# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:52:39 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-[4-(1~{H}-indol-3-ylmethyl)piperazin-1-yl]-1,3-benzothiazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCN1Cc2c[nH]c3ccccc23)c4sc5ccccc5n4
#
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
 JMK  JMK  2-[4-(1~{H}-indol-3-ylmethyl)piperazin-1-yl]-1,3-benzothiazole  ligand  45  25  .  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_JMK
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
 JMK  C1   C  CH2   0  -0.350   2.7471   1.4337  -1.4522
 JMK  C3   C  CR5   0  -0.016   3.8734   1.1710  -0.5104
 JMK  C11  C  CR16  0  -0.366   3.9214  -1.4258  -0.2668
 JMK  C12  C  CR5   0   0.335  -2.4354  -0.1422  -0.2016
 JMK  C16  C  CH2   0  -0.299  -0.6384  -0.1169  -1.8099
 JMK  C17  C  CH2   0  -0.313  -0.1408   0.1688   0.5735
 JMK  C18  C  CR56  0   0.371  -4.5642  -0.6087  -0.5208
 JMK  C19  C  CR56  0  -0.241  -4.6083  -0.4914   0.8785
 JMK  C20  C  CH2   0  -0.289   0.5257   0.8033  -2.1172
 JMK  C21  C  CH2   0  -0.277   1.0030   1.0839   0.1830
 JMK  C22  C  CR16  0  -0.327  -5.7413  -0.9062  -1.2070
 JMK  C23  C  CR16  0  -0.284  -5.7794  -0.6629   1.5990
 JMK  C24  C  CR16  0  -0.257  -6.9158  -1.0794  -0.4928
 JMK  C25  C  CR16  0  -0.280  -6.9394  -0.9600   0.8974
 JMK  N2   N  NT    0  -0.414   1.5470   0.6970  -1.0990
 JMK  C4   C  CR56  0   0.033   4.3427  -0.1064  -0.0594
 JMK  C5   C  CR56  0   0.350   5.4614   0.1346   0.7702
 JMK  N6   N  NR15  0  -0.687   5.6497   1.4849   0.8190
 JMK  C7   C  CR15  0  -0.085   4.6963   2.1010   0.0577
 JMK  C8   C  CR16  0  -0.308   6.1707  -0.9003   1.3792
 JMK  C9   C  CR16  0  -0.284   5.7384  -2.1919   1.1473
 JMK  C10  C  CR16  0  -0.270   4.6227  -2.4533   0.3337
 JMK  N13  N  NT    0  -0.494  -1.1489   0.1369  -0.4709
 JMK  N14  N  N     0  -0.491  -3.3340  -0.4165  -1.0945
 JMK  S15  S  S2    0   0.157  -3.0152  -0.1248   1.4709
 JMK  H1   H  HCH2  0   0.209   2.5663   2.5209  -1.5085
 JMK  H2   H  HCH2  0   0.241   3.0299   1.1192  -2.4626
 JMK  H3   H  HCR6  0   0.238   3.0501  -1.6266  -0.8760
 JMK  H4   H  HCH2  0   0.268  -1.4345   0.0470  -2.5320
 JMK  H5   H  HCH2  0   0.238  -0.3188  -1.1622  -1.8930
 JMK  H6   H  HCH2  0   0.245   0.2397  -0.8408   0.7670
 JMK  H7   H  HCH2  0   0.265  -0.5725   0.5474   1.5010
 JMK  H8   H  HCH2  0   0.248   0.9436   0.5084  -3.0821
 JMK  H9   H  HCH2  0   0.201   0.1554   1.8372  -2.2251
 JMK  H10  H  HCH2  0   0.202   0.6479   2.1291   0.1796
 JMK  H11  H  HCH2  0   0.257   1.7749   1.0053   0.9495
 JMK  H12  H  HCR6  0   0.256  -5.7268  -0.9971  -2.2855
 JMK  H13  H  HCR6  0   0.269  -5.7932  -0.5702   2.6771
 JMK  H14  H  HCR6  0   0.256  -7.8303  -1.3117  -1.0229
 JMK  H15  H  HCR6  0   0.257  -7.8670  -1.1012   1.4359
 JMK  H17  H  HNR5  0   0.407   6.3730   1.9600   1.3318
 JMK  H18  H  HCR5  0   0.281   4.6759   3.1763  -0.0309
 JMK  H19  H  HCR6  0   0.257   7.0280  -0.7022   2.0102
 JMK  H20  H  HCR6  0   0.247   6.2677  -3.0181   1.6047
 JMK  H21  H  HCR6  0   0.243   4.3072  -3.4778   0.1830

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
 JMK  C8   C5   aromatic  1.395  0.020  1.395
 JMK  C8   C9   aromatic  1.382  0.020  1.382
 JMK  N6   C5   aromatic  1.364  0.020  1.364
 JMK  N6   C7   aromatic  1.367  0.020  1.367
 JMK  C5   C4   aromatic  1.413  0.020  1.413
 JMK  C9   C10  aromatic  1.405  0.020  1.405
 JMK  C7   C3   aromatic  1.366  0.020  1.366
 JMK  C4   C3   aromatic  1.434  0.020  1.434
 JMK  C4   C11  aromatic  1.400  0.020  1.400
 JMK  C3   C1   single    1.491  0.020  1.491
 JMK  C10  C11  aromatic  1.381  0.020  1.381
 JMK  C20  C16  single    1.515  0.020  1.515
 JMK  C20  N2   single    1.446  0.020  1.446
 JMK  C1   N2   single    1.452  0.020  1.452
 JMK  C16  N13  single    1.455  0.020  1.455
 JMK  N2   C21  single    1.445  0.020  1.445
 JMK  C21  C17  single    1.516  0.020  1.516
 JMK  N14  C18  aromatic  1.371  0.020  1.371
 JMK  N14  C12  aromatic  1.296  0.020  1.296
 JMK  C22  C18  aromatic  1.395  0.020  1.395
 JMK  C22  C24  aromatic  1.386  0.020  1.386
 JMK  C18  C19  aromatic  1.405  0.020  1.405
 JMK  C12  N13  single    1.344  0.020  1.344
 JMK  C12  S15  aromatic  1.770  0.020  1.770
 JMK  N13  C17  single    1.452  0.020  1.452
 JMK  C24  C25  aromatic  1.396  0.020  1.396
 JMK  C19  S15  aromatic  1.739  0.020  1.739
 JMK  C19  C23  aromatic  1.386  0.020  1.386
 JMK  C25  C23  aromatic  1.388  0.020  1.388
 JMK  C1   H1   single    0.970  0.020  1.090
 JMK  C1   H2   single    0.970  0.020  1.090
 JMK  C11  H3   single    0.930  0.020  1.080
 JMK  C16  H4   single    0.970  0.020  1.090
 JMK  C16  H5   single    0.970  0.020  1.090
 JMK  C17  H6   single    0.970  0.020  1.090
 JMK  C17  H7   single    0.970  0.020  1.090
 JMK  C20  H8   single    0.970  0.020  1.090
 JMK  C20  H9   single    0.970  0.020  1.090
 JMK  C21  H10  single    0.970  0.020  1.090
 JMK  C21  H11  single    0.970  0.020  1.090
 JMK  C22  H12  single    0.930  0.020  1.080
 JMK  C23  H13  single    0.930  0.020  1.080
 JMK  C24  H14  single    0.930  0.020  1.080
 JMK  C25  H15  single    0.930  0.020  1.080
 JMK  N6   H17  single    0.860  0.020  1.020
 JMK  C7   H18  single    0.930  0.020  1.080
 JMK  C8   H19  single    0.930  0.020  1.080
 JMK  C9   H20  single    0.930  0.020  1.080
 JMK  C10  H21  single    0.930  0.020  1.080

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
 JMK  H2   C1   H1   106.15  3.000
 JMK  H2   C1   N2   106.99  3.000
 JMK  H1   C1   N2   112.14  3.000
 JMK  H2   C1   C3   109.69  3.000
 JMK  H1   C1   C3   109.23  3.000
 JMK  N2   C1   C3   112.41  3.000
 JMK  C7   C3   C4   106.18  3.000
 JMK  C4   C3   C1   127.07  3.000
 JMK  C7   C3   C1   126.71  3.000
 JMK  H3   C11  C10  121.03  3.000
 JMK  H3   C11  C4   120.04  3.000
 JMK  C10  C11  C4   118.93  3.000
 JMK  S15  C12  N14  115.21  3.000
 JMK  S15  C12  N13  120.06  3.000
 JMK  N14  C12  N13  124.73  3.000
 JMK  H5   C16  H4   107.87  3.000
 JMK  H5   C16  N13  109.78  3.000
 JMK  H4   C16  N13  109.14  3.000
 JMK  H5   C16  C20  109.85  3.000
 JMK  H4   C16  C20  109.65  3.000
 JMK  N13  C16  C20  110.50  3.000
 JMK  H7   C17  H6   107.88  3.000
 JMK  H7   C17  N13  110.14  3.000
 JMK  H6   C17  N13  110.35  3.000
 JMK  H7   C17  C21  107.94  3.000
 JMK  H6   C17  C21  109.85  3.000
 JMK  N13  C17  C21  110.60  3.000
 JMK  N14  C18  C22  125.55  3.000
 JMK  C22  C18  C19  118.78  3.000
 JMK  N14  C18  C19  115.67  3.000
 JMK  S15  C19  C23  128.56  3.000
 JMK  C23  C19  C18  122.28  3.000
 JMK  S15  C19  C18  109.16  3.000
 JMK  H9   C20  H8   107.15  3.000
 JMK  H9   C20  N2   112.01  3.000
 JMK  H8   C20  N2   109.40  3.000
 JMK  H9   C20  C16  109.33  3.000
 JMK  H8   C20  C16  108.01  3.000
 JMK  N2   C20  C16  110.80  3.000
 JMK  H11  C21  H10  107.34  3.000
 JMK  H11  C21  N2   109.74  3.000
 JMK  H10  C21  N2   111.82  3.000
 JMK  H11  C21  C17  108.02  3.000
 JMK  H10  C21  C17  109.25  3.000
 JMK  N2   C21  C17  110.54  3.000
 JMK  H12  C22  C24  120.96  3.000
 JMK  H12  C22  C18  119.79  3.000
 JMK  C24  C22  C18  119.25  3.000
 JMK  H13  C23  C25  120.75  3.000
 JMK  H13  C23  C19  121.21  3.000
 JMK  C25  C23  C19  118.04  3.000
 JMK  H14  C24  C25  119.48  3.000
 JMK  H14  C24  C22  119.39  3.000
 JMK  C25  C24  C22  121.14  3.000
 JMK  H15  C25  C24  119.94  3.000
 JMK  H15  C25  C23  119.54  3.000
 JMK  C24  C25  C23  120.52  3.000
 JMK  C21  N2   C20  109.82  3.000
 JMK  C21  N2   C1   113.02  3.000
 JMK  C20  N2   C1   112.04  3.000
 JMK  C5   C4   C11  119.06  3.000
 JMK  C11  C4   C3   133.97  3.000
 JMK  C5   C4   C3   106.97  3.000
 JMK  C8   C5   N6   130.44  3.000
 JMK  N6   C5   C4   107.40  3.000
 JMK  C8   C5   C4   122.16  3.000
 JMK  H17  N6   C7   124.93  3.000
 JMK  H17  N6   C5   125.80  3.000
 JMK  C7   N6   C5   109.27  3.000
 JMK  H18  C7   N6   120.53  3.000
 JMK  H18  C7   C3   129.28  3.000
 JMK  N6   C7   C3   110.18  3.000
 JMK  H19  C8   C9   121.10  3.000
 JMK  H19  C8   C5   121.43  3.000
 JMK  C9   C8   C5   117.47  3.000
 JMK  H20  C9   C10  119.40  3.000
 JMK  H20  C9   C8   119.31  3.000
 JMK  C10  C9   C8   121.29  3.000
 JMK  H21  C10  C9   119.21  3.000
 JMK  H21  C10  C11  119.70  3.000
 JMK  C9   C10  C11  121.09  3.000
 JMK  C17  N13  C16  114.96  3.000
 JMK  C17  N13  C12  121.68  3.000
 JMK  C16  N13  C12  118.94  3.000
 JMK  C18  N14  C12  111.32  3.000
 JMK  C19  S15  C12   88.63  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
 JMK  CONST_01  C5   N6   C7   C3      0.00   0.0  0
 JMK  CONST_02  C8   C5   C4   C3    180.00   0.0  0
 JMK  CONST_03  N6   C5   C4   C3      0.00   0.0  0
 JMK  CONST_04  C10  C11  C4   C3    180.00   0.0  0
 JMK  CONST_05  C8   C5   C4   C11     0.00   0.0  0
 JMK  CONST_06  N6   C5   C4   C11   180.00   0.0  0
 JMK  CONST_07  C7   C3   C4   C11   180.00   0.0  0
 JMK  CONST_08  C8   C9   C10  C11     0.00   0.0  0
 JMK  CONST_09  C22  C18  N14  C12   180.00   0.0  0
 JMK  CONST_10  C19  C18  N14  C12     0.00   0.0  0
 JMK  CONST_11  C18  C19  S15  C12     0.00   0.0  0
 JMK  CONST_12  C23  C19  S15  C12   180.00   0.0  0
 JMK  CONST_13  S15  C12  N14  C18     0.00   0.0  0
 JMK  CONST_14  C25  C24  C22  C18     0.00   0.0  0
 JMK  CONST_15  C25  C23  C19  C18     0.00   0.0  0
 JMK  CONST_16  C24  C22  C18  C19     0.00   0.0  0
 JMK  CONST_17  N14  C12  S15  C19     0.00   0.0  0
 JMK  CONST_18  C24  C25  C23  C19     0.00   0.0  0
 JMK  CONST_19  S15  C19  C18  C22   180.00   0.0  0
 JMK  CONST_20  C23  C19  C18  C22     0.00   0.0  0
 JMK  CONST_21  C23  C25  C24  C22     0.00   0.0  0
 JMK  CONST_22  N14  C18  C19  C23   180.00   0.0  0
 JMK  CONST_23  N14  C18  C22  C24   180.00   0.0  0
 JMK  CONST_24  S15  C19  C23  C25   180.00   0.0  0
 JMK  CONST_25  C9   C8   C5   C4      0.00   0.0  0
 JMK  CONST_26  C7   N6   C5   C4      0.00   0.0  0
 JMK  CONST_27  N6   C7   C3   C4      0.00   0.0  0
 JMK  CONST_28  C9   C10  C11  C4      0.00   0.0  0
 JMK  CONST_29  C10  C9   C8   C5      0.00   0.0  0
 JMK  CONST_30  C7   C3   C4   C5      0.00   0.0  0
 JMK  CONST_31  C10  C11  C4   C5      0.00   0.0  0
 JMK  CONST_32  C9   C8   C5   N6    180.00   0.0  0
 JMK  CONST_33  C8   C5   N6   C7    180.00   0.0  0
 JMK  CONST_34  S15  C19  C18  N14     0.00   0.0  0
 JMK  CONST_35  N13  C12  N14  C18   180.00   0.0  0
 JMK  CONST_36  N13  C12  S15  C19   180.00   0.0  0
 JMK  CONST_37  N6   C7   C3   C1    180.00   0.0  0
 JMK  CONST_38  C5   C4   C3   C1    180.00   0.0  0
 JMK  CONST_39  C11  C4   C3   C1      0.00   0.0  0
 JMK  CONST_40  H17  N6   C7   C3    180.00   0.0  0
 JMK  CONST_41  H3   C11  C4   C3      0.00   0.0  0
 JMK  CONST_42  H20  C9   C10  C11   180.00   0.0  0
 JMK  CONST_43  H14  C24  C22  C18   180.00   0.0  0
 JMK  CONST_44  H13  C23  C19  C18   180.00   0.0  0
 JMK  CONST_45  H12  C22  C18  C19   180.00   0.0  0
 JMK  CONST_46  H15  C25  C23  C19   180.00   0.0  0
 JMK  CONST_47  H19  C8   C5   C4    180.00   0.0  0
 JMK  CONST_48  H18  C7   C3   C4    180.00   0.0  0
 JMK  CONST_49  H21  C10  C11  C4    180.00   0.0  0
 JMK  Var_01    C20  C16  N13  C12   153.39  30.0  1
 JMK  Var_02    C21  C17  N13  C12  -153.78  30.0  1
 JMK  Var_03    C21  N2   C20  C16   -60.96  30.0  1
 JMK  Var_04    N14  C12  N13  C16   -12.08  30.0  3
 JMK  Var_05    C20  N2   C21  C17    61.07  30.0  1
 JMK  Var_06    N13  C16  C20  N2     54.25  30.0  1
 JMK  Var_07    N13  C17  C21  N2    -54.74  30.0  1
 JMK  Var_08    C7   C3   C1   N2   -133.98  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
 JMK  plan-1  C1   0.020
 JMK  plan-1  C3   0.020
 JMK  plan-1  C11  0.020
 JMK  plan-1  C4   0.020
 JMK  plan-1  C5   0.020
 JMK  plan-1  N6   0.020
 JMK  plan-1  C7   0.020
 JMK  plan-1  C8   0.020
 JMK  plan-1  C9   0.020
 JMK  plan-1  C10  0.020
 JMK  plan-1  H3   0.020
 JMK  plan-1  H17  0.020
 JMK  plan-1  H18  0.020
 JMK  plan-1  H19  0.020
 JMK  plan-1  H20  0.020
 JMK  plan-1  H21  0.020
 JMK  plan-2  C12  0.020
 JMK  plan-2  C18  0.020
 JMK  plan-2  C19  0.020
 JMK  plan-2  C22  0.020
 JMK  plan-2  C23  0.020
 JMK  plan-2  C24  0.020
 JMK  plan-2  C25  0.020
 JMK  plan-2  N13  0.020
 JMK  plan-2  N14  0.020
 JMK  plan-2  S15  0.020
 JMK  plan-2  H12  0.020
 JMK  plan-2  H13  0.020
 JMK  plan-2  H14  0.020
 JMK  plan-2  H15  0.020

