# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 12:29:08 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (1S,2S)-2-{4-[(dimethylamino)methyl]phenyl}-N-[6-(1H-pyrazol-4-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)c5c[nH]nc5
#
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
 29Y  29Y  (1S,2S)-2-{4-[(dimethylamino)methyl]phenyl}-N-[6-(1H-pyrazol-4-yl)-1,3-benzothiazol-2-yl]cyclopropanecarboxamide  ligand  53  30  .  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_29Y
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
 29Y  C1   C  CH3   0  -0.519    9.2869   1.1838   0.3465
 29Y  N2   N  NT    0  -0.397    8.9462   0.0318   1.1532
 29Y  C3   C  CH3   0  -0.521    9.9745  -0.2421   2.1334
 29Y  C4   C  CH2   0  -0.338    7.6517   0.1841   1.7913
 29Y  C5   C  CR6   0   0.086    6.5229   0.2274   0.7975
 29Y  C6   C  CR16  0  -0.293    5.6934   1.3365   0.6916
 29Y  C7   C  CR16  0  -0.302    4.6489   1.3623  -0.2230
 29Y  C8   C  CR6   0   0.190    4.4037   0.2780  -1.0604
 29Y  C9   C  CR16  0  -0.333    5.2423  -0.8330  -0.9590
 29Y  C10  C  CR16  0  -0.265    6.2848  -0.8547  -0.0473
 29Y  C11  C  CH1   0  -0.338    3.2545   0.3388  -1.9968
 29Y  C13  C  CH2   0  -0.454    3.0351  -0.6297  -3.1006
 29Y  C14  C  CH1   0  -0.433    2.1518  -0.7095  -1.8930
 29Y  C16  C  C     0   0.601    0.7563  -0.2182  -1.9845
 29Y  O17  O  O     0  -0.434    0.3889   0.6109  -2.7868
 29Y  N18  N  NH1   0  -0.738   -0.0744  -0.7817  -1.0391
 29Y  C19  C  CR5   0   0.294   -1.3879  -0.4688  -0.8083
 29Y  N20  N  N     0  -0.416   -2.0995   0.3765  -1.4588
 29Y  C21  C  CR56  0   0.348   -3.3681   0.4464  -0.9349
 29Y  C22  C  CR16  0  -0.292   -4.3951   1.2677  -1.3952
 29Y  C23  C  CR16  0  -0.334   -5.6207   1.2356  -0.7620
 29Y  C24  C  CR6   0   0.098   -5.8713   0.3978   0.3390
 29Y  C25  C  CR16  0  -0.368   -4.8479  -0.4271   0.8013
 29Y  C26  C  CR56  0  -0.220   -3.6205  -0.3910   0.1611
 29Y  S27  S  S2    0   0.208   -2.1859  -1.2948   0.5266
 29Y  C28  C  CR5   0  -0.098   -7.1784   0.3911   0.9911
 29Y  C29  C  CR15  0  -0.012   -8.2686   1.2012   0.7283
 29Y  N30  N  NR15  0  -0.426   -9.2356   0.8290   1.5764
 29Y  N32  N  N     0  -0.260   -8.8755  -0.1638   2.3797
 29Y  C33  C  CR15  0  -0.117   -7.6328  -0.4400   2.0395
 29Y  H1   H  HCH3  0   0.233   10.2583   1.0306  -0.1251
 29Y  H2   H  HCH3  0   0.238    8.5525   1.3272  -0.4460
 29Y  H3   H  HCH3  0   0.190    9.3400   2.1179   0.9289
 29Y  H5   H  HCH3  0   0.191   10.1033   0.5673   2.8697
 29Y  H6   H  HCH3  0   0.233    9.7358  -1.1547   2.6818
 29Y  H7   H  HCH3  0   0.234   10.9335  -0.3912   1.6356
 29Y  H8   H  HCH2  0   0.247    7.5085  -0.6705   2.4596
 29Y  H9   H  HCH2  0   0.209    7.6108   1.0844   2.4285
 29Y  H10  H  HCR6  0   0.248    5.8639   2.1955   1.3301
 29Y  H11  H  HCR6  0   0.249    4.0166   2.2402  -0.2843
 29Y  H13  H  HCR6  0   0.247    5.0876  -1.6950  -1.5969
 29Y  H14  H  HCR6  0   0.245    6.9260  -1.7263   0.0076
 29Y  H12  H  HCH1  0   0.279    2.8902   1.3433  -2.1834
 29Y  H16  H  HCH2  0   0.277    2.5974  -0.2512  -4.0148
 29Y  H17  H  HCH2  0   0.276    3.7403  -1.4388  -3.2401
 29Y  H15  H  HCH1  0   0.298    2.3411  -1.5193  -1.1975
 29Y  H18  H  HNH1  0   0.434    0.3409  -1.4686  -0.4272
 29Y  H19  H  HCR6  0   0.266   -4.2293   1.9219  -2.2409
 29Y  H20  H  HCR6  0   0.250   -6.4075   1.8784  -1.1347
 29Y  H21  H  HCR6  0   0.265   -4.9980  -1.0831   1.6484
 29Y  H22  H  HCR5  0   0.291   -8.4192   1.9997   0.0203
 29Y  H31  H  HNR5  0   0.425  -10.1604   1.2228   1.6463
 29Y  H23  H  HCR5  0   0.258   -7.0980  -1.2278   2.5487

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
 29Y  C7   C6   aromatic  1.389  0.020  1.389
 29Y  C7   C8   aromatic  1.392  0.020  1.392
 29Y  O17  C16  double    1.211  0.020  1.211
 29Y  C11  C13  single    1.485  0.020  1.485
 29Y  C11  C8   single    1.484  0.020  1.484
 29Y  C11  C14  single    1.525  0.020  1.525
 29Y  C6   C5   aromatic  1.389  0.020  1.389
 29Y  C13  C14  single    1.498  0.020  1.498
 29Y  C8   C9   aromatic  1.396  0.020  1.396
 29Y  S27  C26  aromatic  1.735  0.020  1.735
 29Y  S27  C19  aromatic  1.761  0.020  1.761
 29Y  N32  C33  aromatic  1.318  0.020  1.318
 29Y  N32  N30  aromatic  1.327  0.020  1.327
 29Y  C33  C28  aromatic  1.413  0.020  1.413
 29Y  C16  C14  single    1.482  0.020  1.482
 29Y  C16  N18  single    1.379  0.020  1.379
 29Y  C1   N2   single    1.447  0.020  1.447
 29Y  C5   C4   single    1.505  0.020  1.505
 29Y  C5   C10  aromatic  1.393  0.020  1.393
 29Y  C25  C26  aromatic  1.385  0.020  1.385
 29Y  C25  C24  aromatic  1.393  0.020  1.393
 29Y  C9   C10  aromatic  1.385  0.020  1.385
 29Y  C4   N2   single    1.451  0.020  1.451
 29Y  C26  C21  aromatic  1.402  0.020  1.402
 29Y  N30  C29  aromatic  1.339  0.020  1.339
 29Y  C28  C24  single    1.461  0.020  1.461
 29Y  C28  C29  aromatic  1.383  0.020  1.383
 29Y  C19  N18  single    1.370  0.020  1.370
 29Y  C19  N20  aromatic  1.282  0.020  1.282
 29Y  N2   C3   single    1.447  0.020  1.447
 29Y  C24  C23  aromatic  1.406  0.020  1.406
 29Y  C21  N20  aromatic  1.374  0.020  1.374
 29Y  C21  C22  aromatic  1.393  0.020  1.393
 29Y  C23  C22  aromatic  1.380  0.020  1.380
 29Y  C1   H1   single    0.970  0.020  1.090
 29Y  C1   H2   single    0.970  0.020  1.090
 29Y  C1   H3   single    0.970  0.020  1.090
 29Y  C3   H5   single    0.970  0.020  1.090
 29Y  C3   H6   single    0.970  0.020  1.090
 29Y  C3   H7   single    0.970  0.020  1.090
 29Y  C4   H8   single    0.970  0.020  1.090
 29Y  C4   H9   single    0.970  0.020  1.090
 29Y  C6   H10  single    0.930  0.020  1.080
 29Y  C7   H11  single    0.930  0.020  1.080
 29Y  C9   H13  single    0.930  0.020  1.080
 29Y  C10  H14  single    0.930  0.020  1.080
 29Y  C11  H12  single    0.970  0.020  1.090
 29Y  C13  H16  single    0.970  0.020  1.090
 29Y  C13  H17  single    0.970  0.020  1.090
 29Y  C14  H15  single    0.970  0.020  1.090
 29Y  N18  H18  single    0.860  0.020  1.020
 29Y  C22  H19  single    0.930  0.020  1.080
 29Y  C23  H20  single    0.930  0.020  1.080
 29Y  C25  H21  single    0.930  0.020  1.080
 29Y  C29  H22  single    0.930  0.020  1.080
 29Y  N30  H31  single    0.860  0.020  1.020
 29Y  C33  H23  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
 29Y  H3   C1   H2   107.77  3.000
 29Y  H3   C1   H1   107.74  3.000
 29Y  H2   C1   H1   107.71  3.000
 29Y  H3   C1   N2   113.05  3.000
 29Y  H2   C1   N2   110.58  3.000
 29Y  H1   C1   N2   109.81  3.000
 29Y  C4   N2   C3   110.85  3.000
 29Y  C3   N2   C1   111.16  3.000
 29Y  C4   N2   C1   111.81  3.000
 29Y  H7   C3   H6   107.90  3.000
 29Y  H7   C3   H5   107.62  3.000
 29Y  H6   C3   H5   107.71  3.000
 29Y  H7   C3   N2   109.97  3.000
 29Y  H6   C3   N2   110.08  3.000
 29Y  H5   C3   N2   113.38  3.000
 29Y  H9   C4   H8   106.24  3.000
 29Y  H9   C4   C5   109.27  3.000
 29Y  H8   C4   C5   109.12  3.000
 29Y  H9   C4   N2   111.87  3.000
 29Y  H8   C4   N2   107.66  3.000
 29Y  C5   C4   N2   112.45  3.000
 29Y  C10  C5   C6   118.15  3.000
 29Y  C10  C5   C4   120.42  3.000
 29Y  C6   C5   C4   121.42  3.000
 29Y  H10  C6   C7   119.45  3.000
 29Y  H10  C6   C5   119.60  3.000
 29Y  C7   C6   C5   120.95  3.000
 29Y  H11  C7   C8   119.63  3.000
 29Y  H11  C7   C6   119.42  3.000
 29Y  C8   C7   C6   120.95  3.000
 29Y  C11  C8   C9   122.95  3.000
 29Y  C9   C8   C7   118.07  3.000
 29Y  C11  C8   C7   118.96  3.000
 29Y  H13  C9   C10  118.86  3.000
 29Y  H13  C9   C8   120.31  3.000
 29Y  C10  C9   C8   120.83  3.000
 29Y  H14  C10  C9   119.43  3.000
 29Y  H14  C10  C5   119.53  3.000
 29Y  C9   C10  C5   121.04  3.000
 29Y  H12  C11  C14  113.92  3.000
 29Y  H12  C11  C13  115.25  3.000
 29Y  C14  C11  C13   59.69  3.000
 29Y  H12  C11  C8   114.00  3.000
 29Y  C14  C11  C8   119.27  3.000
 29Y  C13  C11  C8   123.84  3.000
 29Y  H17  C13  H16  114.59  3.000
 29Y  H17  C13  C14  116.63  3.000
 29Y  H16  C13  C14  117.46  3.000
 29Y  H17  C13  C11  119.15  3.000
 29Y  H16  C13  C11  117.37  3.000
 29Y  C14  C13  C11   61.49  3.000
 29Y  H15  C14  C16  116.85  3.000
 29Y  H15  C14  C13  116.99  3.000
 29Y  C16  C14  C13  119.18  3.000
 29Y  H15  C14  C11  115.52  3.000
 29Y  C16  C14  C11  116.66  3.000
 29Y  C13  C14  C11   58.82  3.000
 29Y  N18  C16  O17  123.46  3.000
 29Y  N18  C16  C14  112.92  3.000
 29Y  O17  C16  C14  123.61  3.000
 29Y  H18  N18  C19  116.61  3.000
 29Y  H18  N18  C16  116.48  3.000
 29Y  C19  N18  C16  126.86  3.000
 29Y  S27  C19  N20  116.25  3.000
 29Y  N20  C19  N18  126.68  3.000
 29Y  S27  C19  N18  117.07  3.000
 29Y  C21  N20  C19  110.64  3.000
 29Y  C26  C21  C22  118.53  3.000
 29Y  C22  C21  N20  125.77  3.000
 29Y  C26  C21  N20  115.71  3.000
 29Y  H19  C22  C23  120.58  3.000
 29Y  H19  C22  C21  120.12  3.000
 29Y  C23  C22  C21  119.30  3.000
 29Y  H20  C23  C24  119.60  3.000
 29Y  H20  C23  C22  118.29  3.000
 29Y  C24  C23  C22  122.10  3.000
 29Y  C28  C24  C25  120.42  3.000
 29Y  C28  C24  C23  120.78  3.000
 29Y  C25  C24  C23  118.79  3.000
 29Y  H21  C25  C26  120.05  3.000
 29Y  H21  C25  C24  121.12  3.000
 29Y  C26  C25  C24  118.83  3.000
 29Y  S27  C26  C25  128.47  3.000
 29Y  C25  C26  C21  122.44  3.000
 29Y  S27  C26  C21  109.09  3.000
 29Y  C26  S27  C19   88.32  3.000
 29Y  C33  C28  C29  103.42  3.000
 29Y  C29  C28  C24  128.14  3.000
 29Y  C33  C28  C24  128.44  3.000
 29Y  H22  C29  N30  121.40  3.000
 29Y  H22  C29  C28  131.98  3.000
 29Y  N30  C29  C28  106.62  3.000
 29Y  H31  N30  N32  119.96  3.000
 29Y  H31  N30  C29  126.74  3.000
 29Y  N32  N30  C29  113.29  3.000
 29Y  C33  N32  N30  104.86  3.000
 29Y  H23  C33  N32  119.89  3.000
 29Y  H23  C33  C28  128.30  3.000
 29Y  N32  C33  C28  111.81  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
 29Y  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 29Y  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 29Y  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 29Y  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 29Y  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 29Y  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 29Y  CONST_07  C25  C26  S27  C19   180.00   0.0  0
 29Y  CONST_08  C21  C26  S27  C19     0.00   0.0  0
 29Y  CONST_09  C26  C21  N20  C19     0.00   0.0  0
 29Y  CONST_10  C22  C21  N20  C19   180.00   0.0  0
 29Y  CONST_11  C26  S27  C19  N20     0.00   0.0  0
 29Y  CONST_12  S27  C26  C21  N20     0.00   0.0  0
 29Y  CONST_13  C25  C26  C21  N20   180.00   0.0  0
 29Y  CONST_14  C23  C22  C21  N20   180.00   0.0  0
 29Y  CONST_15  C24  C25  C26  C21     0.00   0.0  0
 29Y  CONST_16  S27  C19  N20  C21     0.00   0.0  0
 29Y  CONST_17  C24  C23  C22  C21     0.00   0.0  0
 29Y  CONST_18  S27  C26  C21  C22   180.00   0.0  0
 29Y  CONST_19  C25  C26  C21  C22     0.00   0.0  0
 29Y  CONST_20  C25  C24  C23  C22     0.00   0.0  0
 29Y  CONST_21  C28  C24  C23  C22   180.00   0.0  0
 29Y  CONST_22  C26  C25  C24  C23     0.00   0.0  0
 29Y  CONST_23  C33  C28  C24  C23   180.00   0.0  0
 29Y  CONST_24  C29  C28  C24  C23     0.00   0.0  0
 29Y  CONST_25  C26  C21  C22  C23     0.00   0.0  0
 29Y  CONST_26  S27  C26  C25  C24   180.00   0.0  0
 29Y  CONST_27  N32  C33  C28  C24   180.00   0.0  0
 29Y  CONST_28  N30  C29  C28  C24   180.00   0.0  0
 29Y  CONST_29  C33  C28  C24  C25     0.00   0.0  0
 29Y  CONST_30  C29  C28  C24  C25   180.00   0.0  0
 29Y  CONST_31  C28  C24  C25  C26   180.00   0.0  0
 29Y  CONST_32  N30  N32  C33  C28     0.00   0.0  0
 29Y  CONST_33  N32  N30  C29  C28     0.00   0.0  0
 29Y  CONST_34  C33  N32  N30  C29     0.00   0.0  0
 29Y  CONST_35  N32  C33  C28  C29     0.00   0.0  0
 29Y  CONST_36  C33  C28  C29  N30     0.00   0.0  0
 29Y  CONST_37  C11  C8   C7   C6    180.00   0.0  0
 29Y  CONST_38  C11  C8   C9   C10   180.00   0.0  0
 29Y  CONST_39  C7   C6   C5   C4    180.00   0.0  0
 29Y  CONST_40  C9   C10  C5   C4    180.00   0.0  0
 29Y  CONST_41  C26  S27  C19  N18   180.00   0.0  0
 29Y  CONST_42  C21  N20  C19  N18   180.00   0.0  0
 29Y  CONST_43  H11  C7   C6   C5    180.00   0.0  0
 29Y  CONST_44  H13  C9   C10  C5    180.00   0.0  0
 29Y  CONST_45  H14  C10  C5   C6    180.00   0.0  0
 29Y  CONST_46  H10  C6   C7   C8    180.00   0.0  0
 29Y  CONST_47  H19  C22  C21  N20     0.00   0.0  0
 29Y  CONST_48  H21  C25  C26  C21   180.00   0.0  0
 29Y  CONST_49  H20  C23  C22  C21   180.00   0.0  0
 29Y  CONST_50  H23  C33  C28  C24     0.00   0.0  0
 29Y  CONST_51  H22  C29  C28  C24     0.00   0.0  0
 29Y  CONST_52  H31  N30  C29  C28   180.00   0.0  0
 29Y  CONST_53  C19  N18  C16  C14   180.00   0.0  0
 29Y  CONST_54  S27  C19  N18  C16   180.00   0.0  0
 29Y  CONST_55  N20  C19  N18  C16     0.00   0.0  0
 29Y  CONST_56  H18  N18  C19  N20   180.00   0.0  0
 29Y  CONST_57  C19  N18  C16  O17     0.00   0.0  0
 29Y  Var_01    C13  C11  C8   C7    168.39  30.0  2
 29Y  Var_02    C14  C13  C11  C8    106.85  30.0  1
 29Y  Var_03    C6   C5   C4   N2   -119.13  30.0  3
 29Y  Var_04    O17  C16  C14  C11    42.95  30.0  1
 29Y  Var_05    C5   C4   N2   C1     65.47  30.0  1
 29Y  Var_06    H5   C3   N2   C1     63.41  30.0  3
 29Y  Var_07    H1   C1   N2   C3     56.13  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
 29Y  chir_01  C11  C13  C8   C14  both
 29Y  chir_02  C14  C11  C13  C16  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
 29Y  plan-1  C24  0.020
 29Y  plan-1  C28  0.020
 29Y  plan-1  C29  0.020
 29Y  plan-1  N30  0.020
 29Y  plan-1  N32  0.020
 29Y  plan-1  C33  0.020
 29Y  plan-1  H22  0.020
 29Y  plan-1  H31  0.020
 29Y  plan-1  H23  0.020
 29Y  plan-2  C4   0.020
 29Y  plan-2  C5   0.020
 29Y  plan-2  C6   0.020
 29Y  plan-2  C7   0.020
 29Y  plan-2  C8   0.020
 29Y  plan-2  C9   0.020
 29Y  plan-2  C10  0.020
 29Y  plan-2  C11  0.020
 29Y  plan-2  H10  0.020
 29Y  plan-2  H11  0.020
 29Y  plan-2  H13  0.020
 29Y  plan-2  H14  0.020
 29Y  plan-3  N18  0.020
 29Y  plan-3  C19  0.020
 29Y  plan-3  N20  0.020
 29Y  plan-3  C21  0.020
 29Y  plan-3  C22  0.020
 29Y  plan-3  C23  0.020
 29Y  plan-3  C24  0.020
 29Y  plan-3  C25  0.020
 29Y  plan-3  C26  0.020
 29Y  plan-3  S27  0.020
 29Y  plan-3  C28  0.020
 29Y  plan-3  H19  0.020
 29Y  plan-3  H20  0.020
 29Y  plan-3  H21  0.020
 29Y  plan-4  C14  0.020
 29Y  plan-4  C16  0.020
 29Y  plan-4  O17  0.020
 29Y  plan-4  N18  0.020
 29Y  plan-4  C19  0.020
 29Y  plan-4  H18  0.020

