# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:00:19 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-[2-({[(5-chlorothiophen-2-yl)carbonyl]amino}methyl)phenyl]-5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCc2nc(sc2C1)C(=O)Nc3ccccc3CNC(=O)c4sc(Cl)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
 D46  D46  N-[2-({[(5-chlorothiophen-2-yl)carbonyl]amino}methyl)phenyl]-5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridine-2-carboxamide  ligand  48  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D46
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
 D46  C1    C   CR16  0  -0.247  -2.3002   5.6739   0.4027
 D46  CL1   CL  CL    0  -0.055  -2.2239  -4.1098   1.6599
 D46  C2    C   CR16  0  -0.314  -2.4121   4.6508  -0.5285
 D46  C3    C   CR6   0   0.050  -1.5154   3.5903  -0.5446
 D46  C4    C   CR6   0   0.321  -0.5027   3.5537   0.4253
 D46  C5    C   CR16  0  -0.281  -0.3925   4.5699   1.3677
 D46  C6    C   CR16  0  -0.267  -1.2852   5.6317   1.3462
 D46  C7    C   CH2   0  -0.355  -1.6037   2.5537  -1.6352
 D46  N8    N   NH1   0  -0.697  -1.7356   1.2036  -1.1093
 D46  C9    C   C     0   0.551  -1.2294   0.1293  -1.7723
 D46  C10   C   CR5   0  -0.316  -1.4086  -1.1868  -1.1299
 D46  O11   O   O     0  -0.448  -0.5924   0.2287  -2.8060
 D46  N12   N   NH1   0  -0.770   0.3569   2.4429   0.4336
 D46  C13   C   C     0   0.513   1.6995   2.4430   0.6074
 D46  C14   C   CR5   0  -0.094   2.3037   1.0835   0.5029
 D46  O15   O   O     0  -0.436   2.3825   3.4263   0.8033
 D46  S16   S   S2    0   0.297  -2.1226  -1.4217   0.4249
 D46  C17   C   CR5   0  -0.237  -1.7753  -3.0989   0.3666
 D46  C18   C   CR15  0  -0.122  -1.1425  -3.4688  -0.7814
 D46  C19   C   CR15  0  -0.177  -0.9317  -2.3628  -1.6357
 D46  N20   N   N     0  -0.373   3.5237   0.8905   0.1187
 D46  C21   C   CR5   0   0.340   3.8169  -0.4366   0.0551
 D46  C22   C   CR5   0  -0.276   2.7992  -1.2766   0.3973
 D46  S23   S   S2    0   0.262   1.4230  -0.3684   0.8394
 D46  C24   C   CH2   0  -0.298   2.8942  -2.7647   0.3918
 D46  N25   N   NT    0  -0.419   4.0427  -3.1624  -0.3987
 D46  C26   C   CH2   0  -0.300   5.2430  -2.4451   0.0012
 D46  C27   C   CH2   0  -0.509   5.1436  -0.9686  -0.3690
 D46  C28   C   CH3   0  -0.522   4.2202  -4.5968  -0.3460
 D46  H1    H   HCR6  0   0.261  -3.0032   6.4957   0.3913
 D46  H2    H   HCR6  0   0.262  -3.2030   4.6819  -1.2675
 D46  H5    H   HCR6  0   0.273   0.3755   4.5289   2.1263
 D46  H6    H   HCR6  0   0.264  -1.1900   6.4198   2.0811
 D46  H7    H   HCH2  0   0.282  -2.4386   2.7884  -2.2992
 D46  H7A   H   HCH2  0   0.283  -0.6995   2.5849  -2.2443
 D46  HN8   H   HNH1  0   0.417  -2.4881   1.0645  -0.4492
 D46  HN12  H   HNH1  0   0.411  -0.0791   1.5880   0.1175
 D46  H18   H   HCR5  0   0.299  -0.8425  -4.4818  -1.0034
 D46  H19   H   HCR5  0   0.287  -0.4314  -2.4325  -2.5905
 D46  H24   H   HCH2  0   0.233   2.9544  -3.1297   1.4318
 D46  H24A  H   HCH2  0   0.258   1.9912  -3.2053  -0.0407
 D46  H26   H   HCH2  0   0.209   5.4325  -2.5455   1.0832
 D46  H26A  H   HCH2  0   0.251   6.0978  -2.8887  -0.5109
 D46  H27   H   HCH2  0   0.257   5.2666  -0.8411  -1.4481
 D46  H27A  H   HCH2  0   0.258   5.9496  -0.4098   0.1103
 D46  H28   H   HCH3  0   0.236   3.3123  -5.0969  -0.6868
 D46  H28A  H   HCH3  0   0.241   5.0336  -4.8951  -1.0077
 D46  H28B  H   HCH3  0   0.200   4.4493  -4.9704   0.6636

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
 D46  C1   C2    aromatic  1.388  0.020  1.388
 D46  C1   C6    aromatic  1.386  0.020  1.386
 D46  CL1  C17   single    1.702  0.020  1.702
 D46  C2   C3    aromatic  1.389  0.020  1.389
 D46  C3   C4    aromatic  1.403  0.020  1.403
 D46  C3   C7    single    1.507  0.020  1.507
 D46  C4   C5    aromatic  1.390  0.020  1.390
 D46  C4   N12   single    1.405  0.020  1.405
 D46  C5   C6    aromatic  1.387  0.020  1.387
 D46  C7   N8    single    1.455  0.020  1.455
 D46  N8   C9    single    1.360  0.020  1.360
 D46  C9   C10   single    1.475  0.020  1.475
 D46  C9   O11   double    1.218  0.020  1.218
 D46  C10  S16   aromatic  1.727  0.020  1.727
 D46  C10  C19   aromatic  1.366  0.020  1.366
 D46  N12  C13   single    1.354  0.020  1.354
 D46  C13  C14   single    1.491  0.020  1.491
 D46  C13  O15   double    1.213  0.020  1.213
 D46  C14  N20   aromatic  1.294  0.020  1.294
 D46  C14  S23   aromatic  1.731  0.020  1.731
 D46  S16  C17   aromatic  1.714  0.020  1.714
 D46  C17  C18   aromatic  1.362  0.020  1.362
 D46  C18  C19   aromatic  1.413  0.020  1.413
 D46  N20  C21   aromatic  1.361  0.020  1.361
 D46  C21  C22   aromatic  1.363  0.020  1.363
 D46  C21  C27   single    1.491  0.020  1.491
 D46  C22  S23   aromatic  1.707  0.020  1.707
 D46  C22  C24   single    1.491  0.020  1.491
 D46  C24  N25   single    1.450  0.020  1.450
 D46  N25  C26   single    1.454  0.020  1.454
 D46  N25  C28   single    1.446  0.020  1.446
 D46  C26  C27   single    1.525  0.020  1.525
 D46  C1   H1    single    0.930  0.020  1.080
 D46  C2   H2    single    0.930  0.020  1.080
 D46  C5   H5    single    0.930  0.020  1.080
 D46  C6   H6    single    0.930  0.020  1.080
 D46  C7   H7    single    0.970  0.020  1.090
 D46  C7   H7A   single    0.970  0.020  1.090
 D46  N8   HN8   single    0.890  0.020  1.040
 D46  N12  HN12  single    0.860  0.020  1.020
 D46  C18  H18   single    0.930  0.020  1.080
 D46  C19  H19   single    0.930  0.020  1.080
 D46  C24  H24   single    0.970  0.020  1.090
 D46  C24  H24A  single    0.970  0.020  1.090
 D46  C26  H26   single    0.970  0.020  1.090
 D46  C26  H26A  single    0.970  0.020  1.090
 D46  C27  H27   single    0.970  0.020  1.090
 D46  C27  H27A  single    0.970  0.020  1.090
 D46  C28  H28   single    0.970  0.020  1.090
 D46  C28  H28A  single    0.970  0.020  1.090
 D46  C28  H28B  single    0.970  0.020  1.090

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
 D46  H1    C1   C6    120.41  3.000
 D46  H1    C1   C2    120.05  3.000
 D46  C6    C1   C2    119.55  3.000
 D46  H2    C2   C3    119.05  3.000
 D46  H2    C2   C1    119.71  3.000
 D46  C3    C2   C1    121.24  3.000
 D46  C7    C3   C4    121.64  3.000
 D46  C7    C3   C2    119.72  3.000
 D46  C4    C3   C2    118.56  3.000
 D46  N12   C4   C5    121.70  3.000
 D46  N12   C4   C3    117.82  3.000
 D46  C5    C4   C3    120.45  3.000
 D46  H5    C5   C6    119.82  3.000
 D46  H5    C5   C4    120.31  3.000
 D46  C6    C5   C4    119.86  3.000
 D46  H6    C6   C5    119.37  3.000
 D46  H6    C6   C1    120.30  3.000
 D46  C5    C6   C1    120.33  3.000
 D46  H7A   C7   H7    106.74  3.000
 D46  H7A   C7   N8    107.67  3.000
 D46  H7    C7   N8    110.47  3.000
 D46  H7A   C7   C3    109.63  3.000
 D46  H7    C7   C3    109.68  3.000
 D46  N8    C7   C3    112.46  3.000
 D46  HN8   N8   C9    119.13  3.000
 D46  HN8   N8   C7    115.55  3.000
 D46  C9    N8   C7    121.54  3.000
 D46  O11   C9   C10   120.38  3.000
 D46  O11   C9   N8    122.94  3.000
 D46  C10   C9   N8    116.56  3.000
 D46  C19   C10  S16   111.14  3.000
 D46  C19   C10  C9    124.35  3.000
 D46  S16   C10  C9    124.30  3.000
 D46  HN12  N12  C13   117.91  3.000
 D46  HN12  N12  C4    113.78  3.000
 D46  C13   N12  C4    127.42  3.000
 D46  O15   C13  C14   121.47  3.000
 D46  O15   C13  N12   125.39  3.000
 D46  C14   C13  N12   113.12  3.000
 D46  S23   C14  N20   114.36  3.000
 D46  S23   C14  C13   123.01  3.000
 D46  N20   C14  C13   122.61  3.000
 D46  C17   S16  C10    91.07  3.000
 D46  C18   C17  S16   112.86  3.000
 D46  C18   C17  CL1   127.00  3.000
 D46  S16   C17  CL1   120.14  3.000
 D46  H18   C18  C19   124.65  3.000
 D46  H18   C18  C17   123.86  3.000
 D46  C19   C18  C17   111.49  3.000
 D46  H19   C19  C18   123.57  3.000
 D46  H19   C19  C10   122.99  3.000
 D46  C18   C19  C10   113.44  3.000
 D46  C21   N20  C14   111.26  3.000
 D46  C27   C21  C22   121.05  3.000
 D46  C27   C21  N20   123.58  3.000
 D46  C22   C21  N20   115.36  3.000
 D46  C24   C22  S23   125.68  3.000
 D46  C24   C22  C21   124.50  3.000
 D46  S23   C22  C21   109.82  3.000
 D46  C22   S23  C14    89.18  3.000
 D46  H24A  C24  H24   106.52  3.000
 D46  H24A  C24  N25   109.15  3.000
 D46  H24   C24  N25   112.32  3.000
 D46  H24A  C24  C22   110.54  3.000
 D46  H24   C24  C22   109.27  3.000
 D46  N25   C24  C22   109.04  3.000
 D46  C28   N25  C26   112.20  3.000
 D46  C28   N25  C24   110.45  3.000
 D46  C26   N25  C24   111.63  3.000
 D46  H26A  C26  H26   106.80  3.000
 D46  H26A  C26  C27   109.31  3.000
 D46  H26   C26  C27   109.72  3.000
 D46  H26A  C26  N25   108.49  3.000
 D46  H26   C26  N25   111.50  3.000
 D46  C27   C26  N25   110.90  3.000
 D46  H27A  C27  H27   106.89  3.000
 D46  H27A  C27  C26   109.92  3.000
 D46  H27   C27  C26   110.18  3.000
 D46  H27A  C27  C21   110.45  3.000
 D46  H27   C27  C21   109.83  3.000
 D46  C26   C27  C21   109.53  3.000
 D46  H28B  C28  H28A  107.98  3.000
 D46  H28B  C28  H28   107.71  3.000
 D46  H28A  C28  H28   107.81  3.000
 D46  H28B  C28  N25   113.30  3.000
 D46  H28A  C28  N25   109.93  3.000
 D46  H28   C28  N25   109.94  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
 D46  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 D46  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 D46  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 D46  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 D46  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 D46  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 D46  CONST_07  C18  C17  S16  C10     0.00   0.0  0
 D46  CONST_08  C17  C18  C19  C10     0.00   0.0  0
 D46  CONST_09  C22  C21  N20  C14     0.00   0.0  0
 D46  CONST_10  C21  C22  S23  C14     0.00   0.0  0
 D46  CONST_11  C18  C19  C10  S16     0.00   0.0  0
 D46  CONST_12  C19  C18  C17  S16     0.00   0.0  0
 D46  CONST_13  C19  C10  S16  C17     0.00   0.0  0
 D46  CONST_14  C22  S23  C14  N20     0.00   0.0  0
 D46  CONST_15  S23  C22  C21  N20     0.00   0.0  0
 D46  CONST_16  S23  C14  N20  C21     0.00   0.0  0
 D46  CONST_17  C7   C3   C2   C1    180.00   0.0  0
 D46  CONST_18  C10  S16  C17  CL1   180.00   0.0  0
 D46  CONST_19  C19  C18  C17  CL1   180.00   0.0  0
 D46  CONST_20  N12  C4   C3   C2    180.00   0.0  0
 D46  CONST_21  C7   C3   C4   C5    180.00   0.0  0
 D46  CONST_22  N12  C4   C5   C6    180.00   0.0  0
 D46  CONST_23  C17  S16  C10  C9    180.00   0.0  0
 D46  CONST_24  C18  C19  C10  C9    180.00   0.0  0
 D46  CONST_25  C21  N20  C14  C13   180.00   0.0  0
 D46  CONST_26  C22  S23  C14  C13   180.00   0.0  0
 D46  CONST_27  H5   C5   C6   C1    180.00   0.0  0
 D46  CONST_28  H6   C6   C1   C2    180.00   0.0  0
 D46  CONST_29  H1   C1   C2   C3    180.00   0.0  0
 D46  CONST_30  H2   C2   C3   C4    180.00   0.0  0
 D46  CONST_31  H18  C18  C19  C10   180.00   0.0  0
 D46  CONST_32  H19  C19  C10  S16   180.00   0.0  0
 D46  CONST_33  C14  C13  N12  C4    180.00   0.0  0
 D46  CONST_37  O15  C13  N12  C4      0.00   0.0  0
 D46  CONST_38  C10  C9   N8   C7    180.00   0.0  0
 D46  CONST_40  O11  C9   N8   C7      0.00   0.0  0
 D46  Var_01    C26  C27  C21  N20   166.00  30.0  1
 D46  Var_02    N25  C24  C22  C21   -17.25  30.0  1
 D46  Var_03    N25  C26  C27  C21    47.08  30.0  1
 D46  Var_04    C26  N25  C24  C22    50.34  30.0  1
 D46  Var_05    C27  C26  N25  C24   -68.64  30.0  1
 D46  Var_06    N8   C7   C3   C2   -124.66  30.0  2
 D46  Var_07    S16  C10  C9   N8     -3.83  30.0  2
 D46  Var_08    N20  C14  C13  N12   152.25  30.0  2
 D46  Var_09    H28  C28  N25  C24    56.80  30.0  3
 D46  Var_10    C9   N8   C7   C3   -148.88  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
 D46  plan-1  CL1   0.020
 D46  plan-1  C9    0.020
 D46  plan-1  C10   0.020
 D46  plan-1  S16   0.020
 D46  plan-1  C17   0.020
 D46  plan-1  C18   0.020
 D46  plan-1  C19   0.020
 D46  plan-1  H18   0.020
 D46  plan-1  H19   0.020
 D46  plan-2  C1    0.020
 D46  plan-2  C2    0.020
 D46  plan-2  C3    0.020
 D46  plan-2  C4    0.020
 D46  plan-2  C5    0.020
 D46  plan-2  C6    0.020
 D46  plan-2  C7    0.020
 D46  plan-2  N12   0.020
 D46  plan-2  H1    0.020
 D46  plan-2  H2    0.020
 D46  plan-2  H5    0.020
 D46  plan-2  H6    0.020
 D46  plan-3  C13   0.020
 D46  plan-3  C14   0.020
 D46  plan-3  N20   0.020
 D46  plan-3  C21   0.020
 D46  plan-3  C22   0.020
 D46  plan-3  S23   0.020
 D46  plan-3  C24   0.020
 D46  plan-3  C27   0.020
 D46  plan-4  C7    0.020
 D46  plan-4  N8    0.020
 D46  plan-4  C9    0.020
 D46  plan-4  C10   0.020
 D46  plan-4  O11   0.020
 D46  plan-4  HN8   0.020
 D46  plan-5  C4    0.020
 D46  plan-5  N12   0.020
 D46  plan-5  C13   0.020
 D46  plan-5  C14   0.020
 D46  plan-5  O15   0.020
 D46  plan-5  HN12  0.020

