# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:23:02 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-{[(1S)-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
 2Y7  2Y7  2-{[(1S)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol-4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine  ligand  51  29  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2Y7
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
 2Y7  FAF  F  F     0  -0.378   7.8954  -0.7930   1.8436
 2Y7  CAK  C  CH2   0  -0.034   7.5152  -1.4707   0.6901
 2Y7  CAL  C  CH2   0  -0.245   6.0534  -1.2645   0.4191
 2Y7  OAQ  O  O2    0  -0.467   5.8463   0.0981   0.1041
 2Y7  CAY  C  CR6   0   0.356   4.5910   0.5247  -0.1216
 2Y7  CAJ  C  CR16  0  -0.474   3.4665  -0.2769  -0.0983
 2Y7  CAX  C  CR6   0   0.303   4.4642   1.9028  -0.4029
 2Y7  OAP  O  O2    0  -0.456   5.6090   2.5996  -0.4149
 2Y7  CAA  C  CH3   0  -0.439   5.5482   3.9830  -0.7050
 2Y7  CAH  C  CR16  0  -0.366   3.2048   2.4297  -0.6417
 2Y7  CAG  C  CR16  0  -0.308   2.0784   1.6167  -0.6108
 2Y7  CAW  C  CR6   0   0.103   2.1950   0.2617  -0.3406
 2Y7  CBA  C  CR5   0   0.001   0.9983  -0.5735  -0.3096
 2Y7  NAO  N  N     0  -0.402  -0.1876  -0.1566  -0.6244
 2Y7  SAS  S  S2    0   0.224   1.0270  -2.2348   0.1837
 2Y7  CAV  C  CR5   0  -0.287  -0.6753  -2.3431  -0.0609
 2Y7  CAB  C  CH3   0  -0.722  -1.4206  -3.6165   0.1569
 2Y7  CBB  C  CR5   0   0.427  -1.1309  -1.1320  -0.4902
 2Y7  CBC  C  CH1   0  -0.476  -2.5486  -0.8133  -0.8411
 2Y7  CAC  C  CH3   0  -0.629  -2.7251  -0.5527  -2.3300
 2Y7  SAR  S  S2    0   0.052  -3.0168   0.6496   0.1548
 2Y7  C2   C  CR6   0   0.237  -4.7747   0.5352   0.2220
 2Y7  N3   N  N     0  -0.475  -5.3741  -0.4991  -0.3232
 2Y7  N1   N  N     0  -0.501  -5.3179   1.5570   0.8588
 2Y7  C6   C  CR6   0   0.490  -6.6559   1.5312   0.9722
 2Y7  NAD  N  NH2   0  -0.833  -7.2237   2.5445   1.6522
 2Y7  C5   C  CR16  0  -0.499  -7.4129   0.4880   0.4362
 2Y7  C4   C  CR6   0   0.500  -6.7155  -0.5236  -0.2179
 2Y7  NAE  N  NH2   0  -0.832  -7.3425  -1.5610  -0.8093
 2Y7  H1   H  HCH2  0   0.222   8.1271  -1.1100  -0.1384
 2Y7  H2   H  HCH2  0   0.225   7.7047  -2.5353   0.8313
 2Y7  H3   H  HCH2  0   0.240   5.7650  -1.9118  -0.4170
 2Y7  H4   H  HCH2  0   0.243   5.4613  -1.5625   1.2917
 2Y7  H5   H  HCR6  0   0.282   3.5711  -1.3357   0.1034
 2Y7  H6   H  HCH3  0   0.262   6.5707   4.3498  -0.6696
 2Y7  H7   H  HCH3  0   0.232   5.1382   4.1723  -1.7002
 2Y7  H8   H  HCH3  0   0.232   4.9519   4.5264   0.0320
 2Y7  H9   H  HCR6  0   0.288   3.0770   3.4830  -0.8504
 2Y7  H10  H  HCR6  0   0.261   1.1056   2.0502  -0.7970
 2Y7  H11  H  HCH3  0   0.261  -0.8896  -4.2859   0.8314
 2Y7  H12  H  HCH3  0   0.259  -2.3999  -3.4232   0.5935
 2Y7  H13  H  HCH3  0   0.263  -1.5749  -4.1496  -0.7824
 2Y7  H14  H  HCH1  0   0.293  -3.2039  -1.6273  -0.5319
 2Y7  H15  H  HCH3  0   0.232  -2.0913   0.2689  -2.6619
 2Y7  H16  H  HCH3  0   0.238  -2.4561  -1.4444  -2.8993
 2Y7  H17  H  HCH3  0   0.246  -3.7614  -0.3074  -2.5559
 2Y7  H18  H  HNH2  0   0.392  -6.6629   3.3465   1.8828
 2Y7  H19  H  HNH2  0   0.400  -8.2180   2.6834   1.6138
 2Y7  H20  H  HCR6  0   0.268  -8.4901   0.4639   0.5320
 2Y7  H21  H  HNH2  0   0.391  -6.7880  -2.3562  -1.0773
 2Y7  H22  H  HNH2  0   0.398  -8.3040  -1.7501  -0.5848

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
 2Y7  CAA  OAP  single    1.415  0.020  1.415
 2Y7  OAP  CAX  single    1.340  0.020  1.340
 2Y7  CAH  CAX  aromatic  1.386  0.020  1.386
 2Y7  CAH  CAG  aromatic  1.390  0.020  1.390
 2Y7  CAX  CAY  aromatic  1.412  0.020  1.412
 2Y7  CAG  CAW  aromatic  1.387  0.020  1.387
 2Y7  CAY  OAQ  single    1.345  0.020  1.345
 2Y7  CAY  CAJ  aromatic  1.381  0.020  1.381
 2Y7  OAQ  CAL  single    1.414  0.020  1.414
 2Y7  CAW  CAJ  aromatic  1.402  0.020  1.402
 2Y7  CAW  CBA  single    1.460  0.020  1.460
 2Y7  SAS  CBA  aromatic  1.733  0.020  1.733
 2Y7  SAS  CAV  aromatic  1.723  0.020  1.723
 2Y7  CAK  CAL  single    1.501  0.020  1.501
 2Y7  CAK  FAF  single    1.391  0.020  1.391
 2Y7  CBA  NAO  aromatic  1.296  0.020  1.296
 2Y7  CAV  CAB  single    1.491  0.020  1.491
 2Y7  CAV  CBB  aromatic  1.363  0.020  1.363
 2Y7  NAO  CBB  aromatic  1.364  0.020  1.364
 2Y7  CBB  CBC  single    1.495  0.020  1.495
 2Y7  CBC  CAC  single    1.522  0.020  1.522
 2Y7  CBC  SAR  single    1.831  0.020  1.831
 2Y7  SAR  C2   single    1.763  0.020  1.763
 2Y7  N3   C2   aromatic  1.314  0.020  1.314
 2Y7  N3   C4   aromatic  1.346  0.020  1.346
 2Y7  NAE  C4   single    1.349  0.020  1.349
 2Y7  C2   N1   aromatic  1.321  0.020  1.321
 2Y7  C4   C5   aromatic  1.392  0.020  1.392
 2Y7  N1   C6   aromatic  1.343  0.020  1.343
 2Y7  C5   C6   aromatic  1.396  0.020  1.396
 2Y7  C6   NAD  single    1.346  0.020  1.346
 2Y7  CAK  H1   single    0.970  0.020  1.090
 2Y7  CAK  H2   single    0.970  0.020  1.090
 2Y7  CAL  H3   single    0.970  0.020  1.090
 2Y7  CAL  H4   single    0.970  0.020  1.090
 2Y7  CAJ  H5   single    0.930  0.020  1.080
 2Y7  CAA  H6   single    0.970  0.020  1.090
 2Y7  CAA  H7   single    0.970  0.020  1.090
 2Y7  CAA  H8   single    0.970  0.020  1.090
 2Y7  CAH  H9   single    0.930  0.020  1.080
 2Y7  CAG  H10  single    0.930  0.020  1.080
 2Y7  CAB  H11  single    0.970  0.020  1.090
 2Y7  CAB  H12  single    0.970  0.020  1.090
 2Y7  CAB  H13  single    0.970  0.020  1.090
 2Y7  CBC  H14  single    0.970  0.020  1.090
 2Y7  CAC  H15  single    0.970  0.020  1.090
 2Y7  CAC  H16  single    0.970  0.020  1.090
 2Y7  CAC  H17  single    0.970  0.020  1.090
 2Y7  NAD  H18  single    0.890  0.020  1.040
 2Y7  NAD  H19  single    0.890  0.020  1.040
 2Y7  C5   H20  single    0.930  0.020  1.080
 2Y7  NAE  H21  single    0.890  0.020  1.040
 2Y7  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
 2Y7  H2   CAK  H1   108.88  3.000
 2Y7  H2   CAK  CAL  109.07  3.000
 2Y7  H1   CAK  CAL  111.32  3.000
 2Y7  H2   CAK  FAF  108.71  3.000
 2Y7  H1   CAK  FAF  108.38  3.000
 2Y7  CAL  CAK  FAF  110.43  3.000
 2Y7  H4   CAL  H3   107.74  3.000
 2Y7  H4   CAL  OAQ  111.12  3.000
 2Y7  H3   CAL  OAQ  111.14  3.000
 2Y7  H4   CAL  CAK  110.19  3.000
 2Y7  H3   CAL  CAK  108.23  3.000
 2Y7  OAQ  CAL  CAK  108.38  3.000
 2Y7  CAY  OAQ  CAL  118.68  3.000
 2Y7  CAX  CAY  CAJ  119.78  3.000
 2Y7  CAJ  CAY  OAQ  124.96  3.000
 2Y7  CAX  CAY  OAQ  115.27  3.000
 2Y7  H5   CAJ  CAW  119.70  3.000
 2Y7  H5   CAJ  CAY  119.47  3.000
 2Y7  CAW  CAJ  CAY  120.83  3.000
 2Y7  CAH  CAX  OAP  125.24  3.000
 2Y7  CAH  CAX  CAY  119.14  3.000
 2Y7  OAP  CAX  CAY  115.62  3.000
 2Y7  CAA  OAP  CAX  118.26  3.000
 2Y7  H8   CAA  H7   108.86  3.000
 2Y7  H8   CAA  H6   108.88  3.000
 2Y7  H7   CAA  H6   108.91  3.000
 2Y7  H8   CAA  OAP  111.80  3.000
 2Y7  H7   CAA  OAP  111.85  3.000
 2Y7  H6   CAA  OAP  106.43  3.000
 2Y7  H9   CAH  CAG  118.58  3.000
 2Y7  H9   CAH  CAX  120.73  3.000
 2Y7  CAG  CAH  CAX  120.69  3.000
 2Y7  H10  CAG  CAW  120.07  3.000
 2Y7  H10  CAG  CAH  119.41  3.000
 2Y7  CAW  CAG  CAH  120.52  3.000
 2Y7  CBA  CAW  CAG  119.63  3.000
 2Y7  CBA  CAW  CAJ  121.33  3.000
 2Y7  CAG  CAW  CAJ  119.04  3.000
 2Y7  SAS  CBA  NAO  113.12  3.000
 2Y7  NAO  CBA  CAW  124.13  3.000
 2Y7  SAS  CBA  CAW  122.74  3.000
 2Y7  CBB  NAO  CBA  112.27  3.000
 2Y7  CAV  SAS  CBA   90.20  3.000
 2Y7  CBB  CAV  CAB  129.60  3.000
 2Y7  CBB  CAV  SAS  108.60  3.000
 2Y7  CAB  CAV  SAS  121.77  3.000
 2Y7  H13  CAB  H12  107.73  3.000
 2Y7  H13  CAB  H11  107.58  3.000
 2Y7  H12  CAB  H11  107.41  3.000
 2Y7  H13  CAB  CAV  111.23  3.000
 2Y7  H12  CAB  CAV  110.87  3.000
 2Y7  H11  CAB  CAV  111.83  3.000
 2Y7  CBC  CBB  CAV  125.47  3.000
 2Y7  CBC  CBB  NAO  118.71  3.000
 2Y7  CAV  CBB  NAO  115.81  3.000
 2Y7  H14  CBC  SAR  106.78  3.000
 2Y7  H14  CBC  CAC  109.62  3.000
 2Y7  SAR  CBC  CAC  111.46  3.000
 2Y7  H14  CBC  CBB  110.14  3.000
 2Y7  SAR  CBC  CBB  106.57  3.000
 2Y7  CAC  CBC  CBB  112.10  3.000
 2Y7  H17  CAC  H16  108.09  3.000
 2Y7  H17  CAC  H15  108.70  3.000
 2Y7  H16  CAC  H15  108.29  3.000
 2Y7  H17  CAC  CBC  110.61  3.000
 2Y7  H16  CAC  CBC  109.99  3.000
 2Y7  H15  CAC  CBC  111.08  3.000
 2Y7  C2   SAR  CBC  102.94  3.000
 2Y7  N1   C2   N3   128.42  3.000
 2Y7  N1   C2   SAR  112.23  3.000
 2Y7  N3   C2   SAR  119.35  3.000
 2Y7  C4   N3   C2   115.89  3.000
 2Y7  C6   N1   C2   115.82  3.000
 2Y7  C5   C6   NAD  121.86  3.000
 2Y7  NAD  C6   N1   116.64  3.000
 2Y7  C5   C6   N1   121.48  3.000
 2Y7  H19  NAD  H18  116.78  3.000
 2Y7  H19  NAD  C6   120.14  3.000
 2Y7  H18  NAD  C6   118.76  3.000
 2Y7  H20  C5   C4   121.63  3.000
 2Y7  H20  C5   C6   121.51  3.000
 2Y7  C4   C5   C6   116.86  3.000
 2Y7  NAE  C4   C5   122.15  3.000
 2Y7  C5   C4   N3   121.53  3.000
 2Y7  NAE  C4   N3   116.30  3.000
 2Y7  H22  NAE  H21  115.98  3.000
 2Y7  H22  NAE  C4   119.43  3.000
 2Y7  H21  NAE  C4   117.95  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
 2Y7  CONST_01  CAG  CAH  CAX  CAY     0.00   0.0  0
 2Y7  CONST_02  CAG  CAW  CAJ  CAY     0.00   0.0  0
 2Y7  CONST_03  CBA  CAW  CAJ  CAY   180.00   0.0  0
 2Y7  CONST_04  CAH  CAX  CAY  CAJ     0.00   0.0  0
 2Y7  CONST_05  CAH  CAG  CAW  CAJ     0.00   0.0  0
 2Y7  CONST_06  SAS  CBA  CAW  CAJ     0.00   0.0  0
 2Y7  CONST_07  NAO  CBA  CAW  CAJ   180.00   0.0  0
 2Y7  CONST_08  CAW  CAG  CAH  CAX     0.00   0.0  0
 2Y7  CONST_09  CAW  CAJ  CAY  CAX     0.00   0.0  0
 2Y7  CONST_10  CBA  CAW  CAG  CAH   180.00   0.0  0
 2Y7  CONST_11  SAS  CBA  CAW  CAG   180.00   0.0  0
 2Y7  CONST_12  NAO  CBA  CAW  CAG     0.00   0.0  0
 2Y7  CONST_13  CAV  SAS  CBA  CAW   180.00   0.0  0
 2Y7  CONST_14  CBB  NAO  CBA  CAW   180.00   0.0  0
 2Y7  CONST_15  CBB  CAV  SAS  CBA     0.00   0.0  0
 2Y7  CONST_16  CAV  CBB  NAO  CBA     0.00   0.0  0
 2Y7  CONST_17  CAV  SAS  CBA  NAO     0.00   0.0  0
 2Y7  CONST_18  SAS  CAV  CBB  NAO     0.00   0.0  0
 2Y7  CONST_19  CBB  NAO  CBA  SAS     0.00   0.0  0
 2Y7  CONST_20  C5   C4   N3   C2      0.00   0.0  0
 2Y7  CONST_21  C5   C6   N1   C2      0.00   0.0  0
 2Y7  CONST_22  C6   N1   C2   N3      0.00   0.0  0
 2Y7  CONST_23  C6   C5   C4   N3      0.00   0.0  0
 2Y7  CONST_24  C4   N3   C2   N1      0.00   0.0  0
 2Y7  CONST_25  C4   C5   C6   N1      0.00   0.0  0
 2Y7  CONST_26  CAH  CAX  CAY  OAQ   180.00   0.0  0
 2Y7  CONST_27  CAW  CAJ  CAY  OAQ   180.00   0.0  0
 2Y7  CONST_28  OAP  CAX  CAY  CAJ   180.00   0.0  0
 2Y7  CONST_29  CAG  CAH  CAX  OAP   180.00   0.0  0
 2Y7  CONST_30  CAB  CAV  SAS  CBA   180.00   0.0  0
 2Y7  CONST_31  CBC  CBB  NAO  CBA   180.00   0.0  0
 2Y7  CONST_32  CAB  CAV  CBB  NAO   180.00   0.0  0
 2Y7  CONST_33  CBC  CBB  CAV  SAS   180.00   0.0  0
 2Y7  CONST_34  C4   N3   C2   SAR   180.00   0.0  0
 2Y7  CONST_35  C6   N1   C2   SAR   180.00   0.0  0
 2Y7  CONST_36  NAE  C4   N3   C2    180.00   0.0  0
 2Y7  CONST_37  NAD  C6   N1   C2    180.00   0.0  0
 2Y7  CONST_38  NAE  C4   C5   C6    180.00   0.0  0
 2Y7  CONST_39  C4   C5   C6   NAD   180.00   0.0  0
 2Y7  CONST_40  H9   CAH  CAX  CAY   180.00   0.0  0
 2Y7  CONST_41  H10  CAG  CAW  CAJ   180.00   0.0  0
 2Y7  CONST_42  H5   CAJ  CAY  CAX   180.00   0.0  0
 2Y7  CONST_43  H20  C5   C4   N3    180.00   0.0  0
 2Y7  CONST_45  H22  NAE  C4   N3    180.00   0.0  0
 2Y7  CONST_46  H18  NAD  C6   N1      0.00   0.0  0
 2Y7  CONST_47  H19  NAD  C6   N1    180.00   0.0  0
 2Y7  Var_01    CAX  CAY  OAQ  CAL   178.76  30.0  2
 2Y7  Var_02    CAH  CAX  OAP  CAA    -0.62  30.0  2
 2Y7  Var_03    N3   C2   SAR  CBC     3.50  30.0  2
 2Y7  Var_04    H11  CAB  CAV  SAS    22.91  30.0  2
 2Y7  Var_05    H3   CAL  OAQ  CAY    63.95  30.0  3
 2Y7  Var_06    H6   CAA  OAP  CAX  -179.67  30.0  3
 2Y7  Var_07    OAQ  CAL  CAK  FAF    66.48  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
 2Y7  chir_01  CBC  CBB  CAC  SAR  positiv

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
 2Y7  plan-1  CAW  0.020
 2Y7  plan-1  CBA  0.020
 2Y7  plan-1  NAO  0.020
 2Y7  plan-1  SAS  0.020
 2Y7  plan-1  CAV  0.020
 2Y7  plan-1  CAB  0.020
 2Y7  plan-1  CBB  0.020
 2Y7  plan-1  CBC  0.020
 2Y7  plan-2  OAQ  0.020
 2Y7  plan-2  CAY  0.020
 2Y7  plan-2  CAJ  0.020
 2Y7  plan-2  CAX  0.020
 2Y7  plan-2  OAP  0.020
 2Y7  plan-2  CAH  0.020
 2Y7  plan-2  CAG  0.020
 2Y7  plan-2  CAW  0.020
 2Y7  plan-2  CBA  0.020
 2Y7  plan-2  H5   0.020
 2Y7  plan-2  H9   0.020
 2Y7  plan-2  H10  0.020
 2Y7  plan-3  SAR  0.020
 2Y7  plan-3  C2   0.020
 2Y7  plan-3  N3   0.020
 2Y7  plan-3  N1   0.020
 2Y7  plan-3  C6   0.020
 2Y7  plan-3  NAD  0.020
 2Y7  plan-3  C5   0.020
 2Y7  plan-3  C4   0.020
 2Y7  plan-3  NAE  0.020
 2Y7  plan-3  H20  0.020
 2Y7  plan-4  C6   0.020
 2Y7  plan-4  NAD  0.020
 2Y7  plan-4  H18  0.020
 2Y7  plan-4  H19  0.020
 2Y7  plan-5  C4   0.020
 2Y7  plan-5  NAE  0.020
 2Y7  plan-5  H21  0.020
 2Y7  plan-5  H22  0.020

