# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:57:09 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-[(6-chloro[1,3]thiazolo[5,4-b]pyridin-2-yl)methoxy]-2,6-difluorobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1c(F)ccc(OCc2sc3ncc(Cl)cc3n2)c1F
#
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
 9PC  9PC  3-[(6-chloro[1,3]thiazolo[5,4-b]pyridin-2-yl)methoxy]-2,6-difluorobenzamide  ligand  31  23  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9PC
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
 9PC  C11  C   CR6   0  -0.104   5.7266  -0.0149  -0.0519
 9PC  C12  C   CR16  0  -0.163   4.8014  -0.6819   0.7247
 9PC  N    N   NH2   0  -0.773  -5.5625   0.9232  -2.1834
 9PC  C13  C   CR6   0   0.524  -3.1908   0.3330  -0.2465
 9PC  C1   C   CR6   0  -0.452  -4.5588   0.2167  -0.1345
 9PC  C2   C   CR6   0   0.549  -5.0514  -0.7387   0.7432
 9PC  C3   C   CR16  0  -0.413  -4.2217  -1.5568   1.4714
 9PC  F1   F   F     0  -0.290  -2.6824   1.2533  -1.0701
 9PC  C    C   C     0   0.486  -5.4897   1.1425  -0.8699
 9PC  O    O   O     0  -0.457  -6.1082   2.0033  -0.2704
 9PC  C5   C   CR6   0   0.270  -2.3099  -0.4674   0.4798
 9PC  C4   C   CR16  0  -0.357  -2.8436  -1.4154   1.3396
 9PC  O1   O   O2    0  -0.481  -0.9986  -0.2379   0.2779
 9PC  C6   C   CH2   0  -0.241  -0.0646  -1.0206   0.9794
 9PC  C7   C   CR5   0   0.041   1.2877  -0.5840   0.5264
 9PC  S    S   S2    0   0.252   1.4351   0.5316  -0.8038
 9PC  C9   C   CR56  0  -0.045   3.1589   0.4145  -0.6287
 9PC  N2   N   N     0  -0.394   4.0452   1.0522  -1.3672
 9PC  C10  C   CR16  0  -0.053   5.3175   0.8386  -1.0821
 9PC  CL   CL  CL    0  -0.101   7.4146  -0.2221   0.2364
 9PC  C8   C   CR56  0   0.290   3.4619  -0.4599   0.4253
 9PC  N1   N   N     0  -0.396   2.3778  -1.0069   1.0580
 9PC  H1   H   HCR6  0   0.305   5.0940  -1.3440   1.5286
 9PC  H2   H   HNH2  0   0.420  -5.0645   0.1696  -2.6261
 9PC  H3   H   HNH2  0   0.413  -6.1624   1.4894  -2.7628
 9PC  H4   H   HCR6  0   0.296  -4.6324  -2.3018   2.1392
 9PC  H5   H   HCR6  0   0.314  -2.2009  -2.0603   1.9224
 9PC  H6   H   HCH2  0   0.282  -0.1463  -0.8831   2.0628
 9PC  H7   H   HCH2  0   0.283  -0.1866  -2.0878   0.7618
 9PC  H8   H   HCR6  0   0.294   6.0539   1.3574  -1.6835
 9PC  F    F   F     0  -0.301  -6.3800  -0.8656   0.8552

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
 9PC  O    C    double    1.218  0.020  1.218
 9PC  C    C1   single    1.505  0.020  1.505
 9PC  C    N    single    1.334  0.020  1.334
 9PC  F    C2   single    1.339  0.020  1.339
 9PC  C1   C2   aromatic  1.388  0.020  1.388
 9PC  C1   C13  aromatic  1.378  0.020  1.378
 9PC  C2   C3   aromatic  1.374  0.020  1.374
 9PC  F1   C13  single    1.336  0.020  1.336
 9PC  C13  C5   aromatic  1.394  0.020  1.394
 9PC  C3   C4   aromatic  1.392  0.020  1.392
 9PC  S    C9   aromatic  1.737  0.020  1.737
 9PC  S    C7   aromatic  1.742  0.020  1.742
 9PC  C5   C4   aromatic  1.387  0.020  1.387
 9PC  C5   O1   single    1.347  0.020  1.347
 9PC  N2   C9   aromatic  1.318  0.020  1.318
 9PC  N2   C10  aromatic  1.321  0.020  1.321
 9PC  C6   O1   single    1.406  0.020  1.406
 9PC  C6   C7   single    1.492  0.020  1.492
 9PC  C9   C8   aromatic  1.403  0.020  1.403
 9PC  C7   N1   aromatic  1.284  0.020  1.284
 9PC  C10  C11  aromatic  1.399  0.020  1.399
 9PC  C8   N1   aromatic  1.369  0.020  1.369
 9PC  C8   C12  aromatic  1.390  0.020  1.390
 9PC  C11  C12  aromatic  1.380  0.020  1.380
 9PC  C11  CL   single    1.725  0.020  1.725
 9PC  C12  H1   single    0.930  0.020  1.080
 9PC  N    H2   single    0.860  0.020  1.020
 9PC  N    H3   single    0.860  0.020  1.020
 9PC  C3   H4   single    0.930  0.020  1.080
 9PC  C4   H5   single    0.930  0.020  1.080
 9PC  C6   H6   single    0.970  0.020  1.090
 9PC  C6   H7   single    0.970  0.020  1.090
 9PC  C10  H8   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
 9PC  CL   C11  C10  118.85  3.000
 9PC  CL   C11  C12  120.26  3.000
 9PC  C10  C11  C12  120.88  3.000
 9PC  H1   C12  C8   121.21  3.000
 9PC  H1   C12  C11  122.19  3.000
 9PC  C8   C12  C11  116.59  3.000
 9PC  H3   N    H2   117.54  3.000
 9PC  H3   N    C    120.41  3.000
 9PC  H2   N    C    121.98  3.000
 9PC  C5   C13  F1   118.45  3.000
 9PC  C5   C13  C1   122.45  3.000
 9PC  F1   C13  C1   119.10  3.000
 9PC  C    C1   C2   120.86  3.000
 9PC  C2   C1   C13  117.52  3.000
 9PC  C    C1   C13  121.52  3.000
 9PC  F    C2   C3   119.88  3.000
 9PC  C3   C2   C1   122.05  3.000
 9PC  F    C2   C1   118.05  3.000
 9PC  H4   C3   C4   120.30  3.000
 9PC  H4   C3   C2   120.53  3.000
 9PC  C4   C3   C2   119.16  3.000
 9PC  O    C    C1   120.57  3.000
 9PC  C1   C    N    114.45  3.000
 9PC  O    C    N    124.99  3.000
 9PC  O1   C5   C4   125.76  3.000
 9PC  O1   C5   C13  116.06  3.000
 9PC  C4   C5   C13  118.19  3.000
 9PC  H5   C4   C5   120.88  3.000
 9PC  H5   C4   C3   118.49  3.000
 9PC  C5   C4   C3   120.62  3.000
 9PC  C6   O1   C5   118.50  3.000
 9PC  H7   C6   H6   108.08  3.000
 9PC  H7   C6   C7   109.01  3.000
 9PC  H6   C6   C7   109.35  3.000
 9PC  H7   C6   O1   111.66  3.000
 9PC  H6   C6   O1   111.97  3.000
 9PC  C7   C6   O1   106.72  3.000
 9PC  N1   C7   S    117.06  3.000
 9PC  N1   C7   C6   123.19  3.000
 9PC  S    C7   C6   119.74  3.000
 9PC  C9   S    C7    87.93  3.000
 9PC  C8   C9   N2   125.26  3.000
 9PC  C8   C9   S    109.40  3.000
 9PC  N2   C9   S    125.33  3.000
 9PC  C10  N2   C9   116.64  3.000
 9PC  H8   C10  N2   117.23  3.000
 9PC  H8   C10  C11  120.15  3.000
 9PC  N2   C10  C11  122.62  3.000
 9PC  N1   C8   C9   115.16  3.000
 9PC  N1   C8   C12  126.84  3.000
 9PC  C9   C8   C12  118.00  3.000
 9PC  C8   N1   C7   110.44  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
 9PC  CONST_01  C9   N2   C10  C11     0.00   0.0  0
 9PC  CONST_02  C9   C8   C12  C11     0.00   0.0  0
 9PC  CONST_03  N1   C8   C12  C11   180.00   0.0  0
 9PC  CONST_04  S    C9   C8   C12   180.00   0.0  0
 9PC  CONST_05  N2   C9   C8   C12     0.00   0.0  0
 9PC  CONST_06  C7   N1   C8   C12   180.00   0.0  0
 9PC  CONST_07  N2   C10  C11  C12     0.00   0.0  0
 9PC  CONST_08  C3   C2   C1   C13     0.00   0.0  0
 9PC  CONST_09  C3   C4   C5   C13     0.00   0.0  0
 9PC  CONST_10  C4   C3   C2   C1      0.00   0.0  0
 9PC  CONST_11  C4   C5   C13  C1      0.00   0.0  0
 9PC  CONST_12  C5   C13  C1   C2      0.00   0.0  0
 9PC  CONST_13  C5   C4   C3   C2      0.00   0.0  0
 9PC  CONST_14  N2   C9   S    C7    180.00   0.0  0
 9PC  CONST_15  C8   C9   S    C7      0.00   0.0  0
 9PC  CONST_16  C9   C8   N1   C7      0.00   0.0  0
 9PC  CONST_17  C10  N2   C9   S     180.00   0.0  0
 9PC  CONST_18  N1   C8   C9   S       0.00   0.0  0
 9PC  CONST_19  C8   N1   C7   S       0.00   0.0  0
 9PC  CONST_20  N1   C7   S    C9      0.00   0.0  0
 9PC  CONST_21  N1   C8   C9   N2    180.00   0.0  0
 9PC  CONST_22  C8   C9   N2   C10     0.00   0.0  0
 9PC  CONST_23  C8   C12  C11  C10     0.00   0.0  0
 9PC  CONST_24  F    C2   C1   C13   180.00   0.0  0
 9PC  CONST_25  O1   C5   C13  C1    180.00   0.0  0
 9PC  CONST_26  F1   C13  C1   C2    180.00   0.0  0
 9PC  CONST_27  C    C1   C2   C3    180.00   0.0  0
 9PC  CONST_28  O1   C5   C4   C3    180.00   0.0  0
 9PC  CONST_29  C4   C5   C13  F1    180.00   0.0  0
 9PC  CONST_30  C5   C13  C1   C     180.00   0.0  0
 9PC  CONST_31  F    C2   C3   C4    180.00   0.0  0
 9PC  CONST_32  C9   S    C7   C6    180.00   0.0  0
 9PC  CONST_33  C8   N1   C7   C6    180.00   0.0  0
 9PC  CONST_34  CL   C11  C10  N2    180.00   0.0  0
 9PC  CONST_35  C8   C12  C11  CL    180.00   0.0  0
 9PC  CONST_36  H8   C10  C11  C12   180.00   0.0  0
 9PC  CONST_37  H5   C4   C5   C13   180.00   0.0  0
 9PC  CONST_38  H4   C3   C2   C1    180.00   0.0  0
 9PC  CONST_39  H1   C12  C8   C9    180.00   0.0  0
 9PC  CONST_40  H2   N    C    C1      0.00   0.0  0
 9PC  CONST_41  H3   N    C    C1    180.00   0.0  0
 9PC  Var_01    C2   C1   C    N    -110.84  30.0  2
 9PC  Var_02    C7   C6   O1   C5    178.02  30.0  1
 9PC  Var_03    S    C7   C6   O1     -7.81  30.0  2

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
 9PC  plan-1  C13  0.020
 9PC  plan-1  C1   0.020
 9PC  plan-1  C2   0.020
 9PC  plan-1  C3   0.020
 9PC  plan-1  F1   0.020
 9PC  plan-1  C    0.020
 9PC  plan-1  C5   0.020
 9PC  plan-1  C4   0.020
 9PC  plan-1  O1   0.020
 9PC  plan-1  H4   0.020
 9PC  plan-1  H5   0.020
 9PC  plan-1  F    0.020
 9PC  plan-2  C11  0.020
 9PC  plan-2  C12  0.020
 9PC  plan-2  C6   0.020
 9PC  plan-2  C7   0.020
 9PC  plan-2  S    0.020
 9PC  plan-2  C9   0.020
 9PC  plan-2  N2   0.020
 9PC  plan-2  C10  0.020
 9PC  plan-2  CL   0.020
 9PC  plan-2  C8   0.020
 9PC  plan-2  N1   0.020
 9PC  plan-2  H1   0.020
 9PC  plan-2  H8   0.020
 9PC  plan-3  N    0.020
 9PC  plan-3  C1   0.020
 9PC  plan-3  C    0.020
 9PC  plan-3  O    0.020
 9PC  plan-3  H2   0.020
 9PC  plan-3  H3   0.020

