  CAV  127.98  3.000
 2LK  CAV  CAK  NAL  121.02  3.000
 2LK  CAJ  CAK  NAL  110.99  3.000
 2LK  H6   CAV  H5   108.74  3.000
 2LK  H6   CAV  H4   107.93  3.000
 2LK  H5   CAV  H4   107.34  3.000
 2LK  H6   CAV  CAK  110.83  3.000
 2LK  H5   CAV  CAK  110.64  3.000
 2LK  H4   CAV  CAK  111.23  3.000
 2LK  CAD  CAJ  CAK  127.95  3.000
 2LK  CAD  CAJ  CAN  128.61  3.000
 2LK  CAK  CAJ  CAN  103.43  3.000
 2LK  CAE  CAD  CAC  120.13  3.000
 2LK  CAC  CAD  CAJ  120.25  3.000
 2LK  CAE  CAD  CAJ  119.62  3.000
 2LK  H7   CAC  CAB  120.42  3.000
 2LK  H7   CAC  CAD  121.02  3.000
 2LK  CAB  CAC  CAD  118.55  3.000
 2LK  H8   CAE  CAF  118.78  3.000
 2LK  H8   CAE  CAD  119.00  3.000
 2LK  CAF  CAE  CAD  122.21  3.000
 2LK  H9   CAF  CAA  122.28  3.000
 2LK  H9   CAF  CAE  120.97  3.000
 2LK  CAA  CAF  CAE  116.75  3.000
 2LK  NAG  CAA  CAB  105.03  3.000
 2LK  NAG  CAA  CAF  132.67  3.000
 2LK  CAB  CAA  CAF  122.30  3.000
 2LK  NAI  CAB  CAA  110.00  3.000
 2LK  NAI  CAB  CAC  129.94  3.000
 2LK  CAA  CAB  CAC  120.07  3.000
 2LK  CAH  NAI  CAB  104.63  3.000
 2LK  H10  CAH  NAG  120.81  3.000
 2LK  H10  CAH  NAI  125.24  3.000
 2LK  NAG  CAH  NAI  113.94  3.000
 2LK  CAX  NAG  CAH  126.89  3.000
 2LK  CAX  NAG  CAA  126.69  3.000
 2LK  CAH  NAG  CAA  106.39  3.000
 2LK  H12  CAX  H11  106.96  3.000
 2LK  H12  CAX  CAQ  110.34  3.000
 2LK  H11  CAX  CAQ  110.57  3.000
 2LK  H12  CAX  NAG  109.37  3.000
 2LK  H11  CAX  NAG  107.18  3.000
 2LK  CAQ  CAX  NAG  112.23  3.000
 2LK  CAR  CAQ  CAP  118.87  3.000
 2LK  CAP  CAQ  CAX  120.67  3.000
 2LK  CAR  CAQ  CAX  120.47  3.000
 2LK  H13  CAP  CAO  118.72  3.000
 2LK  H13  CAP  CAQ  120.37  3.000
 2LK  CAO  CAP  CAQ  120.91  3.000
 2LK  H14  CAO  CAT  120.63  3.000
 2LK  H14  CAO  CAP  120.26  3.000
 2LK  CAT  CAO  CAP  119.12  3.000
 2LK  CAS  CAT  CL   119.51  3.000
 2LK  CL   CAT  CAO  119.40  3.000
 2LK  CAS  CAT  CAO  121.09  3.000
 2LK  H15  CAS  CAR  120.27  3.000
 2LK  H15  CAS  CAT  120.74  3.000
 2LK  CAR  CAS  CAT  118.99  3.000
 2LK  H16  CAR  CAS  118.94  3.000
 2LK  H16  CAR  CAQ  120.03  3.000
 2LK  CAS  CAR  CAQ  121.03  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
 2LK  CONST_01  CAK  NAL  OAM  CAN     0.00   0.0  0
 2LK  CONST_02  NAL  CAK  CAJ  CAN     0.00   0.0  0
 2LK  CONST_05  CAJ  CAK  NAL  OAM     0.00   0.0  0
 2LK  CONST_06  CAK  CAJ  CAN  OAM     0.00   0.0  0
 2LK  CONST_07  CAD  CAJ  CAN  OAM   180.00   0.0  0
 2LK  CONST_08  CAJ  CAN  OAM  NAL     0.00   0.0  0
 2LK  CONST_09  CAD  CAJ  CAK  NAL   180.00   0.0  0
 2LK  CONST_12  CAF  CAE  CAD  CAJ   180.00   0.0  0
 2LK  CONST_13  CAB  CAC  CAD  CAJ   180.00   0.0  0
 2LK  CONST_14  CAA  CAF  CAE  CAD     0.00   0.0  0
 2LK  CONST_15  CAA  CAB  CAC  CAD     0.00   0.0  0
 2LK  CONST_16  NAI  CAB  CAC  CAD   180.00   0.0  0
 2LK  CONST_17  CAF  CAE  CAD  CAC     0.00   0.0  0
 2LK  CONST_18  CAF  CAA  CAB  CAC     0.00   0.0  0
 2LK  CONST_19  NAG  CAA  CAB  CAC   180.00   0.0  0
 2LK  CONST_20  CAH  NAI  CAB  CAC   180.00   0.0  0
 2LK  CONST_21  CAB  CAC  CAD  CAE     0.00   0.0  0
 2LK  CONST_22  CAB  CAA  CAF  CAE     0.00   0.0  0
 2LK  CONST_23  NAG  CAA  CAF  CAE   180.00   0.0  0
 2LK  CONST_24  NAI  CAB  CAA  CAF   180.00   0.0  0
 2LK  CONST_25  CAH  NAG  CAA  CAF   180.00   0.0  0
 2LK  CONST_26  CAH  NAI  CAB  CAA     0.00   0.0  0
 2LK  CONST_27  NAI  CAH  NAG  CAA     0.00   0.0  0
 2LK  CONST_28  CAH  NAG  CAA  CAB     0.00   0.0  0
 2LK  CONST_29  NAG  CAH  NAI  CAB     0.00   0.0  0
 2LK  CONST_30  NAG  CAA  CAB  NAI     0.00   0.0  0
 2LK  CONST_31  CAT  CAS  CAR  CAQ     0.00   0.0  0
 2LK  CONST_32  CAT  CAO  CAP  CAQ     0.00   0.0  0
 2LK  CONST_33  CAS  CAR  CAQ  CAP     0.00   0.0  0
 2LK  CONST_34  CAS  CAT  CAO  CAP     0.00   0.0  0
 2LK  CONST_35  CAR  CAS  CAT  CAO     0.00   0.0  0
 2LK  CONST_36  CAR  CAQ  CAP  CAO     0.00   0.0  0
 2LK  CONST_37  NAL  OAM  CAN  CAU   180.00   0.0  0
 2LK  CONST_38  CAK  CAJ  CAN  CAU   180.00   0.0  0
 2LK  CONST_39  CAD  CAJ  CAN  CAU     0.00   0.0  0
 2LK  CONST_40  CAV  CAK  CAJ  CAN   180.00   0.0  0
 2LK  CONST_41  CAV  CAK  NAL  OAM   180.00   0.0  0
 2LK  CONST_42  CAD  CAJ  CAK  CAV     0.00   0.0  0
 2LK  CONST_43  CAX  NAG  CAA  CAF     0.00   0.0  0
 2LK  CONST_44  CAX  NAG  CAA  CAB   180.00   0.0  0
 2LK  CONST_45  CAX  NAG  CAH  NAI   180.00   0.0  0
 2LK  CONST_46  CAS  CAR  CAQ  CAX   180.00   0.0  0
 2LK  CONST_47  CAO  CAP  CAQ  CAX   180.00   0.0  0
 2LK  CONST_48  CL   CAT  CAO  CAP   180.00   0.0  0
 2LK  CONST_49  CAR  CAS  CAT  CL    180.00   0.0  0
 2LK  CONST_50  H8   CAE  CAD  CAJ     0.00   0.0  0
 2LK  CONST_51  H7   CAC  CAD  CAJ     0.00   0.0  0
 2LK  CONST_52  H9   CAF  CAE  CAD   180.00   0.0  0
 2LK  CONST_53  H10  CAH  NAG  CAA   180.00   0.0  0
 2LK  CONST_54  H15  CAS  CAR  CAQ   180.00   0.0  0
 2LK  CONST_55  H14  CAO  CAP  CAQ   180.00   0.0  0
 2LK  CONST_56  H16  CAR  CAQ  CAP   180.00   0.0  0
 2LK  CONST_57  H13  CAP  CAO  CAT   180.00   0.0  0
 2LK  Var_01    CAQ  CAX  NAG  CAA    63.77  30.0  2
 2LK  Var_02    CAR  CAQ  CAX  NAG  -127.97  30.0  2
 2LK  Var_03    H1   CAU  CAN  OAM   -48.94  30.0  2
 2LK  Var_04    H4   CAV  CAK  NAL   107.45  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
 2LK  plan-1  CAU  0.020
 2LK  plan-1  CAN  0.020
 2LK  plan-1  OAM  0.020
 2LK  plan-1  NAL  0.020
 2LK  plan-1  CAK  0.020
 2LK  plan-1  CAV  0.020
 2LK  plan-1  CAJ  0.020
 2LK  plan-1  CAD  0.020
 2LK  plan-2  CAX  0.020
 2LK  plan-2  CAQ  0.020
 2LK  plan-2  CAP  0.020
 2LK  plan-2  CAO  0.020
 2LK  plan-2  CAT  0.020
 2LK  plan-2  CL   0.020
 2LK  plan-2  CAS  0.020
 2LK  plan-2  CAR  0.020
 2LK  plan-2  H13  0.020
 2LK  plan-2  H14  0.020
 2LK  plan-2  H15  0.020
 2LK  plan-2  H16  0.020
 2LK  plan-3  CAJ  0.020
 2LK  plan-3  CAD  0.020
 2LK  plan-3  CAC  0.020
 2LK  plan-3  CAE  0.020
 2LK  plan-3  CAF  0.020
 2LK  plan-3  CAA  0.020
 2LK  plan-3  CAB  0.020
 2LK  plan-3  NAI  0.020
 2LK  plan-3  CAH  0.020
 2LK  plan-3  NAG  0.020
 2LK  plan-3  CAX  0.020
 2LK  plan-3  H7   0.020
 2LK  plan-3  H8   0.020
 2LK  plan-3  H9   0.020
 2LK  plan-3  H10  0.020

