# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 04:35:29 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-[({5-ethyl-2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc(nc1CSc2nc(N)cc(N)n2)c3ccc(OC)c(OCCF)c3
#
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
 1NN  1NN  2-[({5-ethyl-2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine  ligand  51  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1NN
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
 1NN  FAE  F  F     0  -0.379   5.1610  -4.3543   1.4041
 1NN  CAJ  C  CH2   0  -0.033   4.2137  -4.3276   0.3861
 1NN  CAL  C  CH2   0  -0.243   3.5529  -2.9819   0.3161
 1NN  OAR  O  O2    0  -0.467   4.5221  -2.0276  -0.0697
 1NN  CAZ  C  CR6   0   0.356   4.1561  -0.7355  -0.1485
 1NN  CAI  C  CR16  0  -0.437   2.8713  -0.2663   0.0299
 1NN  CAY  C  CR6   0   0.305   5.2010   0.1695  -0.4428
 1NN  OAQ  O  O2    0  -0.456   6.4129  -0.3786  -0.6040
 1NN  CAB  C  CH3   0  -0.439   7.5000   0.4734  -0.9104
 1NN  CAG  C  CR16  0  -0.368   4.9145   1.5211  -0.5419
 1NN  CAF  C  CR16  0  -0.338   3.6166   1.9854  -0.3571
 1NN  CAW  C  CR6   0   0.098   2.5864   1.1038  -0.0732
 1NN  CBC  C  CR5   0   0.014   1.2105   1.5530   0.1150
 1NN  NAP  N  N     0  -0.406   0.2100   0.7624   0.3459
 1NN  SAT  S  S2    0   0.233   0.7589   3.2256   0.0399
 1NN  CBB  C  CR5   0  -0.244  -0.8830   2.7981   0.3327
 1NN  CAK  C  CH2   0  -0.513  -1.9607   3.8256   0.4419
 1NN  CAA  C  CH3   0  -0.649  -2.0694   4.4147   1.8474
 1NN  CBA  C  CR5   0   0.343  -0.9643   1.4447   0.4794
 1NN  CAM  C  CH2   0  -0.645  -2.2243   0.6882   0.7319
 1NN  SAS  S  S2    0   0.041  -2.8772   0.1572  -0.8835
 1NN  C2   C  CR6   0   0.240  -4.3774  -0.6573  -0.4483
 1NN  N3   N  N     0  -0.500  -5.0178  -1.1415  -1.4959
 1NN  N1   N  N     0  -0.483  -4.7203  -0.7077   0.8193
 1NN  C6   C  CR6   0   0.503  -5.8842  -1.3313   1.0854
 1NN  NAC  N  NH2   0  -0.832  -6.2673  -1.3544   2.3767
 1NN  C5   C  CR16  0  -0.500  -6.6588  -1.8904   0.0727
 1NN  C4   C  CR6   0   0.493  -6.1744  -1.7727  -1.2312
 1NN  NAD  N  NH2   0  -0.834  -6.8223  -2.3087  -2.2811
 1NN  H1   H  HCH2  0   0.221   4.7119  -4.5734  -0.5532
 1NN  H2   H  HCH2  0   0.224   3.4567  -5.0854   0.5926
 1NN  H3   H  HCH2  0   0.238   2.7391  -3.0417  -0.4154
 1NN  H4   H  HCH2  0   0.242   3.1119  -2.7227   1.2850
 1NN  H5   H  HCR6  0   0.284   2.0577  -0.9451   0.2462
 1NN  H6   H  HCH3  0   0.263   8.3766  -0.1641  -0.9917
 1NN  H7   H  HCH3  0   0.232   7.3531   0.9947  -1.8596
 1NN  H8   H  HCH3  0   0.232   7.6734   1.2115  -0.1236
 1NN  H9   H  HCR6  0   0.290   5.6939   2.2375  -0.7618
 1NN  H10  H  HCR6  0   0.255   3.4386   3.0503  -0.4441
 1NN  H11  H  HCH2  0   0.262  -1.7861   4.6244  -0.2815
 1NN  H12  H  HCH2  0   0.255  -2.9098   3.3681   0.1558
 1NN  H13  H  HCH3  0   0.239  -2.8662   5.1569   1.8911
 1NN  H14  H  HCH3  0   0.230  -2.2905   3.6385   2.5805
 1NN  H15  H  HCH3  0   0.229  -1.1401   4.9016   2.1441
 1NN  H16  H  HCH2  0   0.300  -2.0260  -0.1874   1.3480
 1NN  H17  H  HCH2  0   0.289  -2.9697   1.2988   1.2370
 1NN  H18  H  HNH2  0   0.399  -7.0195  -1.9561   2.6636
 1NN  H19  H  HNH2  0   0.392  -5.5901  -1.1150   3.0807
 1NN  H20  H  HCR6  0   0.269  -7.5905  -2.3960   0.2879
 1NN  H21  H  HNH2  0   0.401  -7.7596  -2.6555  -2.1771
 1NN  H22  H  HNH2  0   0.393  -6.5235  -2.0703  -3.2108

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
 1NN  CAK  CAA  single    1.528  0.020  1.528
 1NN  CAK  CBB  single    1.493  0.020  1.493
 1NN  SAT  CBB  aromatic  1.722  0.020  1.722
 1NN  SAT  CBC  aromatic  1.734  0.020  1.734
 1NN  CBB  CBA  aromatic  1.364  0.020  1.364
 1NN  NAC  C6   single    1.347  0.020  1.347
 1NN  CAF  CAG  aromatic  1.391  0.020  1.391
 1NN  CAF  CAW  aromatic  1.385  0.020  1.385
 1NN  C6   C5   aromatic  1.392  0.020  1.392
 1NN  C6   N1   aromatic  1.347  0.020  1.347
 1NN  C5   C4   aromatic  1.396  0.020  1.396
 1NN  CAG  CAY  aromatic  1.385  0.020  1.385
 1NN  N1   C2   aromatic  1.314  0.020  1.314
 1NN  CBC  CAW  single    1.460  0.020  1.460
 1NN  CBC  NAP  aromatic  1.296  0.020  1.296
 1NN  C4   NAD  single    1.345  0.020  1.345
 1NN  C4   N3   aromatic  1.344  0.020  1.344
 1NN  CBA  NAP  aromatic  1.365  0.020  1.365
 1NN  CBA  CAM  single    1.491  0.020  1.491
 1NN  C2   N3   aromatic  1.320  0.020  1.320
 1NN  C2   SAS  single    1.762  0.020  1.762
 1NN  CAW  CAI  aromatic  1.403  0.020  1.403
 1NN  CAB  OAQ  single    1.415  0.020  1.415
 1NN  SAS  CAM  single    1.821  0.020  1.821
 1NN  CAY  OAQ  single    1.340  0.020  1.340
 1NN  CAY  CAZ  aromatic  1.413  0.020  1.413
 1NN  CAI  CAZ  aromatic  1.379  0.020  1.379
 1NN  CAZ  OAR  single    1.345  0.020  1.345
 1NN  OAR  CAL  single    1.414  0.020  1.414
 1NN  CAL  CAJ  single    1.501  0.020  1.501
 1NN  CAJ  FAE  single    1.391  0.020  1.391
 1NN  CAJ  H1   single    0.970  0.020  1.090
 1NN  CAJ  H2   single    0.970  0.020  1.090
 1NN  CAL  H3   single    0.970  0.020  1.090
 1NN  CAL  H4   single    0.970  0.020  1.090
 1NN  CAI  H5   single    0.930  0.020  1.080
 1NN  CAB  H6   single    0.970  0.020  1.090
 1NN  CAB  H7   single    0.970  0.020  1.090
 1NN  CAB  H8   single    0.970  0.020  1.090
 1NN  CAG  H9   single    0.930  0.020  1.080
 1NN  CAF  H10  single    0.930  0.020  1.080
 1NN  CAK  H11  single    0.970  0.020  1.090
 1NN  CAK  H12  single    0.970  0.020  1.090
 1NN  CAA  H13  single    0.970  0.020  1.090
 1NN  CAA  H14  single    0.970  0.020  1.090
 1NN  CAA  H15  single    0.970  0.020  1.090
 1NN  CAM  H16  single    0.970  0.020  1.090
 1NN  CAM  H17  single    0.970  0.020  1.090
 1NN  NAC  H18  single    0.890  0.020  1.040
 1NN  NAC  H19  single    0.890  0.020  1.040
 1NN  C5   H20  single    0.930  0.020  1.080
 1NN  NAD  H21  single    0.890  0.020  1.040
 1NN  NAD  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
 1NN  H2   CAJ  H1   108.87  3.000
 1NN  H2   CAJ  CAL  109.03  3.000
 1NN  H1   CAJ  CAL  111.27  3.000
 1NN  H2   CAJ  FAE  108.71  3.000
 1NN  H1   CAJ  FAE  108.34  3.000
 1NN  CAL  CAJ  FAE  110.56  3.000
 1NN  H4   CAL  H3   107.72  3.000
 1NN  H4   CAL  OAR  110.95  3.000
 1NN  H3   CAL  OAR  111.33  3.000
 1NN  H4   CAL  CAJ  110.38  3.000
 1NN  H3   CAL  CAJ  108.01  3.000
 1NN  OAR  CAL  CAJ  108.43  3.000
 1NN  CAZ  OAR  CAL  118.54  3.000
 1NN  CAY  CAZ  CAI  119.86  3.000
 1NN  CAI  CAZ  OAR  124.92  3.000
 1NN  CAY  CAZ  OAR  115.22  3.000
 1NN  H5   CAI  CAW  118.35  3.000
 1NN  H5   CAI  CAZ  120.87  3.000
 1NN  CAW  CAI  CAZ  120.78  3.000
 1NN  CAG  CAY  OAQ  125.28  3.000
 1NN  OAQ  CAY  CAZ  115.59  3.000
 1NN  CAG  CAY  CAZ  119.13  3.000
 1NN  CAB  OAQ  CAY  118.35  3.000
 1NN  H8   CAB  H7   108.94  3.000
 1NN  H8   CAB  H6   108.79  3.000
 1NN  H7   CAB  H6   108.86  3.000
 1NN  H8   CAB  OAQ  111.89  3.000
 1NN  H7   CAB  OAQ  111.84  3.000
 1NN  H6   CAB  OAQ  106.42  3.000
 1NN  H9   CAG  CAF  118.59  3.000
 1NN  H9   CAG  CAY  120.79  3.000
 1NN  CAF  CAG  CAY  120.61  3.000
 1NN  H10  CAF  CAW  121.32  3.000
 1NN  H10  CAF  CAG  118.09  3.000
 1NN  CAW  CAF  CAG  120.58  3.000
 1NN  CBC  CAW  CAF  122.11  3.000
 1NN  CBC  CAW  CAI  118.84  3.000
 1NN  CAF  CAW  CAI  119.04  3.000
 1NN  SAT  CBC  NAP  113.27  3.000
 1NN  NAP  CBC  CAW  124.26  3.000
 1NN  SAT  CBC  CAW  122.46  3.000
 1NN  CBA  NAP  CBC  112.13  3.000
 1NN  CBB  SAT  CBC   90.09  3.000
 1NN  CBA  CBB  CAK  129.20  3.000
 1NN  CBA  CBB  SAT  108.76  3.000
 1NN  CAK  CBB  SAT  122.00  3.000
 1NN  H12  CAK  H11  105.78  3.000
 1NN  H12  CAK  CAA  109.92  3.000
 1NN  H11  CAK  CAA  109.80  3.000
 1NN  H12  CAK  CBB  108.66  3.000
 1NN  H11  CAK  CBB  109.86  3.000
 1NN  CAA  CAK  CBB  112.58  3.000
 1NN  H15  CAA  H14  107.92  3.000
 1NN  H15  CAA  H13  107.95  3.000
 1NN  H14  CAA  H13  108.04  3.000
 1NN  H15  CAA  CAK  111.22  3.000
 1NN  H14  CAA  CAK  111.01  3.000
 1NN  H13  CAA  CAK  110.58  3.000
 1NN  CAM  CBA  CBB  124.90  3.000
 1NN  CAM  CBA  NAP  119.34  3.000
 1NN  CBB  CBA  NAP  115.75  3.000
 1NN  H17  CAM  H16  108.27  3.000
 1NN  H17  CAM  SAS  109.25  3.000
 1NN  H16  CAM  SAS  109.43  3.000
 1NN  H17  CAM  CBA  111.89  3.000
 1NN  H16  CAM  CBA  110.48  3.000
 1NN  SAS  CAM  CBA  107.49  3.000
 1NN  C2   SAS  CAM  102.76  3.000
 1NN  N1   C2   N3   128.67  3.000
 1NN  N3   C2   SAS  112.75  3.000
 1NN  N1   C2   SAS  118.57  3.000
 1NN  C4   N3   C2   115.70  3.000
 1NN  C6   N1   C2   115.71  3.000
 1NN  C5   C6   NAC  122.15  3.000
 1NN  C5   C6   N1   121.53  3.000
 1NN  NAC  C6   N1   116.30  3.000
 1NN  H19  NAC  H18  116.52  3.000
 1NN  H19  NAC  C6   118.38  3.000
 1NN  H18  NAC  C6   119.79  3.000
 1NN  H20  C5   C4   121.61  3.000
 1NN  H20  C5   C6   121.49  3.000
 1NN  C4   C5   C6   116.90  3.000
 1NN  NAD  C4   C5   121.89  3.000
 1NN  NAD  C4   N3   116.61  3.000
 1NN  C5   C4   N3   121.48  3.000
 1NN  H22  NAD  H21  117.05  3.000
 1NN  H22  NAD  C4   118.96  3.000
 1NN  H21  NAD  C4   120.40  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
 1NN  CONST_01  CAF  CAG  CAY  CAZ     0.00   0.0  0
 1NN  CONST_02  CAF  CAW  CAI  CAZ     0.00   0.0  0
 1NN  CONST_03  CBC  CAW  CAI  CAZ   180.00   0.0  0
 1NN  CONST_04  CAG  CAF  CAW  CAI     0.00   0.0  0
 1NN  CONST_05  SAT  CBC  CAW  CAI   180.00   0.0  0
 1NN  CONST_06  NAP  CBC  CAW  CAI     0.00   0.0  0
 1NN  CONST_07  CAG  CAY  CAZ  CAI     0.00   0.0  0
 1NN  CONST_08  CAW  CAF  CAG  CAY     0.00   0.0  0
 1NN  CONST_09  CAW  CAI  CAZ  CAY     0.00   0.0  0
 1NN  CONST_10  CBC  CAW  CAF  CAG   180.00   0.0  0
 1NN  CONST_11  SAT  CBC  CAW  CAF     0.00   0.0  0
 1NN  CONST_12  NAP  CBC  CAW  CAF   180.00   0.0  0
 1NN  CONST_13  CBB  SAT  CBC  CAW   180.00   0.0  0
 1NN  CONST_14  CBA  NAP  CBC  CAW   180.00   0.0  0
 1NN  CONST_15  CBA  CBB  SAT  CBC     0.00   0.0  0
 1NN  CONST_16  CBB  CBA  NAP  CBC     0.00   0.0  0
 1NN  CONST_17  CBB  SAT  CBC  NAP     0.00   0.0  0
 1NN  CONST_18  SAT  CBB  CBA  NAP     0.00   0.0  0
 1NN  CONST_19  CBA  NAP  CBC  SAT     0.00   0.0  0
 1NN  CONST_20  C5   C6   N1   C2      0.00   0.0  0
 1NN  CONST_21  C5   C4   N3   C2      0.00   0.0  0
 1NN  CONST_22  C6   C5   C4   N3      0.00   0.0  0
 1NN  CONST_23  C6   N1   C2   N3      0.00   0.0  0
 1NN  CONST_24  C4   C5   C6   N1      0.00   0.0  0
 1NN  CONST_25  C4   N3   C2   N1      0.00   0.0  0
 1NN  CONST_26  CAG  CAY  CAZ  OAR   180.00   0.0  0
 1NN  CONST_27  CAW  CAI  CAZ  OAR   180.00   0.0  0
 1NN  CONST_28  OAQ  CAY  CAZ  CAI   180.00   0.0  0
 1NN  CONST_29  CAF  CAG  CAY  OAQ   180.00   0.0  0
 1NN  CONST_30  CAK  CBB  SAT  CBC   180.00   0.0  0
 1NN  CONST_31  CAM  CBA  NAP  CBC   180.00   0.0  0
 1NN  CONST_32  CAK  CBB  CBA  NAP   180.00   0.0  0
 1NN  CONST_33  CAM  CBA  CBB  SAT   180.00   0.0  0
 1NN  CONST_34  C6   N1   C2   SAS   180.00   0.0  0
 1NN  CONST_35  C4   N3   C2   SAS   180.00   0.0  0
 1NN  CONST_36  NAC  C6   N1   C2    180.00   0.0  0
 1NN  CONST_37  NAD  C4   N3   C2    180.00   0.0  0
 1NN  CONST_38  NAD  C4   C5   C6    180.00   0.0  0
 1NN  CONST_39  C4   C5   C6   NAC   180.00   0.0  0
 1NN  CONST_40  H9   CAG  CAY  CAZ   180.00   0.0  0
 1NN  CONST_41  H10  CAF  CAW  CAI   180.00   0.0  0
 1NN  CONST_42  H5   CAI  CAZ  CAY   180.00   0.0  0
 1NN  CONST_43  H20  C5   C4   N3    180.00   0.0  0
 1NN  CONST_44  H21  NAD  C4   N3    180.00   0.0  0
 1NN  CONST_45  H22  NAD  C4   N3      0.00   0.0  0
 1NN  CONST_46  H18  NAC  C6   N1    180.00   0.0  0
 1NN  CONST_47  H19  NAC  C6   N1      0.00   0.0  0
 1NN  Var_01    CAY  CAZ  OAR  CAL   175.49  30.0  2
 1NN  Var_02    CAG  CAY  OAQ  CAB    -0.49  30.0  3
 1NN  Var_03    SAS  CAM  CBA  NAP   -85.07  30.0  2
 1NN  Var_04    CAA  CAK  CBB  SAT   -84.51  30.0  1
 1NN  Var_05    N1   C2   SAS  CAM     0.92  30.0  2
 1NN  Var_06    H3   CAL  OAR  CAZ    63.70  30.0  3
 1NN  Var_07    H6   CAB  OAQ  CAY   179.66  30.0  3
 1NN  Var_08    H13  CAA  CAK  CBB  -179.82  30.0  3
 1NN  Var_09    OAR  CAL  CAJ  FAE    65.72  30.0  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
 1NN  plan-1  CAW  0.020
 1NN  plan-1  CBC  0.020
 1NN  plan-1  NAP  0.020
 1NN  plan-1  SAT  0.020
 1NN  plan-1  CBB  0.020
 1NN  plan-1  CAK  0.020
 1NN  plan-1  CBA  0.020
 1NN  plan-1  CAM  0.020
 1NN  plan-2  OAR  0.020
 1NN  plan-2  CAZ  0.020
 1NN  plan-2  CAI  0.020
 1NN  plan-2  CAY  0.020
 1NN  plan-2  OAQ  0.020
 1NN  plan-2  CAG  0.020
 1NN  plan-2  CAF  0.020
 1NN  plan-2  CAW  0.020
 1NN  plan-2  CBC  0.020
 1NN  plan-2  H5   0.020
 1NN  plan-2  H9   0.020
 1NN  plan-2  H10  0.020
 1NN  plan-3  SAS  0.020
 1NN  plan-3  C2   0.020
 1NN  plan-3  N3   0.020
 1NN  plan-3  N1   0.020
 1NN  plan-3  C6   0.020
 1NN  plan-3  NAC  0.020
 1NN  plan-3  C5   0.020
 1NN  plan-3  C4   0.020
 1NN  plan-3  NAD  0.020
 1NN  plan-3  H20  0.020
 1NN  plan-4  C6   0.020
 1NN  plan-4  NAC  0.020
 1NN  plan-4  H18  0.020
 1NN  plan-4  H19  0.020
 1NN  plan-5  C4   0.020
 1NN  plan-5  NAD  0.020
 1NN  plan-5  H21  0.020
 1NN  plan-5  H22  0.020

