# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:56:24 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-{[(1R)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol-4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OCCF)c2sc(C)c(n2)[C@@H](C)Sc3nc(N)cc(N)n3
#
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
 2Y8  2Y8  2-{[(1R)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol-4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine  ligand  51  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2Y8
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
 2Y8  FAF  F  F     0  -0.378  -8.2206   1.2580   0.3212
 2Y8  CAK  C  CH2   0  -0.033  -7.5026   1.4808  -0.8488
 2Y8  CAL  C  CH2   0  -0.247  -6.0384   1.2410  -0.6248
 2Y8  OAQ  O  O2    0  -0.467  -5.8425  -0.1336  -0.3578
 2Y8  CAY  C  CR6   0   0.356  -4.5918  -0.5680  -0.1195
 2Y8  CAJ  C  CR16  0  -0.470  -3.4610   0.2246  -0.1500
 2Y8  CAX  C  CR6   0   0.303  -4.4754  -1.9425   0.1821
 2Y8  OAP  O  O2    0  -0.456  -5.6234  -2.6346   0.1867
 2Y8  CAA  C  CH3   0  -0.439  -5.5684  -4.0194   0.4709
 2Y8  CAH  C  CR16  0  -0.367  -3.2219  -2.4719   0.4462
 2Y8  CAG  C  CR16  0  -0.308  -2.0898  -1.6664   0.4143
 2Y8  CAW  C  CR6   0   0.103  -2.1953  -0.3172   0.1134
 2Y8  CBA  C  CR5   0  -0.001  -0.9947   0.5121   0.0711
 2Y8  NAO  N  N     0  -0.399   0.1697   0.1324   0.4950
 2Y8  SAS  S  S2    0   0.226  -0.9891   2.1127  -0.5949
 2Y8  CAV  C  CR5   0  -0.284   0.6963   2.2477  -0.2704
 2Y8  CAB  C  CH3   0  -0.728   1.4756   3.4769  -0.6006
 2Y8  CBB  C  CR5   0   0.425   1.1215   1.0905   0.3114
 2Y8  CBC  C  CH1   0  -0.479   2.5188   0.8248   0.7693
 2Y8  CAC  C  CH3   0  -0.628   2.6105   0.6664   2.2795
 2Y8  SAR  S  S2    0   0.051   3.0789  -0.6878  -0.0969
 2Y8  C2   C  CR6   0   0.237   4.8355  -0.5332  -0.0577
 2Y8  N3   N  N     0  -0.475   5.3716   0.5622   0.4304
 2Y8  N1   N  N     0  -0.500   5.4439  -1.5893  -0.5665
 2Y8  C6   C  CR6   0   0.488   6.7858  -1.5334  -0.5928
 2Y8  NAD  N  NH2   0  -0.833   7.4246  -2.6154  -1.0792
 2Y8  C5   C  CR16  0  -0.499   7.4801  -0.4231  -0.1105
 2Y8  C4   C  CR6   0   0.504   6.7160   0.6200   0.4071
 2Y8  NAE  N  NH2   0  -0.832   7.2754   1.7253   0.9361
 2Y8  H1   H  HCH2  0   0.222  -7.8977   0.8241  -1.6256
 2Y8  H2   H  HCH2  0   0.225  -7.6483   2.5169  -1.1563
 2Y8  H3   H  HCH2  0   0.239  -5.5024   1.5497  -1.5297
 2Y8  H4   H  HCH2  0   0.244  -5.6730   1.8563   0.2052
 2Y8  H5   H  HCR6  0   0.279  -3.5556   1.2801  -0.3708
 2Y8  H6   H  HCH3  0   0.262  -6.5900  -4.3859   0.4143
 2Y8  H7   H  HCH3  0   0.232  -4.9580  -4.5593  -0.2572
 2Y8  H8   H  HCH3  0   0.232  -5.1777  -4.2139   1.4729
 2Y8  H9   H  HCR6  0   0.289  -3.1038  -3.5216   0.6778
 2Y8  H10  H  HCR6  0   0.261  -1.1214  -2.1021   0.6179
 2Y8  H11  H  HCH3  0   0.263   0.8839   4.1924  -1.1679
 2Y8  H12  H  HCH3  0   0.263   1.8215   3.9791   0.3037
 2Y8  H13  H  HCH3  0   0.261   2.3528   3.2308  -1.1993
 2Y8  H14  H  HCH1  0   0.296   3.1772   1.6314   0.4470
 2Y8  H15  H  HCH3  0   0.233   1.9773  -0.1486   2.6282
 2Y8  H16  H  HCH3  0   0.245   3.6374   0.4672   2.5821
 2Y8  H17  H  HCH3  0   0.237   2.2873   1.5859   2.7714
 2Y8  H18  H  HNH2  0   0.391   6.8892  -3.3020  -1.5824
 2Y8  H19  H  HNH2  0   0.399   8.4028  -2.5596  -1.3017
 2Y8  H20  H  HCR6  0   0.268   8.5607  -0.3768  -0.1338
 2Y8  H21  H  HNH2  0   0.392   6.6845   2.5181   1.1193
 2Y8  H22  H  HNH2  0   0.399   8.2489   1.9181   0.7771

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
 2Y8  FAF  CAK  single    1.391  0.020  1.391
 2Y8  CAK  CAL  single    1.501  0.020  1.501
 2Y8  CAL  OAQ  single    1.414  0.020  1.414
 2Y8  OAQ  CAY  single    1.345  0.020  1.345
 2Y8  CAC  CBC  single    1.521  0.020  1.521
 2Y8  CAY  CAJ  aromatic  1.381  0.020  1.381
 2Y8  CAY  CAX  aromatic  1.412  0.020  1.412
 2Y8  OAP  CAX  single    1.340  0.020  1.340
 2Y8  OAP  CAA  single    1.415  0.020  1.415
 2Y8  CAJ  CAW  aromatic  1.402  0.020  1.402
 2Y8  CAX  CAH  aromatic  1.386  0.020  1.386
 2Y8  NAO  CBB  aromatic  1.363  0.020  1.363
 2Y8  NAO  CBA  aromatic  1.296  0.020  1.296
 2Y8  CBC  SAR  single    1.831  0.020  1.831
 2Y8  CBC  CBB  single    1.494  0.020  1.494
 2Y8  CAW  CBA  single    1.460  0.020  1.460
 2Y8  CAW  CAG  aromatic  1.386  0.020  1.386
 2Y8  SAR  C2   single    1.764  0.020  1.764
 2Y8  CAH  CAG  aromatic  1.390  0.020  1.390
 2Y8  N3   C2   aromatic  1.314  0.020  1.314
 2Y8  N3   C4   aromatic  1.346  0.020  1.346
 2Y8  CBB  CAV  aromatic  1.363  0.020  1.363
 2Y8  CBA  SAS  aromatic  1.734  0.020  1.734
 2Y8  C2   N1   aromatic  1.321  0.020  1.321
 2Y8  NAE  C4   single    1.347  0.020  1.347
 2Y8  C4   C5   aromatic  1.393  0.020  1.393
 2Y8  N1   C6   aromatic  1.343  0.020  1.343
 2Y8  C5   C6   aromatic  1.396  0.020  1.396
 2Y8  C6   NAD  single    1.347  0.020  1.347
 2Y8  CAV  SAS  aromatic  1.722  0.020  1.722
 2Y8  CAV  CAB  single    1.492  0.020  1.492
 2Y8  CAK  H1   single    0.970  0.020  1.090
 2Y8  CAK  H2   single    0.970  0.020  1.090
 2Y8  CAL  H3   single    0.970  0.020  1.090
 2Y8  CAL  H4   single    0.970  0.020  1.090
 2Y8  CAJ  H5   single    0.930  0.020  1.080
 2Y8  CAA  H6   single    0.970  0.020  1.090
 2Y8  CAA  H7   single    0.970  0.020  1.090
 2Y8  CAA  H8   single    0.970  0.020  1.090
 2Y8  CAH  H9   single    0.930  0.020  1.080
 2Y8  CAG  H10  single    0.930  0.020  1.080
 2Y8  CAB  H11  single    0.970  0.020  1.090
 2Y8  CAB  H12  single    0.970  0.020  1.090
 2Y8  CAB  H13  single    0.970  0.020  1.090
 2Y8  CBC  H14  single    0.970  0.020  1.090
 2Y8  CAC  H15  single    0.970  0.020  1.090
 2Y8  CAC  H16  single    0.970  0.020  1.090
 2Y8  CAC  H17  single    0.970  0.020  1.090
 2Y8  NAD  H18  single    0.890  0.020  1.040
 2Y8  NAD  H19  single    0.890  0.020  1.040
 2Y8  C5   H20  single    0.930  0.020  1.080
 2Y8  NAE  H21  single    0.890  0.020  1.040
 2Y8  NAE  H22  single    0.890  0.020  1.040

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
 2Y8  H2   CAK  H1   108.82  3.000
 2Y8  H2   CAK  CAL  108.92  3.000
 2Y8  H1   CAK  CAL  111.31  3.000
 2Y8  H2   CAK  FAF  108.69  3.000
 2Y8  H1   CAK  FAF  108.39  3.000
 2Y8  CAL  CAK  FAF  110.65  3.000
 2Y8  H4   CAL  H3   107.70  3.000
 2Y8  H4   CAL  OAQ  110.90  3.000
 2Y8  H3   CAL  OAQ  111.22  3.000
 2Y8  H4   CAL  CAK  110.40  3.000
 2Y8  H3   CAL  CAK  107.99  3.000
 2Y8  OAQ  CAL  CAK  108.59  3.000
 2Y8  CAY  OAQ  CAL  118.44  3.000
 2Y8  CAX  CAY  CAJ  119.72  3.000
 2Y8  CAX  CAY  OAQ  115.39  3.000
 2Y8  CAJ  CAY  OAQ  124.88  3.000
 2Y8  H5   CAJ  CAW  119.61  3.000
 2Y8  H5   CAJ  CAY  119.50  3.000
 2Y8  CAW  CAJ  CAY  120.89  3.000
 2Y8  CAH  CAX  OAP  125.22  3.000
 2Y8  CAH  CAX  CAY  119.14  3.000
 2Y8  OAP  CAX  CAY  115.64  3.000
 2Y8  CAA  OAP  CAX  118.21  3.000
 2Y8  H8   CAA  H7   108.86  3.000
 2Y8  H8   CAA  H6   108.89  3.000
 2Y8  H7   CAA  H6   108.89  3.000
 2Y8  H8   CAA  OAP  111.86  3.000
 2Y8  H7   CAA  OAP  111.81  3.000
 2Y8  H6   CAA  OAP  106.44  3.000
 2Y8  H9   CAH  CAG  118.59  3.000
 2Y8  H9   CAH  CAX  120.68  3.000
 2Y8  CAG  CAH  CAX  120.73  3.000
 2Y8  H10  CAG  CAW  120.09  3.000
 2Y8  H10  CAG  CAH  119.45  3.000
 2Y8  CAW  CAG  CAH  120.47  3.000
 2Y8  CBA  CAW  CAG  119.77  3.000
 2Y8  CAG  CAW  CAJ  119.05  3.000
 2Y8  CBA  CAW  CAJ  121.18  3.000
 2Y8  SAS  CBA  NAO  113.15  3.000
 2Y8  SAS  CBA  CAW  122.57  3.000
 2Y8  NAO  CBA  CAW  124.26  3.000
 2Y8  CBB  NAO  CBA  112.17  3.000
 2Y8  CAV  SAS  CBA   90.18  3.000
 2Y8  CBB  CAV  CAB  129.10  3.000
 2Y8  CAB  CAV  SAS  122.29  3.000
 2Y8  CBB  CAV  SAS  108.62  3.000
 2Y8  H13  CAB  H12  107.71  3.000
 2Y8  H13  CAB  H11  107.44  3.000
 2Y8  H12  CAB  H11  107.57  3.000
 2Y8  H13  CAB  CAV  110.84  3.000
 2Y8  H12  CAB  CAV  111.19  3.000
 2Y8  H11  CAB  CAV  111.90  3.000
 2Y8  CBC  CBB  CAV  124.99  3.000
 2Y8  CAV  CBB  NAO  115.87  3.000
 2Y8  CBC  CBB  NAO  119.12  3.000
 2Y8  H14  CBC  SAR  106.65  3.000
 2Y8  H14  CBC  CAC  109.53  3.000
 2Y8  SAR  CBC  CAC  111.42  3.000
 2Y8  H14  CBC  CBB  110.04  3.000
 2Y8  SAR  CBC  CBB  106.74  3.000
 2Y8  CAC  CBC  CBB  112.28  3.000
 2Y8  H17  CAC  H16  107.95  3.000
 2Y8  H17  CAC  H15  108.29  3.000
 2Y8  H16  CAC  H15  108.81  3.000
 2Y8  H17  CAC  CBC  109.98  3.000
 2Y8  H16  CAC  CBC  110.59  3.000
 2Y8  H15  CAC  CBC  111.14  3.000
 2Y8  C2   SAR  CBC  102.81  3.000
 2Y8  N1   C2   N3   128.45  3.000
 2Y8  N1   C2   SAR  112.34  3.000
 2Y8  N3   C2   SAR  119.20  3.000
 2Y8  C4   N3   C2   115.92  3.000
 2Y8  C6   N1   C2   115.76  3.000
 2Y8  C5   C6   NAD  121.86  3.000
 2Y8  NAD  C6   N1   116.57  3.000
 2Y8  C5   C6   N1   121.55  3.000
 2Y8  H19  NAD  H18  116.45  3.000
 2Y8  H19  NAD  C6   119.80  3.000
 2Y8  H18  NAD  C6   118.46  3.000
 2Y8  H20  C5   C4   121.59  3.000
 2Y8  H20  C5   C6   121.57  3.000
 2Y8  C4   C5   C6   116.84  3.000
 2Y8  NAE  C4   C5   122.18  3.000
 2Y8  C5   C4   N3   121.49  3.000
 2Y8  NAE  C4   N3   116.32  3.000
 2Y8  H22  NAE  H21  116.53  3.000
 2Y8  H22  NAE  C4   119.84  3.000
 2Y8  H21  NAE  C4   118.32  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
 2Y8  CONST_01  CBA  CAW  CAJ  CAY   180.00   0.0  0
 2Y8  CONST_02  CAG  CAW  CAJ  CAY     0.00   0.0  0
 2Y8  CONST_03  CAG  CAH  CAX  CAY     0.00   0.0  0
 2Y8  CONST_04  CAH  CAX  CAY  CAJ     0.00   0.0  0
 2Y8  CONST_05  NAO  CBA  CAW  CAJ   180.00   0.0  0
 2Y8  CONST_06  SAS  CBA  CAW  CAJ     0.00   0.0  0
 2Y8  CONST_07  CAH  CAG  CAW  CAJ     0.00   0.0  0
 2Y8  CONST_08  CAW  CAJ  CAY  CAX     0.00   0.0  0
 2Y8  CONST_09  CAW  CAG  CAH  CAX     0.00   0.0  0
 2Y8  CONST_10  CBA  CAW  CAG  CAH   180.00   0.0  0
 2Y8  CONST_11  NAO  CBA  CAW  CAG     0.00   0.0  0
 2Y8  CONST_12  SAS  CBA  CAW  CAG   180.00   0.0  0
 2Y8  CONST_13  CBB  NAO  CBA  CAW   180.00   0.0  0
 2Y8  CONST_14  CAV  SAS  CBA  CAW   180.00   0.0  0
 2Y8  CONST_15  CAV  CBB  NAO  CBA     0.00   0.0  0
 2Y8  CONST_16  CBB  CAV  SAS  CBA     0.00   0.0  0
 2Y8  CONST_17  SAS  CAV  CBB  NAO     0.00   0.0  0
 2Y8  CONST_18  CAV  SAS  CBA  NAO     0.00   0.0  0
 2Y8  CONST_19  CBB  NAO  CBA  SAS     0.00   0.0  0
 2Y8  CONST_20  C5   C4   N3   C2      0.00   0.0  0
 2Y8  CONST_21  C5   C6   N1   C2      0.00   0.0  0
 2Y8  CONST_22  C6   N1   C2   N3      0.00   0.0  0
 2Y8  CONST_23  C6   C5   C4   N3      0.00   0.0  0
 2Y8  CONST_24  C4   N3   C2   N1      0.00   0.0  0
 2Y8  CONST_25  C4   C5   C6   N1      0.00   0.0  0
 2Y8  CONST_26  CAW  CAJ  CAY  OAQ   180.00   0.0  0
 2Y8  CONST_27  CAH  CAX  CAY  OAQ   180.00   0.0  0
 2Y8  CONST_28  OAP  CAX  CAY  CAJ   180.00   0.0  0
 2Y8  CONST_29  CAG  CAH  CAX  OAP   180.00   0.0  0
 2Y8  CONST_30  CBC  CBB  NAO  CBA   180.00   0.0  0
 2Y8  CONST_31  CAB  CAV  SAS  CBA   180.00   0.0  0
 2Y8  CONST_32  CAB  CAV  CBB  NAO   180.00   0.0  0
 2Y8  CONST_33  CBC  CBB  CAV  SAS   180.00   0.0  0
 2Y8  CONST_34  C4   N3   C2   SAR   180.00   0.0  0
 2Y8  CONST_35  C6   N1   C2   SAR   180.00   0.0  0
 2Y8  CONST_36  NAE  C4   N3   C2    180.00   0.0  0
 2Y8  CONST_37  NAD  C6   N1   C2    180.00   0.0  0
 2Y8  CONST_38  NAE  C4   C5   C6    180.00   0.0  0
 2Y8  CONST_39  C4   C5   C6   NAD   180.00   0.0  0
 2Y8  CONST_40  H9   CAH  CAX  CAY   180.00   0.0  0
 2Y8  CONST_41  H10  CAG  CAW  CAJ   180.00   0.0  0
 2Y8  CONST_42  H5   CAJ  CAY  CAX   180.00   0.0  0
 2Y8  CONST_43  H20  C5   C4   N3    180.00   0.0  0
 2Y8  CONST_44  H21  NAE  C4   N3      0.00   0.0  0
 2Y8  CONST_45  H22  NAE  C4   N3    180.00   0.0  0
 2Y8  CONST_46  H18  NAD  C6   N1      0.00   0.0  0
 2Y8  CONST_47  H19  NAD  C6   N1    180.00   0.0  0
 2Y8  Var_01    CAJ  CAY  OAQ  CAL    -1.86  30.0  2
 2Y8  Var_02    CAH  CAX  OAP  CAA    -0.56  30.0  2
 2Y8  Var_03    N3   C2   SAR  CBC    -4.96  30.0  2
 2Y8  Var_04    H11  CAB  CAV  SAS    -7.18  30.0  2
 2Y8  Var_05    H3   CAL  OAQ  CAY    61.61  30.0  2
 2Y8  Var_06    H6   CAA  OAP  CAX  -179.42  30.0  3
 2Y8  Var_07    OAQ  CAL  CAK  FAF    66.37  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2Y8  chir_01  CBC  CAC  SAR  CBB  negativ

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
 2Y8  plan-1  CAW  0.020
 2Y8  plan-1  CBA  0.020
 2Y8  plan-1  NAO  0.020
 2Y8  plan-1  SAS  0.020
 2Y8  plan-1  CAV  0.020
 2Y8  plan-1  CAB  0.020
 2Y8  plan-1  CBB  0.020
 2Y8  plan-1  CBC  0.020
 2Y8  plan-2  OAQ  0.020
 2Y8  plan-2  CAY  0.020
 2Y8  plan-2  CAJ  0.020
 2Y8  plan-2  CAX  0.020
 2Y8  plan-2  OAP  0.020
 2Y8  plan-2  CAH  0.020
 2Y8  plan-2  CAG  0.020
 2Y8  plan-2  CAW  0.020
 2Y8  plan-2  CBA  0.020
 2Y8  plan-2  H5   0.020
 2Y8  plan-2  H9   0.020
 2Y8  plan-2  H10  0.020
 2Y8  plan-3  SAR  0.020
 2Y8  plan-3  C2   0.020
 2Y8  plan-3  N3   0.020
 2Y8  plan-3  N1   0.020
 2Y8  plan-3  C6   0.020
 2Y8  plan-3  NAD  0.020
 2Y8  plan-3  C5   0.020
 2Y8  plan-3  C4   0.020
 2Y8  plan-3  NAE  0.020
 2Y8  plan-3  H20  0.020
 2Y8  plan-4  C6   0.020
 2Y8  plan-4  NAD  0.020
 2Y8  plan-4  H18  0.020
 2Y8  plan-4  H19  0.020
 2Y8  plan-5  C4   0.020
 2Y8  plan-5  NAE  0.020
 2Y8  plan-5  H21  0.020
 2Y8  plan-5  H22  0.020

