# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 20:04:33 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 3-[5-(5-ethoxy-6-fluoro-1H-benzimidazol-2-yl)-1H-pyrazol-4-yl]-1,1-diethylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1cc2nc([nH]c2cc1F)c3[nH]ncc3NC(=O)N(CC)CC
#
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
 0JE  0JE  3-[5-(5-ethoxy-6-fluoro-1H-benzimidazol-2-yl)-1H-pyrazol-4-yl]-1,1-diethylurea  ligand  47  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0JE
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
 0JE  CAZ  C  CH3   0  -0.681   5.2521   3.9187   0.0248
 0JE  CAY  C  CH2   0  -0.190   4.0859   2.9616   0.0522
 0JE  OAX  O  O2    0  -0.469   4.5917   1.6363  -0.0406
 0JE  CAB  C  CR6   0   0.242   3.7076   0.6241  -0.0488
 0JE  CAC  C  CR16  0  -0.478   2.3329   0.7581   0.0377
 0JE  CAA  C  CR6   0   0.450   4.2687  -0.6681  -0.1572
 0JE  FAW  F  F     0  -0.314   5.6057  -0.7485  -0.2428
 0JE  CAD  C  CR16  0  -0.462   3.5290  -1.8230  -0.1807
 0JE  CAH  C  CR56  0   0.305   2.1504  -1.6628  -0.0927
 0JE  NAG  N  NR15  0  -0.719   1.1093  -2.5541  -0.0910
 0JE  CAI  C  CR56  0   0.219   1.5545  -0.4020   0.0115
 0JE  NAE  N  N     0  -0.556   0.1943  -0.5372   0.0732
 0JE  CAF  C  CR5   0   0.536  -0.0345  -1.8300   0.0069
 0JE  CAJ  C  CR5   0   0.251  -1.3678  -2.3664   0.0230
 0JE  NAK  N  NR15  0  -0.518  -1.7206  -3.6744   0.0067
 0JE  NAL  N  N     0  -0.233  -3.0238  -3.8496   0.0163
 0JE  CAM  C  CR15  0  -0.133  -3.5615  -2.6397   0.0391
 0JE  CAN  C  CR5   0   0.135  -2.5587  -1.6506   0.0457
 0JE  NAO  N  NH1   0  -0.813  -2.6096  -0.2721   0.0787
 0JE  CAP  C  C     0   0.738  -3.7538   0.4691  -0.0635
 0JE  OAR  O  O     0  -0.534  -4.8458  -0.0642  -0.2252
 0JE  NAQ  N  NT    0  -0.488  -3.5891   1.8147  -0.0135
 0JE  CAU  C  CH2   0  -0.311  -4.7418   2.6716  -0.2390
 0JE  CAV  C  CH3   0  -0.656  -5.4656   3.0424   1.0456
 0JE  CAS  C  CH2   0  -0.363  -2.3263   2.4760   0.2752
 0JE  CAT  C  CH3   0  -0.652  -1.4664   2.7131  -0.9584
 0JE  H1   H  HCH3  0   0.236   5.9263   3.7527   0.8649
 0JE  H2   H  HCH3  0   0.236   5.8200   3.8327  -0.9015
 0JE  H3   H  HCH3  0   0.239   4.8776   4.9396   0.0934
 0JE  H4   H  HCH2  0   0.227   3.5147   3.0792   0.9794
 0JE  H5   H  HCH2  0   0.225   3.4052   3.1616  -0.7825
 0JE  H6   H  HCR6  0   0.282   1.8528   1.7229   0.1260
 0JE  H7   H  HCR6  0   0.293   4.0061  -2.7901  -0.2672
 0JE  H8   H  HNR5  0   0.426   1.1925  -3.5563  -0.1583
 0JE  H10  H  HNR5  0   0.424  -1.1148  -4.4794  -0.0072
 0JE  H11  H  HCR5  0   0.275  -4.6299  -2.5189   0.0497
 0JE  H12  H  HNH1  0   0.450  -1.6912   0.1601   0.1032
 0JE  H13  H  HCH2  0   0.242  -4.3874   3.5727  -0.7442
 0JE  H14  H  HCH2  0   0.249  -5.4266   2.1825  -0.9292
 0JE  H15  H  HCH3  0   0.229  -5.8655   2.1562   1.5377
 0JE  H16  H  HCH3  0   0.224  -4.8002   3.5500   1.7457
 0JE  H17  H  HCH3  0   0.230  -6.2971   3.7148   0.8320
 0JE  H18  H  HCH2  0   0.268  -2.5634   3.4318   0.7445
 0JE  H19  H  HCH2  0   0.246  -1.7685   1.9219   1.0333
 0JE  H20  H  HCH3  0   0.234  -2.0084   3.2900  -1.7083
 0JE  H21  H  HCH3  0   0.233  -0.5703   3.2730  -0.6890
 0JE  H22  H  HCH3  0   0.227  -1.1460   1.7768  -1.4159

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
 0JE  CAZ  CAY  single    1.509  0.020  1.509
 0JE  NAK  NAL  aromatic  1.315  0.020  1.315
 0JE  NAK  CAJ  aromatic  1.355  0.020  1.355
 0JE  CAY  OAX  single    1.422  0.020  1.422
 0JE  NAL  CAM  aromatic  1.324  0.020  1.324
 0JE  NAE  CAI  aromatic  1.368  0.020  1.368
 0JE  NAE  CAF  aromatic  1.315  0.020  1.315
 0JE  CAC  CAI  aromatic  1.397  0.020  1.397
 0JE  CAC  CAB  aromatic  1.384  0.020  1.384
 0JE  OAX  CAB  single    1.344  0.020  1.344
 0JE  CAI  CAH  aromatic  1.398  0.020  1.398
 0JE  CAJ  CAF  single    1.437  0.020  1.437
 0JE  CAJ  CAN  aromatic  1.390  0.020  1.390
 0JE  CAB  CAA  aromatic  1.413  0.020  1.413
 0JE  CAF  NAG  aromatic  1.357  0.020  1.357
 0JE  CAM  CAN  aromatic  1.409  0.020  1.409
 0JE  CAN  NAO  single    1.380  0.020  1.380
 0JE  CAH  NAG  aromatic  1.371  0.020  1.371
 0JE  CAH  CAD  aromatic  1.391  0.020  1.391
 0JE  CAA  CAD  aromatic  1.372  0.020  1.372
 0JE  CAA  FAW  single    1.342  0.020  1.342
 0JE  OAR  CAP  double    1.226  0.020  1.226
 0JE  NAO  CAP  single    1.371  0.020  1.371
 0JE  CAP  NAQ  single    1.357  0.020  1.357
 0JE  CAT  CAS  single    1.522  0.020  1.522
 0JE  CAV  CAU  single    1.520  0.020  1.520
 0JE  NAQ  CAS  single    1.454  0.020  1.454
 0JE  NAQ  CAU  single    1.454  0.020  1.454
 0JE  CAZ  H1   single    0.970  0.020  1.090
 0JE  CAZ  H2   single    0.970  0.020  1.090
 0JE  CAZ  H3   single    0.970  0.020  1.090
 0JE  CAY  H4   single    0.970  0.020  1.090
 0JE  CAY  H5   single    0.970  0.020  1.090
 0JE  CAC  H6   single    0.930  0.020  1.080
 0JE  CAD  H7   single    0.930  0.020  1.080
 0JE  NAG  H8   single    0.860  0.020  1.020
 0JE  NAK  H10  single    0.860  0.020  1.020
 0JE  CAM  H11  single    0.930  0.020  1.080
 0JE  NAO  H12  single    0.860  0.020  1.020
 0JE  CAU  H13  single    0.970  0.020  1.090
 0JE  CAU  H14  single    0.970  0.020  1.090
 0JE  CAV  H15  single    0.970  0.020  1.090
 0JE  CAV  H16  single    0.970  0.020  1.090
 0JE  CAV  H17  single    0.970  0.020  1.090
 0JE  CAS  H18  single    0.970  0.020  1.090
 0JE  CAS  H19  single    0.970  0.020  1.090
 0JE  CAT  H20  single    0.970  0.020  1.090
 0JE  CAT  H21  single    0.970  0.020  1.090
 0JE  CAT  H22  single    0.970  0.020  1.090

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
 0JE  H3   CAZ  H2   107.85  3.000
 0JE  H3   CAZ  H1   107.87  3.000
 0JE  H2   CAZ  H1   108.71  3.000
 0JE  H3   CAZ  CAY  109.12  3.000
 0JE  H2   CAZ  CAY  111.59  3.000
 0JE  H1   CAZ  CAY  111.56  3.000
 0JE  H5   CAY  H4   107.53  3.000
 0JE  H5   CAY  OAX  109.97  3.000
 0JE  H4   CAY  OAX  109.93  3.000
 0JE  H5   CAY  CAZ  110.53  3.000
 0JE  H4   CAY  CAZ  110.50  3.000
 0JE  OAX  CAY  CAZ  108.37  3.000
 0JE  CAB  OAX  CAY  117.93  3.000
 0JE  CAA  CAB  CAC  119.20  3.000
 0JE  CAA  CAB  OAX  115.34  3.000
 0JE  CAC  CAB  OAX  125.46  3.000
 0JE  H6   CAC  CAI  119.67  3.000
 0JE  H6   CAC  CAB  122.18  3.000
 0JE  CAI  CAC  CAB  118.15  3.000
 0JE  CAD  CAA  FAW  119.06  3.000
 0JE  FAW  CAA  CAB  117.08  3.000
 0JE  CAD  CAA  CAB  123.86  3.000
 0JE  H7   CAD  CAH  123.04  3.000
 0JE  H7   CAD  CAA  121.08  3.000
 0JE  CAH  CAD  CAA  115.88  3.000
 0JE  CAI  CAH  NAG  105.22  3.000
 0JE  NAG  CAH  CAD  132.70  3.000
 0JE  CAI  CAH  CAD  122.08  3.000
 0JE  H8   NAG  CAF  127.22  3.000
 0JE  H8   NAG  CAH  125.73  3.000
 0JE  CAF  NAG  CAH  107.05  3.000
 0JE  NAE  CAI  CAH  109.75  3.000
 0JE  CAH  CAI  CAC  120.83  3.000
 0JE  NAE  CAI  CAC  129.42  3.000
 0JE  CAF  NAE  CAI  105.54  3.000
 0JE  CAJ  CAF  NAE  121.86  3.000
 0JE  CAJ  CAF  NAG  125.70  3.000
 0JE  NAE  CAF  NAG  112.44  3.000
 0JE  CAN  CAJ  NAK  105.92  3.000
 0JE  CAN  CAJ  CAF  127.09  3.000
 0JE  NAK  CAJ  CAF  126.99  3.000
 0JE  H10  NAK  NAL  119.31  3.000
 0JE  H10  NAK  CAJ  127.95  3.000
 0JE  NAL  NAK  CAJ  112.74  3.000
 0JE  CAM  NAL  NAK  106.31  3.000
 0JE  H11  CAM  CAN  128.93  3.000
 0JE  H11  CAM  NAL  120.42  3.000
 0JE  CAN  CAM  NAL  110.65  3.000
 0JE  NAO  CAN  CAM  132.49  3.000
 0JE  NAO  CAN  CAJ  123.13  3.000
 0JE  CAM  CAN  CAJ  104.38  3.000
 0JE  H12  NAO  CAP  121.84  3.000
 0JE  H12  NAO  CAN  113.11  3.000
 0JE  CAP  NAO  CAN  124.64  3.000
 0JE  NAQ  CAP  OAR  122.99  3.000
 0JE  NAQ  CAP  NAO  115.54  3.000
 0JE  OAR  CAP  NAO  121.47  3.000
 0JE  CAS  NAQ  CAU  116.82  3.000
 0JE  CAU  NAQ  CAP  118.86  3.000
 0JE  CAS  NAQ  CAP  124.31  3.000
 0JE  H14  CAU  H13  106.36  3.000
 0JE  H14  CAU  CAV  110.24  3.000
 0JE  H13  CAU  CAV  110.12  3.000
 0JE  H14  CAU  NAQ  109.41  3.000
 0JE  H13  CAU  NAQ  107.50  3.000
 0JE  CAV  CAU  NAQ  112.96  3.000
 0JE  H17  CAV  H16  107.69  3.000
 0JE  H17  CAV  H15  108.06  3.000
 0JE  H16  CAV  H15  108.20  3.000
 0JE  H17  CAV  CAU  110.36  3.000
 0JE  H16  CAV  CAU  111.42  3.000
 0JE  H15  CAV  CAU  110.98  3.000
 0JE  H19  CAS  H18  104.88  3.000
 0JE  H19  CAS  CAT  110.67  3.000
 0JE  H18  CAS  CAT  109.57  3.000
 0JE  H19  CAS  NAQ  110.52  3.000
 0JE  H18  CAS  NAQ  107.16  3.000
 0JE  CAT  CAS  NAQ  113.61  3.000
 0JE  H22  CAT  H21  107.64  3.000
 0JE  H22  CAT  H20  108.18  3.000
 0JE  H21  CAT  H20  107.87  3.000
 0JE  H22  CAT  CAS  111.86  3.000
 0JE  H21  CAT  CAS  110.12  3.000
 0JE  H20  CAT  CAS  111.04  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
 0JE  CONST_01  NAE  CAI  CAC  CAB  180.00   0.0  0
 0JE  CONST_02  CAH  CAI  CAC  CAB    0.00   0.0  0
 0JE  CONST_03  CAH  CAD  CAA  CAB    0.00   0.0  0
 0JE  CONST_04  CAF  NAE  CAI  CAC  180.00   0.0  0
 0JE  CONST_05  NAG  CAH  CAI  CAC  180.00   0.0  0
 0JE  CONST_06  CAD  CAH  CAI  CAC    0.00   0.0  0
 0JE  CONST_07  CAD  CAA  CAB  CAC    0.00   0.0  0
 0JE  CONST_08  CAI  CAC  CAB  CAA    0.00   0.0  0
 0JE  CONST_09  CAI  CAH  CAD  CAA    0.00   0.0  0
 0JE  CONST_10  NAG  CAH  CAD  CAA  180.00   0.0  0
 0JE  CONST_11  NAE  CAI  CAH  CAD  180.00   0.0  0
 0JE  CONST_12  CAF  NAG  CAH  CAD  180.00   0.0  0
 0JE  CONST_13  CAF  NAE  CAI  CAH    0.00   0.0  0
 0JE  CONST_14  NAE  CAF  NAG  CAH    0.00   0.0  0
 0JE  CONST_15  CAJ  CAF  NAG  CAH  180.00   0.0  0
 0JE  CONST_16  CAI  NAE  CAF  NAG    0.00   0.0  0
 0JE  CONST_17  NAK  CAJ  CAF  NAG    0.00   0.0  0
 0JE  CONST_18  CAN  CAJ  CAF  NAG  180.00   0.0  0
 0JE  CONST_19  NAE  CAI  CAH  NAG    0.00   0.0  0
 0JE  CONST_20  CAJ  CAF  NAE  CAI  180.00   0.0  0
 0JE  CONST_21  CAF  NAG  CAH  CAI    0.00   0.0  0
 0JE  CONST_22  NAK  CAJ  CAF  NAE  180.00   0.0  0
 0JE  CONST_23  CAN  CAJ  CAF  NAE    0.00   0.0  0
 0JE  CONST_24  NAL  NAK  CAJ  CAF  180.00   0.0  0
 0JE  CONST_25  CAM  CAN  CAJ  CAF  180.00   0.0  0
 0JE  CONST_26  CAM  NAL  NAK  CAJ    0.00   0.0  0
 0JE  CONST_27  NAL  CAM  CAN  CAJ    0.00   0.0  0
 0JE  CONST_28  CAN  CAM  NAL  NAK    0.00   0.0  0
 0JE  CONST_29  CAM  CAN  CAJ  NAK    0.00   0.0  0
 0JE  CONST_30  CAN  CAJ  NAK  NAL    0.00   0.0  0
 0JE  CONST_31  CAI  CAC  CAB  OAX  180.00   0.0  0
 0JE  CONST_32  CAD  CAA  CAB  OAX  180.00   0.0  0
 0JE  CONST_33  FAW  CAA  CAB  CAC  180.00   0.0  0
 0JE  CONST_34  CAH  CAD  CAA  FAW  180.00   0.0  0
 0JE  CONST_35  NAO  CAN  CAJ  CAF    0.00   0.0  0
 0JE  CONST_36  NAO  CAN  CAJ  NAK  180.00   0.0  0
 0JE  CONST_37  NAO  CAN  CAM  NAL  180.00   0.0  0
 0JE  CONST_38  H7   CAD  CAA  CAB  180.00   0.0  0
 0JE  CONST_39  H6   CAC  CAB  CAA  180.00   0.0  0
 0JE  CONST_40  H8   NAG  CAH  CAD    0.00   0.0  0
 0JE  CONST_41  H10  NAK  CAJ  CAF    0.00   0.0  0
 0JE  CONST_42  H11  CAM  CAN  CAJ  180.00   0.0  0
 0JE  CONST_43  CAP  NAO  CAN  CAJ  180.00   0.0  0
 0JE  CONST_44  CAP  NAO  CAN  CAM    0.00   0.0  0
 0JE  CONST_45  H12  NAO  CAN  CAJ    0.00   0.0  0
 0JE  CONST_46  OAR  CAP  NAO  CAN    0.00   0.0  0
 0JE  CONST_47  NAQ  CAP  NAO  CAN  180.00   0.0  0
 0JE  CONST_48  CAS  NAQ  CAP  OAR  180.00   0.0  0
 0JE  CONST_49  CAU  NAQ  CAP  OAR    0.00   0.0  0
 0JE  CONST_50  CAS  NAQ  CAP  NAO    0.00   0.0  0
 0JE  CONST_51  CAU  NAQ  CAP  NAO  180.00   0.0  0
 0JE  Var_01    CAC  CAB  OAX  CAY   -0.60  30.0  2
 0JE  Var_02    H4   CAY  OAX  CAB   59.88  30.0  1
 0JE  Var_03    CAT  CAS  NAQ  CAP   87.54  30.0  3
 0JE  Var_04    CAV  CAU  NAQ  CAP   91.92  30.0  3
 0JE  Var_05    H1   CAZ  CAY  OAX  -61.02  30.0  3
 0JE  Var_06    H20  CAT  CAS  NAQ   56.56  30.0  3
 0JE  Var_07    H15  CAV  CAU  NAQ  -62.42  30.0  3

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
 0JE  plan-1  CAF  0.020
 0JE  plan-1  CAJ  0.020
 0JE  plan-1  NAK  0.020
 0JE  plan-1  NAL  0.020
 0JE  plan-1  CAM  0.020
 0JE  plan-1  CAN  0.020
 0JE  plan-1  NAO  0.020
 0JE  plan-1  H10  0.020
 0JE  plan-1  H11  0.020
 0JE  plan-2  OAX  0.020
 0JE  plan-2  CAB  0.020
 0JE  plan-2  CAC  0.020
 0JE  plan-2  CAA  0.020
 0JE  plan-2  FAW  0.020
 0JE  plan-2  CAD  0.020
 0JE  plan-2  CAH  0.020
 0JE  plan-2  NAG  0.020
 0JE  plan-2  CAI  0.020
 0JE  plan-2  NAE  0.020
 0JE  plan-2  CAF  0.020
 0JE  plan-2  CAJ  0.020
 0JE  plan-2  H6   0.020
 0JE  plan-2  H7   0.020
 0JE  plan-2  H8   0.020
 0JE  plan-3  CAN  0.020
 0JE  plan-3  NAO  0.020
 0JE  plan-3  CAP  0.020
 0JE  plan-3  OAR  0.020
 0JE  plan-3  NAQ  0.020
 0JE  plan-3  CAU  0.020
 0JE  plan-3  CAS  0.020
 0JE  plan-3  H12  0.020

