# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 14:02:21 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (1S,2S)-2-{4-[(dimethylamino)methyl]phenyl}-N-[6-(pyridin-3-yl)-1,3-benzothiazol-2-yl]cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)Cc1ccc(cc1)[C@H]2C[C@@H]2C(=O)Nc3sc4cc(ccc4n3)c5cccnc5
#
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
 29Z  29Z  (1S,2S)-2-{4-[(dimethylamino)methyl]phenyl}-N-[6-(pyridin-3-yl)-1,3-benzothiazol-2-yl]cyclopropanecarboxamide  ligand  55  31  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_29Z
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
 29Z  C1   C  CH3   0  -0.518    7.4241   2.3872  -2.0227
 29Z  N2   N  NT    0  -0.401    8.3691   1.3017  -1.8694
 29Z  C3   C  CH3   0  -0.520    9.6814   1.6844  -2.3445
 29Z  C4   C  CH2   0  -0.321    8.4243   0.8227  -0.5036
 29Z  C5   C  CR6   0   0.072    7.1547   0.1378  -0.0705
 29Z  C6   C  CR16  0  -0.268    6.5261  -0.7899  -0.8964
 29Z  C7   C  CR16  0  -0.309    5.3848  -1.4547  -0.4765
 29Z  C8   C  CR6   0   0.216    4.8349  -1.2197   0.7834
 29Z  C9   C  CR16  0  -0.339    5.4615  -0.2874   1.6067
 29Z  C10  C  CR16  0  -0.293    6.6001   0.3821   1.1813
 29Z  C11  C  CH1   0  -0.354    3.6142  -1.9571   1.1903
 29Z  C12  C  CH2   0  -0.447    3.2761  -2.2267   2.6126
 29Z  C13  C  CH1   0  -0.439    2.4674  -1.2133   1.8594
 29Z  C14  C  C     0   0.606    1.0921  -1.5726   1.4392
 29Z  O15  O  O     0  -0.432    0.7341  -2.7076   1.2191
 29Z  N16  N  NH1   0  -0.739    0.2657  -0.4755   1.3107
 29Z  C17  C  CR5   0   0.297   -1.0476  -0.4759   0.9253
 29Z  N18  N  N     0  -0.417   -1.7463  -1.4987   0.5914
 29Z  C19  C  CR56  0   0.360   -3.0265  -1.1245   0.2644
 29Z  C20  C  CR16  0  -0.298   -4.0420  -1.9850  -0.1467
 29Z  C21  C  CR16  0  -0.304   -5.2847  -1.4642  -0.4470
 29Z  C22  C  CR6   0   0.066   -5.5540  -0.0893  -0.3519
 29Z  C23  C  CR16  0  -0.331   -4.5437   0.7776   0.0563
 29Z  C24  C  CR56  0  -0.229   -3.3008   0.2483   0.3601
 29Z  S25  S  S2    0   0.215   -1.8709   1.0792   0.8813
 29Z  C26  C  CR6   0  -0.002   -6.8943   0.4276  -0.6796
 29Z  C27  C  CR16  0  -0.197   -7.6544  -0.1033  -1.7202
 29Z  C28  C  CR16  0  -0.315   -8.9099   0.4191  -1.9792
 29Z  C29  C  CR16  0  -0.071   -9.3702   1.4640  -1.1920
 29Z  N30  N  N     0  -0.398   -8.6632   1.9811  -0.1937
 29Z  C31  C  CR16  0  -0.101   -7.4652   1.4712   0.0509
 29Z  H1   H  HCH3  0   0.233    7.3637   2.6817  -3.0713
 29Z  H2   H  HCH3  0   0.236    6.4278   2.0761  -1.7083
 29Z  H3   H  HCH3  0   0.192    7.6992   3.2804  -1.4394
 29Z  H5   H  HCH3  0   0.191   10.1176   2.5266  -1.7852
 29Z  H6   H  HCH3  0   0.233   10.3690   0.8410  -2.2676
 29Z  H7   H  HCH3  0   0.233    9.6259   1.9775  -3.3936
 29Z  H8   H  HCH2  0   0.249    9.2467   0.1034  -0.4347
 29Z  H9   H  HCH2  0   0.208    8.6651   1.6289   0.2113
 29Z  H10  H  HCR6  0   0.244    6.9305  -0.9876  -1.8814
 29Z  H11  H  HCR6  0   0.249    4.9128  -2.1722  -1.1376
 29Z  H12  H  HCR6  0   0.248    5.0662  -0.0674   2.5918
 29Z  H13  H  HCR6  0   0.248    7.0656   1.1069   1.8393
 29Z  H14  H  HCH1  0   0.277    3.2997  -2.7183   0.4846
 29Z  H15  H  HCH2  0   0.277    2.8015  -3.1701   2.8482
 29Z  H16  H  HCH2  0   0.275    3.9354  -1.8452   3.3822
 29Z  H17  H  HCH1  0   0.299    2.6507  -0.1704   2.0929
 29Z  H18  H  HNH1  0   0.435    0.6751   0.4225   1.5212
 29Z  H19  H  HCR6  0   0.269   -3.8544  -3.0481  -0.2197
 29Z  H20  H  HCR6  0   0.262   -6.0761  -2.1401  -0.7453
 29Z  H21  H  HCR6  0   0.276   -4.7156   1.8445   0.1149
 29Z  H22  H  HCR6  0   0.272   -7.2625  -0.9054  -2.3331
 29Z  H23  H  HCR6  0   0.274   -9.5201   0.0298  -2.7825
 29Z  H24  H  HCR6  0   0.267  -10.3470   1.8979  -1.3734
 29Z  H25  H  HCR6  0   0.262   -6.9253   1.8997   0.8891

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
 29Z  C28  C27  aromatic  1.384  0.020  1.384
 29Z  C28  C29  aromatic  1.387  0.020  1.387
 29Z  C27  C26  aromatic  1.394  0.020  1.394
 29Z  C29  N30  aromatic  1.328  0.020  1.328
 29Z  C26  C22  single    1.473  0.020  1.473
 29Z  C26  C31  aromatic  1.396  0.020  1.396
 29Z  C21  C22  aromatic  1.404  0.020  1.404
 29Z  C21  C20  aromatic  1.381  0.020  1.381
 29Z  C22  C23  aromatic  1.392  0.020  1.392
 29Z  C20  C19  aromatic  1.393  0.020  1.393
 29Z  N30  C31  aromatic  1.325  0.020  1.325
 29Z  C23  C24  aromatic  1.385  0.020  1.385
 29Z  C19  C24  aromatic  1.403  0.020  1.403
 29Z  C19  N18  aromatic  1.373  0.020  1.373
 29Z  C24  S25  aromatic  1.734  0.020  1.734
 29Z  N18  C17  aromatic  1.283  0.020  1.283
 29Z  C17  S25  aromatic  1.760  0.020  1.760
 29Z  C17  N16  single    1.369  0.020  1.369
 29Z  N16  C14  single    1.380  0.020  1.380
 29Z  O15  C14  double    1.210  0.020  1.210
 29Z  C14  C13  single    1.482  0.020  1.482
 29Z  C12  C13  single    1.499  0.020  1.499
 29Z  C12  C11  single    1.487  0.020  1.487
 29Z  C13  C11  single    1.522  0.020  1.522
 29Z  C11  C8   single    1.483  0.020  1.483
 29Z  C9   C8   aromatic  1.393  0.020  1.393
 29Z  C9   C10  aromatic  1.388  0.020  1.388
 29Z  C8   C7   aromatic  1.395  0.020  1.395
 29Z  C10  C5   aromatic  1.391  0.020  1.391
 29Z  C7   C6   aromatic  1.386  0.020  1.386
 29Z  C5   C6   aromatic  1.392  0.020  1.392
 29Z  C5   C4   single    1.506  0.020  1.506
 29Z  C4   N2   single    1.448  0.020  1.448
 29Z  C1   N2   single    1.447  0.020  1.447
 29Z  N2   C3   single    1.447  0.020  1.447
 29Z  C1   H1   single    0.970  0.020  1.090
 29Z  C1   H2   single    0.970  0.020  1.090
 29Z  C1   H3   single    0.970  0.020  1.090
 29Z  C3   H5   single    0.970  0.020  1.090
 29Z  C3   H6   single    0.970  0.020  1.090
 29Z  C3   H7   single    0.970  0.020  1.090
 29Z  C4   H8   single    0.970  0.020  1.090
 29Z  C4   H9   single    0.970  0.020  1.090
 29Z  C6   H10  single    0.930  0.020  1.080
 29Z  C7   H11  single    0.930  0.020  1.080
 29Z  C9   H12  single    0.930  0.020  1.080
 29Z  C10  H13  single    0.930  0.020  1.080
 29Z  C11  H14  single    0.970  0.020  1.090
 29Z  C12  H15  single    0.970  0.020  1.090
 29Z  C12  H16  single    0.970  0.020  1.090
 29Z  C13  H17  single    0.970  0.020  1.090
 29Z  N16  H18  single    0.860  0.020  1.020
 29Z  C20  H19  single    0.930  0.020  1.080
 29Z  C21  H20  single    0.930  0.020  1.080
 29Z  C23  H21  single    0.930  0.020  1.080
 29Z  C27  H22  single    0.930  0.020  1.080
 29Z  C28  H23  single    0.930  0.020  1.080
 29Z  C29  H24  single    0.930  0.020  1.080
 29Z  C31  H25  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
 29Z  H3   C1   H2   107.87  3.000
 29Z  H3   C1   H1   107.69  3.000
 29Z  H2   C1   H1   107.68  3.000
 29Z  H3   C1   N2   112.89  3.000
 29Z  H2   C1   N2   110.62  3.000
 29Z  H1   C1   N2   109.90  3.000
 29Z  C4   N2   C3   111.25  3.000
 29Z  C3   N2   C1   111.04  3.000
 29Z  C4   N2   C1   111.89  3.000
 29Z  H7   C3   H6   107.91  3.000
 29Z  H7   C3   H5   107.64  3.000
 29Z  H6   C3   H5   107.81  3.000
 29Z  H7   C3   N2   109.92  3.000
 29Z  H6   C3   N2   110.12  3.000
 29Z  H5   C3   N2   113.25  3.000
 29Z  H9   C4   H8   105.97  3.000
 29Z  H9   C4   C5   109.25  3.000
 29Z  H8   C4   C5   108.44  3.000
 29Z  H9   C4   N2   112.18  3.000
 29Z  H8   C4   N2   107.77  3.000
 29Z  C5   C4   N2   112.92  3.000
 29Z  C10  C5   C6   118.10  3.000
 29Z  C6   C5   C4   120.87  3.000
 29Z  C10  C5   C4   121.00  3.000
 29Z  H10  C6   C7   119.70  3.000
 29Z  H10  C6   C5   119.51  3.000
 29Z  C7   C6   C5   120.78  3.000
 29Z  H11  C7   C8   119.40  3.000
 29Z  H11  C7   C6   119.43  3.000
 29Z  C8   C7   C6   121.17  3.000
 29Z  C11  C8   C9   122.75  3.000
 29Z  C9   C8   C7   118.00  3.000
 29Z  C11  C8   C7   119.25  3.000
 29Z  H12  C9   C10  118.68  3.000
 29Z  H12  C9   C8   120.60  3.000
 29Z  C10  C9   C8   120.72  3.000
 29Z  H13  C10  C9   119.26  3.000
 29Z  H13  C10  C5   119.52  3.000
 29Z  C9   C10  C5   121.22  3.000
 29Z  H14  C11  C13  114.24  3.000
 29Z  H14  C11  C12  115.42  3.000
 29Z  C13  C11  C12   59.78  3.000
 29Z  H14  C11  C8   114.15  3.000
 29Z  C13  C11  C8   119.86  3.000
 29Z  C12  C11  C8   122.67  3.000
 29Z  H16  C12  H15  114.80  3.000
 29Z  H16  C12  C13  116.57  3.000
 29Z  H15  C12  C13  117.52  3.000
 29Z  H16  C12  C11  118.54  3.000
 29Z  H15  C12  C11  117.79  3.000
 29Z  C13  C12  C11   61.28  3.000
 29Z  H17  C13  C14  116.81  3.000
 29Z  H17  C13  C12  116.79  3.000
 29Z  C14  C13  C12  118.62  3.000
 29Z  H17  C13  C11  115.93  3.000
 29Z  C12  C13  C11   58.94  3.000
 29Z  C14  C13  C11  117.13  3.000
 29Z  N16  C14  O15  123.48  3.000
 29Z  O15  C14  C13  123.60  3.000
 29Z  N16  C14  C13  112.92  3.000
 29Z  H18  N16  C17  116.63  3.000
 29Z  H18  N16  C14  116.44  3.000
 29Z  C17  N16  C14  126.93  3.000
 29Z  S25  C17  N18  116.30  3.000
 29Z  S25  C17  N16  117.10  3.000
 29Z  N18  C17  N16  126.59  3.000
 29Z  C19  N18  C17  110.64  3.000
 29Z  C24  C19  C20  118.82  3.000
 29Z  C24  C19  N18  115.63  3.000
 29Z  C20  C19  N18  125.56  3.000
 29Z  H19  C20  C21  120.80  3.000
 29Z  H19  C20  C19  120.03  3.000
 29Z  C21  C20  C19  119.16  3.000
 29Z  H20  C21  C22  119.32  3.000
 29Z  H20  C21  C20  118.84  3.000
 29Z  C22  C21  C20  121.82  3.000
 29Z  C26  C22  C23  120.45  3.000
 29Z  C23  C22  C21  119.36  3.000
 29Z  C26  C22  C21  120.19  3.000
 29Z  H21  C23  C24  120.50  3.000
 29Z  H21  C23  C22  120.96  3.000
 29Z  C24  C23  C22  118.53  3.000
 29Z  S25  C24  C23  128.53  3.000
 29Z  S25  C24  C19  109.16  3.000
 29Z  C23  C24  C19  122.31  3.000
 29Z  C24  S25  C17   88.27  3.000
 29Z  C31  C26  C27  116.90  3.000
 29Z  C31  C26  C22  121.19  3.000
 29Z  C27  C26  C22  121.91  3.000
 29Z  H22  C27  C28  120.13  3.000
 29Z  H22  C27  C26  120.49  3.000
 29Z  C28  C27  C26  119.38  3.000
 29Z  H23  C28  C29  120.37  3.000
 29Z  H23  C28  C27  120.99  3.000
 29Z  C29  C28  C27  118.63  3.000
 29Z  H24  C29  N30  116.71  3.000
 29Z  H24  C29  C28  120.37  3.000
 29Z  N30  C29  C28  122.91  3.000
 29Z  C31  N30  C29  118.05  3.000
 29Z  H25  C31  N30  116.14  3.000
 29Z  H25  C31  C26  119.73  3.000
 29Z  N30  C31  C26  124.12  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
 29Z  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 29Z  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 29Z  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 29Z  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 29Z  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 29Z  CONST_06  C10  C5   C6   C7      0.00   0.0  0
 29Z  CONST_07  C20  C19  N18  C17   180.00   0.0  0
 29Z  CONST_08  C24  C19  N18  C17     0.00   0.0  0
 29Z  CONST_09  C23  C24  S25  C17   180.00   0.0  0
 29Z  CONST_10  C19  C24  S25  C17     0.00   0.0  0
 29Z  CONST_11  C21  C20  C19  N18   180.00   0.0  0
 29Z  CONST_12  C23  C24  C19  N18   180.00   0.0  0
 29Z  CONST_13  S25  C24  C19  N18     0.00   0.0  0
 29Z  CONST_14  C24  S25  C17  N18     0.00   0.0  0
 29Z  CONST_15  C22  C21  C20  C19     0.00   0.0  0
 29Z  CONST_16  C22  C23  C24  C19     0.00   0.0  0
 29Z  CONST_17  S25  C17  N18  C19     0.00   0.0  0
 29Z  CONST_18  C26  C22  C21  C20   180.00   0.0  0
 29Z  CONST_19  C23  C22  C21  C20     0.00   0.0  0
 29Z  CONST_20  C23  C24  C19  C20     0.00   0.0  0
 29Z  CONST_21  S25  C24  C19  C20   180.00   0.0  0
 29Z  CONST_24  C24  C23  C22  C21     0.00   0.0  0
 29Z  CONST_25  C24  C19  C20  C21     0.00   0.0  0
 29Z  CONST_26  C28  C27  C26  C22   180.00   0.0  0
 29Z  CONST_27  N30  C31  C26  C22   180.00   0.0  0
 29Z  CONST_28  S25  C24  C23  C22   180.00   0.0  0
 29Z  CONST_31  C26  C22  C23  C24   180.00   0.0  0
 29Z  CONST_32  C29  C28  C27  C26     0.00   0.0  0
 29Z  CONST_33  C29  N30  C31  C26     0.00   0.0  0
 29Z  CONST_34  N30  C29  C28  C27     0.00   0.0  0
 29Z  CONST_35  N30  C31  C26  C27     0.00   0.0  0
 29Z  CONST_36  C31  C26  C27  C28     0.00   0.0  0
 29Z  CONST_37  C31  N30  C29  C28     0.00   0.0  0
 29Z  CONST_38  C11  C8   C7   C6    180.00   0.0  0
 29Z  CONST_39  C11  C8   C9   C10   180.00   0.0  0
 29Z  CONST_40  C9   C10  C5   C4    180.00   0.0  0
 29Z  CONST_41  C7   C6   C5   C4    180.00   0.0  0
 29Z  CONST_42  C19  N18  C17  N16   180.00   0.0  0
 29Z  CONST_43  C24  S25  C17  N16   180.00   0.0  0
 29Z  CONST_44  H12  C9   C10  C5    180.00   0.0  0
 29Z  CONST_45  H11  C7   C6   C5    180.00   0.0  0
 29Z  CONST_46  H13  C10  C5   C6    180.00   0.0  0
 29Z  CONST_47  H10  C6   C7   C8    180.00   0.0  0
 29Z  CONST_48  H19  C20  C19  N18     0.00   0.0  0
 29Z  CONST_49  H20  C21  C20  C19   180.00   0.0  0
 29Z  CONST_50  H21  C23  C24  C19   180.00   0.0  0
 29Z  CONST_51  H22  C27  C26  C22     0.00   0.0  0
 29Z  CONST_52  H25  C31  C26  C22     0.00   0.0  0
 29Z  CONST_53  H23  C28  C27  C26   180.00   0.0  0
 29Z  CONST_54  H24  C29  C28  C27   180.00   0.0  0
 29Z  CONST_55  C17  N16  C14  C13   180.00   0.0  0
 29Z  CONST_56  N18  C17  N16  C14     0.00   0.0  0
 29Z  CONST_57  S25  C17  N16  C14   180.00   0.0  0
 29Z  CONST_58  H18  N16  C17  N18   180.00   0.0  0
 29Z  CONST_59  C17  N16  C14  O15     0.00   0.0  0
 29Z  Var_01    C12  C11  C8   C7    153.92  30.0  2
 29Z  Var_02    C13  C12  C11  C8    108.11  30.0  1
 29Z  Var_03    C10  C5   C4   N2   -136.73  30.0  3
 29Z  Var_04    N16  C14  C13  C11  -139.31  30.0  1
 29Z  Var_05    C5   C4   N2   C1     67.72  30.0  1
 29Z  Var_06    H5   C3   N2   C1     61.97  30.0  3
 29Z  Var_07    H1   C1   N2   C3     58.47  30.0  3

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
 29Z  chir_01  C11  C12  C13  C8   both
 29Z  chir_02  C13  C11  C12  C14  both

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
 29Z  plan-1  C4   0.020
 29Z  plan-1  C5   0.020
 29Z  plan-1  C6   0.020
 29Z  plan-1  C7   0.020
 29Z  plan-1  C8   0.020
 29Z  plan-1  C9   0.020
 29Z  plan-1  C10  0.020
 29Z  plan-1  C11  0.020
 29Z  plan-1  H10  0.020
 29Z  plan-1  H11  0.020
 29Z  plan-1  H12  0.020
 29Z  plan-1  H13  0.020
 29Z  plan-2  C22  0.020
 29Z  plan-2  C26  0.020
 29Z  plan-2  C27  0.020
 29Z  plan-2  C28  0.020
 29Z  plan-2  C29  0.020
 29Z  plan-2  N30  0.020
 29Z  plan-2  C31  0.020
 29Z  plan-2  H22  0.020
 29Z  plan-2  H23  0.020
 29Z  plan-2  H24  0.020
 29Z  plan-2  H25  0.020
 29Z  plan-3  N16  0.020
 29Z  plan-3  C17  0.020
 29Z  plan-3  N18  0.020
 29Z  plan-3  C19  0.020
 29Z  plan-3  C20  0.020
 29Z  plan-3  C21  0.020
 29Z  plan-3  C22  0.020
 29Z  plan-3  C23  0.020
 29Z  plan-3  C24  0.020
 29Z  plan-3  S25  0.020
 29Z  plan-3  C26  0.020
 29Z  plan-3  H19  0.020
 29Z  plan-3  H20  0.020
 29Z  plan-3  H21  0.020
 29Z  plan-4  C13  0.020
 29Z  plan-4  C14  0.020
 29Z  plan-4  O15  0.020
 29Z  plan-4  N16  0.020
 29Z  plan-4  C17  0.020
 29Z  plan-4  H18  0.020

