# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 03:04:00 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 7-(3,4-dimethoxyphenyl)-5-ethylsulfanyl-imidazo[2,1-f]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCSc1nc(cc2nccn12)c3ccc(OC)c(OC)c3
#
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
 KSS  KSS  7-(3,4-dimethoxyphenyl)-5-ethylsulfanyl-imidazo[2,1-f]pyrimidine  ligand  39  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KSS
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
 KSS  C1    C  CR56  0   0.561   2.4376   2.1737  -0.0057
 KSS  N2    N  N     0  -0.557   3.0830   0.9460   0.0074
 KSS  C3    C  CR15  0  -0.120   4.4351   1.1971   0.0066
 KSS  C4    C  CR15  0  -0.190   4.5311   2.5589  -0.0069
 KSS  N5    N  N     0  -0.474   3.3092   3.1571  -0.0146
 KSS  C6    C  CR16  0  -0.440   1.0312   2.1765  -0.0083
 KSS  C7    C  CR6   0   0.278   0.3797   0.9725   0.0043
 KSS  N8    N  N     0  -0.466   1.0749  -0.2027   0.0141
 KSS  C9    C  CR6   0   0.356   2.3593  -0.2116   0.0149
 KSS  S12   S  S2    0   0.062   3.2867  -1.6869   0.0271
 KSS  C13   C  CH2   0  -0.541   1.9671  -2.9370   0.0156
 KSS  C14   C  CH3   0  -0.669   2.6147  -4.3104   0.0380
 KSS  C21   C  CR6   0   0.058  -1.0878   0.8387   0.0051
 KSS  C22   C  CR16  0  -0.356  -1.9327   1.9387   0.0351
 KSS  C23   C  CR16  0  -0.363  -3.3134   1.7755   0.0303
 KSS  C24   C  CR6   0   0.306  -3.8795   0.5107  -0.0040
 KSS  C25   C  CR6   0   0.354  -3.0311  -0.6161  -0.0298
 KSS  C26   C  CR16  0  -0.436  -1.6613  -0.4410  -0.0254
 KSS  O30   O  O2    0  -0.458  -5.1959   0.2520  -0.0145
 KSS  O31   O  O2    0  -0.465  -3.6521  -1.8098  -0.0584
 KSS  C32   C  CH3   0  -0.439  -6.0945   1.3439   0.0025
 KSS  C36   C  CH3   0  -0.439  -2.8544  -2.9755  -0.0806
 KSS  H3    H  HCR5  0   0.313   5.1827   0.4232   0.0160
 KSS  H4    H  HCR5  0   0.266   5.4418   3.1381  -0.0111
 KSS  H6    H  HCR6  0   0.281   0.5177   3.1261  -0.0215
 KSS  H13   H  HCH2  0   0.285   1.3329  -2.7810   0.8866
 KSS  H13A  H  HCH2  0   0.285   1.3636  -2.7952  -0.8795
 KSS  H14   H  HCH3  0   0.244   3.2138  -4.4601   0.9357
 KSS  H14A  H  HCH3  0   0.259   1.8350  -5.0708   0.0265
 KSS  H14B  H  HCH3  0   0.243   3.2511  -4.4722  -0.8316
 KSS  H22   H  HCR6  0   0.253  -1.5439   2.9474   0.0651
 KSS  H23   H  HCR6  0   0.286  -3.9388   2.6573   0.0547
 KSS  H26   H  HCR6  0   0.284  -0.9996  -1.2947  -0.0454
 KSS  H32   H  HCH3  0   0.231  -5.9903   1.9444   0.9099
 KSS  H32A  H  HCH3  0   0.231  -5.9638   1.9936  -0.8667
 KSS  H32B  H  HCH3  0   0.262  -7.0948   0.9193  -0.0236
 KSS  H36   H  HCH3  0   0.263  -3.5397  -3.8192  -0.0946
 KSS  H36A  H  HCH3  0   0.227  -2.2231  -3.0218  -0.9721
 KSS  H36B  H  HCH3  0   0.227  -2.2204  -3.0538   0.8068

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
 KSS  C1   N2    aromatic  1.387  0.020  1.387
 KSS  C1   N5    aromatic  1.314  0.020  1.314
 KSS  C1   C6    aromatic  1.406  0.020  1.406
 KSS  N2   C3    aromatic  1.375  0.020  1.375
 KSS  N2   C9    aromatic  1.365  0.020  1.365
 KSS  C3   C4    aromatic  1.365  0.020  1.365
 KSS  C4   N5    aromatic  1.360  0.020  1.360
 KSS  C6   C7    aromatic  1.369  0.020  1.369
 KSS  C7   N8    aromatic  1.365  0.020  1.365
 KSS  C7   C21   single    1.474  0.020  1.474
 KSS  N8   C9    aromatic  1.284  0.020  1.284
 KSS  C9   S12   single    1.743  0.020  1.743
 KSS  S12  C13   single    1.818  0.020  1.818
 KSS  C13  C14   single    1.519  0.020  1.519
 KSS  C21  C22   aromatic  1.387  0.020  1.387
 KSS  C21  C26   aromatic  1.403  0.020  1.403
 KSS  C22  C23   aromatic  1.390  0.020  1.390
 KSS  C23  C24   aromatic  1.386  0.020  1.386
 KSS  C24  C25   aromatic  1.411  0.020  1.411
 KSS  C24  O30   single    1.342  0.020  1.342
 KSS  C25  C26   aromatic  1.381  0.020  1.381
 KSS  C25  O31   single    1.346  0.020  1.346
 KSS  O30  C32   single    1.414  0.020  1.414
 KSS  O31  C36   single    1.413  0.020  1.413
 KSS  C3   H3    single    0.930  0.020  1.080
 KSS  C4   H4    single    0.930  0.020  1.080
 KSS  C6   H6    single    0.930  0.020  1.080
 KSS  C13  H13   single    0.970  0.020  1.090
 KSS  C13  H13A  single    0.970  0.020  1.090
 KSS  C14  H14   single    0.970  0.020  1.090
 KSS  C14  H14A  single    0.970  0.020  1.090
 KSS  C14  H14B  single    0.970  0.020  1.090
 KSS  C22  H22   single    0.930  0.020  1.080
 KSS  C23  H23   single    0.930  0.020  1.080
 KSS  C26  H26   single    0.930  0.020  1.080
 KSS  C32  H32   single    0.970  0.020  1.090
 KSS  C32  H32A  single    0.970  0.020  1.090
 KSS  C32  H32B  single    0.970  0.020  1.090
 KSS  C36  H36   single    0.970  0.020  1.090
 KSS  C36  H36A  single    0.970  0.020  1.090
 KSS  C36  H36B  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
 KSS  C6    C1   N5    131.43  3.000
 KSS  C6    C1   N2    117.85  3.000
 KSS  N5    C1   N2    110.72  3.000
 KSS  C9    N2   C3    132.54  3.000
 KSS  C9    N2   C1    120.26  3.000
 KSS  C3    N2   C1    107.21  3.000
 KSS  H3    C3   C4    131.96  3.000
 KSS  H3    C3   N2    123.49  3.000
 KSS  C4    C3   N2    104.55  3.000
 KSS  H4    C4   N5    121.46  3.000
 KSS  H4    C4   C3    126.49  3.000
 KSS  N5    C4   C3    112.05  3.000
 KSS  C4    N5   C1    105.46  3.000
 KSS  H6    C6   C7    123.18  3.000
 KSS  H6    C6   C1    118.52  3.000
 KSS  C7    C6   C1    118.30  3.000
 KSS  C21   C7   N8    115.40  3.000
 KSS  C21   C7   C6    123.63  3.000
 KSS  N8    C7   C6    120.98  3.000
 KSS  C9    N8   C7    121.00  3.000
 KSS  S12   C9   N8    122.55  3.000
 KSS  S12   C9   N2    115.83  3.000
 KSS  N8    C9   N2    121.62  3.000
 KSS  C13   S12  C9    101.29  3.000
 KSS  H13A  C13  H13   108.43  3.000
 KSS  H13A  C13  C14   111.49  3.000
 KSS  H13   C13  C14   111.48  3.000
 KSS  H13A  C13  S12   108.55  3.000
 KSS  H13   C13  S12   108.62  3.000
 KSS  C14   C13  S12   108.20  3.000
 KSS  H14B  C14  H14A  107.82  3.000
 KSS  H14B  C14  H14   108.42  3.000
 KSS  H14A  C14  H14   107.84  3.000
 KSS  H14B  C14  C13   111.81  3.000
 KSS  H14A  C14  C13   109.02  3.000
 KSS  H14   C14  C13   111.77  3.000
 KSS  C26   C21  C22   118.35  3.000
 KSS  C26   C21  C7    119.34  3.000
 KSS  C22   C21  C7    122.31  3.000
 KSS  H22   C22  C23   117.82  3.000
 KSS  H22   C22  C21   121.41  3.000
 KSS  C23   C22  C21   120.77  3.000
 KSS  H23   C23  C24   120.56  3.000
 KSS  H23   C23  C22   118.59  3.000
 KSS  C24   C23  C22   120.85  3.000
 KSS  O30   C24  C25   115.85  3.000
 KSS  O30   C24  C23   125.23  3.000
 KSS  C25   C24  C23   118.93  3.000
 KSS  O31   C25  C26   124.76  3.000
 KSS  O31   C25  C24   115.55  3.000
 KSS  C26   C25  C24   119.69  3.000
 KSS  H26   C26  C25   120.49  3.000
 KSS  H26   C26  C21   118.10  3.000
 KSS  C25   C26  C21   121.42  3.000
 KSS  C32   O30  C24   118.33  3.000
 KSS  C36   O31  C25   118.14  3.000
 KSS  H32B  C32  H32A  108.86  3.000
 KSS  H32B  C32  H32   108.80  3.000
 KSS  H32A  C32  H32   108.80  3.000
 KSS  H32B  C32  O30   106.43  3.000
 KSS  H32A  C32  O30   111.92  3.000
 KSS  H32   C32  O30   111.93  3.000
 KSS  H36B  C36  H36A  108.90  3.000
 KSS  H36B  C36  H36   108.69  3.000
 KSS  H36A  C36  H36   108.70  3.000
 KSS  H36B  C36  O31   111.95  3.000
 KSS  H36A  C36  O31   111.95  3.000
 KSS  H36   C36  O31   106.54  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
 KSS  CONST_01  C4   C3   N2   C1      0.00   0.0  0
 KSS  CONST_02  N8   C9   N2   C1      0.00   0.0  0
 KSS  CONST_03  C3   C4   N5   C1      0.00   0.0  0
 KSS  CONST_04  N8   C7   C6   C1      0.00   0.0  0
 KSS  CONST_05  C21  C7   C6   C1    180.00   0.0  0
 KSS  CONST_06  C4   N5   C1   N2      0.00   0.0  0
 KSS  CONST_07  C7   C6   C1   N2      0.00   0.0  0
 KSS  CONST_08  N5   C4   C3   N2      0.00   0.0  0
 KSS  CONST_09  C7   N8   C9   N2      0.00   0.0  0
 KSS  CONST_10  N5   C1   N2   C3      0.00   0.0  0
 KSS  CONST_11  C6   C1   N2   C3    180.00   0.0  0
 KSS  CONST_12  N8   C9   N2   C3    180.00   0.0  0
 KSS  CONST_13  C9   N2   C3   C4    180.00   0.0  0
 KSS  CONST_14  C6   C1   N5   C4    180.00   0.0  0
 KSS  CONST_15  C9   N2   C1   N5    180.00   0.0  0
 KSS  CONST_16  C7   C6   C1   N5    180.00   0.0  0
 KSS  CONST_17  C9   N2   C1   C6      0.00   0.0  0
 KSS  CONST_18  C9   N8   C7   C6      0.00   0.0  0
 KSS  CONST_19  C22  C21  C7   C6      0.00   0.0  0
 KSS  CONST_20  C26  C21  C7   C6    180.00   0.0  0
 KSS  CONST_21  C23  C22  C21  C7    180.00   0.0  0
 KSS  CONST_22  C25  C26  C21  C7    180.00   0.0  0
 KSS  CONST_23  C22  C21  C7   N8    180.00   0.0  0
 KSS  CONST_24  C26  C21  C7   N8      0.00   0.0  0
 KSS  CONST_25  C21  C7   N8   C9    180.00   0.0  0
 KSS  CONST_26  C24  C23  C22  C21     0.00   0.0  0
 KSS  CONST_27  C24  C25  C26  C21     0.00   0.0  0
 KSS  CONST_28  C25  C26  C21  C22     0.00   0.0  0
 KSS  CONST_29  C25  C24  C23  C22     0.00   0.0  0
 KSS  CONST_30  C26  C21  C22  C23     0.00   0.0  0
 KSS  CONST_31  C26  C25  C24  C23     0.00   0.0  0
 KSS  CONST_32  S12  C9   N2   C1    180.00   0.0  0
 KSS  CONST_33  S12  C9   N2   C3      0.00   0.0  0
 KSS  CONST_34  S12  C9   N8   C7    180.00   0.0  0
 KSS  CONST_35  O31  C25  C26  C21   180.00   0.0  0
 KSS  CONST_36  O30  C24  C23  C22   180.00   0.0  0
 KSS  CONST_37  O31  C25  C24  C23   180.00   0.0  0
 KSS  CONST_38  O30  C24  C25  C26   180.00   0.0  0
 KSS  CONST_39  H3   C3   N2   C1    180.00   0.0  0
 KSS  CONST_40  H4   C4   N5   C1    180.00   0.0  0
 KSS  CONST_41  H6   C6   C1   N2    180.00   0.0  0
 KSS  CONST_42  H22  C22  C21  C7      0.00   0.0  0
 KSS  CONST_43  H26  C26  C21  C7      0.00   0.0  0
 KSS  CONST_44  H23  C23  C22  C21   180.00   0.0  0
 KSS  Var_01    C14  C13  S12  C9   -179.47  30.0  3
 KSS  Var_02    H32  C32  O30  C24   -62.01  30.0  3
 KSS  Var_03    H36  C36  O31  C25   179.61  30.0  3
 KSS  Var_04    H14  C14  C13  S12    61.15  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
 KSS  plan-1  C7   0.020
 KSS  plan-1  C21  0.020
 KSS  plan-1  C22  0.020
 KSS  plan-1  C23  0.020
 KSS  plan-1  C24  0.020
 KSS  plan-1  C25  0.020
 KSS  plan-1  C26  0.020
 KSS  plan-1  O30  0.020
 KSS  plan-1  O31  0.020
 KSS  plan-1  H22  0.020
 KSS  plan-1  H23  0.020
 KSS  plan-1  H26  0.020
 KSS  plan-2  C1   0.020
 KSS  plan-2  N2   0.020
 KSS  plan-2  C3   0.020
 KSS  plan-2  C4   0.020
 KSS  plan-2  N5   0.020
 KSS  plan-2  C6   0.020
 KSS  plan-2  C7   0.020
 KSS  plan-2  N8   0.020
 KSS  plan-2  C9   0.020
 KSS  plan-2  S12  0.020
 KSS  plan-2  C21  0.020
 KSS  plan-2  H3   0.020
 KSS  plan-2  H4   0.020
 KSS  plan-2  H6   0.020

