# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:07:47 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: N-(2-chloro-6-methylphenyl)-2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-1,3-thiazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(Nc2sc(cn2)C(=O)Nc3c(C)cccc3Cl)cc(n1)N4CCN(CCO)CC4
#
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
 1N1  1N1  N-(2-chloro-6-methylphenyl)-2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-1,3-thiazole-5-carboxamide  ligand  59  33  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1N1
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
 1N1  C1    C   CR15  0   0.043   -2.4393   1.5936   0.8274
 1N1  C2    C   CR5   0  -0.392   -3.1212   0.5434   0.2930
 1N1  C3    C   C     0   0.533   -4.5822   0.4274   0.2247
 1N1  N6    N   NT    0  -0.418    7.9454  -0.9610  -0.4156
 1N1  C7    C   CR16  0  -0.245   -9.1812  -1.5397  -0.4105
 1N1  C8    C   CR16  0  -0.310   -8.4514  -2.0715   0.6415
 1N1  C9    C   CR6   0   0.075   -7.0874  -1.8266   0.7655
 1N1  C10   C   CH3   0  -0.731   -6.3026  -2.3904   1.9118
 1N1  C11   C   CR6   0   0.547    1.7762   0.6402   0.3365
 1N1  C12   C   CR16  0  -0.541    2.9469  -0.0885   0.1839
 1N1  C13   C   CR6   0   0.587    4.1456   0.6001   0.4113
 1N1  C14   C   CR6   0   0.357    2.9376   2.4750   0.9089
 1N1  C15   C   CH3   0  -0.729    2.9224   3.9183   1.3056
 1N1  C16   C   CH2   0  -0.304    6.5629   0.6424   0.8037
 1N1  C19   C   CH2   0  -0.309    5.5411  -1.3493  -0.1344
 1N1  C20   C   CH2   0  -0.294    9.1203  -1.1995  -1.2325
 1N1  C21   C   CH2   0  -0.172   10.4332  -1.0145  -0.5006
 1N1  N     N   NH1   0  -0.749    0.5841  -0.0223   0.1013
 1N1  C     C   CR5   0   0.323   -0.6914   0.4083   0.2776
 1N1  N1    N   N     0  -0.393   -1.0870   1.5172   0.8239
 1N1  S     S   S2    0   0.203   -1.9781  -0.6264  -0.2852
 1N1  N2    N   NH1   0  -0.764   -5.0724  -0.7949  -0.1101
 1N1  C4    C   CR6   0   0.356   -6.4554  -1.0426  -0.2041
 1N1  C5    C   CR6   0  -0.072   -7.1955  -0.5274  -1.2652
 1N1  C6    C   CR16  0  -0.251   -8.5561  -0.7630  -1.3740
 1N1  CL    CL  CL    0  -0.112   -6.4035   0.3987  -2.4901
 1N1  O     O   O     0  -0.453   -5.3016   1.3817   0.4604
 1N1  N3    N   N     0  -0.498    4.1122   1.8883   0.7965
 1N1  N4    N   N     0  -0.459    1.7501   1.9170   0.6870
 1N1  N5    N   NT    0  -0.506    5.3639   0.0347   0.2535
 1N1  C17   C   CH2   0  -0.294    7.7470   0.4435  -0.1213
 1N1  C18   C   CH2   0  -0.277    6.7531  -1.4959  -1.0378
 1N1  O1    O   OH1   0  -0.670   10.5079  -1.9294   0.5686
 1N1  H1    H   HCR5  0   0.286   -2.9187   2.4609   1.2590
 1N1  H7    H   HCR6  0   0.269  -10.2426  -1.7335  -0.4878
 1N1  H8    H   HCR6  0   0.260   -8.9498  -2.6773   1.3876
 1N1  H101  H   HCH3  0   0.253   -5.5406  -3.0948   1.5727
 1N1  H102  H   HCH3  0   0.255   -5.7890  -1.6076   2.4711
 1N1  H103  H   HCH3  0   0.258   -6.9550  -2.9221   2.6016
 1N1  H12   H   HCR6  0   0.286    2.9068  -1.1354  -0.0762
 1N1  H151  H   HCH3  0   0.256    2.5856   4.5320   0.4680
 1N1  H152  H   HCH3  0   0.251    2.2228   4.0851   2.1244
 1N1  H153  H   HCH3  0   0.246    3.9113   4.2567   1.6037
 1N1  H161  H   HCH2  0   0.272    6.3918   1.7028   0.9588
 1N1  H162  H   HCH2  0   0.230    6.7862   0.1908   1.7780
 1N1  H191  H   HCH2  0   0.236    5.6536  -1.9836   0.7532
 1N1  H192  H   HCH2  0   0.263    4.6738  -1.7056  -0.6849
 1N1  H201  H   HCH2  0   0.235    9.0737  -2.2279  -1.6014
 1N1  H202  H   HCH2  0   0.199    9.1370  -0.5503  -2.1245
 1N1  H211  H   HCH2  0   0.206   11.2357  -1.1747  -1.2320
 1N1  H212  H   HCH2  0   0.196   10.5401   0.0209  -0.1530
 1N1  HN    H   HNH1  0   0.432    0.6883  -0.9653  -0.2419
 1N1  HN2   H   HNH1  0   0.409   -4.4606  -1.5974  -0.1205
 1N1  H6    H   HCR6  0   0.281   -9.1160  -0.3504  -2.2018
 1N1  H171  H   HCH2  0   0.246    8.6280   0.8495   0.3785
 1N1  H172  H   HCH2  0   0.198    7.5999   1.0327  -1.0437
 1N1  H181  H   HCH2  0   0.197    6.5350  -1.0051  -2.0024
 1N1  H182  H   HCH2  0   0.247    6.8986  -2.5585  -1.2434
 1N1  HO1   H   HOH1  0   0.452   11.3765  -1.8440   0.9706

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
 1N1  C1   C2    aromatic  1.361  0.020  1.361
 1N1  C1   N1    aromatic  1.354  0.020  1.354
 1N1  C1   H1    single    0.930  0.020  1.080
 1N1  C2   C3    single    1.467  0.020  1.467
 1N1  C2   S     aromatic  1.735  0.020  1.735
 1N1  C3   N2    single    1.359  0.020  1.359
 1N1  C3   O     double    1.218  0.020  1.218
 1N1  N6   C20   single    1.451  0.020  1.451
 1N1  N6   C17   single    1.449  0.020  1.449
 1N1  N6   C18   single    1.447  0.020  1.447
 1N1  C7   C8    aromatic  1.386  0.020  1.386
 1N1  C7   C6    aromatic  1.387  0.020  1.387
 1N1  C7   H7    single    0.930  0.020  1.080
 1N1  C8   C9    aromatic  1.391  0.020  1.391
 1N1  C8   H8    single    0.930  0.020  1.080
 1N1  C9   C10   single    1.499  0.020  1.499
 1N1  C9   C4    aromatic  1.398  0.020  1.398
 1N1  C10  H101  single    0.970  0.020  1.090
 1N1  C10  H102  single    0.970  0.020  1.090
 1N1  C10  H103  single    0.970  0.020  1.090
 1N1  C11  C12   aromatic  1.387  0.020  1.387
 1N1  C11  N     single    1.384  0.020  1.384
 1N1  C11  N4    aromatic  1.324  0.020  1.324
 1N1  C12  C13   aromatic  1.401  0.020  1.401
 1N1  C12  H12   single    0.930  0.020  1.080
 1N1  C13  N3    aromatic  1.345  0.020  1.345
 1N1  C13  N5    single    1.352  0.020  1.352
 1N1  C14  C15   single    1.497  0.020  1.497
 1N1  C14  N3    aromatic  1.318  0.020  1.318
 1N1  C14  N4    aromatic  1.331  0.020  1.331
 1N1  C15  H151  single    0.970  0.020  1.090
 1N1  C15  H152  single    0.970  0.020  1.090
 1N1  C15  H153  single    0.970  0.020  1.090
 1N1  C16  N5    single    1.452  0.020  1.452
 1N1  C16  C17   single    1.516  0.020  1.516
 1N1  C16  H161  single    0.970  0.020  1.090
 1N1  C16  H162  single    0.970  0.020  1.090
 1N1  C19  N5    single    1.448  0.020  1.448
 1N1  C19  C18   single    1.519  0.020  1.519
 1N1  C19  H191  single    0.970  0.020  1.090
 1N1  C19  H192  single    0.970  0.020  1.090
 1N1  C20  C21   single    1.514  0.020  1.514
 1N1  C20  H201  single    0.970  0.020  1.090
 1N1  C20  H202  single    0.970  0.020  1.090
 1N1  C21  O1    single    1.409  0.020  1.409
 1N1  C21  H211  single    0.970  0.020  1.090
 1N1  C21  H212  single    0.970  0.020  1.090
 1N1  N    C     single    1.358  0.020  1.358
 1N1  N    HN    single    0.860  0.020  1.020
 1N1  C    N1    aromatic  1.298  0.020  1.298
 1N1  C    S     aromatic  1.744  0.020  1.744
 1N1  N2   C4    single    1.408  0.020  1.408
 1N1  N2   HN2   single    0.860  0.020  1.020
 1N1  C4   C5    aromatic  1.393  0.020  1.393
 1N1  C5   C6    aromatic  1.385  0.020  1.385
 1N1  C5   CL    single    1.728  0.020  1.728
 1N1  C6   H6    single    0.930  0.020  1.080
 1N1  C17  H171  single    0.970  0.020  1.090
 1N1  C17  H172  single    0.970  0.020  1.090
 1N1  C18  H181  single    0.970  0.020  1.090
 1N1  C18  H182  single    0.970  0.020  1.090
 1N1  O1   HO1   single    0.850  0.020  0.980

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
 1N1  H1    C1   N1    119.28  3.000
 1N1  H1    C1   C2    123.61  3.000
 1N1  N1    C1   C2    117.10  3.000
 1N1  S     C2   C3    125.97  3.000
 1N1  S     C2   C1    108.72  3.000
 1N1  C3    C2   C1    125.31  3.000
 1N1  O     C3   N2    122.64  3.000
 1N1  O     C3   C2    121.14  3.000
 1N1  N2    C3   C2    116.22  3.000
 1N1  C18   N6   C17   109.43  3.000
 1N1  C18   N6   C20   111.37  3.000
 1N1  C17   N6   C20   112.62  3.000
 1N1  H7    C7   C6    119.54  3.000
 1N1  H7    C7   C8    120.13  3.000
 1N1  C6    C7   C8    120.32  3.000
 1N1  H8    C8   C9    119.24  3.000
 1N1  H8    C8   C7    119.68  3.000
 1N1  C9    C8   C7    121.07  3.000
 1N1  C4    C9   C10   120.30  3.000
 1N1  C4    C9   C8    118.70  3.000
 1N1  C10   C9   C8    121.00  3.000
 1N1  H103  C10  H102  107.93  3.000
 1N1  H103  C10  H101  107.46  3.000
 1N1  H102  C10  H101  107.08  3.000
 1N1  H103  C10  C9    110.77  3.000
 1N1  H102  C10  C9    111.64  3.000
 1N1  H101  C10  C9    111.75  3.000
 1N1  N4    C11  N     119.31  3.000
 1N1  N4    C11  C12   123.51  3.000
 1N1  N     C11  C12   117.18  3.000
 1N1  H12   C12  C13   123.20  3.000
 1N1  H12   C12  C11   120.30  3.000
 1N1  C13   C12  C11   116.49  3.000
 1N1  N5    C13  N3    117.15  3.000
 1N1  N5    C13  C12   123.12  3.000
 1N1  N3    C13  C12   119.73  3.000
 1N1  N4    C14  N3    126.48  3.000
 1N1  N4    C14  C15   116.06  3.000
 1N1  N3    C14  C15   117.45  3.000
 1N1  H153  C15  H152  109.29  3.000
 1N1  H153  C15  H151  108.42  3.000
 1N1  H152  C15  H151  107.00  3.000
 1N1  H153  C15  C14   111.32  3.000
 1N1  H152  C15  C14   110.69  3.000
 1N1  H151  C15  C14   109.99  3.000
 1N1  H162  C16  H161  107.90  3.000
 1N1  H162  C16  C17   109.22  3.000
 1N1  H161  C16  C17   109.79  3.000
 1N1  H162  C16  N5    109.41  3.000
 1N1  H161  C16  N5    109.44  3.000
 1N1  C17   C16  N5    111.03  3.000
 1N1  H192  C19  H191  107.58  3.000
 1N1  H192  C19  C18   107.68  3.000
 1N1  H191  C19  C18   110.11  3.000
 1N1  H192  C19  N5    110.55  3.000
 1N1  H191  C19  N5    110.40  3.000
 1N1  C18   C19  N5    110.44  3.000
 1N1  H202  C20  H201  106.33  3.000
 1N1  H202  C20  C21   107.80  3.000
 1N1  H201  C20  C21   108.35  3.000
 1N1  H202  C20  N6    111.77  3.000
 1N1  H201  C20  N6    108.06  3.000
 1N1  C21   C20  N6    114.20  3.000
 1N1  H212  C21  H211  106.12  3.000
 1N1  H212  C21  O1    111.53  3.000
 1N1  H211  C21  O1    111.84  3.000
 1N1  H212  C21  C20   110.66  3.000
 1N1  H211  C21  C20   107.10  3.000
 1N1  O1    C21  C20   109.47  3.000
 1N1  HN    N    C     115.96  3.000
 1N1  HN    N    C11   114.60  3.000
 1N1  C     N    C11   129.44  3.000
 1N1  S     C    N1    114.69  3.000
 1N1  S     C    N     117.58  3.000
 1N1  N1    C    N     127.73  3.000
 1N1  C     N1   C1    110.71  3.000
 1N1  C     S    C2     88.77  3.000
 1N1  HN2   N2   C4    117.05  3.000
 1N1  HN2   N2   C3    119.95  3.000
 1N1  C4    N2   C3    121.94  3.000
 1N1  C5    C4   N2    120.52  3.000
 1N1  C5    C4   C9    119.71  3.000
 1N1  N2    C4   C9    119.76  3.000
 1N1  CL    C5   C6    119.06  3.000
 1N1  CL    C5   C4    119.66  3.000
 1N1  C6    C5   C4    121.27  3.000
 1N1  H6    C6   C5    120.26  3.000
 1N1  H6    C6   C7    120.82  3.000
 1N1  C5    C6   C7    118.92  3.000
 1N1  C14   N3   C13   118.23  3.000
 1N1  C14   N4   C11   115.52  3.000
 1N1  C19   N5   C16   113.59  3.000
 1N1  C19   N5   C13   122.76  3.000
 1N1  C16   N5   C13   121.64  3.000
 1N1  H172  C17  H171  106.95  3.000
 1N1  H172  C17  C16   109.62  3.000
 1N1  H171  C17  C16   107.60  3.000
 1N1  H172  C17  N6    111.47  3.000
 1N1  H171  C17  N6    110.07  3.000
 1N1  C16   C17  N6    110.99  3.000
 1N1  H182  C18  H181  107.12  3.000
 1N1  H182  C18  C19   108.19  3.000
 1N1  H181  C18  C19   108.62  3.000
 1N1  H182  C18  N6    109.31  3.000
 1N1  H181  C18  N6    111.97  3.000
 1N1  C19   C18  N6    111.47  3.000
 1N1  HO1   O1   C21   107.92  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
 1N1  CONST_01  C     S    C2   C1      0.00   0.0  0
 1N1  CONST_02  S     C    N1   C1      0.00   0.0  0
 1N1  CONST_03  C     N1   C1   C2      0.00   0.0  0
 1N1  CONST_04  N1    C    S    C2      0.00   0.0  0
 1N1  CONST_05  C4    C9   C8   C7      0.00   0.0  0
 1N1  CONST_06  C4    C5   C6   C7      0.00   0.0  0
 1N1  CONST_07  C5    C6   C7   C8      0.00   0.0  0
 1N1  CONST_08  C5    C4   C9   C8      0.00   0.0  0
 1N1  CONST_09  C6    C7   C8   C9      0.00   0.0  0
 1N1  CONST_10  C6    C5   C4   C9      0.00   0.0  0
 1N1  CONST_11  N3    C13  C12  C11     0.00   0.0  0
 1N1  CONST_12  N3    C14  N4   C11     0.00   0.0  0
 1N1  CONST_13  C14   N4   C11  C12     0.00   0.0  0
 1N1  CONST_14  C14   N3   C13  C12     0.00   0.0  0
 1N1  CONST_15  N4    C11  C12  C13     0.00   0.0  0
 1N1  CONST_16  N4    C14  N3   C13     0.00   0.0  0
 1N1  CONST_17  S     C2   C1   N1      0.00   0.0  0
 1N1  CONST_18  N5    C13  C12  C11   180.00   0.0  0
 1N1  CONST_19  N5    C13  N3   C14   180.00   0.0  0
 1N1  CONST_20  N     C    N1   C1    180.00   0.0  0
 1N1  CONST_21  N     C    S    C2    180.00   0.0  0
 1N1  CONST_22  N1    C1   C2   C3    180.00   0.0  0
 1N1  CONST_23  C     S    C2   C3    180.00   0.0  0
 1N1  CONST_24  C10   C9   C8   C7    180.00   0.0  0
 1N1  CONST_25  CL    C5   C6   C7    180.00   0.0  0
 1N1  CONST_26  N2    C4   C9   C8    180.00   0.0  0
 1N1  CONST_27  CL    C5   C4   C9    180.00   0.0  0
 1N1  CONST_28  C5    C4   C9   C10   180.00   0.0  0
 1N1  CONST_29  C15   C14  N4   C11   180.00   0.0  0
 1N1  CONST_30  N     C11  C12  C13   180.00   0.0  0
 1N1  CONST_31  C15   C14  N3   C13   180.00   0.0  0
 1N1  CONST_32  N     C11  N4   C14   180.00   0.0  0
 1N1  CONST_33  C6    C5   C4   N2    180.00   0.0  0
 1N1  CONST_34  H6    C6   C7   C8    180.00   0.0  0
 1N1  CONST_35  H7    C7   C8   C9    180.00   0.0  0
 1N1  CONST_36  H1    C1   N1   C     180.00   0.0  0
 1N1  CONST_37  H8    C8   C9   C4    180.00   0.0  0
 1N1  CONST_38  H12   C12  C13  N3    180.00   0.0  0
 1N1  CONST_39  C4    N2   C3   C2    180.00   0.0  0
 1N1  CONST_43  O     C3   N2   C4      0.00   0.0  0
 1N1  Var_01    N5    C16  C17  N6    -55.15  30.0  1
 1N1  Var_02    N5    C19  C18  N6     55.40  30.0  1
 1N1  Var_03    C16   N5   C13  C12  -164.41  30.0  2
 1N1  Var_04    C17   C16  N5   C13  -143.85  30.0  1
 1N1  Var_05    C18   C19  N5   C13   144.28  30.0  1
 1N1  Var_06    C18   N6   C17  C16    59.12  30.0  1
 1N1  Var_07    C17   N6   C18  C19   -59.50  30.0  1
 1N1  Var_08    N1    C    N    C11    -6.56  30.0  2
 1N1  Var_09    C     N    C11  C12   174.14  30.0  2
 1N1  Var_10    N2    C3   C2   C1   -167.95  30.0  2
 1N1  Var_11    H101  C10  C9   C8    116.25  30.0  2
 1N1  Var_12    H151  C15  C14  N3    111.25  30.0  2
 1N1  Var_13    O1    C21  C20  N6     61.21  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
 1N1  plan-1  C1   0.020
 1N1  plan-1  C2   0.020
 1N1  plan-1  C3   0.020
 1N1  plan-1  N    0.020
 1N1  plan-1  C    0.020
 1N1  plan-1  N1   0.020
 1N1  plan-1  S    0.020
 1N1  plan-1  H1   0.020
 1N1  plan-2  C7   0.020
 1N1  plan-2  C8   0.020
 1N1  plan-2  C9   0.020
 1N1  plan-2  C10  0.020
 1N1  plan-2  N2   0.020
 1N1  plan-2  C4   0.020
 1N1  plan-2  C5   0.020
 1N1  plan-2  C6   0.020
 1N1  plan-2  CL   0.020
 1N1  plan-2  H7   0.020
 1N1  plan-2  H8   0.020
 1N1  plan-2  H6   0.020
 1N1  plan-3  C11  0.020
 1N1  plan-3  C12  0.020
 1N1  plan-3  C13  0.020
 1N1  plan-3  C14  0.020
 1N1  plan-3  C15  0.020
 1N1  plan-3  N    0.020
 1N1  plan-3  N3   0.020
 1N1  plan-3  N4   0.020
 1N1  plan-3  N5   0.020
 1N1  plan-3  H12  0.020
 1N1  plan-4  C2   0.020
 1N1  plan-4  C3   0.020
 1N1  plan-4  N2   0.020
 1N1  plan-4  C4   0.020
 1N1  plan-4  O    0.020
 1N1  plan-4  HN2  0.020

