# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:07:09 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (2S)-1,3-benzothiazol-2-yl{2-[(2-pyridin-3-ylethyl)amino]pyrimidin-4-yl}ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#C[C@@H](c1sc2ccccc2n1)c3ccnc(NCCc4cccnc4)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
 JN5  JN5  (2S)-1,3-benzothiazol-2-yl{2-[(2-pyridin-3-ylethyl)amino]pyrimidin-4-yl}ethanenitrile  ligand  43  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JN5
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
 JN5  C1W   C  CR16  0  -0.190  -5.6254   2.1553  -0.3771
 JN5  C1X   C  CR16  0  -0.318  -6.8822   2.3762  -0.9173
 JN5  C1Y   C  CR16  0  -0.073  -7.8963   1.4775  -0.6216
 JN5  N1Z   N  N     0  -0.401  -7.7193   0.4175   0.1583
 JN5  C2A   C  CR16  0  -0.100  -6.5110   0.2187   0.6697
 JN5  C1V   C  CR6   0   0.026  -5.4188   1.0505   0.4416
 JN5  C1U   C  CH2   0  -0.554  -4.0711   0.7370   1.0201
 JN5  C1T   C  CH2   0  -0.236  -3.2175  -0.0355   0.0180
 JN5  N1S   N  NH1   0  -0.664  -1.9091  -0.2913   0.5730
 JN5  C2    C  CR6   0   0.610  -1.0407  -1.1860   0.0786
 JN5  N3    N  N     0  -0.459   0.1786  -1.2108   0.6322
 JN5  N1    N  N     0  -0.457  -1.4503  -1.9869  -0.9147
 JN5  C6    C  CR16  0   0.004  -0.5762  -2.8701  -1.3545
 JN5  C5    C  CR16  0  -0.412   0.7130  -2.9876  -0.8504
 JN5  C4    C  CR6   0   0.311   1.0304  -2.1000   0.1628
 JN5  C1J   C  CH1   0  -0.496   2.4043  -2.0250   0.8084
 JN5  C1K   C  CSP   0   0.142   3.2837  -3.1202   0.4130
 JN5  N1L   N  NS    0  -0.232   3.9891  -3.9743   0.1075
 JN5  C1I   C  CR5   0   0.094   3.0559  -0.7033   0.4973
 JN5  N1G   N  N     0  -0.374   3.4453   0.1209   1.3959
 JN5  C1E   C  CR56  0   0.346   3.9888   1.2490   0.8240
 JN5  C1C   C  CR16  0  -0.303   4.5008   2.3429   1.5220
 JN5  C1A   C  CR16  0  -0.256   5.0103   3.4063   0.8036
 JN5  C1B   C  CR16  0  -0.261   5.0173   3.3942  -0.5965
 JN5  C1D   C  CR16  0  -0.274   4.5152   2.3187  -1.3061
 JN5  C1F   C  CR56  0  -0.231   4.0021   1.2502  -0.5800
 JN5  S1H   S  S2    0   0.258   3.3004  -0.2206  -1.1596
 JN5  H1W   H  HCR6  0   0.268  -4.8117   2.8403  -0.5849
 JN5  H1X   H  HCR6  0   0.271  -7.0766   3.2289  -1.5534
 JN5  H1Y   H  HCR6  0   0.263  -8.8912   1.6210  -1.0283
 JN5  H2A   H  HCR6  0   0.257  -6.3956  -0.6525   1.3080
 JN5  H1U   H  HCH2  0   0.262  -3.5641   1.6656   1.2962
 JN5  H1UA  H  HCH2  0   0.262  -4.1792   0.1471   1.9330
 JN5  H1T   H  HCH2  0   0.250  -3.6994  -0.9835  -0.2223
 JN5  H1TA  H  HCH2  0   0.237  -3.1443   0.5295  -0.9181
 JN5  HN1S  H  HNH1  0   0.398  -1.5332   0.3709   1.2335
 JN5  H6    H  HCR6  0   0.281  -0.9071  -3.5193  -2.1579
 JN5  H5    H  HCR6  0   0.280   1.4035  -3.7178  -1.2444
 JN5  H1J   H  HCH1  0   0.384   2.2839  -2.0757   1.8940
 JN5  H1C   H  HCR6  0   0.272   4.4923   2.3461   2.6039
 JN5  H1A   H  HCR6  0   0.268   5.4120   4.2629   1.3281
 JN5  H1B   H  HCR6  0   0.270   5.4229   4.2410  -1.1337
 JN5  H1D   H  HCR6  0   0.279   4.5215   2.3123  -2.3874

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
 JN5  C1V  C1W   aromatic  1.391  0.020  1.391
 JN5  C1W  C1X   aromatic  1.386  0.020  1.386
 JN5  C1W  H1W   single    0.930  0.020  1.080
 JN5  C1Y  C1X   aromatic  1.387  0.020  1.387
 JN5  C1X  H1X   single    0.930  0.020  1.080
 JN5  N1Z  C1Y   aromatic  1.328  0.020  1.328
 JN5  C1Y  H1Y   single    0.930  0.020  1.080
 JN5  C2A  N1Z   aromatic  1.327  0.020  1.327
 JN5  C2A  C1V   aromatic  1.392  0.020  1.392
 JN5  C2A  H2A   single    0.930  0.020  1.080
 JN5  C1U  C1V   single    1.500  0.020  1.500
 JN5  C1U  C1T   single    1.526  0.020  1.526
 JN5  C1U  H1U   single    0.970  0.020  1.090
 JN5  C1U  H1UA  single    0.970  0.020  1.090
 JN5  N1S  C1T   single    1.444  0.020  1.444
 JN5  C1T  H1T   single    0.970  0.020  1.090
 JN5  C1T  H1TA  single    0.970  0.020  1.090
 JN5  N1S  C2    single    1.341  0.020  1.341
 JN5  N1S  HN1S  single    0.860  0.020  1.020
 JN5  N1   C2    aromatic  1.340  0.020  1.340
 JN5  C2   N3    aromatic  1.339  0.020  1.339
 JN5  N3   C4    aromatic  1.318  0.020  1.318
 JN5  N1   C6    aromatic  1.318  0.020  1.318
 JN5  C6   C5    aromatic  1.389  0.020  1.389
 JN5  C6   H6    single    0.930  0.020  1.080
 JN5  C5   C4    aromatic  1.384  0.020  1.384
 JN5  C5   H5    single    0.930  0.020  1.080
 JN5  C4   C1J   single    1.520  0.020  1.520
 JN5  C1J  C1I   single    1.506  0.020  1.506
 JN5  C1J  C1K   single    1.459  0.020  1.459
 JN5  C1J  H1J   single    0.970  0.020  1.090
 JN5  C1K  N1L   triple    1.149  0.020  1.149
 JN5  S1H  C1I   aromatic  1.743  0.020  1.743
 JN5  C1I  N1G   aromatic  1.280  0.020  1.280
 JN5  N1G  C1E   aromatic  1.377  0.020  1.377
 JN5  C1F  C1E   aromatic  1.404  0.020  1.404
 JN5  C1E  C1C   aromatic  1.395  0.020  1.395
 JN5  C1C  C1A   aromatic  1.381  0.020  1.381
 JN5  C1C  H1C   single    0.930  0.020  1.080
 JN5  C1B  C1A   aromatic  1.400  0.020  1.400
 JN5  C1A  H1A   single    0.930  0.020  1.080
 JN5  C1D  C1B   aromatic  1.383  0.020  1.383
 JN5  C1B  H1B   single    0.930  0.020  1.080
 JN5  C1F  C1D   aromatic  1.390  0.020  1.390
 JN5  C1D  H1D   single    0.930  0.020  1.080
 JN5  S1H  C1F   aromatic  1.730  0.020  1.730

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
 JN5  H1W   C1W  C1V  120.23  3.000
 JN5  H1W   C1W  C1X  120.36  3.000
 JN5  C1V   C1W  C1X  119.40  3.000
 JN5  H1X   C1X  C1Y  120.33  3.000
 JN5  H1X   C1X  C1W  121.20  3.000
 JN5  C1Y   C1X  C1W  118.47  3.000
 JN5  H1Y   C1Y  N1Z  116.63  3.000
 JN5  H1Y   C1Y  C1X  120.34  3.000
 JN5  N1Z   C1Y  C1X  123.03  3.000
 JN5  C2A   N1Z  C1Y  117.86  3.000
 JN5  H2A   C2A  C1V  119.50  3.000
 JN5  H2A   C2A  N1Z  116.32  3.000
 JN5  C1V   C2A  N1Z  124.19  3.000
 JN5  C1U   C1V  C2A  121.14  3.000
 JN5  C1U   C1V  C1W  121.78  3.000
 JN5  C2A   C1V  C1W  117.05  3.000
 JN5  H1UA  C1U  H1U  107.07  3.000
 JN5  H1UA  C1U  C1T  109.32  3.000
 JN5  H1U   C1U  C1T  109.65  3.000
 JN5  H1UA  C1U  C1V  110.26  3.000
 JN5  H1U   C1U  C1V  109.67  3.000
 JN5  C1T   C1U  C1V  110.80  3.000
 JN5  H1TA  C1T  H1T  106.83  3.000
 JN5  H1TA  C1T  N1S  111.05  3.000
 JN5  H1T   C1T  N1S  109.34  3.000
 JN5  H1TA  C1T  C1U  109.71  3.000
 JN5  H1T   C1T  C1U  109.73  3.000
 JN5  N1S   C1T  C1U  110.13  3.000
 JN5  HN1S  N1S  C2   115.99  3.000
 JN5  HN1S  N1S  C1T  118.25  3.000
 JN5  C2    N1S  C1T  124.27  3.000
 JN5  N1    C2   N3   125.00  3.000
 JN5  N3    C2   N1S  116.71  3.000
 JN5  N1    C2   N1S  118.29  3.000
 JN5  C4    N3   C2   116.98  3.000
 JN5  C6    N1   C2   116.43  3.000
 JN5  H6    C6   C5   120.08  3.000
 JN5  H6    C6   N1   116.48  3.000
 JN5  C5    C6   N1   123.43  3.000
 JN5  H5    C5   C4   123.67  3.000
 JN5  H5    C5   C6   121.22  3.000
 JN5  C4    C5   C6   115.10  3.000
 JN5  C1J   C4   C5   123.36  3.000
 JN5  C1J   C4   N3   113.56  3.000
 JN5  C5    C4   N3   123.05  3.000
 JN5  H1J   C1J  C1I  107.06  3.000
 JN5  H1J   C1J  C1K  107.49  3.000
 JN5  C1I   C1J  C1K  109.99  3.000
 JN5  H1J   C1J  C4   108.66  3.000
 JN5  C1K   C1J  C4   113.12  3.000
 JN5  C1I   C1J  C4   110.28  3.000
 JN5  N1L   C1K  C1J  180.00  3.000
 JN5  S1H   C1I  N1G  116.51  3.000
 JN5  N1G   C1I  C1J  123.48  3.000
 JN5  S1H   C1I  C1J  120.01  3.000
 JN5  C1E   N1G  C1I  110.86  3.000
 JN5  C1F   C1E  C1C  119.75  3.000
 JN5  C1C   C1E  N1G  125.42  3.000
 JN5  C1F   C1E  N1G  114.83  3.000
 JN5  H1C   C1C  C1A  121.39  3.000
 JN5  H1C   C1C  C1E  119.99  3.000
 JN5  C1A   C1C  C1E  118.62  3.000
 JN5  H1A   C1A  C1B  119.33  3.000
 JN5  H1A   C1A  C1C  119.64  3.000
 JN5  C1B   C1A  C1C  121.03  3.000
 JN5  H1B   C1B  C1D  119.34  3.000
 JN5  H1B   C1B  C1A  119.46  3.000
 JN5  C1D   C1B  C1A  121.20  3.000
 JN5  H1D   C1D  C1F  121.33  3.000
 JN5  H1D   C1D  C1B  121.04  3.000
 JN5  C1F   C1D  C1B  117.63  3.000
 JN5  S1H   C1F  C1D  128.93  3.000
 JN5  S1H   C1F  C1E  109.30  3.000
 JN5  C1D   C1F  C1E  121.77  3.000
 JN5  C1F   S1H  C1I   88.50  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
 JN5  CONST_01  N1Z   C2A  C1V  C1W    0.00   0.0  0
 JN5  CONST_02  N1Z   C1Y  C1X  C1W    0.00   0.0  0
 JN5  CONST_03  C2A   C1V  C1W  C1X    0.00   0.0  0
 JN5  CONST_04  C2A   N1Z  C1Y  C1X    0.00   0.0  0
 JN5  CONST_05  C1V   C1W  C1X  C1Y    0.00   0.0  0
 JN5  CONST_06  C1V   C2A  N1Z  C1Y    0.00   0.0  0
 JN5  CONST_07  C5    C6   N1   C2     0.00   0.0  0
 JN5  CONST_08  C5    C4   N3   C2     0.00   0.0  0
 JN5  CONST_09  C6    N1   C2   N3     0.00   0.0  0
 JN5  CONST_10  C6    C5   C4   N3     0.00   0.0  0
 JN5  CONST_11  C4    N3   C2   N1     0.00   0.0  0
 JN5  CONST_12  C4    C5   C6   N1     0.00   0.0  0
 JN5  CONST_13  C1E   C1F  S1H  C1I    0.00   0.0  0
 JN5  CONST_14  C1D   C1F  S1H  C1I  180.00   0.0  0
 JN5  CONST_15  C1F   C1E  N1G  C1I    0.00   0.0  0
 JN5  CONST_16  C1C   C1E  N1G  C1I  180.00   0.0  0
 JN5  CONST_17  C1F   S1H  C1I  N1G    0.00   0.0  0
 JN5  CONST_18  C1D   C1F  C1E  N1G  180.00   0.0  0
 JN5  CONST_19  S1H   C1F  C1E  N1G    0.00   0.0  0
 JN5  CONST_20  C1A   C1C  C1E  N1G  180.00   0.0  0
 JN5  CONST_21  S1H   C1I  N1G  C1E    0.00   0.0  0
 JN5  CONST_22  C1B   C1D  C1F  C1E    0.00   0.0  0
 JN5  CONST_23  C1B   C1A  C1C  C1E    0.00   0.0  0
 JN5  CONST_24  C1D   C1F  C1E  C1C    0.00   0.0  0
 JN5  CONST_25  S1H   C1F  C1E  C1C  180.00   0.0  0
 JN5  CONST_26  C1D   C1B  C1A  C1C    0.00   0.0  0
 JN5  CONST_27  C1F   C1E  C1C  C1A    0.00   0.0  0
 JN5  CONST_28  C1F   C1D  C1B  C1A    0.00   0.0  0
 JN5  CONST_29  S1H   C1F  C1D  C1B  180.00   0.0  0
 JN5  CONST_30  C1U   C1V  C1W  C1X  180.00   0.0  0
 JN5  CONST_31  C1U   C1V  C2A  N1Z  180.00   0.0  0
 JN5  CONST_32  C6    N1   C2   N1S  180.00   0.0  0
 JN5  CONST_33  C4    N3   C2   N1S  180.00   0.0  0
 JN5  CONST_34  C1J   C4   N3   C2   180.00   0.0  0
 JN5  CONST_35  C1J   C4   C5   C6   180.00   0.0  0
 JN5  CONST_36  C1F   S1H  C1I  C1J  180.00   0.0  0
 JN5  CONST_37  C1E   N1G  C1I  C1J  180.00   0.0  0
 JN5  CONST_38  H2A   C2A  C1V  C1W  180.00   0.0  0
 JN5  CONST_39  H1Y   C1Y  C1X  C1W  180.00   0.0  0
 JN5  CONST_40  H1W   C1W  C1X  C1Y  180.00   0.0  0
 JN5  CONST_41  H1X   C1X  C1Y  N1Z  180.00   0.0  0
 JN5  CONST_42  H6    C6   N1   C2   180.00   0.0  0
 JN5  CONST_43  H5    C5   C4   N3   180.00   0.0  0
 JN5  CONST_44  H1C   C1C  C1E  N1G    0.00   0.0  0
 JN5  CONST_45  H1D   C1D  C1F  C1E  180.00   0.0  0
 JN5  CONST_46  H1A   C1A  C1C  C1E  180.00   0.0  0
 JN5  CONST_47  H1B   C1B  C1A  C1C  180.00   0.0  0
 JN5  CONST_48  N1    C2   N1S  C1T    0.00   0.0  0
 JN5  CONST_49  N3    C2   N1S  C1T  180.00   0.0  0
 JN5  CONST_50  HN1S  N1S  C2   N3     0.00   0.0  0
 JN5  Var_01    C1T   C1U  C1V  C1W  -83.62  30.0  3
 JN5  Var_02    N1S   C1T  C1U  C1V  178.13  30.0  3
 JN5  Var_03    C2    N1S  C1T  C1U  164.57  30.0  2

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
 JN5  chir_01  C1J  C4  C1I  C1K  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
 JN5  plan-1  C1W   0.020
 JN5  plan-1  C1X   0.020
 JN5  plan-1  C1Y   0.020
 JN5  plan-1  N1Z   0.020
 JN5  plan-1  C2A   0.020
 JN5  plan-1  C1V   0.020
 JN5  plan-1  C1U   0.020
 JN5  plan-1  H1W   0.020
 JN5  plan-1  H1X   0.020
 JN5  plan-1  H1Y   0.020
 JN5  plan-1  H2A   0.020
 JN5  plan-2  N1S   0.020
 JN5  plan-2  C2    0.020
 JN5  plan-2  N3    0.020
 JN5  plan-2  N1    0.020
 JN5  plan-2  C6    0.020
 JN5  plan-2  C5    0.020
 JN5  plan-2  C4    0.020
 JN5  plan-2  C1J   0.020
 JN5  plan-2  H6    0.020
 JN5  plan-2  H5    0.020
 JN5  plan-3  C1J   0.020
 JN5  plan-3  C1I   0.020
 JN5  plan-3  N1G   0.020
 JN5  plan-3  C1E   0.020
 JN5  plan-3  C1C   0.020
 JN5  plan-3  C1A   0.020
 JN5  plan-3  C1B   0.020
 JN5  plan-3  C1D   0.020
 JN5  plan-3  C1F   0.020
 JN5  plan-3  S1H   0.020
 JN5  plan-3  H1C   0.020
 JN5  plan-3  H1A   0.020
 JN5  plan-3  H1B   0.020
 JN5  plan-3  H1D   0.020
 JN5  plan-4  C1T   0.020
 JN5  plan-4  N1S   0.020
 JN5  plan-4  C2    0.020
 JN5  plan-4  HN1S  0.020

