# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 14:27:19 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: 4-azanyl-6-[[(1~{S})-1-[6-[3-[(dimethylamino)methyl]phenyl]-3-methyl-5-oxidanylidene-[1,3]thiazolo[3,2-a]pyridin-7-yl]ethyl]amino]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1ncnc(N)c1C#N)C2=C(C(=O)N3C(=CSC3=C2)C)c4cccc(CN(C)C)c4
#
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
 8TN  8TN  4-azanyl-6-[[(1~{S})-1-[6-[3-[(dimethylamino)methyl]phenyl]-3-methyl-5-oxidanylidene-[1,3]thiazolo[3,2-a]pyridin-7-yl]ethyl]amino]pyrimidine-5-carbonitrile  ligand  58  33  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8TN
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
 8TN  C1   C  CSP   0   0.011  -4.1882   1.8833   1.4040
 8TN  C2   C  CR16  0  -0.230   1.4080  -2.8133  -2.5123
 8TN  C3   C  CR16  0  -0.301   1.3832  -1.4434  -2.2747
 8TN  C7   C  CR6   0  -0.246  -4.2357   0.6218   0.7810
 8TN  C8   C  CR6   0   0.068   1.3011  -0.9605  -0.9739
 8TN  C9   C  CR6   0   0.116   1.2692  -3.2383  -0.1438
 8TN  C10  C  CR6   0   0.537  -5.2833  -0.2862   1.0463
 8TN  C11  C  CR6   0   0.601  -3.2299   0.2117  -0.1262
 8TN  C12  C  CR16  0  -0.495   0.2037   2.6566  -0.6752
 8TN  C13  C  CR15  0  -0.595   3.2720   4.5030   0.5935
 8TN  C14  C  CR6   0  -0.304   1.2779   0.4985  -0.7097
 8TN  C15  C  CR6   0   0.310   0.1560   1.2697  -0.9010
 8TN  C16  C  CR5   0   0.474   3.5854   3.2053   0.4834
 8TN  C19  C  CH3   0  -0.696   4.9179   2.6469   0.8498
 8TN  C20  C  CH3   0  -0.643  -1.4960   1.0863  -2.7867
 8TN  C21  C  CH3   0  -0.519   3.5827  -4.3951   1.2873
 8TN  C22  C  CH3   0  -0.520   2.1588  -6.1880   1.9591
 8TN  C24  C  CH1   0  -0.195  -1.1475   0.6573  -1.3640
 8TN  N25  N  NS    0  -0.254  -4.1447   2.9206   1.9130
 8TN  N26  N  N     0  -0.475  -5.3091  -1.4878   0.4509
 8TN  C4   C  CR16  0  -0.294   1.3556  -3.7049  -1.4535
 8TN  C5   C  CR16  0  -0.325   1.2494  -1.8693   0.0814
 8TN  C6   C  CR16  0   0.083  -4.3193  -1.7530  -0.3771
 8TN  C17  C  CR56  0   0.226   1.3711   3.1999  -0.2262
 8TN  C18  C  CR6   0   0.565   2.5183   1.0604  -0.2495
 8TN  C23  C  CH2   0  -0.338   1.2076  -4.2146   1.0013
 8TN  N27  N  N     0  -0.487  -3.2930  -0.9908  -0.7066
 8TN  N28  N  N     0  -0.644   2.4942   2.4496   0.0027
 8TN  N30  N  NH1   0  -0.673  -2.1945   1.0050  -0.4162
 8TN  N31  N  NT    0  -0.398   2.3515  -5.1065   1.0176
 8TN  O32  O  O     0  -0.466   3.5428   0.4181  -0.0712
 8TN  S33  S  S2    0   0.268   1.6456   4.8659   0.1276
 8TN  H1   H  HCR6  0   0.252   1.4721  -3.1812  -3.5285
 8TN  H2   H  HCR6  0   0.249   1.4280  -0.7483  -3.1046
 8TN  H3   H  HCR6  0   0.290  -0.6441   3.3043  -0.8517
 8TN  H4   H  HCR5  0   0.321   3.9277   5.2864   0.9379
 8TN  H6   H  HCH3  0   0.252   5.5312   3.4654   1.2227
 8TN  H7   H  HCH3  0   0.261   4.8450   1.8954   1.6324
 8TN  H8   H  HCH3  0   0.261   5.4286   2.1994   0.0004
 8TN  H9   H  HCH3  0   0.248  -2.4126   0.5931  -3.1096
 8TN  H10  H  HCH3  0   0.234  -1.6402   2.1645  -2.8607
 8TN  H11  H  HCH3  0   0.241  -0.6983   0.8017  -3.4732
 8TN  H12  H  HCH3  0   0.233   4.4270  -5.0844   1.2467
 8TN  H13  H  HCH3  0   0.238   3.7497  -3.6202   0.5385
 8TN  H14  H  HCH3  0   0.190   3.5907  -3.9111   2.2771
 8TN  H15  H  HCH3  0   0.191   2.0649  -5.8466   3.0020
 8TN  H16  H  HCH3  0   0.232   1.2559  -6.7471   1.7091
 8TN  H17  H  HCH3  0   0.234   3.0034  -6.8763   1.9112
 8TN  H18  H  HCH1  0   0.288  -1.0562  -0.4260  -1.3444
 8TN  H19  H  HNH2  0   0.418  -6.3303   0.8689   2.3889
 8TN  H20  H  HNH2  0   0.411  -6.9840  -0.6903   2.0652
 8TN  H21  H  HCR6  0   0.244   1.3836  -4.7717  -1.6391
 8TN  H22  H  HCR6  0   0.239   1.1896  -1.4983   1.0986
 8TN  H23  H  HCR6  0   0.264  -4.3523  -2.7273  -0.8546
 8TN  H24  H  HCH2  0   0.208   1.1004  -3.6623   1.9508
 8TN  H25  H  HCH2  0   0.248   0.3071  -4.8282   0.9006
 8TN  H26  H  HNH1  0   0.410  -2.1917   1.9385  -0.0349
 8TN  N29  N  NH2   0  -0.820  -6.2775   0.0020   1.8820

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
 8TN  C19  C16  single    1.490  0.020  1.490
 8TN  C13  C16  double    1.340  0.020  1.340
 8TN  C13  S33  single    1.730  0.020  1.730
 8TN  C16  N28  single    1.412  0.020  1.412
 8TN  S33  C17  single    1.725  0.020  1.725
 8TN  N28  C17  single    1.370  0.020  1.370
 8TN  N28  C18  single    1.412  0.020  1.412
 8TN  C17  C12  double    1.364  0.020  1.364
 8TN  O32  C18  double    1.222  0.020  1.222
 8TN  C18  C14  single    1.437  0.020  1.437
 8TN  C12  C15  single    1.406  0.020  1.406
 8TN  C22  N31  single    1.447  0.020  1.447
 8TN  C14  C15  double    1.375  0.020  1.375
 8TN  C14  C8   single    1.483  0.020  1.483
 8TN  C21  N31  single    1.447  0.020  1.447
 8TN  N31  C23  single    1.451  0.020  1.451
 8TN  C15  C24  single    1.513  0.020  1.513
 8TN  C5   C8   aromatic  1.394  0.020  1.394
 8TN  C5   C9   aromatic  1.388  0.020  1.388
 8TN  C8   C3   aromatic  1.390  0.020  1.390
 8TN  C23  C9   single    1.506  0.020  1.506
 8TN  C20  C24  single    1.526  0.020  1.526
 8TN  C9   C4   aromatic  1.393  0.020  1.393
 8TN  C24  N30  single    1.454  0.020  1.454
 8TN  C3   C2   aromatic  1.391  0.020  1.391
 8TN  N30  C11  single    1.336  0.020  1.336
 8TN  C4   C2   aromatic  1.385  0.020  1.385
 8TN  C11  N27  aromatic  1.337  0.020  1.337
 8TN  C11  C7   aromatic  1.415  0.020  1.415
 8TN  N25  C1   triple    1.156  0.020  1.156
 8TN  C1   C7   single    1.408  0.020  1.408
 8TN  N27  C6   aromatic  1.320  0.020  1.320
 8TN  C7   C10  aromatic  1.411  0.020  1.411
 8TN  C6   N26  aromatic  1.317  0.020  1.317
 8TN  C10  N26  aromatic  1.341  0.020  1.341
 8TN  C10  N29  single    1.330  0.020  1.330
 8TN  C2   H1   single    0.930  0.020  1.080
 8TN  C3   H2   single    0.930  0.020  1.080
 8TN  C12  H3   single    0.930  0.020  1.080
 8TN  C13  H4   single    0.930  0.020  1.080
 8TN  C19  H6   single    0.970  0.020  1.090
 8TN  C19  H7   single    0.970  0.020  1.090
 8TN  C19  H8   single    0.970  0.020  1.090
 8TN  C20  H9   single    0.970  0.020  1.090
 8TN  C20  H10  single    0.970  0.020  1.090
 8TN  C20  H11  single    0.970  0.020  1.090
 8TN  C21  H12  single    0.970  0.020  1.090
 8TN  C21  H13  single    0.970  0.020  1.090
 8TN  C21  H14  single    0.970  0.020  1.090
 8TN  C22  H15  single    0.970  0.020  1.090
 8TN  C22  H16  single    0.970  0.020  1.090
 8TN  C22  H17  single    0.970  0.020  1.090
 8TN  C24  H18  single    0.970  0.020  1.090
 8TN  N29  H19  single    0.860  0.020  1.020
 8TN  N29  H20  single    0.860  0.020  1.020
 8TN  C4   H21  single    0.930  0.020  1.080
 8TN  C5   H22  single    0.930  0.020  1.080
 8TN  C6   H23  single    0.930  0.020  1.080
 8TN  C23  H24  single    0.970  0.020  1.090
 8TN  C23  H25  single    0.970  0.020  1.090
 8TN  N30  H26  single    0.860  0.020  1.020

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
 8TN  N25  C1   C7   180.00  3.000
 8TN  H1   C2   C4   120.06  3.000
 8TN  H1   C2   C3   119.75  3.000
 8TN  C4   C2   C3   120.19  3.000
 8TN  H2   C3   C8   119.76  3.000
 8TN  H2   C3   C2   120.02  3.000
 8TN  C8   C3   C2   120.21  3.000
 8TN  C11  C7   C10  117.49  3.000
 8TN  C10  C7   C1   121.21  3.000
 8TN  C11  C7   C1   121.30  3.000
 8TN  C5   C8   C14  120.41  3.000
 8TN  C5   C8   C3   118.96  3.000
 8TN  C14  C8   C3   120.63  3.000
 8TN  C23  C9   C5   121.04  3.000
 8TN  C23  C9   C4   120.02  3.000
 8TN  C5   C9   C4   118.94  3.000
 8TN  N29  C10  N26  117.29  3.000
 8TN  N29  C10  C7   122.24  3.000
 8TN  N26  C10  C7   120.47  3.000
 8TN  N30  C11  N27  118.45  3.000
 8TN  N27  C11  C7   120.36  3.000
 8TN  N30  C11  C7   121.18  3.000
 8TN  H3   C12  C17  119.09  3.000
 8TN  H3   C12  C15  122.55  3.000
 8TN  C17  C12  C15  118.36  3.000
 8TN  H4   C13  S33  120.35  3.000
 8TN  H4   C13  C16  126.01  3.000
 8TN  S33  C13  C16  113.64  3.000
 8TN  C18  C14  C15  121.97  3.000
 8TN  C15  C14  C8   122.68  3.000
 8TN  C18  C14  C8   115.35  3.000
 8TN  C24  C15  C14  121.24  3.000
 8TN  C24  C15  C12  118.54  3.000
 8TN  C14  C15  C12  120.22  3.000
 8TN  N28  C16  C19  125.04  3.000
 8TN  N28  C16  C13  111.45  3.000
 8TN  C19  C16  C13  123.50  3.000
 8TN  H8   C19  H7   108.01  3.000
 8TN  H8   C19  H6   108.20  3.000
 8TN  H7   C19  H6   108.10  3.000
 8TN  H8   C19  C16  112.46  3.000
 8TN  H7   C19  C16  112.08  3.000
 8TN  H6   C19  C16  107.83  3.000
 8TN  H11  C20  H10  108.19  3.000
 8TN  H11  C20  H9   108.10  3.000
 8TN  H10  C20  H9   108.43  3.000
 8TN  H11  C20  C24  110.27  3.000
 8TN  H10  C20  C24  111.80  3.000
 8TN  H9   C20  C24  109.94  3.000
 8TN  H14  C21  H13  107.67  3.000
 8TN  H14  C21  H12  107.78  3.000
 8TN  H13  C21  H12  107.76  3.000
 8TN  H14  C21  N31  112.93  3.000
 8TN  H13  C21  N31  110.58  3.000
 8TN  H12  C21  N31  109.94  3.000
 8TN  H17  C22  H16  107.91  3.000
 8TN  H17  C22  H15  107.65  3.000
 8TN  H16  C22  H15  107.77  3.000
 8TN  H17  C22  N31  109.88  3.000
 8TN  H16  C22  N31  110.13  3.000
 8TN  H15  C22  N31  113.32  3.000
 8TN  H18  C24  N30  106.68  3.000
 8TN  H18  C24  C20  108.42  3.000
 8TN  N30  C24  C20  112.08  3.000
 8TN  H18  C24  C15  108.99  3.000
 8TN  N30  C24  C15  108.91  3.000
 8TN  C20  C24  C15  111.61  3.000
 8TN  C6   N26  C10  116.42  3.000
 8TN  H21  C4   C9   119.52  3.000
 8TN  H21  C4   C2   120.13  3.000
 8TN  C9   C4   C2   120.36  3.000
 8TN  H22  C5   C9   119.38  3.000
 8TN  H22  C5   C8   119.29  3.000
 8TN  C9   C5   C8   121.34  3.000
 8TN  H23  C6   N27  115.60  3.000
 8TN  H23  C6   N26  115.74  3.000
 8TN  N27  C6   N26  128.66  3.000
 8TN  S33  C17  N28  111.35  3.000
 8TN  N28  C17  C12  122.59  3.000
 8TN  S33  C17  C12  126.05  3.000
 8TN  O32  C18  N28  120.35  3.000
 8TN  O32  C18  C14  124.37  3.000
 8TN  N28  C18  C14  115.28  3.000
 8TN  H25  C23  H24  106.25  3.000
 8TN  H25  C23  N31  107.76  3.000
 8TN  H24  C23  N31  112.00  3.000
 8TN  H25  C23  C9   109.10  3.000
 8TN  H24  C23  C9   109.49  3.000
 8TN  N31  C23  C9   112.02  3.000
 8TN  C6   N27  C11  116.60  3.000
 8TN  C18  N28  C17  121.53  3.000
 8TN  C18  N28  C16  125.05  3.000
 8TN  C17  N28  C16  113.42  3.000
 8TN  H26  N30  C24  117.76  3.000
 8TN  H26  N30  C11  118.01  3.000
 8TN  C24  N30  C11  123.87  3.000
 8TN  C23  N31  C22  111.22  3.000
 8TN  C23  N31  C21  111.76  3.000
 8TN  C22  N31  C21  111.07  3.000
 8TN  C17  S33  C13   90.13  3.000
 8TN  H20  N29  H19  117.69  3.000
 8TN  H20  N29  C10  119.35  3.000
 8TN  H19  N29  C10  122.86  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
 8TN  CONST_01  C5   C8   C3   C2      0.00   0.0  0
 8TN  CONST_02  C5   C9   C4   C2      0.00   0.0  0
 8TN  CONST_03  C9   C5   C8   C3      0.00   0.0  0
 8TN  CONST_04  C9   C4   C2   C3      0.00   0.0  0
 8TN  CONST_05  C6   N27  C11  C7      0.00   0.0  0
 8TN  CONST_06  C6   N26  C10  C7      0.00   0.0  0
 8TN  CONST_07  C4   C9   C5   C8      0.00   0.0  0
 8TN  CONST_08  C4   C2   C3   C8      0.00   0.0  0
 8TN  CONST_09  N27  C11  C7   C10     0.00   0.0  0
 8TN  CONST_10  N27  C6   N26  C10     0.00   0.0  0
 8TN  CONST_11  N26  C6   N27  C11     0.00   0.0  0
 8TN  CONST_12  N26  C10  C7   C11     0.00   0.0  0
 8TN  CONST_13  C14  C8   C3   C2    180.00   0.0  0
 8TN  CONST_14  C14  C8   C5   C9    180.00   0.0  0
 8TN  CONST_15  C16  N28  C18  C14   180.00   0.0  0
 8TN  CONST_16  C17  N28  C18  C14     0.00   0.0  0
 8TN  CONST_17  N27  C11  C7   C1    180.00   0.0  0
 8TN  CONST_18  N26  C10  C7   C1    180.00   0.0  0
 8TN  CONST_19  C23  C9   C4   C2    180.00   0.0  0
 8TN  CONST_20  C23  C9   C5   C8    180.00   0.0  0
 8TN  CONST_21  N30  C11  C7   C10   180.00   0.0  0
 8TN  CONST_22  N29  C10  C7   C11   180.00   0.0  0
 8TN  CONST_23  C6   N26  C10  N29   180.00   0.0  0
 8TN  CONST_24  N30  C11  N27  C6    180.00   0.0  0
 8TN  CONST_25  O32  C18  N28  C16     0.00   0.0  0
 8TN  CONST_26  O32  C18  N28  C17   180.00   0.0  0
 8TN  CONST_27  H22  C5   C8   C3    180.00   0.0  0
 8TN  CONST_28  H21  C4   C2   C3    180.00   0.0  0
 8TN  CONST_29  H1   C2   C3   C8    180.00   0.0  0
 8TN  CONST_30  H23  C6   N26  C10   180.00   0.0  0
 8TN  CONST_31  H2   C3   C8   C14     0.00   0.0  0
 8TN  CONST_32  C24  N30  C11  C7    180.00   0.0  0
 8TN  CONST_33  N27  C11  N30  C24     0.00   0.0  0
 8TN  CONST_34  H26  N30  C11  C7      0.00   0.0  0
 8TN  CONST_35  H19  N29  C10  C7      0.00   0.0  0
 8TN  CONST_36  H20  N29  C10  C7    180.00   0.0  0
 8TN  Var_01    C18  C14  C8   C3   -102.35  30.0  2
 8TN  Var_02    N31  C23  C9   C4     57.46  30.0  1
 8TN  Var_03    H6   C19  C16  C13     1.20  30.0  3
 8TN  Var_04    C22  N31  C23  C9   -169.28  30.0  2
 8TN  Var_05    H15  C22  N31  C21    62.28  30.0  3
 8TN  Var_06    H12  C21  N31  C22    57.78  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
 8TN  chir_01  C24  C15  C20  N30  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
 8TN  plan-1  C1   0.020
 8TN  plan-1  C7   0.020
 8TN  plan-1  C10  0.020
 8TN  plan-1  C11  0.020
 8TN  plan-1  N25  0.020
 8TN  plan-1  N26  0.020
 8TN  plan-1  C6   0.020
 8TN  plan-1  N27  0.020
 8TN  plan-1  N30  0.020
 8TN  plan-1  H23  0.020
 8TN  plan-1  N29  0.020
 8TN  plan-2  C2   0.020
 8TN  plan-2  C3   0.020
 8TN  plan-2  C8   0.020
 8TN  plan-2  C9   0.020
 8TN  plan-2  C14  0.020
 8TN  plan-2  C4   0.020
 8TN  plan-2  C5   0.020
 8TN  plan-2  C23  0.020
 8TN  plan-2  H1   0.020
 8TN  plan-2  H2   0.020
 8TN  plan-2  H21  0.020
 8TN  plan-2  H22  0.020
 8TN  plan-3  C8   0.020
 8TN  plan-3  C12  0.020
 8TN  plan-3  C13  0.020
 8TN  plan-3  C14  0.020
 8TN  plan-3  C15  0.020
 8TN  plan-3  C16  0.020
 8TN  plan-3  C19  0.020
 8TN  plan-3  C24  0.020
 8TN  plan-3  C17  0.020
 8TN  plan-3  C18  0.020
 8TN  plan-3  N28  0.020
 8TN  plan-3  O32  0.020
 8TN  plan-3  S33  0.020
 8TN  plan-3  H3   0.020
 8TN  plan-3  H4   0.020
 8TN  plan-4  C11  0.020
 8TN  plan-4  C24  0.020
 8TN  plan-4  N30  0.020
 8TN  plan-4  H26  0.020
 8TN  plan-5  C10  0.020
 8TN  plan-5  H19  0.020
 8TN  plan-5  H20  0.020
 8TN  plan-5  N29  0.020

