# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 07:50:10 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: ~{N}-(6-methyl-1,3-benzothiazol-2-yl)-2-[(4-oxidanylidene-3-phenyl-6,7-dihydrothieno[3,2-d]pyrimidin-2-yl)sulfanyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2nc(NC(=O)CSC3=NC4=C(SCC4)C(=O)N3c5ccccc5)sc2c1
#
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
 9XK  9XK  ~{N}-(6-methyl-1,3-benzothiazol-2-yl)-2-[(4-oxidanylidene-3-phenyl-6,7-dihydrothieno[3,2-d]pyrimidin-2-yl)sulfanyl]ethanamide  ligand  49  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9XK
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
 9XK  C01   C  CH3   0  -0.722   9.9291   0.1221  -0.1391
 9XK  C02   C  CR6   0   0.083   8.4464  -0.0902  -0.0419
 9XK  C03   C  CR16  0  -0.330   7.5620   0.9669  -0.2052
 9XK  C04   C  CR56  0  -0.225   6.1990   0.7178  -0.1125
 9XK  C05   C  CR56  0   0.347   5.6890  -0.5619   0.1415
 9XK  C06   C  CR16  0  -0.298   6.5820  -1.6195   0.3076
 9XK  C07   C  CR16  0  -0.290   7.9374  -1.3734   0.2148
 9XK  N08   N  N     0  -0.413   4.3174  -0.6523   0.2093
 9XK  C09   C  CR5   0   0.291   3.7813   0.4942   0.0131
 9XK  N10   N  NH1   0  -0.722   2.4350   0.7728   0.0084
 9XK  C11   C  C     0   0.574   1.4176  -0.1435   0.0141
 9XK  O12   O  O     0  -0.412   1.5716  -1.3409   0.0193
 9XK  C13   C  CH2   0  -0.704   0.0524   0.5061   0.0117
 9XK  S14   S  S2    0   0.114  -1.1588  -0.8343  -0.0139
 9XK  C15   C  CR6   0   0.351  -2.6253   0.1232   0.0062
 9XK  N16   N  N     0  -0.454  -2.5833   1.4158   0.0343
 9XK  C17   C  CR56  0   0.309  -3.7687   2.0637   0.0471
 9XK  C18   C  CR56  0  -0.348  -4.9715   1.4325   0.0304
 9XK  S19   S  S2    0   0.060  -6.3660   2.4891   0.0701
 9XK  C20   C  CH2   0  -0.563  -5.2814   3.9230  -0.3143
 9XK  C21   C  CH2   0  -0.489  -3.8708   3.5541   0.1453
 9XK  C22   C  CR6   0   0.572  -5.0525   0.0085   0.0134
 9XK  O23   O  O     0  -0.454  -6.0669  -0.6631   0.0175
 9XK  N24   N  NR6   0  -0.629  -3.7836  -0.5970  -0.0072
 9XK  C25   C  CR6   0   0.214  -3.7388  -2.0271  -0.0364
 9XK  C26   C  CR16  0  -0.227  -3.7169  -2.6811  -1.2586
 9XK  C27   C  CR16  0  -0.262  -3.6625  -4.0670  -1.2827
 9XK  C28   C  CR16  0  -0.236  -3.6333  -4.7826  -0.0927
 9XK  C29   C  CR16  0  -0.262  -3.6586  -4.1158   1.1255
 9XK  C30   C  CR16  0  -0.227  -3.7128  -2.7302   1.1582
 9XK  S31   S  S2    0   0.213   4.8812   1.8327  -0.2805
 9XK  H013  H  HCH3  0   0.249  10.4267  -0.1334   0.7978
 9XK  H011  H  HCH3  0   0.248  10.3657  -0.5086  -0.9149
 9XK  H012  H  HCH3  0   0.246  10.1722   1.1568  -0.3755
 9XK  H031  H  HCR6  0   0.269   7.9299   1.9649  -0.4072
 9XK  H061  H  HCR6  0   0.264   6.2089  -2.6159   0.5056
 9XK  H071  H  HCR6  0   0.255   8.6317  -2.1953   0.3415
 9XK  H101  H  HNH1  0   0.441   2.1711   1.7473  -0.0290
 9XK  H211  H  HCH2  0   0.281  -3.7057   3.8451   1.1877
 9XK  H212  H  HCH2  0   0.282  -3.1137   4.0580  -0.4556
 9XK  H261  H  HCR6  0   0.276  -3.7392  -2.1105  -2.1782
 9XK  H271  H  HCR6  0   0.269  -3.6426  -4.5869  -2.2310
 9XK  H281  H  HCR6  0   0.268  -3.5911  -5.8634  -0.1148
 9XK  H291  H  HCR6  0   0.269  -3.6364  -4.6745   2.0515
 9XK  H301  H  HCR6  0   0.275  -3.7293  -2.1981   2.1005
 9XK  H131  H  HCH2  0   0.334  -0.0765   1.1262   0.9005
 9XK  H132  H  HCH2  0   0.333  -0.0676   1.1514  -0.8599
 9XK  H201  H  HCH2  0   0.289  -5.3120   4.0917  -1.3902
 9XK  H202  H  HCH2  0   0.291  -5.6724   4.8032   0.1895

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
 9XK  C01  C02   single    1.501  0.020  1.501
 9XK  C02  C03   aromatic  1.388  0.020  1.388
 9XK  C02  C07   aromatic  1.404  0.020  1.404
 9XK  C03  C04   aromatic  1.389  0.020  1.389
 9XK  C04  C05   aromatic  1.401  0.020  1.401
 9XK  C04  S31   aromatic  1.734  0.020  1.734
 9XK  C05  C06   aromatic  1.394  0.020  1.394
 9XK  C05  N08   aromatic  1.376  0.020  1.376
 9XK  C06  C07   aromatic  1.381  0.020  1.381
 9XK  N08  C09   aromatic  1.281  0.020  1.281
 9XK  C09  N10   single    1.375  0.020  1.375
 9XK  C09  S31   aromatic  1.757  0.020  1.757
 9XK  N10  C11   single    1.369  0.020  1.369
 9XK  C11  O12   double    1.207  0.020  1.207
 9XK  C11  C13   single    1.512  0.020  1.512
 9XK  C13  S14   single    1.807  0.020  1.807
 9XK  S14  C15   single    1.752  0.020  1.752
 9XK  C15  N16   double    1.294  0.020  1.294
 9XK  C15  N24   single    1.364  0.020  1.364
 9XK  N16  C17   single    1.351  0.020  1.351
 9XK  C17  C18   double    1.358  0.020  1.358
 9XK  C17  C21   single    1.497  0.020  1.497
 9XK  C18  S19   single    1.750  0.020  1.750
 9XK  C18  C22   single    1.426  0.020  1.426
 9XK  S19  C20   single    1.839  0.020  1.839
 9XK  C20  C21   single    1.529  0.020  1.529
 9XK  C22  O23   double    1.217  0.020  1.217
 9XK  C22  N24   single    1.406  0.020  1.406
 9XK  N24  C25   single    1.431  0.020  1.431
 9XK  C25  C26   aromatic  1.386  0.020  1.386
 9XK  C25  C30   aromatic  1.386  0.020  1.386
 9XK  C26  C27   aromatic  1.387  0.020  1.387
 9XK  C27  C28   aromatic  1.389  0.020  1.389
 9XK  C28  C29   aromatic  1.389  0.020  1.389
 9XK  C29  C30   aromatic  1.387  0.020  1.387
 9XK  C01  H013  single    0.970  0.020  1.090
 9XK  C01  H011  single    0.970  0.020  1.090
 9XK  C01  H012  single    0.970  0.020  1.090
 9XK  C03  H031  single    0.930  0.020  1.080
 9XK  C06  H061  single    0.930  0.020  1.080
 9XK  C07  H071  single    0.930  0.020  1.080
 9XK  N10  H101  single    0.860  0.020  1.020
 9XK  C13  H131  single    0.970  0.020  1.090
 9XK  C13  H132  single    0.970  0.020  1.090
 9XK  C20  H201  single    0.970  0.020  1.090
 9XK  C20  H202  single    0.970  0.020  1.090
 9XK  C21  H211  single    0.970  0.020  1.090
 9XK  C21  H212  single    0.970  0.020  1.090
 9XK  C26  H261  single    0.930  0.020  1.080
 9XK  C27  H271  single    0.930  0.020  1.080
 9XK  C28  H281  single    0.930  0.020  1.080
 9XK  C29  H291  single    0.930  0.020  1.080
 9XK  C30  H301  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
 9XK  H012  C01  H011  107.80  3.000
 9XK  H012  C01  H013  107.89  3.000
 9XK  H011  C01  H013  107.02  3.000
 9XK  H012  C01  C02   111.66  3.000
 9XK  H011  C01  C02   111.07  3.000
 9XK  H013  C01  C02   111.21  3.000
 9XK  C07   C02  C03   119.11  3.000
 9XK  C07   C02  C01   119.95  3.000
 9XK  C03   C02  C01   120.93  3.000
 9XK  H031  C03  C04   120.75  3.000
 9XK  H031  C03  C02   120.49  3.000
 9XK  C04   C03  C02   118.75  3.000
 9XK  S31   C04  C05   109.16  3.000
 9XK  S31   C04  C03   128.61  3.000
 9XK  C05   C04  C03   122.23  3.000
 9XK  N08   C05  C06   125.64  3.000
 9XK  N08   C05  C04   115.58  3.000
 9XK  C06   C05  C04   118.78  3.000
 9XK  H061  C06  C07   120.98  3.000
 9XK  H061  C06  C05   119.97  3.000
 9XK  C07   C06  C05   119.05  3.000
 9XK  H071  C07  C06   119.08  3.000
 9XK  H071  C07  C02   118.84  3.000
 9XK  C06   C07  C02   122.08  3.000
 9XK  C09   N08  C05   110.54  3.000
 9XK  S31   C09  N10   117.26  3.000
 9XK  S31   C09  N08   116.46  3.000
 9XK  N10   C09  N08   126.28  3.000
 9XK  H101  N10  C11   116.85  3.000
 9XK  H101  N10  C09   116.83  3.000
 9XK  C11   N10  C09   126.30  3.000
 9XK  C13   C11  O12   122.78  3.000
 9XK  C13   C11  N10   112.54  3.000
 9XK  O12   C11  N10   124.68  3.000
 9XK  H132  C13  H131  107.55  3.000
 9XK  H132  C13  S14   110.71  3.000
 9XK  H131  C13  S14   110.72  3.000
 9XK  H132  C13  C11   110.77  3.000
 9XK  H131  C13  C11   110.46  3.000
 9XK  S14   C13  C11   106.65  3.000
 9XK  C15   S14  C13    98.95  3.000
 9XK  N24   C15  N16   123.74  3.000
 9XK  N24   C15  S14   114.97  3.000
 9XK  N16   C15  S14   121.28  3.000
 9XK  C17   N16  C15   116.80  3.000
 9XK  C21   C17  C18   113.77  3.000
 9XK  C21   C17  N16   122.54  3.000
 9XK  C18   C17  N16   123.64  3.000
 9XK  C22   C18  S19   123.90  3.000
 9XK  C22   C18  C17   120.95  3.000
 9XK  S19   C18  C17   115.13  3.000
 9XK  C20   S19  C18    89.77  3.000
 9XK  H202  C20  H201  108.80  3.000
 9XK  H202  C20  C21   112.83  3.000
 9XK  H201  C20  C21   111.11  3.000
 9XK  H202  C20  S19   108.81  3.000
 9XK  H201  C20  S19   108.10  3.000
 9XK  C21   C20  S19   107.05  3.000
 9XK  H212  C21  H211  107.29  3.000
 9XK  H212  C21  C20   111.32  3.000
 9XK  H211  C21  C20   111.18  3.000
 9XK  H212  C21  C17   112.13  3.000
 9XK  H211  C21  C17   108.47  3.000
 9XK  C20   C21  C17   106.46  3.000
 9XK  N24   C22  O23   120.98  3.000
 9XK  N24   C22  C18   112.26  3.000
 9XK  O23   C22  C18   126.76  3.000
 9XK  C25   N24  C22   117.31  3.000
 9XK  C25   N24  C15   120.09  3.000
 9XK  C22   N24  C15   122.60  3.000
 9XK  C30   C25  C26   121.34  3.000
 9XK  C30   C25  N24   119.33  3.000
 9XK  C26   C25  N24   119.33  3.000
 9XK  H261  C26  C27   120.85  3.000
 9XK  H261  C26  C25   119.99  3.000
 9XK  C27   C26  C25   119.16  3.000
 9XK  H271  C27  C28   120.20  3.000
 9XK  H271  C27  C26   119.75  3.000
 9XK  C28   C27  C26   120.05  3.000
 9XK  H281  C28  C29   119.88  3.000
 9XK  H281  C28  C27   119.87  3.000
 9XK  C29   C28  C27   120.25  3.000
 9XK  H291  C29  C30   119.77  3.000
 9XK  H291  C29  C28   120.16  3.000
 9XK  C30   C29  C28   120.06  3.000
 9XK  H301  C30  C29   120.81  3.000
 9XK  H301  C30  C25   120.04  3.000
 9XK  C29   C30  C25   119.15  3.000
 9XK  C09   S31  C04    88.27  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
 9XK  CONST_01  C05   C04  C03  C02     0.00   0.0  0
 9XK  CONST_02  S31   C04  C03  C02   180.00   0.0  0
 9XK  CONST_03  C05   C06  C07  C02     0.00   0.0  0
 9XK  CONST_04  C06   C07  C02  C03     0.00   0.0  0
 9XK  CONST_05  C06   C05  C04  C03     0.00   0.0  0
 9XK  CONST_06  N08   C05  C04  C03   180.00   0.0  0
 9XK  CONST_07  C09   S31  C04  C03   180.00   0.0  0
 9XK  CONST_08  C07   C02  C03  C04     0.00   0.0  0
 9XK  CONST_09  C07   C06  C05  C04     0.00   0.0  0
 9XK  CONST_10  C09   N08  C05  C04     0.00   0.0  0
 9XK  CONST_11  N08   C09  S31  C04     0.00   0.0  0
 9XK  CONST_12  C09   S31  C04  C05     0.00   0.0  0
 9XK  CONST_13  S31   C09  N08  C05     0.00   0.0  0
 9XK  CONST_14  S31   C04  C05  C06   180.00   0.0  0
 9XK  CONST_15  C09   N08  C05  C06   180.00   0.0  0
 9XK  CONST_16  N08   C05  C06  C07   180.00   0.0  0
 9XK  CONST_17  S31   C04  C05  N08     0.00   0.0  0
 9XK  CONST_18  C28   C27  C26  C25     0.00   0.0  0
 9XK  CONST_19  C28   C29  C30  C25     0.00   0.0  0
 9XK  CONST_20  C29   C30  C25  C26     0.00   0.0  0
 9XK  CONST_21  C29   C28  C27  C26     0.00   0.0  0
 9XK  CONST_22  C30   C25  C26  C27     0.00   0.0  0
 9XK  CONST_23  C30   C29  C28  C27     0.00   0.0  0
 9XK  CONST_24  C27   C26  C25  N24   180.00   0.0  0
 9XK  CONST_25  C29   C30  C25  N24   180.00   0.0  0
 9XK  CONST_26  C18   C22  N24  C15     0.00   0.0  0
 9XK  CONST_27  C22   N24  C15  N16     0.00   0.0  0
 9XK  CONST_28  C25   N24  C15  N16   180.00   0.0  0
 9XK  CONST_29  N24   C15  N16  C17     0.00   0.0  0
 9XK  CONST_30  C25   N24  C22  C18   180.00   0.0  0
 9XK  CONST_31  C04   C03  C02  C01   180.00   0.0  0
 9XK  CONST_32  C06   C07  C02  C01   180.00   0.0  0
 9XK  CONST_33  N10   C09  S31  C04   180.00   0.0  0
 9XK  CONST_34  N10   C09  N08  C05   180.00   0.0  0
 9XK  CONST_35  C17   N16  C15  S14   180.00   0.0  0
 9XK  CONST_36  C22   N24  C15  S14   180.00   0.0  0
 9XK  CONST_37  C25   N24  C15  S14     0.00   0.0  0
 9XK  CONST_38  O23   C22  N24  C15   180.00   0.0  0
 9XK  CONST_39  C25   N24  C22  O23     0.00   0.0  0
 9XK  CONST_40  H061  C06  C07  C02   180.00   0.0  0
 9XK  CONST_41  H071  C07  C02  C03   180.00   0.0  0
 9XK  CONST_42  H031  C03  C04  C05   180.00   0.0  0
 9XK  CONST_43  H261  C26  C25  N24     0.00   0.0  0
 9XK  CONST_44  H301  C30  C25  N24     0.00   0.0  0
 9XK  CONST_45  H271  C27  C26  C25   180.00   0.0  0
 9XK  CONST_46  H291  C29  C30  C25   180.00   0.0  0
 9XK  CONST_47  H281  C28  C27  C26   180.00   0.0  0
 9XK  CONST_48  C11   N10  C09  N08     0.00   0.0  0
 9XK  CONST_49  S31   C09  N10  C11   180.00   0.0  0
 9XK  CONST_50  H101  N10  C09  N08   180.00   0.0  0
 9XK  CONST_51  O12   C11  N10  C09     0.00   0.0  0
 9XK  CONST_52  C13   C11  N10  C09   180.00   0.0  0
 9XK  Var_01    C26   C25  N24  C15   -89.91  30.0  2
 9XK  Var_02    C20   C21  C17  N16   162.27  30.0  1
 9XK  Var_03    S19   C20  C21  C17    28.52  30.0  1
 9XK  Var_04    C21   C20  S19  C18   -24.06  30.0  1
 9XK  Var_05    C22   C18  S19  C20  -167.98  30.0  1
 9XK  Var_06    N16   C15  S14  C13    -0.13  30.0  3
 9XK  Var_07    H013  C01  C02  C03   118.70  30.0  2
 9XK  Var_08    H131  C13  S14  C15    59.14  30.0  1
 9XK  Var_09    S14   C13  C11  N10   178.88  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
 9XK  plan-1  N24   0.020
 9XK  plan-1  C25   0.020
 9XK  plan-1  C26   0.020
 9XK  plan-1  C27   0.020
 9XK  plan-1  C28   0.020
 9XK  plan-1  C29   0.020
 9XK  plan-1  C30   0.020
 9XK  plan-1  H261  0.020
 9XK  plan-1  H271  0.020
 9XK  plan-1  H281  0.020
 9XK  plan-1  H291  0.020
 9XK  plan-1  H301  0.020
 9XK  plan-2  C01   0.020
 9XK  plan-2  C02   0.020
 9XK  plan-2  C03   0.020
 9XK  plan-2  C04   0.020
 9XK  plan-2  C05   0.020
 9XK  plan-2  C06   0.020
 9XK  plan-2  C07   0.020
 9XK  plan-2  N08   0.020
 9XK  plan-2  C09   0.020
 9XK  plan-2  N10   0.020
 9XK  plan-2  S31   0.020
 9XK  plan-2  H031  0.020
 9XK  plan-2  H061  0.020
 9XK  plan-2  H071  0.020
 9XK  plan-3  C09   0.020
 9XK  plan-3  N10   0.020
 9XK  plan-3  C11   0.020
 9XK  plan-3  O12   0.020
 9XK  plan-3  C13   0.020
 9XK  plan-3  H101  0.020
 9XK  plan-4  S14   0.020
 9XK  plan-4  C15   0.020
 9XK  plan-4  N16   0.020
 9XK  plan-4  C17   0.020
 9XK  plan-4  C18   0.020
 9XK  plan-4  S19   0.020
 9XK  plan-4  C21   0.020
 9XK  plan-4  C22   0.020
 9XK  plan-4  O23   0.020
 9XK  plan-4  N24   0.020
 9XK  plan-4  C25   0.020

