# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 16:09:53 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 1-[4-(3-methylbutyl)-5-oxo-6-(pyridin-3-yl)-4,5-dihydro[1,3]thiazolo[5,4-b]pyridin-2-yl]-3-prop-2-en-1-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCN1C(=O)C(=Cc2nc(NC(=O)NCC=C)sc12)c3cccnc3
#
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
 2B7  2B7  1-[4-(3-methylbutyl)-5-oxo-6-(pyridin-3-yl)-4,5-dihydro[1,3]thiazolo[5,4-b]pyridin-2-yl]-3-prop-2-en-1-ylurea  ligand  51  28  .  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_2B7
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
 2B7  C1   C  CH3   0  -0.662   3.8005  -4.6079  -0.6338
 2B7  C2   C  CH1   0  -0.240   2.6310  -4.4135   0.3275
 2B7  C3   C  CH3   0  -0.651   2.9030  -5.1207   1.6509
 2B7  N6   N  NR6   0  -0.560   1.5516  -0.7942  -0.3739
 2B7  C7   C  CR6   0   0.540   2.5476   0.1808  -0.3958
 2B7  C9   C  CR6   0  -0.181   2.1273   1.5356  -0.0654
 2B7  C10  C  CR16  0  -0.213   0.8399   1.8116   0.2873
 2B7  C11  C  CR56  0   0.283  -0.1193   0.7813   0.3225
 2B7  C12  C  CR56  0   0.058   0.2849  -0.4890  -0.0162
 2B7  C14  C  CR5   0   0.296  -2.0404  -0.2199   0.6147
 2B7  C20  C  CH2   0  -0.356  -6.8106   0.7368   0.7060
 2B7  C21  C  C1    0  -0.167  -7.4043   0.3187  -0.6064
 2B7  C22  C  C2    0  -0.525  -8.6293  -0.1725  -0.7431
 2B7  C24  C  CR16  0  -0.191   3.2567   3.4906   0.9906
 2B7  C4   C  CH2   0  -0.414   2.3310  -2.9361   0.5837
 2B7  C5   C  CH2   0  -0.347   1.9167  -2.1798  -0.6715
 2B7  O8   O  O     0  -0.481   3.6984  -0.1310  -0.6741
 2B7  S13  S  S2    0   0.228  -1.0444  -1.5820   0.0885
 2B7  N15  N  N     0  -0.399  -1.4356   0.9062   0.6840
 2B7  N16  N  NH1   0  -0.770  -3.3607  -0.4591   0.8871
 2B7  C17  C  C     0   0.734  -4.3838   0.4409   0.5980
 2B7  O18  O  O     0  -0.495  -4.1849   1.4963   0.0289
 2B7  N19  N  NH1   0  -0.665  -5.5924   0.0209   1.0221
 2B7  C23  C  CR6   0   0.007   3.1466   2.5991  -0.0724
 2B7  C25  C  CR16  0  -0.319   4.2012   4.5033   0.9364
 2B7  C26  C  CR16  0  -0.070   5.0122   4.5897  -0.1829
 2B7  N27  N  N     0  -0.403   4.9202   3.7497  -1.2092
 2B7  C28  C  CR16  0  -0.073   4.0147   2.7848  -1.1505
 2B7  H1   H  HCH3  0   0.232   4.0225  -5.6683  -0.7628
 2B7  H2   H  HCH3  0   0.230   3.5997  -4.1988  -1.6248
 2B7  H3   H  HCH3  0   0.217   4.7036  -4.1256  -0.2520
 2B7  H4   H  HCH1  0   0.221   1.7388  -4.8664  -0.1213
 2B7  H5   H  HCH3  0   0.227   2.0601  -5.0208   2.3364
 2B7  H6   H  HCH3  0   0.228   3.0858  -6.1856   1.4998
 2B7  H7   H  HCH3  0   0.216   3.7835  -4.7005   2.1433
 2B7  H8   H  HCR6  0   0.285   0.5379   2.8221   0.5349
 2B7  H9   H  HCH2  0   0.262  -6.5910   1.8050   0.6949
 2B7  H10  H  HCH2  0   0.266  -7.5208   0.5661   1.5154
 2B7  H11  H  H     0   0.251  -6.7700   0.4439  -1.4792
 2B7  H12  H  H     0   0.243  -9.0257  -0.4483  -1.7114
 2B7  H13  H  H     0   0.239  -9.2853  -0.3106   0.1086
 2B7  H14  H  HCR6  0   0.271   2.6187   3.3867   1.8597
 2B7  H15  H  HCH2  0   0.235   1.5305  -2.8603   1.3268
 2B7  H16  H  HCH2  0   0.236   3.2109  -2.4540   1.0211
 2B7  H17  H  HCH2  0   0.265   1.0596  -2.6583  -1.1524
 2B7  H18  H  HCH2  0   0.285   2.7145  -2.1573  -1.4085
 2B7  H19  H  HNH1  0   0.426  -3.6054  -1.3765   1.2294
 2B7  H20  H  HNH1  0   0.405  -5.6953  -0.9051   1.4052
 2B7  H21  H  HCR6  0   0.273   4.3120   5.2069   1.7498
 2B7  H22  H  HCR6  0   0.266   5.7653   5.3659  -0.2564
 2B7  H23  H  HCR6  0   0.259   3.9595   2.1306  -2.0122

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
 2B7  C21  C20  single    1.500  0.020  1.500
 2B7  C21  C22  double    1.327  0.020  1.327
 2B7  C20  N19  single    1.448  0.020  1.448
 2B7  N19  C17  single    1.348  0.020  1.348
 2B7  C17  O18  double    1.215  0.020  1.215
 2B7  C17  N16  single    1.393  0.020  1.393
 2B7  N16  C14  single    1.369  0.020  1.369
 2B7  C14  S13  aromatic  1.768  0.020  1.768
 2B7  C14  N15  aromatic  1.280  0.020  1.280
 2B7  S13  C12  aromatic  1.724  0.020  1.724
 2B7  N15  C11  aromatic  1.371  0.020  1.371
 2B7  C3   C2   single    1.525  0.020  1.525
 2B7  C2   C4   single    1.529  0.020  1.529
 2B7  C2   C1   single    1.526  0.020  1.526
 2B7  C4   C5   single    1.523  0.020  1.523
 2B7  C11  C12  aromatic  1.375  0.020  1.375
 2B7  C11  C10  single    1.408  0.020  1.408
 2B7  C12  N6   single    1.351  0.020  1.351
 2B7  C10  C9   double    1.363  0.020  1.363
 2B7  N6   C5   single    1.464  0.020  1.464
 2B7  N6   C7   single    1.394  0.020  1.394
 2B7  C9   C7   single    1.457  0.020  1.457
 2B7  C9   C23  single    1.473  0.020  1.473
 2B7  C7   O8   double    1.224  0.020  1.224
 2B7  C23  C24  aromatic  1.392  0.020  1.392
 2B7  C23  C28  aromatic  1.397  0.020  1.397
 2B7  C24  C25  aromatic  1.386  0.020  1.386
 2B7  C28  N27  aromatic  1.324  0.020  1.324
 2B7  C25  C26  aromatic  1.385  0.020  1.385
 2B7  N27  C26  aromatic  1.329  0.020  1.329
 2B7  C1   H1   single    0.970  0.020  1.090
 2B7  C1   H2   single    0.970  0.020  1.090
 2B7  C1   H3   single    0.970  0.020  1.090
 2B7  C2   H4   single    0.970  0.020  1.090
 2B7  C3   H5   single    0.970  0.020  1.090
 2B7  C3   H6   single    0.970  0.020  1.090
 2B7  C3   H7   single    0.970  0.020  1.090
 2B7  C10  H8   single    0.930  0.020  1.080
 2B7  C20  H9   single    0.970  0.020  1.090
 2B7  C20  H10  single    0.970  0.020  1.090
 2B7  C21  H11  single    0.930  0.020  1.080
 2B7  C22  H12  single    0.930  0.020  1.080
 2B7  C22  H13  single    0.930  0.020  1.080
 2B7  C24  H14  single    0.930  0.020  1.080
 2B7  C4   H15  single    0.970  0.020  1.090
 2B7  C4   H16  single    0.970  0.020  1.090
 2B7  C5   H17  single    0.970  0.020  1.090
 2B7  C5   H18  single    0.970  0.020  1.090
 2B7  N16  H19  single    0.860  0.020  1.020
 2B7  N19  H20  single    0.860  0.020  1.020
 2B7  C25  H21  single    0.930  0.020  1.080
 2B7  C26  H22  single    0.930  0.020  1.080
 2B7  C28  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
 2B7  H3   C1   H2   107.70  3.000
 2B7  H3   C1   H1   107.59  3.000
 2B7  H2   C1   H1   107.13  3.000
 2B7  H3   C1   C2   110.91  3.000
 2B7  H2   C1   C2   112.54  3.000
 2B7  H1   C1   C2   110.75  3.000
 2B7  H4   C2   C4   107.94  3.000
 2B7  H4   C2   C3   107.98  3.000
 2B7  C4   C2   C3   109.74  3.000
 2B7  H4   C2   C1   108.24  3.000
 2B7  C4   C2   C1   112.27  3.000
 2B7  C3   C2   C1   110.54  3.000
 2B7  H7   C3   H6   107.62  3.000
 2B7  H7   C3   H5   107.71  3.000
 2B7  H6   C3   H5   107.81  3.000
 2B7  H7   C3   C2   110.87  3.000
 2B7  H6   C3   C2   111.25  3.000
 2B7  H5   C3   C2   111.41  3.000
 2B7  C5   N6   C12  120.10  3.000
 2B7  C5   N6   C7   118.73  3.000
 2B7  C12  N6   C7   121.07  3.000
 2B7  O8   C7   C9   124.03  3.000
 2B7  O8   C7   N6   119.81  3.000
 2B7  C9   C7   N6   116.16  3.000
 2B7  C23  C9   C10  120.57  3.000
 2B7  C23  C9   C7   118.09  3.000
 2B7  C10  C9   C7   121.30  3.000
 2B7  H8   C10  C11  119.13  3.000
 2B7  H8   C10  C9   120.75  3.000
 2B7  C11  C10  C9   120.11  3.000
 2B7  N15  C11  C12  115.55  3.000
 2B7  C12  C11  C10  118.00  3.000
 2B7  N15  C11  C10  126.44  3.000
 2B7  S13  C12  C11  110.12  3.000
 2B7  C11  C12  N6   123.32  3.000
 2B7  S13  C12  N6   126.56  3.000
 2B7  N16  C14  N15  126.76  3.000
 2B7  N15  C14  S13  115.33  3.000
 2B7  N16  C14  S13  117.90  3.000
 2B7  H10  C20  H9   106.98  3.000
 2B7  H10  C20  N19  107.97  3.000
 2B7  H9   C20  N19  108.48  3.000
 2B7  H10  C20  C21  110.37  3.000
 2B7  H9   C20  C21  110.11  3.000
 2B7  N19  C20  C21  112.72  3.000
 2B7  H11  C21  C22  119.93  3.000
 2B7  H11  C21  C20  116.10  3.000
 2B7  C22  C21  C20  123.97  3.000
 2B7  H13  C22  H12  116.67  3.000
 2B7  H13  C22  C21  121.67  3.000
 2B7  H12  C22  C21  121.66  3.000
 2B7  H14  C24  C25  120.19  3.000
 2B7  H14  C24  C23  120.32  3.000
 2B7  C25  C24  C23  119.48  3.000
 2B7  H16  C4   H15  106.62  3.000
 2B7  H16  C4   C5   109.23  3.000
 2B7  H15  C4   C5   109.04  3.000
 2B7  H16  C4   C2   109.56  3.000
 2B7  H15  C4   C2   108.91  3.000
 2B7  C5   C4   C2   113.27  3.000
 2B7  H18  C5   H17  106.64  3.000
 2B7  H18  C5   C4   111.70  3.000
 2B7  H17  C5   C4   111.01  3.000
 2B7  H18  C5   N6   107.55  3.000
 2B7  H17  C5   N6   107.96  3.000
 2B7  C4   C5   N6   111.74  3.000
 2B7  C14  S13  C12   87.93  3.000
 2B7  C14  N15  C11  111.05  3.000
 2B7  H19  N16  C17  118.66  3.000
 2B7  H19  N16  C14  117.39  3.000
 2B7  C17  N16  C14  123.65  3.000
 2B7  N19  C17  O18  124.37  3.000
 2B7  O18  C17  N16  122.55  3.000
 2B7  N19  C17  N16  113.08  3.000
 2B7  H20  N19  C17  119.85  3.000
 2B7  H20  N19  C20  116.84  3.000
 2B7  C17  N19  C20  122.12  3.000
 2B7  C28  C23  C24  117.09  3.000
 2B7  C28  C23  C9   121.99  3.000
 2B7  C24  C23  C9   120.90  3.000
 2B7  H21  C25  C26  120.49  3.000
 2B7  H21  C25  C24  121.06  3.000
 2B7  C26  C25  C24  118.44  3.000
 2B7  H22  C26  N27  116.63  3.000
 2B7  H22  C26  C25  120.41  3.000
 2B7  N27  C26  C25  122.95  3.000
 2B7  C28  N27  C26  118.26  3.000
 2B7  H23  C28  N27  116.08  3.000
 2B7  H23  C28  C23  120.13  3.000
 2B7  N27  C28  C23  123.78  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
 2B7  CONST_01  S13  C14  N15  C11     0.00   0.0  0
 2B7  CONST_02  C14  S13  C12  C11     0.00   0.0  0
 2B7  CONST_03  N15  C14  S13  C12     0.00   0.0  0
 2B7  CONST_04  C14  N15  C11  C12     0.00   0.0  0
 2B7  CONST_05  N27  C28  C23  C24     0.00   0.0  0
 2B7  CONST_06  N27  C26  C25  C24     0.00   0.0  0
 2B7  CONST_07  N15  C11  C12  S13     0.00   0.0  0
 2B7  CONST_08  C26  C25  C24  C23     0.00   0.0  0
 2B7  CONST_09  C26  N27  C28  C23     0.00   0.0  0
 2B7  CONST_10  C28  C23  C24  C25     0.00   0.0  0
 2B7  CONST_11  C28  N27  C26  C25     0.00   0.0  0
 2B7  CONST_12  C25  C24  C23  C9    180.00   0.0  0
 2B7  CONST_13  N27  C28  C23  C9    180.00   0.0  0
 2B7  CONST_14  C12  N6   C7   C9      0.00   0.0  0
 2B7  CONST_15  N16  C14  N15  C11   180.00   0.0  0
 2B7  CONST_16  N16  C14  S13  C12   180.00   0.0  0
 2B7  CONST_17  C5   N6   C7   C9    180.00   0.0  0
 2B7  CONST_18  O8   C7   N6   C12   180.00   0.0  0
 2B7  CONST_19  H14  C24  C23  C9      0.00   0.0  0
 2B7  CONST_20  H23  C28  C23  C9      0.00   0.0  0
 2B7  CONST_21  H22  C26  C25  C24   180.00   0.0  0
 2B7  CONST_22  H21  C25  C24  C23   180.00   0.0  0
 2B7  CONST_25  O8   C7   N6   C5      0.00   0.0  0
 2B7  CONST_27  O18  C17  N16  C14     0.00   0.0  0
 2B7  CONST_28  N19  C17  N16  C14   180.00   0.0  0
 2B7  CONST_29  O18  C17  N19  C20     0.00   0.0  0
 2B7  CONST_30  N16  C17  N19  C20   180.00   0.0  0
 2B7  CONST_31  H20  N19  C17  O18   180.00   0.0  0
 2B7  CONST_32  H12  C22  C21  C20   180.00   0.0  0
 2B7  CONST_33  H13  C22  C21  C20     0.00   0.0  0
 2B7  Var_01    C24  C23  C9   C7   -131.80  30.0  2
 2B7  Var_02    C4   C5   N6   C7     89.14  30.0  3
 2B7  Var_03    N6   C5   C4   C2    176.18  30.0  3
 2B7  Var_04    C5   C4   C2   C1     62.15  30.0  3
 2B7  Var_05    C17  N19  C20  C21    87.15  30.0  3
 2B7  Var_06    N19  C20  C21  C22   121.56  30.0  3
 2B7  Var_07    H5   C3   C2   C1   -177.97  30.0  3
 2B7  Var_08    H1   C1   C2   C3     54.48  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
 2B7  plan-1  C9   0.020
 2B7  plan-1  C24  0.020
 2B7  plan-1  C23  0.020
 2B7  plan-1  C25  0.020
 2B7  plan-1  C26  0.020
 2B7  plan-1  N27  0.020
 2B7  plan-1  C28  0.020
 2B7  plan-1  H14  0.020
 2B7  plan-1  H21  0.020
 2B7  plan-1  H22  0.020
 2B7  plan-1  H23  0.020
 2B7  plan-2  C20  0.020
 2B7  plan-2  C21  0.020
 2B7  plan-2  C22  0.020
 2B7  plan-2  H11  0.020
 2B7  plan-2  H12  0.020
 2B7  plan-2  H13  0.020
 2B7  plan-3  N6   0.020
 2B7  plan-3  C7   0.020
 2B7  plan-3  C9   0.020
 2B7  plan-3  C10  0.020
 2B7  plan-3  C11  0.020
 2B7  plan-3  C12  0.020
 2B7  plan-3  C14  0.020
 2B7  plan-3  C5   0.020
 2B7  plan-3  O8   0.020
 2B7  plan-3  S13  0.020
 2B7  plan-3  N15  0.020
 2B7  plan-3  N16  0.020
 2B7  plan-3  C23  0.020
 2B7  plan-3  H8   0.020
 2B7  plan-4  C14  0.020
 2B7  plan-4  C20  0.020
 2B7  plan-4  N16  0.020
 2B7  plan-4  C17  0.020
 2B7  plan-4  O18  0.020
 2B7  plan-4  N19  0.020
 2B7  plan-4  H19  0.020
 2B7  plan-4  H20  0.020

