# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 13 08:02:19 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: ~{N}-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-methyl-phenyl]-2-fluoranyl-prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)c(Cl)c(COc2cnc(Nc3c(C)cccc3NC(=O)C(F)=C)nc2)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
 HHL  HHL  ~{N}-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-methyl-phenyl]-2-fluoranyl-prop-2-enamide  ligand  55  34  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HHL
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
 HHL  CBH  C   C2    0  -0.614  132.6665   0.4612  85.9282
 HHL  CBE  C   C     0   0.384  131.9462   1.5593  86.0642
 HHL  FBG  F   F     0  -0.312  132.5351   2.7427  86.3203
 HHL  CBD  C   C     0   0.440  130.4609   1.6160  85.9247
 HHL  OBF  O   O     0  -0.446  129.8186   0.5949  85.7789
 HHL  NBC  N   NH1   0  -0.739  129.9295   2.8589  85.9721
 HHL  CAW  C   CR6   0   0.330  128.5945   3.1294  85.6246
 HHL  CAX  C   CR16  0  -0.315  127.5429   2.5458  86.3186
 HHL  CAY  C   CR16  0  -0.250  126.2389   2.8705  85.9861
 HHL  CAZ  C   CR16  0  -0.317  125.9837   3.7789  84.9692
 HHL  CBA  C   CR6   0   0.069  127.0211   4.3643  84.2513
 HHL  CBB  C   CH3   0  -0.734  126.7381   5.3223  83.1323
 HHL  CAV  C   CR6   0   0.242  128.3381   4.0235  84.5791
 HHL  NAU  N   NH1   0  -0.757  129.4070   4.6092  83.8817
 HHL  CAR  C   CR6   0   0.558  130.3025   3.9175  83.1115
 HHL  NAS  N   N     0  -0.427  130.2117   2.5994  83.0575
 HHL  CAT  C   CR16  0  -0.121  131.1204   1.9492  82.3396
 HHL  NAQ  N   N     0  -0.428  131.2172   4.6539  82.4753
 HHL  CAP  C   CR16  0  -0.099  132.1027   4.0056  81.7482
 HHL  CAO  C   CR6   0   0.260  132.1164   2.6149  81.6429
 HHL  OAN  O   O2    0  -0.459  133.0792   2.0505  80.8873
 HHL  CAM  C   CH2   0  -0.263  132.9819   0.6577  80.6422
 HHL  CAB  C   CR6   0   0.276  133.9450   0.3325  79.5400
 HHL  CAC  C   CR6   0  -0.296  135.1588  -0.3018  79.7780
 HHL  CL1  CL  CL    0  -0.103  135.6449  -0.7353  81.3805
 HHL  CAA  C   CR6   0  -0.275  133.6261   0.6830  78.2318
 HHL  CL2  CL  CL    0  -0.100  132.1426   1.4974  77.8795
 HHL  CAF  C   CR6   0   0.527  134.4788   0.3850  77.1690
 HHL  OAH  O   O2    0  -0.452  134.0754   0.7517  75.9510
 HHL  CAL  C   CH3   0  -0.443  134.8919   0.4433  74.8351
 HHL  CAE  C   CR16  0  -0.567  135.6807  -0.2656  77.4287
 HHL  CAD  C   CR6   0   0.530  136.0307  -0.6102  78.7291
 HHL  OAG  O   O2    0  -0.452  137.1689  -1.2273  79.0543
 HHL  CAK  C   CH3   0  -0.443  138.0798  -1.5760  78.0265
 HHL  H1   H   H     0   0.285  133.7434   0.4764  86.0178
 HHL  H2   H   H     0   0.283  132.1816  -0.4799  85.7217
 HHL  H5   H   HNH1  0   0.411  130.5591   3.6484  85.9586
 HHL  H6   H   HCR6  0   0.263  127.7467   1.8641  87.1326
 HHL  H7   H   HCR6  0   0.257  125.4178   2.4215  86.5291
 HHL  H8   H   HCR6  0   0.252  124.9607   4.0302  84.7176
 HHL  H9   H   HCH3  0   0.249  127.0945   6.3299  83.3577
 HHL  H10  H   HCH3  0   0.251  127.2244   5.0114  82.2064
 HHL  H11  H   HCH3  0   0.254  125.6683   5.3902  82.9433
 HHL  H12  H   HNH1  0   0.402  129.3774   5.6043  83.7187
 HHL  H13  H   HCR6  0   0.289  131.0299   0.8687  82.3313
 HHL  H14  H   HCR6  0   0.280  132.8438   4.5986  81.2206
 HHL  H15  H   HCH2  0   0.254  131.9690   0.3873  80.3279
 HHL  H16  H   HCH2  0   0.259  133.2056   0.0900  81.5474
 HHL  H17  H   HCH3  0   0.268  134.3663   0.8193  73.9616
 HHL  H18  H   HCH3  0   0.237  135.8670   0.9319  74.8982
 HHL  H19  H   HCH3  0   0.237  135.0367  -0.6338  74.7246
 HHL  H20  H   HCR6  0   0.323  136.3500  -0.5020  76.6139
 HHL  H21  H   HCH3  0   0.268  138.9157  -2.0683  78.5158
 HHL  H22  H   HCH3  0   0.237  137.6334  -2.2662  77.3071
 HHL  H23  H   HCH3  0   0.237  138.4490  -0.6949  77.4964

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
 HHL  CAL  OAH  single    1.417  0.020  1.417
 HHL  OAH  CAF  single    1.334  0.020  1.334
 HHL  CAK  OAG  single    1.417  0.020  1.417
 HHL  CAE  CAF  aromatic  1.391  0.020  1.391
 HHL  CAE  CAD  aromatic  1.390  0.020  1.390
 HHL  CAF  CAA  aromatic  1.395  0.020  1.395
 HHL  OAG  CAD  single    1.335  0.020  1.335
 HHL  CAD  CAC  aromatic  1.398  0.020  1.398
 HHL  CAA  CL2  single    1.729  0.020  1.729
 HHL  CAA  CAB  aromatic  1.391  0.020  1.391
 HHL  CAC  CAB  aromatic  1.390  0.020  1.390
 HHL  CAC  CL1  single    1.730  0.020  1.730
 HHL  CAB  CAM  single    1.499  0.020  1.499
 HHL  CAM  OAN  single    1.418  0.020  1.418
 HHL  OAN  CAO  single    1.348  0.020  1.348
 HHL  CAO  CAT  aromatic  1.386  0.020  1.386
 HHL  CAO  CAP  aromatic  1.395  0.020  1.395
 HHL  CAT  NAS  aromatic  1.328  0.020  1.328
 HHL  CAP  NAQ  aromatic  1.316  0.020  1.316
 HHL  CBB  CBA  single    1.500  0.020  1.500
 HHL  NAS  CAR  aromatic  1.322  0.020  1.322
 HHL  NAQ  CAR  aromatic  1.336  0.020  1.336
 HHL  CAR  NAU  single    1.369  0.020  1.369
 HHL  CBA  CAZ  aromatic  1.391  0.020  1.391
 HHL  CBA  CAV  aromatic  1.399  0.020  1.399
 HHL  NAU  CAV  single    1.404  0.020  1.404
 HHL  CAZ  CAY  aromatic  1.387  0.020  1.387
 HHL  CAV  CAW  aromatic  1.399  0.020  1.399
 HHL  CAY  CAX  aromatic  1.384  0.020  1.384
 HHL  CAW  NBC  single    1.406  0.020  1.406
 HHL  CAW  CAX  aromatic  1.389  0.020  1.389
 HHL  NBC  CBD  single    1.353  0.020  1.353
 HHL  CBD  OBF  double    1.215  0.020  1.215
 HHL  CBD  CBE  single    1.493  0.020  1.493
 HHL  FBG  CBE  single    1.346  0.020  1.346
 HHL  CBH  CBE  double    1.320  0.020  1.320
 HHL  CBH  H1   single    0.930  0.020  1.080
 HHL  CBH  H2   single    0.930  0.020  1.080
 HHL  NBC  H5   single    0.890  0.020  1.040
 HHL  CAX  H6   single    0.930  0.020  1.080
 HHL  CAY  H7   single    0.930  0.020  1.080
 HHL  CAZ  H8   single    0.930  0.020  1.080
 HHL  CBB  H9   single    0.970  0.020  1.090
 HHL  CBB  H10  single    0.970  0.020  1.090
 HHL  CBB  H11  single    0.970  0.020  1.090
 HHL  NAU  H12  single    0.860  0.020  1.020
 HHL  CAT  H13  single    0.930  0.020  1.080
 HHL  CAP  H14  single    0.930  0.020  1.080
 HHL  CAM  H15  single    0.970  0.020  1.090
 HHL  CAM  H16  single    0.970  0.020  1.090
 HHL  CAL  H17  single    0.970  0.020  1.090
 HHL  CAL  H18  single    0.970  0.020  1.090
 HHL  CAL  H19  single    0.970  0.020  1.090
 HHL  CAE  H20  single    0.930  0.020  1.080
 HHL  CAK  H21  single    0.970  0.020  1.090
 HHL  CAK  H22  single    0.970  0.020  1.090
 HHL  CAK  H23  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
 HHL  H2   CBH  H1   118.42  3.000
 HHL  H2   CBH  CBE  120.01  3.000
 HHL  H1   CBH  CBE  121.56  3.000
 HHL  CBD  CBE  FBG  114.81  3.000
 HHL  FBG  CBE  CBH  120.79  3.000
 HHL  CBD  CBE  CBH  124.39  3.000
 HHL  NBC  CBD  OBF  124.66  3.000
 HHL  OBF  CBD  CBE  120.34  3.000
 HHL  NBC  CBD  CBE  114.99  3.000
 HHL  H5   NBC  CAW  116.00  3.000
 HHL  H5   NBC  CBD  118.23  3.000
 HHL  CAW  NBC  CBD  122.77  3.000
 HHL  CAV  CAW  CAX  120.21  3.000
 HHL  CAX  CAW  NBC  120.98  3.000
 HHL  CAV  CAW  NBC  118.79  3.000
 HHL  H6   CAX  CAY  120.42  3.000
 HHL  H6   CAX  CAW  119.91  3.000
 HHL  CAY  CAX  CAW  119.65  3.000
 HHL  H7   CAY  CAZ  120.01  3.000
 HHL  H7   CAY  CAX  119.79  3.000
 HHL  CAZ  CAY  CAX  120.20  3.000
 HHL  H8   CAZ  CBA  119.14  3.000
 HHL  H8   CAZ  CAY  119.74  3.000
 HHL  CBA  CAZ  CAY  121.12  3.000
 HHL  CAV  CBA  CBB  120.52  3.000
 HHL  CAV  CBA  CAZ  118.60  3.000
 HHL  CBB  CBA  CAZ  120.87  3.000
 HHL  H11  CBB  H10  107.96  3.000
 HHL  H11  CBB  H9   107.40  3.000
 HHL  H10  CBB  H9   107.00  3.000
 HHL  H11  CBB  CBA  110.79  3.000
 HHL  H10  CBB  CBA  111.53  3.000
 HHL  H9   CBB  CBA  111.94  3.000
 HHL  NAU  CAV  CBA  119.91  3.000
 HHL  NAU  CAV  CAW  119.87  3.000
 HHL  CBA  CAV  CAW  120.20  3.000
 HHL  H12  NAU  CAR  115.26  3.000
 HHL  H12  NAU  CAV  117.99  3.000
 HHL  CAR  NAU  CAV  124.52  3.000
 HHL  NAQ  CAR  NAS  125.25  3.000
 HHL  NAQ  CAR  NAU  115.94  3.000
 HHL  NAS  CAR  NAU  118.80  3.000
 HHL  CAT  NAS  CAR  117.59  3.000
 HHL  H13  CAT  CAO  122.33  3.000
 HHL  H13  CAT  NAS  115.78  3.000
 HHL  CAO  CAT  NAS  121.90  3.000
 HHL  CAP  NAQ  CAR  116.89  3.000
 HHL  H14  CAP  CAO  120.07  3.000
 HHL  H14  CAP  NAQ  117.29  3.000
 HHL  CAO  CAP  NAQ  122.64  3.000
 HHL  OAN  CAO  CAP  117.84  3.000
 HHL  CAP  CAO  CAT  115.71  3.000
 HHL  OAN  CAO  CAT  126.45  3.000
 HHL  CAM  OAN  CAO  117.35  3.000
 HHL  H16  CAM  H15  107.41  3.000
 HHL  H16  CAM  CAB  111.42  3.000
 HHL  H15  CAM  CAB  109.26  3.000
 HHL  H16  CAM  OAN  110.70  3.000
 HHL  H15  CAM  OAN  110.85  3.000
 HHL  CAB  CAM  OAN  107.22  3.000
 HHL  CAA  CAB  CAC  118.42  3.000
 HHL  CAC  CAB  CAM  122.28  3.000
 HHL  CAA  CAB  CAM  119.30  3.000
 HHL  CAD  CAC  CL1  117.67  3.000
 HHL  CL1  CAC  CAB  121.22  3.000
 HHL  CAD  CAC  CAB  121.11  3.000
 HHL  CAF  CAA  CL2  118.04  3.000
 HHL  CL2  CAA  CAB  120.46  3.000
 HHL  CAF  CAA  CAB  121.50  3.000
 HHL  CAE  CAF  OAH  124.06  3.000
 HHL  CAE  CAF  CAA  119.07  3.000
 HHL  OAH  CAF  CAA  116.87  3.000
 HHL  CAL  OAH  CAF  119.01  3.000
 HHL  H19  CAL  H18  109.18  3.000
 HHL  H19  CAL  H17  108.90  3.000
 HHL  H18  CAL  H17  108.87  3.000
 HHL  H19  CAL  OAH  111.76  3.000
 HHL  H18  CAL  OAH  111.81  3.000
 HHL  H17  CAL  OAH  106.21  3.000
 HHL  H20  CAE  CAD  119.68  3.000
 HHL  H20  CAE  CAF  119.78  3.000
 HHL  CAD  CAE  CAF  120.54  3.000
 HHL  OAG  CAD  CAE  123.86  3.000
 HHL  OAG  CAD  CAC  116.80  3.000
 HHL  CAE  CAD  CAC  119.34  3.000
 HHL  CAK  OAG  CAD  119.02  3.000
 HHL  H23  CAK  H22  109.16  3.000
 HHL  H23  CAK  H21  108.90  3.000
 HHL  H22  CAK  H21  108.95  3.000
 HHL  H23  CAK  OAG  111.76  3.000
 HHL  H22  CAK  OAG  111.75  3.000
 HHL  H21  CAK  OAG  106.22  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
 HHL  CONST_01  CAZ  CBA  CAV  CAW     0.00   0.0  0
 HHL  CONST_02  CAZ  CAY  CAX  CAW     0.00   0.0  0
 HHL  CONST_03  CBA  CAZ  CAY  CAX     0.00   0.0  0
 HHL  CONST_04  CBA  CAV  CAW  CAX     0.00   0.0  0
 HHL  CONST_05  CAV  CBA  CAZ  CAY     0.00   0.0  0
 HHL  CONST_06  CAV  CAW  CAX  CAY     0.00   0.0  0
 HHL  CONST_07  CAO  CAT  NAS  CAR     0.00   0.0  0
 HHL  CONST_08  CAO  CAP  NAQ  CAR     0.00   0.0  0
 HHL  CONST_09  CAP  CAO  CAT  NAS     0.00   0.0  0
 HHL  CONST_10  CAP  NAQ  CAR  NAS     0.00   0.0  0
 HHL  CONST_11  NAQ  CAP  CAO  CAT     0.00   0.0  0
 HHL  CONST_12  NAQ  CAR  NAS  CAT     0.00   0.0  0
 HHL  CONST_13  CAE  CAF  CAA  CAB     0.00   0.0  0
 HHL  CONST_14  CAE  CAD  CAC  CAB     0.00   0.0  0
 HHL  CONST_15  CAF  CAE  CAD  CAC     0.00   0.0  0
 HHL  CONST_16  CAF  CAA  CAB  CAC     0.00   0.0  0
 HHL  CONST_17  CAD  CAE  CAF  CAA     0.00   0.0  0
 HHL  CONST_18  CAD  CAC  CAB  CAA     0.00   0.0  0
 HHL  CONST_19  CBA  CAV  CAW  NBC   180.00   0.0  0
 HHL  CONST_20  CAY  CAX  CAW  NBC   180.00   0.0  0
 HHL  CONST_21  CBB  CBA  CAV  CAW   180.00   0.0  0
 HHL  CONST_22  NAU  CAV  CAW  CAX   180.00   0.0  0
 HHL  CONST_23  CBB  CBA  CAZ  CAY   180.00   0.0  0
 HHL  CONST_24  NAU  CAV  CBA  CAZ   180.00   0.0  0
 HHL  CONST_25  CAT  NAS  CAR  NAU   180.00   0.0  0
 HHL  CONST_26  CAP  NAQ  CAR  NAU   180.00   0.0  0
 HHL  CONST_27  OAN  CAO  CAT  NAS   180.00   0.0  0
 HHL  CONST_28  OAN  CAO  CAP  NAQ   180.00   0.0  0
 HHL  CONST_29  CAF  CAA  CAB  CAM   180.00   0.0  0
 HHL  CONST_30  CAD  CAC  CAB  CAM   180.00   0.0  0
 HHL  CONST_31  OAH  CAF  CAA  CAB   180.00   0.0  0
 HHL  CONST_32  OAG  CAD  CAC  CAB   180.00   0.0  0
 HHL  CONST_33  CL2  CAA  CAB  CAC   180.00   0.0  0
 HHL  CONST_34  CAE  CAD  CAC  CL1   180.00   0.0  0
 HHL  CONST_35  CAA  CAB  CAC  CL1   180.00   0.0  0
 HHL  CONST_36  CAE  CAF  CAA  CL2   180.00   0.0  0
 HHL  CONST_37  OAG  CAD  CAE  CAF   180.00   0.0  0
 HHL  CONST_38  CAD  CAE  CAF  OAH   180.00   0.0  0
 HHL  CONST_39  H7   CAY  CAX  CAW   180.00   0.0  0
 HHL  CONST_40  H8   CAZ  CAY  CAX   180.00   0.0  0
 HHL  CONST_41  H6   CAX  CAY  CAZ   180.00   0.0  0
 HHL  CONST_42  H13  CAT  NAS  CAR   180.00   0.0  0
 HHL  CONST_43  H14  CAP  NAQ  CAR   180.00   0.0  0
 HHL  CONST_44  H20  CAE  CAD  CAC   180.00   0.0  0
 HHL  CONST_48  CAW  NBC  CBD  CBE   180.00   0.0  0
 HHL  CONST_49  CAW  NBC  CBD  OBF     0.00   0.0  0
 HHL  Var_01    CAR  NAU  CAV  CAW    64.77  30.0  2
 HHL  Var_02    NAS  CAR  NAU  CAV    -3.40  30.0  3
 HHL  Var_03    CAB  CAM  OAN  CAO   166.73  30.0  1
 HHL  Var_04    CAA  CAB  CAM  OAN   -75.11  30.0  2
 HHL  Var_05    CAE  CAF  OAH  CAL     1.47  30.0  2
 HHL  Var_06    H9   CBB  CBA  CAZ   114.76  30.0  2
 HHL  Var_07    H17  CAL  OAH  CAF   179.26  30.0  3
 HHL  Var_08    H21  CAK  OAG  CAD  -179.47  30.0  3
 HHL  Var_09    NBC  CBD  CBE  CBH  -173.81  30.0  2
 HHL  Var_10    H1   CBH  CBE  FBG     0.03   0.0  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
 HHL  plan-1  NBC  0.020
 HHL  plan-1  CAW  0.020
 HHL  plan-1  CAX  0.020
 HHL  plan-1  CAY  0.020
 HHL  plan-1  CAZ  0.020
 HHL  plan-1  CBA  0.020
 HHL  plan-1  CBB  0.020
 HHL  plan-1  CAV  0.020
 HHL  plan-1  NAU  0.020
 HHL  plan-1  H6   0.020
 HHL  plan-1  H7   0.020
 HHL  plan-1  H8   0.020
 HHL  plan-2  NAU  0.020
 HHL  plan-2  CAR  0.020
 HHL  plan-2  NAS  0.020
 HHL  plan-2  CAT  0.020
 HHL  plan-2  NAQ  0.020
 HHL  plan-2  CAP  0.020
 HHL  plan-2  CAO  0.020
 HHL  plan-2  OAN  0.020
 HHL  plan-2  H13  0.020
 HHL  plan-2  H14  0.020
 HHL  plan-3  CAM  0.020
 HHL  plan-3  CAB  0.020
 HHL  plan-3  CAC  0.020
 HHL  plan-3  CL1  0.020
 HHL  plan-3  CAA  0.020
 HHL  plan-3  CL2  0.020
 HHL  plan-3  CAF  0.020
 HHL  plan-3  OAH  0.020
 HHL  plan-3  CAE  0.020
 HHL  plan-3  CAD  0.020
 HHL  plan-3  OAG  0.020
 HHL  plan-3  H20  0.020
 HHL  plan-4  CBE  0.020
 HHL  plan-4  CBD  0.020
 HHL  plan-4  OBF  0.020
 HHL  plan-4  NBC  0.020
 HHL  plan-4  CAW  0.020
 HHL  plan-4  H5   0.020
 HHL  plan-5  CBH  0.020
 HHL  plan-5  CBE  0.020
 HHL  plan-5  FBG  0.020
 HHL  plan-5  CBD  0.020
 HHL  plan-5  H1   0.020
 HHL  plan-5  H2   0.020

