# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 08:18:45 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 6-[(1,3-benzothiazol-6-yl)amino]-4-{[(2S)-1-hydroxy-3-phenylpropan-2-yl]amino}-N-methylpyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cnc(Nc2ccc3ncsc3c2)cc1N[C@H](CO)Cc4ccccc4
#
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
 9YS  9YS  6-[(1,3-benzothiazol-6-yl)amino]-4-{[(2S)-1-hydroxy-3-phenylpropan-2-yl]amino}-N-methylpyridine-3-carboxamide  ligand  54  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9YS
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
 9YS  C13  C  CH1   0  -0.113  -3.2253   1.1092   1.4007
 9YS  C18  C  CR16  0  -0.310  -4.4663   2.6556  -1.2306
 9YS  C17  C  CR6   0   0.160  -4.6934   1.4244  -0.6183
 9YS  C15  C  CH2   0  -0.153  -3.1432   1.2077   2.9183
 9YS  C19  C  CR16  0  -0.240  -4.4580   2.7748  -2.6137
 9YS  C20  C  CR16  0  -0.274  -4.6778   1.6578  -3.4098
 9YS  C21  C  CR16  0  -0.243  -4.9058   0.4255  -2.8117
 9YS  C22  C  CR16  0  -0.311  -4.9118   0.3118  -1.4275
 9YS  C23  C  CR6   0   0.369   3.2313   1.0918   0.4709
 9YS  C24  C  CR16  0  -0.350   3.9507   0.0070  -0.0234
 9YS  C12  C  CH3   0  -0.511  -2.5302  -5.1695  -0.4872
 9YS  C27  C  CR16  0  -0.288   5.2810   2.3940   0.7033
 9YS  C1   C  CR6   0  -0.258  -1.0558  -1.7577   0.2081
 9YS  C2   C  CR16  0  -0.067   0.2894  -1.9466  -0.0681
 9YS  N3   N  N     0  -0.501   1.2528  -1.0489   0.0514
 9YS  C4   C  CR6   0   0.575   0.8964   0.1601   0.4867
 9YS  C5   C  CR16  0  -0.549  -0.4181   0.4977   0.7947
 9YS  C6   C  CR6   0   0.517  -1.4398  -0.4476   0.6527
 9YS  N7   N  NH1   0  -0.700  -2.7203  -0.1509   0.9112
 9YS  C9   C  C     0   0.585  -2.0509  -2.8462   0.0582
 9YS  N10  N  NH1   0  -0.655  -1.6232  -4.0566  -0.3317
 9YS  O11  O  O     0  -0.524  -3.2523  -2.6676   0.2877
 9YS  C14  C  CH2   0  -0.543  -4.6554   1.3055   0.8793
 9YS  O16  O  OH1   0  -0.669  -3.9449   0.1995   3.4839
 9YS  C25  C  CR56  0  -0.217   5.3295   0.1447  -0.1396
 9YS  C26  C  CR56  0   0.310   6.0168   1.3137   0.2121
 9YS  C28  C  CR16  0  -0.370   3.9181   2.2765   0.8268
 9YS  S29  S  S2    0   0.201   6.4711  -1.0228  -0.7139
 9YS  C30  C  CR15  0  -0.228   7.7407   0.1323  -0.4340
 9YS  N31  N  N     0  -0.375   7.3796   1.2720   0.0329
 9YS  H1   H  HCH1  0   0.259  -2.6209   1.9256   0.9949
 9YS  H2   H  HCR6  0   0.246  -4.2974   3.5330  -0.6164
 9YS  H3   H  HCH2  0   0.211  -2.0936   1.1086   3.2265
 9YS  H4   H  HCH2  0   0.204  -3.4697   2.2121   3.2185
 9YS  H5   H  HCR6  0   0.252  -4.2824   3.7409  -3.0695
 9YS  H6   H  HCR6  0   0.253  -4.6749   1.7478  -4.4885
 9YS  H7   H  HCR6  0   0.252  -5.0796  -0.4508  -3.4234
 9YS  H8   H  HCR6  0   0.242  -5.0890  -0.6564  -0.9739
 9YS  H9   H  HCR6  0   0.300   3.4524  -0.9050  -0.3068
 9YS  H10  H  HCH3  0   0.249  -1.9579  -6.0256  -0.8324
 9YS  H11  H  HCH3  0   0.237  -3.0127  -5.4369   0.4539
 9YS  H12  H  HCH3  0   0.238  -3.3074  -4.9585  -1.2218
 9YS  H13  H  HCR6  0   0.269   5.7795   3.3116   0.9865
 9YS  H14  H  HCR6  0   0.244   0.6443  -2.9080  -0.4225
 9YS  H15  H  HCR6  0   0.276  -0.6348   1.4983   1.1412
 9YS  H16  H  HNH1  0   0.412  -3.3602  -0.9316   0.8236
 9YS  H17  H  HNH1  0   0.415   1.5049   2.0033   0.9867
 9YS  H18  H  HNH1  0   0.411  -0.6492  -4.2370  -0.4900
 9YS  H19  H  HCH2  0   0.258  -5.2874   0.4783   1.2113
 9YS  H20  H  HCH2  0   0.259  -5.0602   2.2119   1.3357
 9YS  H21  H  HOH1  0   0.458  -3.8659   0.2536   4.4402
 9YS  H22  H  HCR6  0   0.273   3.3525   3.1164   1.2122
 9YS  H23  H  HCR5  0   0.303   8.7660  -0.1319  -0.6552
 9YS  N8   N  NH1   0  -0.788   1.8573   1.1217   0.6476

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
 9YS  C12  N10  single    1.444  0.020  1.444
 9YS  N3   C2   aromatic  1.322  0.020  1.322
 9YS  N3   C4   aromatic  1.333  0.020  1.333
 9YS  C2   C1   aromatic  1.386  0.020  1.386
 9YS  N10  C9   single    1.342  0.020  1.342
 9YS  C9   C1   single    1.482  0.020  1.482
 9YS  C9   O11  double    1.236  0.020  1.236
 9YS  N8   C4   single    1.369  0.020  1.369
 9YS  N8   C23  single    1.386  0.020  1.386
 9YS  C1   C6   aromatic  1.436  0.020  1.436
 9YS  C4   C5   aromatic  1.392  0.020  1.392
 9YS  C28  C23  aromatic  1.415  0.020  1.415
 9YS  C28  C27  aromatic  1.373  0.020  1.373
 9YS  C23  C24  aromatic  1.392  0.020  1.392
 9YS  C6   C5   aromatic  1.399  0.020  1.399
 9YS  C6   N7   single    1.340  0.020  1.340
 9YS  C27  C26  aromatic  1.396  0.020  1.396
 9YS  C24  C25  aromatic  1.390  0.020  1.390
 9YS  N7   C13  single    1.443  0.020  1.443
 9YS  C26  C25  aromatic  1.401  0.020  1.401
 9YS  C26  N31  aromatic  1.375  0.020  1.375
 9YS  C25  S29  aromatic  1.731  0.020  1.731
 9YS  C13  C14  single    1.535  0.020  1.535
 9YS  C13  C15  single    1.523  0.020  1.523
 9YS  N31  C30  aromatic  1.283  0.020  1.283
 9YS  C14  C17  single    1.503  0.020  1.503
 9YS  S29  C30  aromatic  1.739  0.020  1.739
 9YS  O16  C15  single    1.407  0.020  1.407
 9YS  C17  C22  aromatic  1.393  0.020  1.393
 9YS  C17  C18  aromatic  1.394  0.020  1.394
 9YS  C22  C21  aromatic  1.389  0.020  1.389
 9YS  C18  C19  aromatic  1.388  0.020  1.388
 9YS  C21  C20  aromatic  1.389  0.020  1.389
 9YS  C19  C20  aromatic  1.389  0.020  1.389
 9YS  C13  H1   single    0.970  0.020  1.090
 9YS  C18  H2   single    0.930  0.020  1.080
 9YS  C15  H3   single    0.970  0.020  1.090
 9YS  C15  H4   single    0.970  0.020  1.090
 9YS  C19  H5   single    0.930  0.020  1.080
 9YS  C20  H6   single    0.930  0.020  1.080
 9YS  C21  H7   single    0.930  0.020  1.080
 9YS  C22  H8   single    0.930  0.020  1.080
 9YS  C24  H9   single    0.930  0.020  1.080
 9YS  C12  H10  single    0.970  0.020  1.090
 9YS  C12  H11  single    0.970  0.020  1.090
 9YS  C12  H12  single    0.970  0.020  1.090
 9YS  C27  H13  single    0.930  0.020  1.080
 9YS  C2   H14  single    0.930  0.020  1.080
 9YS  C5   H15  single    0.930  0.020  1.080
 9YS  N7   H16  single    0.860  0.020  1.020
 9YS  N8   H17  single    0.860  0.020  1.020
 9YS  N10  H18  single    0.860  0.020  1.020
 9YS  C14  H19  single    0.970  0.020  1.090
 9YS  C14  H20  single    0.970  0.020  1.090
 9YS  O16  H21  single    0.850  0.020  0.980
 9YS  C28  H22  single    0.930  0.020  1.080
 9YS  C30  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
 9YS  H1   C13  C14  107.06  3.000
 9YS  H1   C13  N7   109.42  3.000
 9YS  C14  C13  N7   108.81  3.000
 9YS  H1   C13  C15  106.95  3.000
 9YS  C14  C13  C15  112.36  3.000
 9YS  N7   C13  C15  112.06  3.000
 9YS  H2   C18  C19  119.60  3.000
 9YS  H2   C18  C17  119.43  3.000
 9YS  C19  C18  C17  120.97  3.000
 9YS  C14  C17  C22  121.31  3.000
 9YS  C22  C17  C18  118.42  3.000
 9YS  C14  C17  C18  120.24  3.000
 9YS  H4   C15  H3   106.86  3.000
 9YS  H4   C15  O16  112.10  3.000
 9YS  H3   C15  O16  111.53  3.000
 9YS  H4   C15  C13  108.40  3.000
 9YS  H3   C15  C13  108.98  3.000
 9YS  O16  C15  C13  108.88  3.000
 9YS  H5   C19  C20  120.12  3.000
 9YS  H5   C19  C18  119.81  3.000
 9YS  C20  C19  C18  120.07  3.000
 9YS  H6   C20  C21  120.23  3.000
 9YS  H6   C20  C19  120.25  3.000
 9YS  C21  C20  C19  119.51  3.000
 9YS  H7   C21  C22  119.75  3.000
 9YS  H7   C21  C20  120.08  3.000
 9YS  C22  C21  C20  120.17  3.000
 9YS  H8   C22  C21  119.40  3.000
 9YS  H8   C22  C17  119.74  3.000
 9YS  C21  C22  C17  120.86  3.000
 9YS  C28  C23  N8   115.54  3.000
 9YS  C28  C23  C24  119.40  3.000
 9YS  N8   C23  C24  125.06  3.000
 9YS  H9   C24  C25  121.37  3.000
 9YS  H9   C24  C23  120.93  3.000
 9YS  C25  C24  C23  117.70  3.000
 9YS  H12  C12  H11  108.27  3.000
 9YS  H12  C12  H10  108.30  3.000
 9YS  H11  C12  H10  108.31  3.000
 9YS  H12  C12  N10  111.79  3.000
 9YS  H11  C12  N10  111.95  3.000
 9YS  H10  C12  N10  108.10  3.000
 9YS  H13  C27  C28  120.41  3.000
 9YS  H13  C27  C26  120.36  3.000
 9YS  C28  C27  C26  119.23  3.000
 9YS  C9   C1   C6   121.45  3.000
 9YS  C6   C1   C2   116.46  3.000
 9YS  C9   C1   C2   122.09  3.000
 9YS  H14  C2   N3   113.14  3.000
 9YS  H14  C2   C1   120.24  3.000
 9YS  N3   C2   C1   126.62  3.000
 9YS  C4   N3   C2   116.77  3.000
 9YS  N8   C4   C5   117.81  3.000
 9YS  C5   C4   N3   123.00  3.000
 9YS  N8   C4   N3   119.19  3.000
 9YS  H15  C5   C6   120.77  3.000
 9YS  H15  C5   C4   119.01  3.000
 9YS  C6   C5   C4   120.22  3.000
 9YS  N7   C6   C5   121.92  3.000
 9YS  N7   C6   C1   121.17  3.000
 9YS  C5   C6   C1   116.91  3.000
 9YS  H16  N7   C6   114.60  3.000
 9YS  H16  N7   C13  118.77  3.000
 9YS  C6   N7   C13  126.40  3.000
 9YS  O11  C9   N10  119.61  3.000
 9YS  O11  C9   C1   121.85  3.000
 9YS  N10  C9   C1   118.54  3.000
 9YS  H18  N10  C9   121.17  3.000
 9YS  H18  N10  C12  117.02  3.000
 9YS  C9   N10  C12  121.76  3.000
 9YS  H20  C14  H19  106.66  3.000
 9YS  H20  C14  C17  109.95  3.000
 9YS  H19  C14  C17  110.37  3.000
 9YS  H20  C14  C13  108.03  3.000
 9YS  H19  C14  C13  109.81  3.000
 9YS  C17  C14  C13  111.86  3.000
 9YS  H21  O16  C15  108.24  3.000
 9YS  S29  C25  C26  108.82  3.000
 9YS  S29  C25  C24  127.94  3.000
 9YS  C26  C25  C24  123.24  3.000
 9YS  N31  C26  C25  115.35  3.000
 9YS  N31  C26  C27  126.27  3.000
 9YS  C25  C26  C27  118.38  3.000
 9YS  H22  C28  C27  118.92  3.000
 9YS  H22  C28  C23  119.02  3.000
 9YS  C27  C28  C23  122.05  3.000
 9YS  C30  S29  C25   88.86  3.000
 9YS  H23  C30  N31  123.92  3.000
 9YS  H23  C30  S29  119.79  3.000
 9YS  N31  C30  S29  116.29  3.000
 9YS  C30  N31  C26  110.68  3.000
 9YS  H17  N8   C4   114.11  3.000
 9YS  H17  N8   C23  114.11  3.000
 9YS  C4   N8   C23  131.75  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
 9YS  CONST_01  C21  C22  C17  C18    0.00   0.0  0
 9YS  CONST_02  C21  C20  C19  C18    0.00   0.0  0
 9YS  CONST_03  C20  C21  C22  C17    0.00   0.0  0
 9YS  CONST_04  C20  C19  C18  C17    0.00   0.0  0
 9YS  CONST_05  C22  C17  C18  C19    0.00   0.0  0
 9YS  CONST_06  C22  C21  C20  C19    0.00   0.0  0
 9YS  CONST_07  C26  C27  C28  C23    0.00   0.0  0
 9YS  CONST_08  C26  C25  C24  C23    0.00   0.0  0
 9YS  CONST_09  S29  C25  C24  C23  180.00   0.0  0
 9YS  CONST_10  C27  C28  C23  C24    0.00   0.0  0
 9YS  CONST_11  C27  C26  C25  C24    0.00   0.0  0
 9YS  CONST_12  N31  C26  C25  C24  180.00   0.0  0
 9YS  CONST_13  C30  S29  C25  C24  180.00   0.0  0
 9YS  CONST_14  S29  C25  C26  C27  180.00   0.0  0
 9YS  CONST_15  C30  N31  C26  C27  180.00   0.0  0
 9YS  CONST_16  C4   N3   C2   C1     0.00   0.0  0
 9YS  CONST_17  C4   C5   C6   C1     0.00   0.0  0
 9YS  CONST_18  C5   C4   N3   C2     0.00   0.0  0
 9YS  CONST_19  C5   C6   C1   C2     0.00   0.0  0
 9YS  CONST_20  C6   C1   C2   N3     0.00   0.0  0
 9YS  CONST_21  C6   C5   C4   N3     0.00   0.0  0
 9YS  CONST_22  C28  C23  C24  C25    0.00   0.0  0
 9YS  CONST_23  C28  C27  C26  C25    0.00   0.0  0
 9YS  CONST_24  C30  N31  C26  C25    0.00   0.0  0
 9YS  CONST_25  N31  C30  S29  C25    0.00   0.0  0
 9YS  CONST_26  C30  S29  C25  C26    0.00   0.0  0
 9YS  CONST_27  S29  C30  N31  C26    0.00   0.0  0
 9YS  CONST_28  N31  C26  C27  C28  180.00   0.0  0
 9YS  CONST_29  N31  C26  C25  S29    0.00   0.0  0
 9YS  CONST_30  C14  C17  C18  C19  180.00   0.0  0
 9YS  CONST_31  C14  C17  C22  C21  180.00   0.0  0
 9YS  CONST_32  N8   C23  C28  C27  180.00   0.0  0
 9YS  CONST_33  N8   C4   N3   C2   180.00   0.0  0
 9YS  CONST_34  N7   C6   C1   C2   180.00   0.0  0
 9YS  CONST_35  C9   C1   C2   N3   180.00   0.0  0
 9YS  CONST_36  N7   C6   C5   C4   180.00   0.0  0
 9YS  CONST_37  C9   C1   C6   C5   180.00   0.0  0
 9YS  CONST_38  N8   C4   C5   C6   180.00   0.0  0
 9YS  CONST_39  C25  C24  C23  N8   180.00   0.0  0
 9YS  CONST_40  H8   C22  C17  C18  180.00   0.0  0
 9YS  CONST_41  H6   C20  C19  C18  180.00   0.0  0
 9YS  CONST_42  H7   C21  C22  C17  180.00   0.0  0
 9YS  CONST_43  H5   C19  C18  C17  180.00   0.0  0
 9YS  CONST_44  H2   C18  C19  C20  180.00   0.0  0
 9YS  CONST_45  H13  C27  C28  C23  180.00   0.0  0
 9YS  CONST_46  H22  C28  C23  C24  180.00   0.0  0
 9YS  CONST_47  H15  C5   C6   C1   180.00   0.0  0
 9YS  CONST_48  H14  C2   N3   C4   180.00   0.0  0
 9YS  CONST_49  H23  C30  S29  C25  180.00   0.0  0
 9YS  CONST_50  H9   C24  C25  C26  180.00   0.0  0
 9YS  CONST_51  C1   C6   N7   C13  180.00   0.0  0
 9YS  CONST_52  C5   C6   N7   C13    0.00   0.0  0
 9YS  CONST_53  H16  N7   C6   C1     0.00   0.0  0
 9YS  CONST_54  C1   C9   N10  C12  180.00   0.0  0
 9YS  CONST_55  H18  N10  C9   C1     0.00   0.0  0
 9YS  CONST_56  O11  C9   N10  C12    0.00   0.0  0
 9YS  Var_01    N3   C4   N8   C23   -1.96  30.0  2
 9YS  Var_02    C4   N8   C23  C24    4.43  30.0  2
 9YS  Var_03    C22  C17  C14  C13   93.46  30.0  2
 9YS  Var_04    N10  C9   C1   C2     1.37  30.0  2
 9YS  Var_05    H10  C12  N10  C9   178.55  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
 9YS  chir_01  C13  N7  C14  C15  negativ

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
 9YS  plan-1  C18  0.020
 9YS  plan-1  C17  0.020
 9YS  plan-1  C19  0.020
 9YS  plan-1  C20  0.020
 9YS  plan-1  C21  0.020
 9YS  plan-1  C22  0.020
 9YS  plan-1  C14  0.020
 9YS  plan-1  H2   0.020
 9YS  plan-1  H5   0.020
 9YS  plan-1  H6   0.020
 9YS  plan-1  H7   0.020
 9YS  plan-1  H8   0.020
 9YS  plan-2  C1   0.020
 9YS  plan-2  C2   0.020
 9YS  plan-2  N3   0.020
 9YS  plan-2  C4   0.020
 9YS  plan-2  C5   0.020
 9YS  plan-2  C6   0.020
 9YS  plan-2  N7   0.020
 9YS  plan-2  C9   0.020
 9YS  plan-2  H14  0.020
 9YS  plan-2  H15  0.020
 9YS  plan-2  N8   0.020
 9YS  plan-3  C23  0.020
 9YS  plan-3  C24  0.020
 9YS  plan-3  C27  0.020
 9YS  plan-3  C25  0.020
 9YS  plan-3  C26  0.020
 9YS  plan-3  C28  0.020
 9YS  plan-3  S29  0.020
 9YS  plan-3  C30  0.020
 9YS  plan-3  N31  0.020
 9YS  plan-3  H9   0.020
 9YS  plan-3  H13  0.020
 9YS  plan-3  H22  0.020
 9YS  plan-3  H23  0.020
 9YS  plan-3  N8   0.020
 9YS  plan-4  C12  0.020
 9YS  plan-4  C1   0.020
 9YS  plan-4  C9   0.020
 9YS  plan-4  N10  0.020
 9YS  plan-4  O11  0.020
 9YS  plan-4  H18  0.020
 9YS  plan-5  C13  0.020
 9YS  plan-5  C6   0.020
 9YS  plan-5  N7   0.020
 9YS  plan-5  H16  0.020

