# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:52:23 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 2-({5-bromo-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}oxy)-N-methylbenzene-1-carboximidic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Nc2ncc(Br)c(Oc3ccccc3C(O)=NC)n2)cc(OC)c1OC
#
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
 EDJ  EDJ  '2-({5-bromo-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}oxy)-N-methylbenzene-1-carboximidic acid'  ligand  52  31  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EDJ
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
 EDJ  C4   C   CR6   0   0.623   2.2070  -0.4792  -0.3916
 EDJ  C5   C   CR6   0  -0.298   2.1563  -1.8403  -0.0612
 EDJ  C6   C   CR16  0   0.021   0.9046  -2.3503   0.1882
 EDJ  N1   N   N     0  -0.481  -0.2012  -1.6147   0.1220
 EDJ  N3   N   N     0  -0.487   1.1280   0.2477  -0.4819
 EDJ  CAB  C   CH3   0  -0.440  -5.0091   3.5804  -0.6367
 EDJ  CBA  C   CR6   0   0.350  -4.6575   1.3046  -0.0723
 EDJ  CAL  C   CR16  0  -0.543  -3.2860   1.4058  -0.2675
 EDJ  CBE  C   CR6   0   0.151  -5.2277   0.0896   0.3177
 EDJ  OAT  O   O2    0  -0.482  -6.5666  -0.0027   0.5429
 EDJ  CAD  C   CH3   0  -0.408  -7.3300  -0.3321  -0.6091
 EDJ  CBB  C   CR6   0   0.378  -4.4026  -1.0219   0.4864
 EDJ  OAS  O   O2    0  -0.467  -5.0277  -2.1549   0.8502
 EDJ  CAC  C   CH3   0  -0.439  -4.2519  -3.3146   1.0784
 EDJ  CAM  C   CR16  0  -0.518  -3.0243  -0.9338   0.2933
 EDJ  CAW  C   CR6   0   0.423  -2.4700   0.2864  -0.0838
 EDJ  C2   C   CR6   0   0.625  -0.0423  -0.3409  -0.2078
 EDJ  BR5  BR  BR    0  -0.015   3.7058  -2.8707   0.0923
 EDJ  OAU  O   O2    0  -0.486   3.3902   0.0548  -0.6792
 EDJ  CAZ  C   CR6   0   0.337   3.5168   1.4237  -0.7183
 EDJ  CAI  C   CR16  0  -0.311   3.7313   1.9813  -1.9663
 EDJ  CAG  C   CR16  0  -0.258   3.9412   3.3454  -2.0929
 EDJ  CAH  C   CR16  0  -0.239   3.9256   4.1468  -0.9621
 EDJ  CAJ  C   CR16  0  -0.293   3.7132   3.5803   0.2837
 EDJ  CBC  C   CR6   0  -0.023   3.5048   2.2073   0.4424
 EDJ  CAV  C   C     0   0.467   3.3005   1.6410   1.7978
 EDJ  OAE  O   OH1   0  -0.623   3.3694   2.5851   2.7519
 EDJ  NAP  N   N     0  -0.430   3.0870   0.4101   1.9785
 EDJ  CAA  C   CH3   0  -0.605   2.8750  -0.1092   3.3063
 EDJ  H1   H   HCR6  0   0.289   0.7752  -3.3917   0.4611
 EDJ  H2   H   HCH3  0   0.230  -4.5172   3.5231  -1.6112
 EDJ  H3   H   HCH3  0   0.263  -5.8644   4.2466  -0.7161
 EDJ  H4   H   HCH3  0   0.230  -4.3061   3.9954   0.0901
 EDJ  H5   H   HCR6  0   0.290  -2.8363   2.3446  -0.5635
 EDJ  H6   H   HCH3  0   0.235  -8.3730  -0.3841  -0.3007
 EDJ  H7   H   HCH3  0   0.219  -7.2352   0.4261  -1.3900
 EDJ  H8   H   HCH3  0   0.219  -7.0407  -1.3008  -1.0247
 EDJ  H9   H   HCH3  0   0.228  -3.7301  -3.6424   0.1758
 EDJ  H10  H   HCH3  0   0.229  -3.5181  -3.1646   1.8743
 EDJ  H11  H   HCH3  0   0.262  -4.9463  -4.0935   1.3836
 EDJ  H12  H   HCR6  0   0.311  -2.3828  -1.7885   0.4265
 EDJ  H13  H   HNH1  0   0.414  -0.8543   1.4341  -0.5542
 EDJ  H14  H   HCR6  0   0.277   3.7359   1.3378  -2.8365
 EDJ  H15  H   HCR6  0   0.270   4.1097   3.7751  -3.0711
 EDJ  H16  H   HCR6  0   0.266   4.0821   5.2136  -1.0450
 EDJ  H17  H   HCR6  0   0.270   3.7112   4.2260   1.1496
 EDJ  H19  H   HCH3  0   0.235   3.7259   0.0576   3.9765
 EDJ  H20  H   HCH3  0   0.239   1.9874   0.3138   3.7899
 EDJ  H21  H   HCH3  0   0.251   2.7228  -1.1850   3.2450
 EDJ  H22  H   HOH1  0   0.492   3.2440   2.2041   3.6298
 EDJ  NAQ  N   NH1   0  -0.778  -1.1103   0.4924  -0.2993
 EDJ  OAR  O   O2    0  -0.465  -5.5161   2.3261  -0.2262

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
 EDJ  CAD  OAT  single    1.421  0.020  1.421
 EDJ  CAB  OAR  single    1.414  0.020  1.414
 EDJ  OAS  CBB  single    1.344  0.020  1.344
 EDJ  OAS  CAC  single    1.414  0.020  1.414
 EDJ  CAM  CBB  aromatic  1.395  0.020  1.395
 EDJ  CAM  CAW  aromatic  1.392  0.020  1.392
 EDJ  CBB  CBE  aromatic  1.394  0.020  1.394
 EDJ  NAQ  CAW  single    1.392  0.020  1.392
 EDJ  NAQ  C2   single    1.358  0.020  1.358
 EDJ  CAW  CAL  aromatic  1.397  0.020  1.397
 EDJ  CBE  OAT  single    1.361  0.020  1.361
 EDJ  CBE  CBA  aromatic  1.398  0.020  1.398
 EDJ  CAL  CBA  aromatic  1.389  0.020  1.389
 EDJ  CBA  OAR  single    1.343  0.020  1.343
 EDJ  CAH  CAG  aromatic  1.386  0.020  1.386
 EDJ  CAH  CAJ  aromatic  1.385  0.020  1.385
 EDJ  CAG  CAI  aromatic  1.386  0.020  1.386
 EDJ  C2   N1   aromatic  1.325  0.020  1.325
 EDJ  C2   N3   aromatic  1.338  0.020  1.338
 EDJ  N1   C6   aromatic  1.330  0.020  1.330
 EDJ  CAJ  CBC  aromatic  1.398  0.020  1.398
 EDJ  CAI  CAZ  aromatic  1.384  0.020  1.384
 EDJ  N3   C4   aromatic  1.304  0.020  1.304
 EDJ  C6   C5   aromatic  1.374  0.020  1.374
 EDJ  CBC  CAZ  aromatic  1.401  0.020  1.401
 EDJ  CBC  CAV  single    1.483  0.020  1.483
 EDJ  CAZ  OAU  single    1.375  0.020  1.375
 EDJ  C4   C5   aromatic  1.402  0.020  1.402
 EDJ  C4   OAU  single    1.330  0.020  1.330
 EDJ  C5   BR5  single    1.867  0.020  1.867
 EDJ  CAV  OAE  single    1.344  0.020  1.344
 EDJ  CAV  NAP  double    1.262  0.020  1.262
 EDJ  NAP  CAA  single    1.441  0.020  1.441
 EDJ  C6   H1   single    0.930  0.020  1.080
 EDJ  CAB  H2   single    0.970  0.020  1.090
 EDJ  CAB  H3   single    0.970  0.020  1.090
 EDJ  CAB  H4   single    0.970  0.020  1.090
 EDJ  CAL  H5   single    0.930  0.020  1.080
 EDJ  CAD  H6   single    0.970  0.020  1.090
 EDJ  CAD  H7   single    0.970  0.020  1.090
 EDJ  CAD  H8   single    0.970  0.020  1.090
 EDJ  CAC  H9   single    0.970  0.020  1.090
 EDJ  CAC  H10  single    0.970  0.020  1.090
 EDJ  CAC  H11  single    0.970  0.020  1.090
 EDJ  CAM  H12  single    0.930  0.020  1.080
 EDJ  NAQ  H13  single    0.860  0.020  1.020
 EDJ  CAI  H14  single    0.930  0.020  1.080
 EDJ  CAG  H15  single    0.930  0.020  1.080
 EDJ  CAH  H16  single    0.930  0.020  1.080
 EDJ  CAJ  H17  single    0.930  0.020  1.080
 EDJ  CAA  H19  single    0.970  0.020  1.090
 EDJ  CAA  H20  single    0.970  0.020  1.090
 EDJ  CAA  H21  single    0.970  0.020  1.090
 EDJ  OAE  H22  single    0.850  0.020  0.980

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
 EDJ  OAU  C4   N3   119.83  3.000
 EDJ  OAU  C4   C5   118.24  3.000
 EDJ  N3   C4   C5   121.85  3.000
 EDJ  BR5  C5   C6   122.42  3.000
 EDJ  BR5  C5   C4   121.69  3.000
 EDJ  C6   C5   C4   115.85  3.000
 EDJ  H1   C6   N1   116.40  3.000
 EDJ  H1   C6   C5   120.71  3.000
 EDJ  N1   C6   C5   122.89  3.000
 EDJ  C2   N1   C6   116.39  3.000
 EDJ  C2   N3   C4   117.66  3.000
 EDJ  H4   CAB  H3   108.78  3.000
 EDJ  H4   CAB  H2   108.86  3.000
 EDJ  H3   CAB  H2   108.73  3.000
 EDJ  H4   CAB  OAR  111.99  3.000
 EDJ  H3   CAB  OAR  106.43  3.000
 EDJ  H2   CAB  OAR  111.94  3.000
 EDJ  CBE  CBA  CAL  120.35  3.000
 EDJ  CAL  CBA  OAR  124.03  3.000
 EDJ  CBE  CBA  OAR  115.62  3.000
 EDJ  H5   CAL  CAW  119.22  3.000
 EDJ  H5   CAL  CBA  120.79  3.000
 EDJ  CAW  CAL  CBA  119.98  3.000
 EDJ  CBB  CBE  OAT  120.54  3.000
 EDJ  OAT  CBE  CBA  120.43  3.000
 EDJ  CBB  CBE  CBA  119.03  3.000
 EDJ  CAD  OAT  CBE  114.22  3.000
 EDJ  H8   CAD  H7   108.68  3.000
 EDJ  H8   CAD  H6   108.60  3.000
 EDJ  H7   CAD  H6   108.58  3.000
 EDJ  H8   CAD  OAT  111.81  3.000
 EDJ  H7   CAD  OAT  111.84  3.000
 EDJ  H6   CAD  OAT  107.22  3.000
 EDJ  CAM  CBB  OAS  123.39  3.000
 EDJ  CAM  CBB  CBE  121.18  3.000
 EDJ  OAS  CBB  CBE  115.43  3.000
 EDJ  CAC  OAS  CBB  118.68  3.000
 EDJ  H11  CAC  H10  108.83  3.000
 EDJ  H11  CAC  H9   108.78  3.000
 EDJ  H10  CAC  H9   108.78  3.000
 EDJ  H11  CAC  OAS  106.42  3.000
 EDJ  H10  CAC  OAS  111.93  3.000
 EDJ  H9   CAC  OAS  112.01  3.000
 EDJ  H12  CAM  CAW  119.47  3.000
 EDJ  H12  CAM  CBB  121.43  3.000
 EDJ  CAW  CAM  CBB  119.10  3.000
 EDJ  NAQ  CAW  CAM  124.08  3.000
 EDJ  NAQ  CAW  CAL  115.57  3.000
 EDJ  CAM  CAW  CAL  120.35  3.000
 EDJ  NAQ  C2   N3   113.84  3.000
 EDJ  N3   C2   N1   125.34  3.000
 EDJ  NAQ  C2   N1   120.82  3.000
 EDJ  CAZ  OAU  C4   119.20  3.000
 EDJ  CBC  CAZ  CAI  121.56  3.000
 EDJ  CBC  CAZ  OAU  122.18  3.000
 EDJ  CAI  CAZ  OAU  116.17  3.000
 EDJ  H14  CAI  CAG  120.74  3.000
 EDJ  H14  CAI  CAZ  119.09  3.000
 EDJ  CAG  CAI  CAZ  120.17  3.000
 EDJ  H15  CAG  CAH  120.65  3.000
 EDJ  H15  CAG  CAI  119.82  3.000
 EDJ  CAH  CAG  CAI  119.53  3.000
 EDJ  H16  CAH  CAJ  119.64  3.000
 EDJ  H16  CAH  CAG  120.42  3.000
 EDJ  CAJ  CAH  CAG  119.94  3.000
 EDJ  H17  CAJ  CBC  119.74  3.000
 EDJ  H17  CAJ  CAH  118.48  3.000
 EDJ  CBC  CAJ  CAH  121.79  3.000
 EDJ  CAV  CBC  CAJ  119.96  3.000
 EDJ  CAV  CBC  CAZ  123.02  3.000
 EDJ  CAJ  CBC  CAZ  117.02  3.000
 EDJ  NAP  CAV  OAE  126.30  3.000
 EDJ  NAP  CAV  CBC  121.77  3.000
 EDJ  OAE  CAV  CBC  111.93  3.000
 EDJ  H22  OAE  CAV  111.21  3.000
 EDJ  CAA  NAP  CAV  120.54  3.000
 EDJ  H21  CAA  H20  107.05  3.000
 EDJ  H21  CAA  H19  107.06  3.000
 EDJ  H20  CAA  H19  107.48  3.000
 EDJ  H21  CAA  NAP  108.96  3.000
 EDJ  H20  CAA  NAP  112.74  3.000
 EDJ  H19  CAA  NAP  113.22  3.000
 EDJ  H13  NAQ  C2   112.98  3.000
 EDJ  H13  NAQ  CAW  115.16  3.000
 EDJ  C2   NAQ  CAW  131.85  3.000
 EDJ  CBA  OAR  CAB  118.61  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
 EDJ  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 EDJ  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 EDJ  CONST_03  C2   N1   C6   C5      0.00   0.0  0
 EDJ  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 EDJ  CONST_05  N3   C2   N1   C6      0.00   0.0  0
 EDJ  CONST_06  N3   C4   C5   C6      0.00   0.0  0
 EDJ  CONST_07  CAM  CBB  CBE  CBA     0.00   0.0  0
 EDJ  CONST_08  CAM  CAW  CAL  CBA     0.00   0.0  0
 EDJ  CONST_09  CBB  CAM  CAW  CAL     0.00   0.0  0
 EDJ  CONST_10  CBB  CBE  CBA  CAL     0.00   0.0  0
 EDJ  CONST_11  CAW  CAM  CBB  CBE     0.00   0.0  0
 EDJ  CONST_12  CAW  CAL  CBA  CBE     0.00   0.0  0
 EDJ  CONST_13  CAH  CAG  CAI  CAZ     0.00   0.0  0
 EDJ  CONST_14  CAH  CAJ  CBC  CAZ     0.00   0.0  0
 EDJ  CONST_15  CAJ  CAH  CAG  CAI     0.00   0.0  0
 EDJ  CONST_16  CAJ  CBC  CAZ  CAI     0.00   0.0  0
 EDJ  CONST_17  CBC  CAJ  CAH  CAG     0.00   0.0  0
 EDJ  CONST_18  CBC  CAZ  CAI  CAG     0.00   0.0  0
 EDJ  CONST_19  NAQ  C2   N3   C4    180.00   0.0  0
 EDJ  CONST_20  NAQ  C2   N1   C6    180.00   0.0  0
 EDJ  CONST_21  OAU  C4   C5   C6    180.00   0.0  0
 EDJ  CONST_22  BR5  C5   C6   N1    180.00   0.0  0
 EDJ  CONST_23  BR5  C5   C4   N3    180.00   0.0  0
 EDJ  CONST_24  CBB  CBE  CBA  OAR   180.00   0.0  0
 EDJ  CONST_25  CAW  CAL  CBA  OAR   180.00   0.0  0
 EDJ  CONST_26  OAS  CBB  CBE  CBA   180.00   0.0  0
 EDJ  CONST_27  NAQ  CAW  CAL  CBA   180.00   0.0  0
 EDJ  CONST_28  OAT  CBE  CBA  CAL   180.00   0.0  0
 EDJ  CONST_29  CAM  CBB  CBE  OAT   180.00   0.0  0
 EDJ  CONST_30  NAQ  CAW  CAM  CBB   180.00   0.0  0
 EDJ  CONST_31  CAW  CAM  CBB  OAS   180.00   0.0  0
 EDJ  CONST_32  OAU  C4   N3   C2    180.00   0.0  0
 EDJ  CONST_33  CAG  CAI  CAZ  OAU   180.00   0.0  0
 EDJ  CONST_34  CAJ  CBC  CAZ  OAU   180.00   0.0  0
 EDJ  CONST_35  CAV  CBC  CAZ  CAI   180.00   0.0  0
 EDJ  CONST_36  CAV  CBC  CAJ  CAH   180.00   0.0  0
 EDJ  CONST_37  H1   C6   C5   C4    180.00   0.0  0
 EDJ  CONST_38  H12  CAM  CAW  CAL   180.00   0.0  0
 EDJ  CONST_39  H5   CAL  CBA  CBE   180.00   0.0  0
 EDJ  CONST_40  H15  CAG  CAI  CAZ   180.00   0.0  0
 EDJ  CONST_41  H17  CAJ  CBC  CAZ   180.00   0.0  0
 EDJ  CONST_42  H16  CAH  CAG  CAI   180.00   0.0  0
 EDJ  CONST_43  H14  CAI  CAG  CAH   180.00   0.0  0
 EDJ  Var_01    CAI  CAZ  OAU  C4   -110.92  30.0  2
 EDJ  Var_02    CAW  NAQ  C2   N1      1.10  30.0  2
 EDJ  Var_03    C2   NAQ  CAW  CAL   179.45  30.0  2
 EDJ  Var_04    CBE  CBA  OAR  CAB  -179.18  30.0  2
 EDJ  Var_05    CBB  CBE  OAT  CAD   -91.66  30.0  2
 EDJ  Var_06    CAM  CBB  OAS  CAC     1.39  30.0  2
 EDJ  Var_07    OAE  CAV  CBC  CAZ   178.18  30.0  2
 EDJ  Var_08    H2   CAB  OAR  CBA    60.23  30.0  3
 EDJ  Var_09    H6   CAD  OAT  CBE   179.52  30.0  3
 EDJ  Var_10    H9   CAC  OAS  CBB   -62.74  30.0  3
 EDJ  Var_11    H19  CAA  NAP  CAV   -60.27  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
 EDJ  plan-1  CBA  0.020
 EDJ  plan-1  CAL  0.020
 EDJ  plan-1  CBE  0.020
 EDJ  plan-1  OAT  0.020
 EDJ  plan-1  CBB  0.020
 EDJ  plan-1  OAS  0.020
 EDJ  plan-1  CAM  0.020
 EDJ  plan-1  CAW  0.020
 EDJ  plan-1  H5   0.020
 EDJ  plan-1  H12  0.020
 EDJ  plan-1  NAQ  0.020
 EDJ  plan-1  OAR  0.020
 EDJ  plan-2  C4   0.020
 EDJ  plan-2  C5   0.020
 EDJ  plan-2  C6   0.020
 EDJ  plan-2  N1   0.020
 EDJ  plan-2  N3   0.020
 EDJ  plan-2  C2   0.020
 EDJ  plan-2  BR5  0.020
 EDJ  plan-2  OAU  0.020
 EDJ  plan-2  H1   0.020
 EDJ  plan-2  NAQ  0.020
 EDJ  plan-3  OAU  0.020
 EDJ  plan-3  CAZ  0.020
 EDJ  plan-3  CAI  0.020
 EDJ  plan-3  CAG  0.020
 EDJ  plan-3  CAH  0.020
 EDJ  plan-3  CAJ  0.020
 EDJ  plan-3  CBC  0.020
 EDJ  plan-3  CAV  0.020
 EDJ  plan-3  H14  0.020
 EDJ  plan-3  H15  0.020
 EDJ  plan-3  H16  0.020
 EDJ  plan-3  H17  0.020
 EDJ  plan-4  CBC  0.020
 EDJ  plan-4  CAV  0.020
 EDJ  plan-4  OAE  0.020
 EDJ  plan-4  NAP  0.020
 EDJ  plan-4  CAA  0.020

