# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 17:33:24 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 1-(2-methoxyethyl)-N-oxo-4-[4-[4-(trifluoromethoxy)phenoxy]phenyl]sulfonyl-piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN1CCC(CC1)(C(=O)N=O)[S](=O)(=O)c2ccc(Oc3ccc(OC(F)(F)F)cc3)cc2
#
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
 3KR  3KR  1-(2-methoxyethyl)-N-oxo-4-[4-[4-(trifluoromethoxy)phenoxy]phenyl]sulfonyl-piperidine-4-carboxamide  ligand  58  35  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3KR
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
 3KR  S1    S  S     0   1.222   2.3756   0.0152  -1.8022
 3KR  C2    C  CR6   0  -0.196   0.8815  -0.6752  -1.1785
 3KR  C3    C  CR16  0  -0.211  -0.2845   0.0777  -1.1961
 3KR  C4    C  CR16  0  -0.333  -1.4629  -0.4642  -0.7131
 3KR  C5    C  CR6   0   0.396  -1.4653  -1.7642  -0.2146
 3KR  C6    C  CR16  0  -0.314  -0.2933  -2.5221  -0.2075
 3KR  C7    C  CR16  0  -0.219   0.8774  -1.9809  -0.6927
 3KR  C8    C  CT    0  -0.413   3.1963   0.8310  -0.3649
 3KR  C9    C  C     0   0.505   2.2874   2.0160  -0.0978
 3KR  N10   N  N     0   0.019   2.4726   3.1861  -1.0372
 3KR  O11   O  O     0  -0.198   1.4855   3.8363  -1.1112
 3KR  O12   O  OS    0  -0.622   3.2093  -1.0681  -2.3058
 3KR  O13   O  OS    0  -0.649   2.0297   1.1226  -2.6972
 3KR  O14   O  O     0  -0.293   1.5223   2.1085   0.8088
 3KR  C15   C  CH2   0  -0.432   3.2890  -0.0671   0.8671
 3KR  C16   C  CH2   0  -0.286   4.4002  -1.1011   0.7838
 3KR  N17   N  NT    0  -0.416   5.6750  -0.4567   0.5378
 3KR  C18   C  CH2   0  -0.284   5.6595   0.2227  -0.7424
 3KR  C19   C  CH2   0  -0.445   4.5972   1.3111  -0.7919
 3KR  C20   C  CH2   0  -0.307   6.7793  -1.3929   0.6385
 3KR  C21   C  CH2   0  -0.151   8.1240  -0.7276   0.8466
 3KR  O22   O  O2    0  -0.480   8.1352  -0.0633   2.0837
 3KR  C23   C  CH3   0  -0.395   9.3502   0.5943   2.3292
 3KR  O24   O  O2    0  -0.498  -2.5616  -2.3709   0.2852
 3KR  C25   C  CR6   0   0.288  -3.7800  -1.7357   0.2114
 3KR  C26   C  CR16  0  -0.284  -4.5505  -1.8580  -0.9342
 3KR  C27   C  CR16  0  -0.322  -5.7937  -1.2536  -0.9834
 3KR  C28   C  CR6   0   0.355  -6.2564  -0.5319   0.1085
 3KR  C29   C  CR16  0  -0.337  -5.4878  -0.4076   1.2563
 3KR  C30   C  CR16  0  -0.288  -4.2390  -1.0151   1.2978
 3KR  O31   O  O2    0  -0.504  -7.5115   0.0133  -0.0737
 3KR  C32   C  CT    0   1.082  -8.1201   0.7794   0.8374
 3KR  F33   F  F     0  -0.302  -7.4320   1.8840   1.1283
 3KR  F34   F  F     0  -0.271  -9.2863   1.1411   0.3290
 3KR  F35   F  F     0  -0.302  -8.3490   0.1385   1.9844
 3KR  H3    H  HCR6  0   0.290  -0.2987   1.0834  -1.5938
 3KR  H4    H  HCR6  0   0.299  -2.3620   0.1358  -0.7362
 3KR  H6    H  HCR6  0   0.291  -0.3090  -3.5348   0.1729
 3KR  H7    H  HCR6  0   0.296   1.7768  -2.5823  -0.6917
 3KR  H15   H  HCH2  0   0.279   3.5053   0.5868   1.7152
 3KR  H15A  H  HCH2  0   0.277   2.3347  -0.5457   1.0880
 3KR  H16   H  HCH2  0   0.256   4.4437  -1.6134   1.7468
 3KR  H16A  H  HCH2  0   0.207   4.1727  -1.8721   0.0312
 3KR  H18   H  HCH2  0   0.253   6.6190   0.7155  -0.9040
 3KR  H18A  H  HCH2  0   0.218   5.5300  -0.4841  -1.5733
 3KR  H19   H  HCH2  0   0.281   4.5856   1.7691  -1.7808
 3KR  H19A  H  HCH2  0   0.281   4.8852   2.1001  -0.0913
 3KR  H20   H  HCH2  0   0.240   6.5923  -2.0597   1.4845
 3KR  H20A  H  HCH2  0   0.205   6.8531  -2.0397  -0.2515
 3KR  H21   H  HCH2  0   0.208   8.8999  -1.5060   0.8091
 3KR  H21A  H  HCH2  0   0.200   8.3522  -0.0285   0.0289
 3KR  H23   H  HCH3  0   0.231   9.2803   1.0825   3.3010
 3KR  H23A  H  HCH3  0   0.201  10.2012  -0.0978   2.3524
 3KR  H23B  H  HCH3  0   0.202   9.5640   1.3604   1.5736
 3KR  H26   H  HCR6  0   0.290  -4.1907  -2.4252  -1.7829
 3KR  H27   H  HCR6  0   0.293  -6.4072  -1.3430  -1.8701
 3KR  H29   H  HCR6  0   0.297  -5.8104   0.1417   2.1283
 3KR  H30   H  HCR6  0   0.292  -3.6319  -0.9249   2.1890

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
 3KR  S1   C2    single    1.760  0.020  1.760
 3KR  S1   C8    single    1.845  0.020  1.845
 3KR  S1   O12   double    1.457  0.020  1.457
 3KR  S1   O13   double    1.465  0.020  1.465
 3KR  C2   C3    aromatic  1.388  0.020  1.388
 3KR  C2   C7    aromatic  1.393  0.020  1.393
 3KR  C3   C4    aromatic  1.384  0.020  1.384
 3KR  C4   C5    aromatic  1.392  0.020  1.392
 3KR  C5   C6    aromatic  1.396  0.020  1.396
 3KR  C5   O24   single    1.349  0.020  1.349
 3KR  C6   C7    aromatic  1.378  0.020  1.378
 3KR  C8   C9    single    1.517  0.020  1.517
 3KR  C8   C15   single    1.527  0.020  1.527
 3KR  C8   C19   single    1.541  0.020  1.541
 3KR  C9   N10   single    1.512  0.020  1.512
 3KR  C9   O14   double    1.190  0.020  1.190
 3KR  N10  O11   double    1.184  0.020  1.184
 3KR  C15  C16   single    1.520  0.020  1.520
 3KR  C16  N17   single    1.449  0.020  1.449
 3KR  N17  C18   single    1.449  0.020  1.449
 3KR  N17  C20   single    1.451  0.020  1.451
 3KR  C18  C19   single    1.522  0.020  1.522
 3KR  C20  C21   single    1.515  0.020  1.515
 3KR  C21  O22   single    1.404  0.020  1.404
 3KR  O22  C23   single    1.403  0.020  1.403
 3KR  O24  C25   single    1.376  0.020  1.376
 3KR  C25  C26   aromatic  1.386  0.020  1.386
 3KR  C25  C30   aromatic  1.382  0.020  1.382
 3KR  C26  C27   aromatic  1.383  0.020  1.383
 3KR  C27  C28   aromatic  1.388  0.020  1.388
 3KR  C28  C29   aromatic  1.387  0.020  1.387
 3KR  C28  O31   single    1.381  0.020  1.381
 3KR  C29  C30   aromatic  1.389  0.020  1.389
 3KR  O31  C32   single    1.337  0.020  1.337
 3KR  C32  F33   single    1.333  0.020  1.333
 3KR  C32  F34   single    1.323  0.020  1.323
 3KR  C32  F35   single    1.334  0.020  1.334
 3KR  C3   H3    single    0.930  0.020  1.080
 3KR  C4   H4    single    0.930  0.020  1.080
 3KR  C6   H6    single    0.930  0.020  1.080
 3KR  C7   H7    single    0.930  0.020  1.080
 3KR  C15  H15   single    0.970  0.020  1.090
 3KR  C15  H15A  single    0.970  0.020  1.090
 3KR  C16  H16   single    0.970  0.020  1.090
 3KR  C16  H16A  single    0.970  0.020  1.090
 3KR  C18  H18   single    0.970  0.020  1.090
 3KR  C18  H18A  single    0.970  0.020  1.090
 3KR  C19  H19   single    0.970  0.020  1.090
 3KR  C19  H19A  single    0.970  0.020  1.090
 3KR  C20  H20   single    0.970  0.020  1.090
 3KR  C20  H20A  single    0.970  0.020  1.090
 3KR  C21  H21   single    0.970  0.020  1.090
 3KR  C21  H21A  single    0.970  0.020  1.090
 3KR  C23  H23   single    0.970  0.020  1.090
 3KR  C23  H23A  single    0.970  0.020  1.090
 3KR  C23  H23B  single    0.970  0.020  1.090
 3KR  C26  H26   single    0.930  0.020  1.080
 3KR  C27  H27   single    0.930  0.020  1.080
 3KR  C29  H29   single    0.930  0.020  1.080
 3KR  C30  H30   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
 3KR  O13   S1   O12   119.07  3.000
 3KR  O13   S1   C8    104.28  3.000
 3KR  O12   S1   C8    110.09  3.000
 3KR  O13   S1   C2    108.21  3.000
 3KR  O12   S1   C2    108.46  3.000
 3KR  C8    S1   C2    105.96  3.000
 3KR  C7    C2   C3    120.68  3.000
 3KR  C7    C2   S1    119.59  3.000
 3KR  C3    C2   S1    119.73  3.000
 3KR  H3    C3   C4    118.76  3.000
 3KR  H3    C3   C2    121.33  3.000
 3KR  C4    C3   C2    119.90  3.000
 3KR  H4    C4   C5    121.63  3.000
 3KR  H4    C4   C3    118.90  3.000
 3KR  C5    C4   C3    119.47  3.000
 3KR  O24   C5   C6    115.87  3.000
 3KR  O24   C5   C4    123.64  3.000
 3KR  C6    C5   C4    120.49  3.000
 3KR  H6    C6   C7    120.25  3.000
 3KR  H6    C6   C5    119.86  3.000
 3KR  C7    C6   C5    119.89  3.000
 3KR  H7    C7   C6    119.18  3.000
 3KR  H7    C7   C2    121.25  3.000
 3KR  C6    C7   C2    119.57  3.000
 3KR  C19   C8   C15   110.58  3.000
 3KR  C19   C8   C9    110.49  3.000
 3KR  C15   C8   C9    110.71  3.000
 3KR  C19   C8   S1    109.04  3.000
 3KR  C15   C8   S1    113.28  3.000
 3KR  C9    C8   S1    102.47  3.000
 3KR  O14   C9   N10   119.47  3.000
 3KR  O14   C9   C8    125.46  3.000
 3KR  N10   C9   C8    114.94  3.000
 3KR  O11   N10  C9    111.20  3.000
 3KR  H15A  C15  H15   106.19  3.000
 3KR  H15A  C15  C16   110.63  3.000
 3KR  H15   C15  C16   107.75  3.000
 3KR  H15A  C15  C8    111.63  3.000
 3KR  H15   C15  C8    106.63  3.000
 3KR  C16   C15  C8    113.58  3.000
 3KR  H16A  C16  H16   106.41  3.000
 3KR  H16A  C16  N17   112.15  3.000
 3KR  H16   C16  N17   108.86  3.000
 3KR  H16A  C16  C15   111.27  3.000
 3KR  H16   C16  C15   107.46  3.000
 3KR  N17   C16  C15   110.48  3.000
 3KR  C20   N17  C18   111.83  3.000
 3KR  C20   N17  C16   111.76  3.000
 3KR  C18   N17  C16   110.42  3.000
 3KR  H18A  C18  H18   106.40  3.000
 3KR  H18A  C18  C19   110.70  3.000
 3KR  H18   C18  C19   106.62  3.000
 3KR  H18A  C18  N17   111.57  3.000
 3KR  H18   C18  N17   109.46  3.000
 3KR  C19   C18  N17   111.81  3.000
 3KR  H19A  C19  H19   106.32  3.000
 3KR  H19A  C19  C18   108.14  3.000
 3KR  H19   C19  C18   109.73  3.000
 3KR  H19A  C19  C8    106.65  3.000
 3KR  H19   C19  C8    111.87  3.000
 3KR  C18   C19  C8    113.75  3.000
 3KR  H20A  C20  H20   106.16  3.000
 3KR  H20A  C20  C21   108.01  3.000
 3KR  H20   C20  C21   108.26  3.000
 3KR  H20A  C20  N17   111.92  3.000
 3KR  H20   C20  N17   108.48  3.000
 3KR  C21   C20  N17   113.69  3.000
 3KR  H21A  C21  H21   106.16  3.000
 3KR  H21A  C21  O22   110.64  3.000
 3KR  H21   C21  O22   111.06  3.000
 3KR  H21A  C21  C20   111.18  3.000
 3KR  H21   C21  C20   108.11  3.000
 3KR  O22   C21  C20   109.63  3.000
 3KR  C23   O22  C21   112.51  3.000
 3KR  H23B  C23  H23A  107.69  3.000
 3KR  H23B  C23  H23   108.29  3.000
 3KR  H23A  C23  H23   108.27  3.000
 3KR  H23B  C23  O22   112.05  3.000
 3KR  H23A  C23  O22   112.31  3.000
 3KR  H23   C23  O22   108.09  3.000
 3KR  C25   O24  C5    119.48  3.000
 3KR  C30   C25  C26   120.74  3.000
 3KR  C30   C25  O24   119.51  3.000
 3KR  C26   C25  O24   119.72  3.000
 3KR  H26   C26  C27   119.99  3.000
 3KR  H26   C26  C25   120.64  3.000
 3KR  C27   C26  C25   119.37  3.000
 3KR  H27   C27  C28   119.90  3.000
 3KR  H27   C27  C26   120.18  3.000
 3KR  C28   C27  C26   119.91  3.000
 3KR  O31   C28  C29   125.29  3.000
 3KR  O31   C28  C27   113.86  3.000
 3KR  C29   C28  C27   120.85  3.000
 3KR  H29   C29  C30   117.82  3.000
 3KR  H29   C29  C28   123.25  3.000
 3KR  C30   C29  C28   118.92  3.000
 3KR  H30   C30  C29   119.50  3.000
 3KR  H30   C30  C25   120.30  3.000
 3KR  C29   C30  C25   120.20  3.000
 3KR  C32   O31  C28   123.38  3.000
 3KR  F35   C32  F34   108.10  3.000
 3KR  F35   C32  F33   107.40  3.000
 3KR  F34   C32  F33   108.20  3.000
 3KR  F35   C32  O31   112.88  3.000
 3KR  F34   C32  O31   107.22  3.000
 3KR  F33   C32  O31   112.85  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
 3KR  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 3KR  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 3KR  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 3KR  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 3KR  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 3KR  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 3KR  CONST_07  C28  C27  C26  C25     0.00   0.0  0
 3KR  CONST_08  C28  C29  C30  C25     0.00   0.0  0
 3KR  CONST_09  C29  C30  C25  C26     0.00   0.0  0
 3KR  CONST_10  C29  C28  C27  C26     0.00   0.0  0
 3KR  CONST_11  C30  C25  C26  C27     0.00   0.0  0
 3KR  CONST_12  C30  C29  C28  C27     0.00   0.0  0
 3KR  CONST_13  C4   C3   C2   S1    180.00   0.0  0
 3KR  CONST_14  C6   C7   C2   S1    180.00   0.0  0
 3KR  CONST_15  O24  C5   C4   C3    180.00   0.0  0
 3KR  CONST_16  O24  C5   C6   C7    180.00   0.0  0
 3KR  CONST_17  C27  C26  C25  O24   180.00   0.0  0
 3KR  CONST_18  C29  C30  C25  O24   180.00   0.0  0
 3KR  CONST_19  O31  C28  C27  C26   180.00   0.0  0
 3KR  CONST_20  O31  C28  C29  C30   180.00   0.0  0
 3KR  CONST_21  H4   C4   C3   C2    180.00   0.0  0
 3KR  CONST_22  H6   C6   C7   C2    180.00   0.0  0
 3KR  CONST_23  H7   C7   C2   C3    180.00   0.0  0
 3KR  CONST_24  H3   C3   C4   C5    180.00   0.0  0
 3KR  CONST_25  H27  C27  C26  C25   180.00   0.0  0
 3KR  CONST_26  H29  C29  C30  C25   180.00   0.0  0
 3KR  CONST_27  H30  C30  C25  C26   180.00   0.0  0
 3KR  CONST_28  H26  C26  C27  C28   180.00   0.0  0
 3KR  Var_01    N17  C16  C15  C8     55.61  30.0  1
 3KR  Var_02    N17  C18  C19  C8    -51.37  30.0  1
 3KR  Var_03    C18  N17  C16  C15   -62.87  30.0  1
 3KR  Var_04    C19  C18  N17  C16    61.13  30.0  1
 3KR  Var_05    C8   S1   C2   C3     90.50  30.0  2
 3KR  Var_06    C26  C25  O24  C5     85.55  30.0  2
 3KR  Var_07    C21  C20  N17  C16  -160.94  30.0  3
 3KR  Var_08    O22  C21  C20  N17    64.38  30.0  3
 3KR  Var_09    F33  C32  O31  C28    60.02  30.0  3
 3KR  Var_10    H23  C23  O22  C21   179.98  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 3KR  chir_01  C8  C9  C15  C19  positiv

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
 3KR  plan-1  S1   0.020
 3KR  plan-1  C2   0.020
 3KR  plan-1  C3   0.020
 3KR  plan-1  C4   0.020
 3KR  plan-1  C5   0.020
 3KR  plan-1  C6   0.020
 3KR  plan-1  C7   0.020
 3KR  plan-1  O24  0.020
 3KR  plan-1  H3   0.020
 3KR  plan-1  H4   0.020
 3KR  plan-1  H6   0.020
 3KR  plan-1  H7   0.020
 3KR  plan-2  O24  0.020
 3KR  plan-2  C25  0.020
 3KR  plan-2  C26  0.020
 3KR  plan-2  C27  0.020
 3KR  plan-2  C28  0.020
 3KR  plan-2  C29  0.020
 3KR  plan-2  C30  0.020
 3KR  plan-2  O31  0.020
 3KR  plan-2  H26  0.020
 3KR  plan-2  H27  0.020
 3KR  plan-2  H29  0.020
 3KR  plan-2  H30  0.020
 3KR  plan-3  C8   0.020
 3KR  plan-3  C9   0.020
 3KR  plan-3  N10  0.020
 3KR  plan-3  O11  0.020
 3KR  plan-3  O14  0.020

