# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 05:17:39 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-[({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: COc1ccc(cc1OCCF)c2scc(CSc3nc(N)cc(N)n3)n2
#
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
 1NM  1NM  2-[({2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine  ligand  45  27  .  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_1NM
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
 1NM  FAD  F  F     0  -0.378  -8.1252   1.0828   0.2579
 1NM  CAJ  C  CH2   0  -0.033  -7.3726   1.5170  -0.8276
 1NM  CAK  C  CH2   0  -0.246  -5.9080   1.3203  -0.5652
 1NM  OAQ  O  O2    0  -0.467  -5.6478  -0.0676  -0.4880
 1NM  CAZ  C  CR6   0   0.357  -4.3956  -0.4713  -0.2102
 1NM  CAI  C  CR16  0  -0.471  -3.3125   0.3687  -0.0428
 1NM  CAY  C  CR6   0   0.305  -4.2218  -1.8683  -0.0958
 1NM  OAP  O  O2    0  -0.455  -5.3254  -2.6052  -0.2770
 1NM  CAA  C  CH3   0  -0.439  -5.2201  -4.0120  -0.1634
 1NM  CAF  C  CR16  0  -0.367  -2.9615  -2.3715   0.1865
 1NM  CAE  C  CR16  0  -0.305  -1.8786  -1.5178   0.3585
 1NM  CAW  C  CR6   0   0.104  -2.0408  -0.1455   0.2473
 1NM  CBA  C  CR5   0   0.010  -0.8935   0.7379   0.4337
 1NM  NAO  N  N     0  -0.397   0.3276   0.3256   0.5803
 1NM  SAS  S  S2    0   0.232  -1.0523   2.4657   0.5000
 1NM  CAG  C  CR15  0  -0.546   0.6379   2.5977   0.7302
 1NM  CAV  C  CR5   0   0.355   1.1999   1.3597   0.7517
 1NM  CAL  C  CH2   0  -0.630   2.6526   1.0784   0.9281
 1NM  SAR  S  S2    0   0.041   3.3097   0.5016  -0.6693
 1NM  C2   C  CR6   0   0.241   4.9521   0.0187  -0.2548
 1NM  N3   N  N     0  -0.498   5.6165  -0.4634  -1.2888
 1NM  N1   N  N     0  -0.482   5.3594   0.1679   0.9853
 1NM  C6   C  CR6   0   0.503   6.6215  -0.2286   1.2387
 1NM  NAB  N  NH2   0  -0.831   7.0618  -0.0520   2.4994
 1NM  C5   C  CR16  0  -0.498   7.4302  -0.7622   0.2387
 1NM  C4   C  CR6   0   0.488   6.8754  -0.8587  -1.0381
 1NM  NAC  N  NH2   0  -0.832   7.5824  -1.3263  -2.0859
 1NM  H1   H  HCH2  0   0.222  -7.6952   0.9655  -1.7121
 1NM  H2   H  HCH2  0   0.225  -7.5644   2.5790  -0.9850
 1NM  H3   H  HCH2  0   0.240  -5.3501   1.7818  -1.3879
 1NM  H4   H  HCH2  0   0.243  -5.6160   1.8251   0.3625
 1NM  H5   H  HCR6  0   0.281  -3.4462   1.4380  -0.1473
 1NM  H6   H  HCH3  0   0.233  -4.5359  -4.4304  -0.9057
 1NM  H7   H  HCH3  0   0.232  -4.8902  -4.3152   0.8332
 1NM  H8   H  HCH3  0   0.263  -6.2159  -4.4094  -0.3410
 1NM  H9   H  HCR6  0   0.289  -2.8016  -3.4367   0.2804
 1NM  H10  H  HCR6  0   0.261  -0.9069  -1.9330   0.5866
 1NM  H11  H  HCR5  0   0.310   1.1224   3.5554   0.8372
 1NM  H12  H  HCH2  0   0.293   3.1863   1.9723   1.2444
 1NM  H13  H  HCH2  0   0.296   2.8074   0.2990   1.6732
 1NM  H14  H  HNH2  0   0.399   7.9117  -0.4987   2.7963
 1NM  H15  H  HNH2  0   0.392   6.3853   0.1439   3.2175
 1NM  H16  H  HCR6  0   0.269   8.4417  -1.0868   0.4419
 1NM  H17  H  HNH2  0   0.399   8.4415  -1.8220  -1.9219
 1NM  H18  H  HNH2  0   0.391   7.0863  -1.5618  -2.9285

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
 1NM  NAB  C6   single    1.347  0.020  1.347
 1NM  C6   C5   aromatic  1.392  0.020  1.392
 1NM  C6   N1   aromatic  1.347  0.020  1.347
 1NM  C5   C4   aromatic  1.396  0.020  1.396
 1NM  N1   C2   aromatic  1.314  0.020  1.314
 1NM  C4   NAC  single    1.348  0.020  1.348
 1NM  C4   N3   aromatic  1.343  0.020  1.343
 1NM  C2   N3   aromatic  1.320  0.020  1.320
 1NM  C2   SAR  single    1.761  0.020  1.761
 1NM  SAR  CAL  single    1.821  0.020  1.821
 1NM  CAL  CAV  single    1.490  0.020  1.490
 1NM  FAD  CAJ  single    1.390  0.020  1.390
 1NM  CAV  NAO  aromatic  1.364  0.020  1.364
 1NM  CAV  CAG  aromatic  1.360  0.020  1.360
 1NM  NAO  CBA  aromatic  1.297  0.020  1.297
 1NM  CAG  SAS  aromatic  1.711  0.020  1.711
 1NM  CAJ  CAK  single    1.501  0.020  1.501
 1NM  CBA  SAS  aromatic  1.736  0.020  1.736
 1NM  CBA  CAW  single    1.460  0.020  1.460
 1NM  CAK  OAQ  single    1.414  0.020  1.414
 1NM  CAW  CAI  aromatic  1.402  0.020  1.402
 1NM  CAW  CAE  aromatic  1.386  0.020  1.386
 1NM  CAI  CAZ  aromatic  1.381  0.020  1.381
 1NM  CAZ  OAQ  single    1.345  0.020  1.345
 1NM  CAZ  CAY  aromatic  1.412  0.020  1.412
 1NM  CAE  CAF  aromatic  1.390  0.020  1.390
 1NM  CAY  CAF  aromatic  1.386  0.020  1.386
 1NM  CAY  OAP  single    1.339  0.020  1.339
 1NM  OAP  CAA  single    1.415  0.020  1.415
 1NM  CAJ  H1   single    0.970  0.020  1.090
 1NM  CAJ  H2   single    0.970  0.020  1.090
 1NM  CAK  H3   single    0.970  0.020  1.090
 1NM  CAK  H4   single    0.970  0.020  1.090
 1NM  CAI  H5   single    0.930  0.020  1.080
 1NM  CAA  H6   single    0.970  0.020  1.090
 1NM  CAA  H7   single    0.970  0.020  1.090
 1NM  CAA  H8   single    0.970  0.020  1.090
 1NM  CAF  H9   single    0.930  0.020  1.080
 1NM  CAE  H10  single    0.930  0.020  1.080
 1NM  CAG  H11  single    0.930  0.020  1.080
 1NM  CAL  H12  single    0.970  0.020  1.090
 1NM  CAL  H13  single    0.970  0.020  1.090
 1NM  NAB  H14  single    0.890  0.020  1.040
 1NM  NAB  H15  single    0.890  0.020  1.040
 1NM  C5   H16  single    0.930  0.020  1.080
 1NM  NAC  H17  single    0.890  0.020  1.040
 1NM  NAC  H18  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
 1NM  H2   CAJ  H1   108.86  3.000
 1NM  H2   CAJ  CAK  108.93  3.000
 1NM  H1   CAJ  CAK  111.35  3.000
 1NM  H2   CAJ  FAD  108.76  3.000
 1NM  H1   CAJ  FAD  108.36  3.000
 1NM  CAK  CAJ  FAD  110.53  3.000
 1NM  H4   CAK  H3   107.81  3.000
 1NM  H4   CAK  OAQ  110.91  3.000
 1NM  H3   CAK  OAQ  111.14  3.000
 1NM  H4   CAK  CAJ  110.35  3.000
 1NM  H3   CAK  CAJ  108.08  3.000
 1NM  OAQ  CAK  CAJ  108.53  3.000
 1NM  CAZ  OAQ  CAK  118.51  3.000
 1NM  CAY  CAZ  CAI  119.69  3.000
 1NM  CAY  CAZ  OAQ  115.36  3.000
 1NM  CAI  CAZ  OAQ  124.95  3.000
 1NM  H5   CAI  CAW  119.62  3.000
 1NM  H5   CAI  CAZ  119.49  3.000
 1NM  CAW  CAI  CAZ  120.89  3.000
 1NM  CAF  CAY  OAP  125.24  3.000
 1NM  OAP  CAY  CAZ  115.59  3.000
 1NM  CAF  CAY  CAZ  119.17  3.000
 1NM  CAA  OAP  CAY  118.34  3.000
 1NM  H8   CAA  H7   108.92  3.000
 1NM  H8   CAA  H6   108.82  3.000
 1NM  H7   CAA  H6   108.92  3.000
 1NM  H8   CAA  OAP  106.39  3.000
 1NM  H7   CAA  OAP  111.81  3.000
 1NM  H6   CAA  OAP  111.88  3.000
 1NM  H9   CAF  CAE  118.64  3.000
 1NM  H9   CAF  CAY  120.65  3.000
 1NM  CAE  CAF  CAY  120.71  3.000
 1NM  H10  CAE  CAW  120.15  3.000
 1NM  H10  CAE  CAF  119.38  3.000
 1NM  CAW  CAE  CAF  120.47  3.000
 1NM  CBA  CAW  CAE  119.79  3.000
 1NM  CAE  CAW  CAI  119.06  3.000
 1NM  CBA  CAW  CAI  121.15  3.000
 1NM  SAS  CBA  NAO  113.46  3.000
 1NM  SAS  CBA  CAW  122.35  3.000
 1NM  NAO  CBA  CAW  124.19  3.000
 1NM  CAV  NAO  CBA  112.04  3.000
 1NM  CAG  SAS  CBA   89.51  3.000
 1NM  H11  CAG  CAV  128.40  3.000
 1NM  H11  CAG  SAS  121.71  3.000
 1NM  CAV  CAG  SAS  109.89  3.000
 1NM  CAL  CAV  CAG  125.22  3.000
 1NM  CAG  CAV  NAO  115.09  3.000
 1NM  CAL  CAV  NAO  119.68  3.000
 1NM  H13  CAL  H12  108.62  3.000
 1NM  H13  CAL  SAR  108.79  3.000
 1NM  H12  CAL  SAR  109.77  3.000
 1NM  H13  CAL  CAV  110.77  3.000
 1NM  H12  CAL  CAV  110.94  3.000
 1NM  SAR  CAL  CAV  107.92  3.000
 1NM  C2   SAR  CAL  102.52  3.000
 1NM  N1   C2   N3   128.66  3.000
 1NM  N3   C2   SAR  112.65  3.000
 1NM  N1   C2   SAR  118.69  3.000
 1NM  C4   N3   C2   115.66  3.000
 1NM  C6   N1   C2   115.76  3.000
 1NM  C5   C6   NAB  122.18  3.000
 1NM  C5   C6   N1   121.46  3.000
 1NM  NAB  C6   N1   116.34  3.000
 1NM  H15  NAB  H14  116.39  3.000
 1NM  H15  NAB  C6   118.29  3.000
 1NM  H14  NAB  C6   119.64  3.000
 1NM  H16  C5   C4   121.53  3.000
 1NM  H16  C5   C6   121.55  3.000
 1NM  C4   C5   C6   116.92  3.000
 1NM  NAC  C4   C5   121.79  3.000
 1NM  NAC  C4   N3   116.66  3.000
 1NM  C5   C4   N3   121.54  3.000
 1NM  H18  NAC  H17  116.28  3.000
 1NM  H18  NAC  C4   118.28  3.000
 1NM  H17  NAC  C4   119.51  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
 1NM  CONST_01  CBA  CAW  CAI  CAZ  180.00   0.0  0
 1NM  CONST_02  CAE  CAW  CAI  CAZ    0.00   0.0  0
 1NM  CONST_03  CAE  CAF  CAY  CAZ    0.00   0.0  0
 1NM  CONST_04  NAO  CBA  CAW  CAI  180.00   0.0  0
 1NM  CONST_05  SAS  CBA  CAW  CAI    0.00   0.0  0
 1NM  CONST_06  CAF  CAE  CAW  CAI    0.00   0.0  0
 1NM  CONST_07  CAF  CAY  CAZ  CAI    0.00   0.0  0
 1NM  CONST_08  CAW  CAI  CAZ  CAY    0.00   0.0  0
 1NM  CONST_09  CAW  CAE  CAF  CAY    0.00   0.0  0
 1NM  CONST_10  CBA  CAW  CAE  CAF  180.00   0.0  0
 1NM  CONST_11  NAO  CBA  CAW  CAE    0.00   0.0  0
 1NM  CONST_12  SAS  CBA  CAW  CAE  180.00   0.0  0
 1NM  CONST_13  CAV  NAO  CBA  CAW  180.00   0.0  0
 1NM  CONST_14  CAG  SAS  CBA  CAW  180.00   0.0  0
 1NM  CONST_15  CAG  CAV  NAO  CBA    0.00   0.0  0
 1NM  CONST_16  CAV  CAG  SAS  CBA    0.00   0.0  0
 1NM  CONST_17  SAS  CAG  CAV  NAO    0.00   0.0  0
 1NM  CONST_18  CAG  SAS  CBA  NAO    0.00   0.0  0
 1NM  CONST_19  CAV  NAO  CBA  SAS    0.00   0.0  0
 1NM  CONST_20  C5   C6   N1   C2     0.00   0.0  0
 1NM  CONST_21  C5   C4   N3   C2     0.00   0.0  0
 1NM  CONST_22  C6   C5   C4   N3     0.00   0.0  0
 1NM  CONST_23  C6   N1   C2   N3     0.00   0.0  0
 1NM  CONST_24  C4   C5   C6   N1     0.00   0.0  0
 1NM  CONST_25  C4   N3   C2   N1     0.00   0.0  0
 1NM  CONST_26  CAW  CAI  CAZ  OAQ  180.00   0.0  0
 1NM  CONST_27  CAF  CAY  CAZ  OAQ  180.00   0.0  0
 1NM  CONST_28  OAP  CAY  CAZ  CAI  180.00   0.0  0
 1NM  CONST_29  CAE  CAF  CAY  OAP  180.00   0.0  0
 1NM  CONST_30  CAL  CAV  NAO  CBA  180.00   0.0  0
 1NM  CONST_31  CAL  CAV  CAG  SAS  180.00   0.0  0
 1NM  CONST_32  C6   N1   C2   SAR  180.00   0.0  0
 1NM  CONST_33  C4   N3   C2   SAR  180.00   0.0  0
 1NM  CONST_34  NAB  C6   N1   C2   180.00   0.0  0
 1NM  CONST_35  NAC  C4   N3   C2   180.00   0.0  0
 1NM  CONST_36  NAC  C4   C5   C6   180.00   0.0  0
 1NM  CONST_37  C4   C5   C6   NAB  180.00   0.0  0
 1NM  CONST_38  H9   CAF  CAY  CAZ  180.00   0.0  0
 1NM  CONST_39  H10  CAE  CAW  CAI  180.00   0.0  0
 1NM  CONST_40  H5   CAI  CAZ  CAY  180.00   0.0  0
 1NM  CONST_41  H11  CAG  SAS  CBA  180.00   0.0  0
 1NM  CONST_42  H16  C5   C4   N3   180.00   0.0  0
 1NM  CONST_43  H17  NAC  C4   N3   180.00   0.0  0
 1NM  CONST_44  H18  NAC  C4   N3     0.00   0.0  0
 1NM  CONST_45  H14  NAB  C6   N1   180.00   0.0  0
 1NM  CONST_46  H15  NAB  C6   N1     0.00   0.0  0
 1NM  Var_01    CAI  CAZ  OAQ  CAK   -2.73  30.0  2
 1NM  Var_02    CAF  CAY  OAP  CAA    0.61  30.0  2
 1NM  Var_03    SAR  CAL  CAV  NAO   70.78  30.0  2
 1NM  Var_04    N1   C2   SAR  CAL   -0.99  30.0  2
 1NM  Var_05    H3   CAK  OAQ  CAZ   63.58  30.0  1
 1NM  Var_06    H6   CAA  OAP  CAY  -61.46  30.0  3
 1NM  Var_07    OAQ  CAK  CAJ  FAD   66.01  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
 1NM  plan-1  CAW  0.020
 1NM  plan-1  CBA  0.020
 1NM  plan-1  NAO  0.020
 1NM  plan-1  SAS  0.020
 1NM  plan-1  CAG  0.020
 1NM  plan-1  CAV  0.020
 1NM  plan-1  CAL  0.020
 1NM  plan-1  H11  0.020
 1NM  plan-2  OAQ  0.020
 1NM  plan-2  CAZ  0.020
 1NM  plan-2  CAI  0.020
 1NM  plan-2  CAY  0.020
 1NM  plan-2  OAP  0.020
 1NM  plan-2  CAF  0.020
 1NM  plan-2  CAE  0.020
 1NM  plan-2  CAW  0.020
 1NM  plan-2  CBA  0.020
 1NM  plan-2  H5   0.020
 1NM  plan-2  H9   0.020
 1NM  plan-2  H10  0.020
 1NM  plan-3  SAR  0.020
 1NM  plan-3  C2   0.020
 1NM  plan-3  N3   0.020
 1NM  plan-3  N1   0.020
 1NM  plan-3  C6   0.020
 1NM  plan-3  NAB  0.020
 1NM  plan-3  C5   0.020
 1NM  plan-3  C4   0.020
 1NM  plan-3  NAC  0.020
 1NM  plan-3  H16  0.020
 1NM  plan-4  C6   0.020
 1NM  plan-4  NAB  0.020
 1NM  plan-4  H14  0.020
 1NM  plan-4  H15  0.020
 1NM  plan-5  C4   0.020
 1NM  plan-5  NAC  0.020
 1NM  plan-5  H17  0.020
 1NM  plan-5  H18  0.020

