# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:35:26 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 2-{[3-(1,4-diazepan-1-yl)phenyl]amino}-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1sc(c(C)n1)c2nc(Nc3cccc(c3)N4CCCNCC4)ncc2C#N
#
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
 T3C  T3C  2-{[3-(1,4-diazepan-1-yl)phenyl]amino}-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile  ligand  54  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_T3C
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
 T3C  C01   C  CH3   0  -0.516   8.5602  -0.7881   0.2179
 T3C  N02   N  NH1   0  -0.638   7.5707   0.2657   0.2200
 T3C  C03   C  CR5   0   0.359   6.2678   0.0099   0.2224
 T3C  N04   N  N     0  -0.457   5.7687  -1.2031   0.2268
 T3C  C05   C  CR5   0   0.392   4.4187  -1.1929   0.2286
 T3C  C06   C  CH3   0  -0.726   3.7344  -2.5194   0.2333
 T3C  C07   C  CR5   0  -0.389   3.8248   0.0606   0.2265
 T3C  C08   C  CR6   0   0.398   2.4240   0.3766   0.2290
 T3C  N09   N  N     0  -0.514   1.5835  -0.6475   0.2075
 T3C  C10   C  CR6   0   0.621   0.2705  -0.4297   0.2147
 T3C  N11   N  NH1   0  -0.768  -0.4746  -1.5562   0.1932
 T3C  C12   C  CR6   0   0.386  -1.8526  -1.7787   0.2209
 T3C  C13   C  CR16  0  -0.390  -2.2499  -3.1210   0.2511
 T3C  C14   C  CR16  0  -0.231  -3.5973  -3.4219   0.2649
 T3C  C15   C  CR16  0  -0.383  -4.5654  -2.4273   0.2650
 T3C  C16   C  CR6   0   0.406  -4.1827  -1.0804   0.2304
 T3C  N17   N  NT    0  -0.507  -5.1073  -0.0476   0.2000
 T3C  C18   C  CH2   0  -0.303  -6.4918  -0.3434  -0.0984
 T3C  C19   C  CH2   0  -0.448  -7.2382   0.8112  -0.7588
 T3C  C20   C  CH2   0  -0.320  -7.4267   2.0490   0.1209
 T3C  N21   N  NH1   0  -0.600  -6.3262   2.9949   0.1929
 T3C  C22   C  CH2   0  -0.272  -4.9757   2.4494   0.2629
 T3C  C23   C  CH2   0  -0.354  -4.8766   1.1311   1.0214
 T3C  C24   C  CR16  0  -0.420  -2.8110  -0.7736   0.1974
 T3C  N25   N  N     0  -0.470  -0.3229   0.7685   0.2397
 T3C  C26   C  CR16  0   0.049   0.4916   1.7990   0.2597
 T3C  C27   C  CR6   0  -0.153   1.8806   1.6918   0.2561
 T3C  C28   C  CSP   0  -0.036   2.6249   2.8936   0.2810
 T3C  N29   N  NS    0  -0.243   3.1760   3.9081   0.3074
 T3C  S30   S  S2    0   0.169   5.0892   1.2800   0.2224
 T3C  H011  H  HCH3  0   0.246   8.4657  -1.4240   1.0980
 T3C  H012  H  HCH3  0   0.246   8.4761  -1.4137  -0.6710
 T3C  H013  H  HCH3  0   0.261   9.5424  -0.3262   0.2264
 T3C  H02   H  HNH1  0   0.419   7.8874   1.2205   0.2079
 T3C  H061  H  HCH3  0   0.256   3.0747  -2.6277   1.0927
 T3C  H062  H  HCH3  0   0.256   3.1131  -2.6507  -0.6514
 T3C  H063  H  HCH3  0   0.249   4.4844  -3.3066   0.2592
 T3C  H11   H  HNH1  0   0.413   0.0904  -2.3925   0.1739
 T3C  H13   H  HCR6  0   0.262  -1.5106  -3.9123   0.2657
 T3C  H24   H  HCR6  0   0.291  -2.4911   0.2527   0.1245
 T3C  H14   H  HCR6  0   0.254  -3.9065  -4.4590   0.2987
 T3C  H15   H  HCR6  0   0.262  -5.6064  -2.7127   0.3205
 T3C  H181  H  HCH2  0   0.246  -6.5228  -1.1905  -0.7835
 T3C  H182  H  HCH2  0   0.208  -7.0422  -0.6447   0.8066
 T3C  H231  H  HCH2  0   0.242  -5.5672   1.1328   1.8759
 T3C  H232  H  HCH2  0   0.263  -3.8824   1.0652   1.4576
 T3C  H191  H  HCH2  0   0.227  -6.7545   1.0804  -1.7024
 T3C  H192  H  HCH2  0   0.237  -8.2275   0.4242  -1.0180
 T3C  H201  H  HCH2  0   0.240  -8.2935   2.6094  -0.2339
 T3C  H202  H  HCH2  0   0.210  -7.6893   1.7120   1.1305
 T3C  H21   H  HNH1  0   0.347  -6.3788   3.6228  -0.5963
 T3C  H221  H  HCH2  0   0.205  -4.5284   2.2883  -0.7265
 T3C  H222  H  HCH2  0   0.223  -4.3405   3.1818   0.7710
 T3C  H26   H  HCR6  0   0.295   0.0341   2.7820   0.2807

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
 T3C  C01  N02   single    1.446  0.020  1.446
 T3C  N02  C03   single    1.328  0.020  1.328
 T3C  C03  N04   aromatic  1.312  0.020  1.312
 T3C  C03  S30   aromatic  1.733  0.020  1.733
 T3C  N04  C05   aromatic  1.350  0.020  1.350
 T3C  C05  C06   single    1.493  0.020  1.493
 T3C  C05  C07   aromatic  1.387  0.020  1.387
 T3C  C07  C08   single    1.436  0.020  1.436
 T3C  C07  S30   aromatic  1.757  0.020  1.757
 T3C  C08  N09   aromatic  1.325  0.020  1.325
 T3C  C08  C27   aromatic  1.423  0.020  1.423
 T3C  N09  C10   aromatic  1.331  0.020  1.331
 T3C  C10  N11   single    1.351  0.020  1.351
 T3C  C10  N25   aromatic  1.337  0.020  1.337
 T3C  N11  C12   single    1.396  0.020  1.396
 T3C  C12  C13   aromatic  1.400  0.020  1.400
 T3C  C12  C24   aromatic  1.389  0.020  1.389
 T3C  C13  C14   aromatic  1.381  0.020  1.381
 T3C  C14  C15   aromatic  1.388  0.020  1.388
 T3C  C15  C16   aromatic  1.401  0.020  1.401
 T3C  C16  N17   single    1.387  0.020  1.387
 T3C  C16  C24   aromatic  1.406  0.020  1.406
 T3C  N17  C18   single    1.447  0.020  1.447
 T3C  N17  C23   single    1.455  0.020  1.455
 T3C  C18  C19   single    1.525  0.020  1.525
 T3C  C19  C20   single    1.530  0.020  1.530
 T3C  C20  N21   single    1.453  0.020  1.453
 T3C  N21  C22   single    1.458  0.020  1.458
 T3C  C22  C23   single    1.524  0.020  1.524
 T3C  N25  C26   aromatic  1.314  0.020  1.314
 T3C  C26  C27   aromatic  1.393  0.020  1.393
 T3C  C27  C28   single    1.414  0.020  1.414
 T3C  C28  N29   triple    1.155  0.020  1.155
 T3C  C01  H011  single    0.970  0.020  1.090
 T3C  C01  H012  single    0.970  0.020  1.090
 T3C  C01  H013  single    0.970  0.020  1.090
 T3C  N02  H02   single    0.860  0.020  1.020
 T3C  C06  H061  single    0.970  0.020  1.090
 T3C  C06  H062  single    0.970  0.020  1.090
 T3C  C06  H063  single    0.970  0.020  1.090
 T3C  N11  H11   single    0.860  0.020  1.020
 T3C  C13  H13   single    0.930  0.020  1.080
 T3C  C24  H24   single    0.930  0.020  1.080
 T3C  C14  H14   single    0.930  0.020  1.080
 T3C  C15  H15   single    0.930  0.020  1.080
 T3C  C18  H181  single    0.970  0.020  1.090
 T3C  C18  H182  single    0.970  0.020  1.090
 T3C  C23  H231  single    0.970  0.020  1.090
 T3C  C23  H232  single    0.970  0.020  1.090
 T3C  C19  H191  single    0.970  0.020  1.090
 T3C  C19  H192  single    0.970  0.020  1.090
 T3C  C20  H201  single    0.970  0.020  1.090
 T3C  C20  H202  single    0.970  0.020  1.090
 T3C  N21  H21   single    0.890  0.020  1.040
 T3C  C22  H221  single    0.970  0.020  1.090
 T3C  C22  H222  single    0.970  0.020  1.090
 T3C  C26  H26   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
 T3C  H013  C01  H012  108.69  3.000
 T3C  H013  C01  H011  108.68  3.000
 T3C  H012  C01  H011  108.48  3.000
 T3C  H013  C01  N02   108.01  3.000
 T3C  H012  C01  N02   111.51  3.000
 T3C  H011  C01  N02   111.39  3.000
 T3C  H02   N02  C03   119.47  3.000
 T3C  H02   N02  C01   118.44  3.000
 T3C  C03   N02  C01   122.09  3.000
 T3C  S30   C03  N04   114.77  3.000
 T3C  S30   C03  N02   121.75  3.000
 T3C  N04   C03  N02   123.48  3.000
 T3C  C05   N04  C03   111.93  3.000
 T3C  C07   C05  C06   127.36  3.000
 T3C  C07   C05  N04   115.78  3.000
 T3C  C06   C05  N04   116.86  3.000
 T3C  H063  C06  H062  108.99  3.000
 T3C  H063  C06  H061  109.09  3.000
 T3C  H062  C06  H061  106.47  3.000
 T3C  H063  C06  C05   109.09  3.000
 T3C  H062  C06  C05   111.48  3.000
 T3C  H061  C06  C05   111.63  3.000
 T3C  S30   C07  C08   123.32  3.000
 T3C  S30   C07  C05   108.62  3.000
 T3C  C08   C07  C05   128.06  3.000
 T3C  C27   C08  N09   118.18  3.000
 T3C  C27   C08  C07   125.16  3.000
 T3C  N09   C08  C07   116.66  3.000
 T3C  C10   N09  C08   119.95  3.000
 T3C  N25   C10  N11   120.18  3.000
 T3C  N25   C10  N09   125.77  3.000
 T3C  N11   C10  N09   114.05  3.000
 T3C  H11   N11  C12   114.88  3.000
 T3C  H11   N11  C10   112.49  3.000
 T3C  C12   N11  C10   132.61  3.000
 T3C  C24   C12  C13   119.89  3.000
 T3C  C24   C12  N11   124.43  3.000
 T3C  C13   C12  N11   115.68  3.000
 T3C  H13   C13  C14   120.45  3.000
 T3C  H13   C13  C12   120.47  3.000
 T3C  C14   C13  C12   119.08  3.000
 T3C  H14   C14  C15   119.15  3.000
 T3C  H14   C14  C13   119.20  3.000
 T3C  C15   C14  C13   121.64  3.000
 T3C  H15   C15  C16   121.22  3.000
 T3C  H15   C15  C14   118.86  3.000
 T3C  C16   C15  C14   119.90  3.000
 T3C  C24   C16  N17   119.18  3.000
 T3C  C24   C16  C15   118.49  3.000
 T3C  N17   C16  C15   122.32  3.000
 T3C  C23   N17  C18   115.71  3.000
 T3C  C23   N17  C16   119.03  3.000
 T3C  C18   N17  C16   119.37  3.000
 T3C  H182  C18  H181  106.84  3.000
 T3C  H182  C18  C19   108.56  3.000
 T3C  H181  C18  C19   107.59  3.000
 T3C  H182  C18  N17   111.39  3.000
 T3C  H181  C18  N17   108.41  3.000
 T3C  C19   C18  N17   113.76  3.000
 T3C  H192  C19  H191  106.42  3.000
 T3C  H192  C19  C20   108.13  3.000
 T3C  H191  C19  C20   110.56  3.000
 T3C  H192  C19  C18   106.11  3.000
 T3C  H191  C19  C18   110.08  3.000
 T3C  C20   C19  C18   115.07  3.000
 T3C  H202  C20  H201  105.48  3.000
 T3C  H202  C20  N21   109.63  3.000
 T3C  H201  C20  N21   106.46  3.000
 T3C  H202  C20  C19   108.07  3.000
 T3C  H201  C20  C19   109.04  3.000
 T3C  N21   C20  C19   117.51  3.000
 T3C  H21   N21  C22   108.56  3.000
 T3C  H21   N21  C20   109.06  3.000
 T3C  C22   N21  C20   117.41  3.000
 T3C  H222  C22  H221  106.26  3.000
 T3C  H222  C22  C23   108.06  3.000
 T3C  H221  C22  C23   107.16  3.000
 T3C  H222  C22  N21   108.03  3.000
 T3C  H221  C22  N21   112.90  3.000
 T3C  C23   C22  N21   114.06  3.000
 T3C  H232  C23  H231  105.23  3.000
 T3C  H232  C23  C22   108.15  3.000
 T3C  H231  C23  C22   110.17  3.000
 T3C  H232  C23  N17   108.80  3.000
 T3C  H231  C23  N17   109.91  3.000
 T3C  C22   C23  N17   114.17  3.000
 T3C  H24   C24  C16   119.94  3.000
 T3C  H24   C24  C12   119.04  3.000
 T3C  C16   C24  C12   120.99  3.000
 T3C  C26   N25  C10   115.34  3.000
 T3C  H26   C26  C27   119.37  3.000
 T3C  H26   C26  N25   116.73  3.000
 T3C  C27   C26  N25   123.90  3.000
 T3C  C28   C27  C26   117.35  3.000
 T3C  C28   C27  C08   125.79  3.000
 T3C  C26   C27  C08   116.86  3.000
 T3C  N29   C28  C27   180.00  3.000
 T3C  C07   S30  C03    88.89  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
 T3C  CONST_01  C07   C05  N04  C03     0.00   0.0  0
 T3C  CONST_02  C05   C07  S30  C03     0.00   0.0  0
 T3C  CONST_03  C08   C07  S30  C03   180.00   0.0  0
 T3C  CONST_04  C07   S30  C03  N04     0.00   0.0  0
 T3C  CONST_05  C08   C07  C05  N04   180.00   0.0  0
 T3C  CONST_06  S30   C07  C05  N04     0.00   0.0  0
 T3C  CONST_07  S30   C03  N04  C05     0.00   0.0  0
 T3C  CONST_08  N09   C08  C07  C05     0.00   0.0  0
 T3C  CONST_09  C27   C08  C07  C05   180.00   0.0  0
 T3C  CONST_10  C10   N09  C08  C07   180.00   0.0  0
 T3C  CONST_11  C26   C27  C08  C07   180.00   0.0  0
 T3C  CONST_12  N25   C10  N09  C08     0.00   0.0  0
 T3C  CONST_13  N25   C26  C27  C08     0.00   0.0  0
 T3C  CONST_14  S30   C07  C08  N09   180.00   0.0  0
 T3C  CONST_15  C26   C27  C08  N09     0.00   0.0  0
 T3C  CONST_16  C26   N25  C10  N09     0.00   0.0  0
 T3C  CONST_17  C27   C08  N09  C10     0.00   0.0  0
 T3C  CONST_18  C27   C26  N25  C10     0.00   0.0  0
 T3C  CONST_19  C15   C14  C13  C12     0.00   0.0  0
 T3C  CONST_20  C15   C16  C24  C12     0.00   0.0  0
 T3C  CONST_21  C16   C24  C12  C13     0.00   0.0  0
 T3C  CONST_22  C16   C15  C14  C13     0.00   0.0  0
 T3C  CONST_23  C24   C12  C13  C14     0.00   0.0  0
 T3C  CONST_24  C24   C16  C15  C14     0.00   0.0  0
 T3C  CONST_25  S30   C07  C08  C27     0.00   0.0  0
 T3C  CONST_26  N17   C16  C24  C12   180.00   0.0  0
 T3C  CONST_27  N17   C16  C15  C14   180.00   0.0  0
 T3C  CONST_28  C05   N04  C03  N02   180.00   0.0  0
 T3C  CONST_29  C07   S30  C03  N02   180.00   0.0  0
 T3C  CONST_30  C06   C05  N04  C03   180.00   0.0  0
 T3C  CONST_31  C08   C07  C05  C06     0.00   0.0  0
 T3C  CONST_32  S30   C07  C05  C06   180.00   0.0  0
 T3C  CONST_33  C28   C27  C08  C07     0.00   0.0  0
 T3C  CONST_34  N11   C10  N09  C08   180.00   0.0  0
 T3C  CONST_35  C28   C27  C08  N09   180.00   0.0  0
 T3C  CONST_36  C26   N25  C10  N11   180.00   0.0  0
 T3C  CONST_37  C14   C13  C12  N11   180.00   0.0  0
 T3C  CONST_38  C16   C24  C12  N11   180.00   0.0  0
 T3C  CONST_39  C28   C27  C26  N25   180.00   0.0  0
 T3C  CONST_40  H26   C26  C27  C08   180.00   0.0  0
 T3C  CONST_41  H14   C14  C13  C12   180.00   0.0  0
 T3C  CONST_42  H24   C24  C12  C13   180.00   0.0  0
 T3C  CONST_43  H15   C15  C14  C13   180.00   0.0  0
 T3C  CONST_44  H13   C13  C14  C15   180.00   0.0  0
 T3C  CONST_45  N04   C03  N02  C01     0.00   0.0  0
 T3C  CONST_46  S30   C03  N02  C01   180.00   0.0  0
 T3C  CONST_47  H02   N02  C03  N04   180.00   0.0  0
 T3C  Var_01    C12   N11  C10  N09   178.36  30.0  2
 T3C  Var_02    C13   C12  N11  C10  -176.89  30.0  2
 T3C  Var_03    H061  C06  C05  N04   122.01  30.0  2
 T3C  Var_04    H011  C01  N02  C03   -60.14  30.0  3

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
 T3C  plan-1  N02  0.020
 T3C  plan-1  C03  0.020
 T3C  plan-1  N04  0.020
 T3C  plan-1  C05  0.020
 T3C  plan-1  C06  0.020
 T3C  plan-1  C07  0.020
 T3C  plan-1  C08  0.020
 T3C  plan-1  S30  0.020
 T3C  plan-2  C07  0.020
 T3C  plan-2  C08  0.020
 T3C  plan-2  N09  0.020
 T3C  plan-2  C10  0.020
 T3C  plan-2  N11  0.020
 T3C  plan-2  N25  0.020
 T3C  plan-2  C26  0.020
 T3C  plan-2  C27  0.020
 T3C  plan-2  C28  0.020
 T3C  plan-2  N29  0.020
 T3C  plan-2  H26  0.020
 T3C  plan-3  N11  0.020
 T3C  plan-3  C12  0.020
 T3C  plan-3  C13  0.020
 T3C  plan-3  C14  0.020
 T3C  plan-3  C15  0.020
 T3C  plan-3  C16  0.020
 T3C  plan-3  N17  0.020
 T3C  plan-3  C24  0.020
 T3C  plan-3  H13  0.020
 T3C  plan-3  H24  0.020
 T3C  plan-3  H14  0.020
 T3C  plan-3  H15  0.020
 T3C  plan-4  C01  0.020
 T3C  plan-4  N02  0.020
 T3C  plan-4  C03  0.020
 T3C  plan-4  H02  0.020

