# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 04:09:50 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-[({2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OCCF)c2sc(C)c(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
 1NO  1NO  2-[({2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine  ligand  48  28  .  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_1NO
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
 1NO  FAN  F  F     0  -0.378   7.8512  -1.2738   1.5339
 1NO  CAM  C  CH2   0  -0.033   7.4333  -1.7178   0.2838
 1NO  CAL  C  CH2   0  -0.245   5.9814  -1.4022   0.0715
 1NO  OAK  O  O2    0  -0.468   5.8333   0.0024   0.0033
 1NO  CAV  C  CR6   0   0.357   4.5967   0.5146  -0.1274
 1NO  CAU  C  CR16  0  -0.475   3.4414  -0.2315  -0.2555
 1NO  CAW  C  CR6   0   0.303   4.5233   1.9247  -0.1311
 1NO  OAX  O  O2    0  -0.456   5.6916   2.5671   0.0064
 1NO  CAY  C  CH3   0  -0.439   5.6802   3.9816   0.0350
 1NO  CBB  C  CR16  0  -0.366   3.2869   2.5353  -0.2700
 1NO  CBA  C  CR16  0  -0.307   2.1296   1.7765  -0.3964
 1NO  CAT  C  CR6   0   0.105   2.1921   0.3914  -0.3868
 1NO  CAS  C  CR5   0   0.007   0.9652  -0.3917  -0.5013
 1NO  NAR  N  N     0  -0.400  -0.2077   0.1151  -0.7213
 1NO  SAZ  S  S2    0   0.234   0.9424  -2.1165  -0.3287
 1NO  CAP  C  CR5   0  -0.259  -0.7592  -2.1242  -0.5739
 1NO  CAO  C  CH3   0  -0.723  -1.5707  -3.3729  -0.5139
 1NO  CAQ  C  CR5   0   0.344  -1.1792  -0.8406  -0.7684
 1NO  CAJ  C  CH2   0  -0.637  -2.6000  -0.4381  -0.9702
 1NO  SAI  S  S2    0   0.040  -3.2822  -0.0260   0.6692
 1NO  C2   C  CR6   0   0.240  -4.9744   0.3105   0.3183
 1NO  N1   N  N     0  -0.498  -5.6680   0.6150   1.3998
 1NO  N3   N  N     0  -0.482  -5.3889   0.2286  -0.9260
 1NO  C4   C  CR6   0   0.502  -6.6968   0.4813  -1.1248
 1NO  NAF  N  NH2   0  -0.831  -7.1296   0.4303  -2.3998
 1NO  C5   C  CR16  0  -0.497  -7.5437   0.8069  -0.0684
 1NO  C6   C  CR6   0   0.487  -6.9720   0.8685   1.2030
 1NO  NAA  N  NH2   0  -0.832  -7.6911   1.2125   2.2901
 1NO  H1   H  HCH2  0   0.222   8.0579  -1.2459  -0.4762
 1NO  H2   H  HCH2  0   0.224   7.5719  -2.7985   0.2323
 1NO  H3   H  HCH2  0   0.240   5.6621  -1.8808  -0.8615
 1NO  H4   H  HCH2  0   0.244   5.3791  -1.8217   0.8851
 1NO  H5   H  HCR6  0   0.281   3.5046  -1.3124  -0.2617
 1NO  H6   H  HCH3  0   0.263   6.7122   4.2939   0.1718
 1NO  H7   H  HCH3  0   0.232   5.3043   4.4060  -0.8994
 1NO  H8   H  HCH3  0   0.232   5.0820   4.3673   0.8645
 1NO  H9   H  HCR6  0   0.288   3.2020   3.6131  -0.2754
 1NO  H10  H  HCR6  0   0.260   1.1767   2.2770  -0.4983
 1NO  H11  H  HCH3  0   0.263  -0.9539  -4.2659  -0.5935
 1NO  H12  H  HCH3  0   0.263  -2.1221  -3.4345   0.4260
 1NO  H13  H  HCH3  0   0.260  -2.2980  -3.4040  -1.3253
 1NO  H14  H  HCH2  0   0.298  -2.6684   0.4317  -1.6213
 1NO  H15  H  HCH2  0   0.289  -3.1885  -1.2429  -1.4064
 1NO  H16  H  HNH2  0   0.399  -8.1168   0.4052  -2.5887
 1NO  H17  H  HNH2  0   0.392  -6.5310   0.0071  -3.0882
 1NO  H18  H  HCR6  0   0.269  -8.5956   1.0041  -0.2253
 1NO  H19  H  HNH2  0   0.399  -8.6952   1.2048   2.2420
 1NO  H20  H  HNH2  0   0.391  -7.2885   1.0457   3.1967

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
 1NO  CAO  CAP  single    1.490  0.020  1.490
 1NO  SAZ  CAP  aromatic  1.719  0.020  1.719
 1NO  SAZ  CAS  aromatic  1.734  0.020  1.734
 1NO  CAP  CAQ  aromatic  1.365  0.020  1.365
 1NO  NAF  C4   single    1.347  0.020  1.347
 1NO  CBA  CBB  aromatic  1.390  0.020  1.390
 1NO  CBA  CAT  aromatic  1.387  0.020  1.387
 1NO  C4   C5   aromatic  1.393  0.020  1.393
 1NO  C4   N3   aromatic  1.347  0.020  1.347
 1NO  CBB  CAW  aromatic  1.386  0.020  1.386
 1NO  C5   C6   aromatic  1.395  0.020  1.395
 1NO  N3   C2   aromatic  1.314  0.020  1.314
 1NO  CAS  CAT  single    1.460  0.020  1.460
 1NO  CAS  NAR  aromatic  1.296  0.020  1.296
 1NO  C6   NAA  single    1.348  0.020  1.348
 1NO  C6   N1   aromatic  1.343  0.020  1.343
 1NO  CAT  CAU  aromatic  1.402  0.020  1.402
 1NO  C2   N1   aromatic  1.320  0.020  1.320
 1NO  C2   SAI  single    1.761  0.020  1.761
 1NO  CAQ  NAR  aromatic  1.364  0.020  1.364
 1NO  CAQ  CAJ  single    1.490  0.020  1.490
 1NO  SAI  CAJ  single    1.823  0.020  1.823
 1NO  CAY  OAX  single    1.415  0.020  1.415
 1NO  CAW  OAX  single    1.340  0.020  1.340
 1NO  CAW  CAV  aromatic  1.412  0.020  1.412
 1NO  CAU  CAV  aromatic  1.381  0.020  1.381
 1NO  CAV  OAK  single    1.345  0.020  1.345
 1NO  OAK  CAL  single    1.414  0.020  1.414
 1NO  CAL  CAM  single    1.501  0.020  1.501
 1NO  CAM  FAN  single    1.391  0.020  1.391
 1NO  CAM  H1   single    0.970  0.020  1.090
 1NO  CAM  H2   single    0.970  0.020  1.090
 1NO  CAL  H3   single    0.970  0.020  1.090
 1NO  CAL  H4   single    0.970  0.020  1.090
 1NO  CAU  H5   single    0.930  0.020  1.080
 1NO  CAY  H6   single    0.970  0.020  1.090
 1NO  CAY  H7   single    0.970  0.020  1.090
 1NO  CAY  H8   single    0.970  0.020  1.090
 1NO  CBB  H9   single    0.930  0.020  1.080
 1NO  CBA  H10  single    0.930  0.020  1.080
 1NO  CAO  H11  single    0.970  0.020  1.090
 1NO  CAO  H12  single    0.970  0.020  1.090
 1NO  CAO  H13  single    0.970  0.020  1.090
 1NO  CAJ  H14  single    0.970  0.020  1.090
 1NO  CAJ  H15  single    0.970  0.020  1.090
 1NO  NAF  H16  single    0.890  0.020  1.040
 1NO  NAF  H17  single    0.890  0.020  1.040
 1NO  C5   H18  single    0.930  0.020  1.080
 1NO  NAA  H19  single    0.890  0.020  1.040
 1NO  NAA  H20  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
 1NO  H2   CAM  H1   108.84  3.000
 1NO  H2   CAM  CAL  108.94  3.000
 1NO  H1   CAM  CAL  111.36  3.000
 1NO  H2   CAM  FAN  108.70  3.000
 1NO  H1   CAM  FAN  108.42  3.000
 1NO  CAL  CAM  FAN  110.53  3.000
 1NO  H4   CAL  H3   107.74  3.000
 1NO  H4   CAL  OAK  111.01  3.000
 1NO  H3   CAL  OAK  111.23  3.000
 1NO  H4   CAL  CAM  110.26  3.000
 1NO  H3   CAL  CAM  108.08  3.000
 1NO  OAK  CAL  CAM  108.48  3.000
 1NO  CAV  OAK  CAL  118.64  3.000
 1NO  CAW  CAV  CAU  119.72  3.000
 1NO  CAU  CAV  OAK  124.92  3.000
 1NO  CAW  CAV  OAK  115.36  3.000
 1NO  H5   CAU  CAT  119.66  3.000
 1NO  H5   CAU  CAV  119.40  3.000
 1NO  CAT  CAU  CAV  120.93  3.000
 1NO  CBB  CAW  OAX  125.22  3.000
 1NO  OAX  CAW  CAV  115.66  3.000
 1NO  CBB  CAW  CAV  119.12  3.000
 1NO  CAY  OAX  CAW  118.31  3.000
 1NO  H8   CAY  H7   108.88  3.000
 1NO  H8   CAY  H6   108.83  3.000
 1NO  H7   CAY  H6   108.82  3.000
 1NO  H8   CAY  OAX  111.87  3.000
 1NO  H7   CAY  OAX  111.95  3.000
 1NO  H6   CAY  OAX  106.39  3.000
 1NO  H9   CBB  CBA  118.59  3.000
 1NO  H9   CBB  CAW  120.65  3.000
 1NO  CBA  CBB  CAW  120.77  3.000
 1NO  H10  CBA  CAT  120.19  3.000
 1NO  H10  CBA  CBB  119.33  3.000
 1NO  CAT  CBA  CBB  120.48  3.000
 1NO  CAS  CAT  CBA  119.83  3.000
 1NO  CAS  CAT  CAU  121.19  3.000
 1NO  CBA  CAT  CAU  118.99  3.000
 1NO  SAZ  CAS  NAR  113.20  3.000
 1NO  NAR  CAS  CAT  124.32  3.000
 1NO  SAZ  CAS  CAT  122.47  3.000
 1NO  CAQ  NAR  CAS  112.11  3.000
 1NO  CAP  SAZ  CAS   90.19  3.000
 1NO  CAQ  CAP  CAO  128.78  3.000
 1NO  CAQ  CAP  SAZ  108.71  3.000
 1NO  CAO  CAP  SAZ  122.47  3.000
 1NO  H13  CAO  H12  107.60  3.000
 1NO  H13  CAO  H11  107.47  3.000
 1NO  H12  CAO  H11  107.65  3.000
 1NO  H13  CAO  CAP  110.92  3.000
 1NO  H12  CAO  CAP  110.92  3.000
 1NO  H11  CAO  CAP  112.08  3.000
 1NO  CAJ  CAQ  CAP  124.52  3.000
 1NO  CAJ  CAQ  NAR  119.64  3.000
 1NO  CAP  CAQ  NAR  115.79  3.000
 1NO  H15  CAJ  H14  108.50  3.000
 1NO  H15  CAJ  SAI  108.98  3.000
 1NO  H14  CAJ  SAI  109.49  3.000
 1NO  H15  CAJ  CAQ  111.72  3.000
 1NO  H14  CAJ  CAQ  110.89  3.000
 1NO  SAI  CAJ  CAQ  107.22  3.000
 1NO  C2   SAI  CAJ  102.93  3.000
 1NO  N3   C2   N1   128.62  3.000
 1NO  N1   C2   SAI  112.69  3.000
 1NO  N3   C2   SAI  118.69  3.000
 1NO  C6   N1   C2   115.70  3.000
 1NO  C4   N3   C2   115.75  3.000
 1NO  C5   C4   NAF  122.10  3.000
 1NO  C5   C4   N3   121.50  3.000
 1NO  NAF  C4   N3   116.39  3.000
 1NO  H17  NAF  H16  116.45  3.000
 1NO  H17  NAF  C4   118.19  3.000
 1NO  H16  NAF  C4   119.61  3.000
 1NO  H18  C5   C6   121.50  3.000
 1NO  H18  C5   C4   121.60  3.000
 1NO  C6   C5   C4   116.89  3.000
 1NO  NAA  C6   C5   121.84  3.000
 1NO  NAA  C6   N1   116.61  3.000
 1NO  C5   C6   N1   121.53  3.000
 1NO  H20  NAA  H19  116.21  3.000
 1NO  H20  NAA  C6   118.10  3.000
 1NO  H19  NAA  C6   119.49  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
 1NO  CONST_01  CBA  CBB  CAW  CAV    0.00   0.0  0
 1NO  CONST_02  CBA  CAT  CAU  CAV    0.00   0.0  0
 1NO  CONST_03  CAS  CAT  CAU  CAV  180.00   0.0  0
 1NO  CONST_04  CBB  CBA  CAT  CAU    0.00   0.0  0
 1NO  CONST_05  SAZ  CAS  CAT  CAU    0.00   0.0  0
 1NO  CONST_06  NAR  CAS  CAT  CAU  180.00   0.0  0
 1NO  CONST_07  CBB  CAW  CAV  CAU    0.00   0.0  0
 1NO  CONST_08  CAT  CBA  CBB  CAW    0.00   0.0  0
 1NO  CONST_09  CAT  CAU  CAV  CAW    0.00   0.0  0
 1NO  CONST_10  CAS  CAT  CBA  CBB  180.00   0.0  0
 1NO  CONST_11  SAZ  CAS  CAT  CBA  180.00   0.0  0
 1NO  CONST_12  NAR  CAS  CAT  CBA    0.00   0.0  0
 1NO  CONST_13  CAP  SAZ  CAS  CAT  180.00   0.0  0
 1NO  CONST_14  CAQ  NAR  CAS  CAT  180.00   0.0  0
 1NO  CONST_15  CAQ  CAP  SAZ  CAS    0.00   0.0  0
 1NO  CONST_16  CAP  CAQ  NAR  CAS    0.00   0.0  0
 1NO  CONST_17  CAP  SAZ  CAS  NAR    0.00   0.0  0
 1NO  CONST_18  SAZ  CAP  CAQ  NAR    0.00   0.0  0
 1NO  CONST_19  CAQ  NAR  CAS  SAZ    0.00   0.0  0
 1NO  CONST_20  C5   C4   N3   C2     0.00   0.0  0
 1NO  CONST_21  C5   C6   N1   C2     0.00   0.0  0
 1NO  CONST_22  C4   C5   C6   N1     0.00   0.0  0
 1NO  CONST_23  C4   N3   C2   N1     0.00   0.0  0
 1NO  CONST_24  C6   C5   C4   N3     0.00   0.0  0
 1NO  CONST_25  C6   N1   C2   N3     0.00   0.0  0
 1NO  CONST_26  CBB  CAW  CAV  OAK  180.00   0.0  0
 1NO  CONST_27  CAT  CAU  CAV  OAK  180.00   0.0  0
 1NO  CONST_28  OAX  CAW  CAV  CAU  180.00   0.0  0
 1NO  CONST_29  CBA  CBB  CAW  OAX  180.00   0.0  0
 1NO  CONST_30  CAO  CAP  SAZ  CAS  180.00   0.0  0
 1NO  CONST_31  CAJ  CAQ  NAR  CAS  180.00   0.0  0
 1NO  CONST_32  CAO  CAP  CAQ  NAR  180.00   0.0  0
 1NO  CONST_33  CAJ  CAQ  CAP  SAZ  180.00   0.0  0
 1NO  CONST_34  C4   N3   C2   SAI  180.00   0.0  0
 1NO  CONST_35  C6   N1   C2   SAI  180.00   0.0  0
 1NO  CONST_36  NAF  C4   N3   C2   180.00   0.0  0
 1NO  CONST_37  NAA  C6   N1   C2   180.00   0.0  0
 1NO  CONST_38  NAA  C6   C5   C4   180.00   0.0  0
 1NO  CONST_39  C6   C5   C4   NAF  180.00   0.0  0
 1NO  CONST_40  H9   CBB  CAW  CAV  180.00   0.0  0
 1NO  CONST_41  H10  CBA  CAT  CAU  180.00   0.0  0
 1NO  CONST_42  H5   CAU  CAV  CAW  180.00   0.0  0
 1NO  CONST_43  H18  C5   C6   N1   180.00   0.0  0
 1NO  CONST_44  H19  NAA  C6   N1   180.00   0.0  0
 1NO  CONST_45  H20  NAA  C6   N1     0.00   0.0  0
 1NO  CONST_46  H16  NAF  C4   N3   180.00   0.0  0
 1NO  CONST_47  H17  NAF  C4   N3     0.00   0.0  0
 1NO  Var_01    CAW  CAV  OAK  CAL  177.40  30.0  2
 1NO  Var_02    CBB  CAW  OAX  CAY    1.04  30.0  2
 1NO  Var_03    SAI  CAJ  CAQ  NAR  -85.21  30.0  2
 1NO  Var_04    N3   C2   SAI  CAJ   -0.74  30.0  2
 1NO  Var_05    H11  CAO  CAP  SAZ  -16.71  30.0  2
 1NO  Var_06    H3   CAL  OAK  CAV   64.06  30.0  3
 1NO  Var_07    H6   CAY  OAX  CAW  178.87  30.0  3
 1NO  Var_08    OAK  CAL  CAM  FAN   66.55  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
 1NO  plan-1  CAT  0.020
 1NO  plan-1  CAS  0.020
 1NO  plan-1  NAR  0.020
 1NO  plan-1  SAZ  0.020
 1NO  plan-1  CAP  0.020
 1NO  plan-1  CAO  0.020
 1NO  plan-1  CAQ  0.020
 1NO  plan-1  CAJ  0.020
 1NO  plan-2  OAK  0.020
 1NO  plan-2  CAV  0.020
 1NO  plan-2  CAU  0.020
 1NO  plan-2  CAW  0.020
 1NO  plan-2  OAX  0.020
 1NO  plan-2  CBB  0.020
 1NO  plan-2  CBA  0.020
 1NO  plan-2  CAT  0.020
 1NO  plan-2  CAS  0.020
 1NO  plan-2  H5   0.020
 1NO  plan-2  H9   0.020
 1NO  plan-2  H10  0.020
 1NO  plan-3  SAI  0.020
 1NO  plan-3  C2   0.020
 1NO  plan-3  N1   0.020
 1NO  plan-3  N3   0.020
 1NO  plan-3  C4   0.020
 1NO  plan-3  NAF  0.020
 1NO  plan-3  C5   0.020
 1NO  plan-3  C6   0.020
 1NO  plan-3  NAA  0.020
 1NO  plan-3  H18  0.020
 1NO  plan-4  C4   0.020
 1NO  plan-4  NAF  0.020
 1NO  plan-4  H16  0.020
 1NO  plan-4  H17  0.020
 1NO  plan-5  C6   0.020
 1NO  plan-5  NAA  0.020
 1NO  plan-5  H19  0.020
 1NO  plan-5  H20  0.020

