# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 05:49:18 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: ~{N}-[3-[2-azanyl-5-(4-piperazin-1-ylphenyl)pyridin-3-yl]-5-methoxy-phenyl]methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(N[S](C)(=O)=O)cc(c1)c2cc(cnc2N)c3ccc(cc3)N4CCNCC4
#
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
 KRE  KRE  ~{N}-[3-[2-azanyl-5-(4-piperazin-1-ylphenyl)pyridin-3-yl]-5-methoxy-phenyl]methanesulfonamide  ligand  59  32  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KRE
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
 KRE  C15   C  CH3   0  -0.442   4.6642   1.8950  -3.8537
 KRE  C19   C  CR16  0  -0.112  -1.1445  -3.0713   0.2100
 KRE  O11   O  OS    0  -0.651   5.9415   2.5041   0.5893
 KRE  C12   C  CR16  0  -0.401   4.5902   0.6084  -1.3680
 KRE  C13   C  CR6   0   0.415   3.5322   0.5404  -2.2677
 KRE  C16   C  CR16  0  -0.390   2.3912  -0.2008  -1.9512
 KRE  C17   C  CR16  0  -0.236  -0.1523  -1.0094  -0.3613
 KRE  C02   C  CR6   0   0.406   1.1189  -3.0226  -0.1517
 KRE  C03   C  CR6   0  -0.058   1.0792  -1.6317  -0.4061
 KRE  C04   C  CR6   0   0.071   2.2987  -0.8638  -0.7378
 KRE  C05   C  CR16  0  -0.384   3.3467  -0.7732   0.1809
 KRE  C06   C  CR6   0   0.322   4.4804  -0.0439  -0.1429
 KRE  C10   C  CH3   0  -0.795   4.4777   1.7344   2.6254
 KRE  C20   C  CR6   0  -0.003  -1.3163  -1.7183  -0.0528
 KRE  C21   C  CR6   0   0.058  -2.6368  -1.0729   0.0125
 KRE  C22   C  CR16  0  -0.305  -3.7873  -1.7208  -0.4294
 KRE  C23   C  CR16  0  -0.341  -5.0376  -1.1238  -0.3531
 KRE  C24   C  CR16  0  -0.307  -2.7917   0.2192   0.5229
 KRE  C25   C  CR16  0  -0.309  -4.0292   0.8284   0.5885
 KRE  C26   C  CR6   0   0.347  -5.1908   0.1705   0.1557
 KRE  C28   C  CH2   0  -0.302  -7.5569   0.1744  -0.4250
 KRE  C29   C  CH2   0  -0.298  -8.7045   1.1576  -0.5729
 KRE  C31   C  CH2   0  -0.300  -7.9465   2.3889   1.3127
 KRE  C32   C  CH2   0  -0.299  -6.7863   1.4293   1.4884
 KRE  N07   N  NC1   0  -0.824   5.5641   0.0204   0.7688
 KRE  N18   N  N     0  -0.447   0.0188  -3.7036   0.1593
 KRE  N27   N  NT    0  -0.515  -6.4241   0.8184   0.2134
 KRE  N30   N  NH1   0  -0.598  -9.0702   1.6872   0.7251
 KRE  O09   O  OS    0  -0.662   7.0434   1.1673   2.4080
 KRE  O14   O  O2    0  -0.470   3.5332   1.1347  -3.4718
 KRE  S08   S  S     0   1.317   5.8834   1.4425   1.5785
 KRE  H153  H  HCH3  0   0.264   4.4510   2.2875  -4.8445
 KRE  H151  H  HCH3  0   0.232   4.8406   2.7319  -3.1734
 KRE  H152  H  HCH3  0   0.232   5.5680   1.2830  -3.9038
 KRE  H191  H  HCR6  0   0.254  -1.9971  -3.6810   0.4942
 KRE  H121  H  HCR6  0   0.289   5.5021   1.1354  -1.6055
 KRE  H161  H  HCR6  0   0.265   1.5848  -0.2669  -2.6711
 KRE  H171  H  HCR6  0   0.259  -0.2069   0.0525  -0.5727
 KRE  H051  H  HCR6  0   0.276   3.2693  -1.2504   1.1509
 KRE  H101  H  HCH3  0   0.298   4.3945   0.9257   3.3477
 KRE  H103  H  HCH3  0   0.311   4.6346   2.6810   3.1397
 KRE  H102  H  HCH3  0   0.293   3.5783   1.7915   2.0158
 KRE  H221  H  HCR6  0   0.247  -3.7177  -2.7165  -0.8512
 KRE  H231  H  HCR6  0   0.266  -5.8931  -1.6891  -0.6963
 KRE  H241  H  HCR6  0   0.248  -1.9279   0.7639   0.8856
 KRE  H251  H  HCR6  0   0.260  -4.0889   1.8383   0.9728
 KRE  H282  H  HCH2  0   0.209  -7.8998  -0.7051   0.1413
 KRE  H281  H  HCH2  0   0.248  -7.2655  -0.1680  -1.4188
 KRE  H291  H  HCH2  0   0.195  -8.4034   1.9436  -1.2834
 KRE  H292  H  HCH2  0   0.238  -9.5584   0.6360  -1.0084
 KRE  H311  H  HCH2  0   0.238  -8.2314   2.7796   2.2912
 KRE  H312  H  HCH2  0   0.196  -7.6084   3.2424   0.7036
 KRE  H322  H  HCH2  0   0.252  -5.9387   1.9750   1.8979
 KRE  H321  H  HCH2  0   0.213  -7.0586   0.6541   2.2196
 KRE  H011  H  HNH2  0   0.399   3.1530  -3.2674  -0.2666
 KRE  H012  H  HNH2  0   0.387   2.2710  -4.6579   0.1437
 KRE  H071  H  HNC1  0   0.423   5.6314  -0.7789   1.3916
 KRE  H301  H  HNH1  0   0.356  -9.8569   2.3156   0.6304
 KRE  N01   N  NH2   0  -0.834   2.2670  -3.7423  -0.2737

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
 KRE  C29  N30   single    1.449  0.020  1.449
 KRE  C29  C28   single    1.518  0.020  1.518
 KRE  N30  C31   single    1.449  0.020  1.449
 KRE  C28  N27   single    1.451  0.020  1.451
 KRE  C31  C32   single    1.516  0.020  1.516
 KRE  N27  C32   single    1.460  0.020  1.460
 KRE  N27  C26   single    1.394  0.020  1.394
 KRE  C25  C26   aromatic  1.403  0.020  1.403
 KRE  C25  C24   aromatic  1.381  0.020  1.381
 KRE  C26  C23   aromatic  1.399  0.020  1.399
 KRE  C24  C21   aromatic  1.398  0.020  1.398
 KRE  C23  C22   aromatic  1.388  0.020  1.388
 KRE  C21  C22   aromatic  1.392  0.020  1.392
 KRE  C21  C20   single    1.471  0.020  1.471
 KRE  C19  C20   aromatic  1.389  0.020  1.389
 KRE  C19  N18   aromatic  1.325  0.020  1.325
 KRE  C20  C17   aromatic  1.397  0.020  1.397
 KRE  N18  C02   aromatic  1.331  0.020  1.331
 KRE  C17  C03   aromatic  1.380  0.020  1.380
 KRE  C02  C03   aromatic  1.415  0.020  1.415
 KRE  C02  N01   single    1.360  0.020  1.360
 KRE  C03  C04   single    1.479  0.020  1.479
 KRE  C04  C16   aromatic  1.386  0.020  1.386
 KRE  C04  C05   aromatic  1.397  0.020  1.397
 KRE  C16  C13   aromatic  1.397  0.020  1.397
 KRE  C05  C06   aromatic  1.386  0.020  1.386
 KRE  C13  O14   single    1.343  0.020  1.343
 KRE  C13  C12   aromatic  1.390  0.020  1.390
 KRE  C06  C12   aromatic  1.392  0.020  1.392
 KRE  C06  N07   single    1.418  0.020  1.418
 KRE  O14  C15   single    1.415  0.020  1.415
 KRE  C10  S08   single    1.777  0.020  1.777
 KRE  O09  S08   double    1.452  0.020  1.452
 KRE  N07  S08   single    1.667  0.020  1.667
 KRE  S08  O11   double    1.452  0.020  1.452
 KRE  C15  H153  single    0.970  0.020  1.090
 KRE  C15  H151  single    0.970  0.020  1.090
 KRE  C15  H152  single    0.970  0.020  1.090
 KRE  C19  H191  single    0.930  0.020  1.080
 KRE  C12  H121  single    0.930  0.020  1.080
 KRE  C16  H161  single    0.930  0.020  1.080
 KRE  C17  H171  single    0.930  0.020  1.080
 KRE  C05  H051  single    0.930  0.020  1.080
 KRE  C10  H101  single    0.970  0.020  1.090
 KRE  C10  H103  single    0.970  0.020  1.090
 KRE  C10  H102  single    0.970  0.020  1.090
 KRE  C22  H221  single    0.930  0.020  1.080
 KRE  C23  H231  single    0.930  0.020  1.080
 KRE  C24  H241  single    0.930  0.020  1.080
 KRE  C25  H251  single    0.930  0.020  1.080
 KRE  C28  H282  single    0.970  0.020  1.090
 KRE  C28  H281  single    0.970  0.020  1.090
 KRE  C29  H291  single    0.970  0.020  1.090
 KRE  C29  H292  single    0.970  0.020  1.090
 KRE  C31  H311  single    0.970  0.020  1.090
 KRE  C31  H312  single    0.970  0.020  1.090
 KRE  C32  H322  single    0.970  0.020  1.090
 KRE  C32  H321  single    0.970  0.020  1.090
 KRE  N01  H011  single    0.890  0.020  1.040
 KRE  N01  H012  single    0.890  0.020  1.040
 KRE  N07  H071  single    0.890  0.020  1.040
 KRE  N30  H301  single    0.890  0.020  1.040

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
 KRE  H152  C15  H151  108.90  3.000
 KRE  H152  C15  H153  108.82  3.000
 KRE  H151  C15  H153  108.82  3.000
 KRE  H152  C15  O14   111.87  3.000
 KRE  H151  C15  O14   111.87  3.000
 KRE  H153  C15  O14   106.46  3.000
 KRE  H191  C19  N18   115.55  3.000
 KRE  H191  C19  C20   119.95  3.000
 KRE  N18   C19  C20   124.49  3.000
 KRE  H121  C12  C06   119.26  3.000
 KRE  H121  C12  C13   121.62  3.000
 KRE  C06   C12  C13   119.11  3.000
 KRE  O14   C13  C16   116.02  3.000
 KRE  O14   C13  C12   123.92  3.000
 KRE  C16   C13  C12   120.06  3.000
 KRE  H161  C16  C04   120.20  3.000
 KRE  H161  C16  C13   119.34  3.000
 KRE  C04   C16  C13   120.45  3.000
 KRE  H171  C17  C20   119.87  3.000
 KRE  H171  C17  C03   118.70  3.000
 KRE  C20   C17  C03   121.44  3.000
 KRE  N18   C02  N01   116.61  3.000
 KRE  N01   C02  C03   121.85  3.000
 KRE  N18   C02  C03   121.46  3.000
 KRE  C04   C03  C02   121.85  3.000
 KRE  C04   C03  C17   120.58  3.000
 KRE  C02   C03  C17   117.55  3.000
 KRE  C05   C04  C03   120.33  3.000
 KRE  C05   C04  C16   119.66  3.000
 KRE  C03   C04  C16   119.99  3.000
 KRE  H051  C05  C06   119.94  3.000
 KRE  H051  C05  C04   120.43  3.000
 KRE  C06   C05  C04   119.61  3.000
 KRE  N07   C06  C05   119.92  3.000
 KRE  N07   C06  C12   118.97  3.000
 KRE  C05   C06  C12   121.09  3.000
 KRE  H102  C10  H103  109.76  3.000
 KRE  H102  C10  H101  110.36  3.000
 KRE  H103  C10  H101  110.11  3.000
 KRE  H102  C10  S08   109.42  3.000
 KRE  H103  C10  S08   107.89  3.000
 KRE  H101  C10  S08   109.25  3.000
 KRE  C21   C20  C17   122.34  3.000
 KRE  C17   C20  C19   115.65  3.000
 KRE  C21   C20  C19   122.00  3.000
 KRE  C24   C21  C22   117.03  3.000
 KRE  C22   C21  C20   121.56  3.000
 KRE  C24   C21  C20   121.41  3.000
 KRE  H221  C22  C23   118.33  3.000
 KRE  H221  C22  C21   119.87  3.000
 KRE  C23   C22  C21   121.79  3.000
 KRE  H231  C23  C26   120.83  3.000
 KRE  H231  C23  C22   118.06  3.000
 KRE  C26   C23  C22   121.11  3.000
 KRE  H241  C24  C25   118.47  3.000
 KRE  H241  C24  C21   119.90  3.000
 KRE  C25   C24  C21   121.63  3.000
 KRE  H251  C25  C26   120.09  3.000
 KRE  H251  C25  C24   118.55  3.000
 KRE  C26   C25  C24   121.35  3.000
 KRE  N27   C26  C25   120.10  3.000
 KRE  C25   C26  C23   117.08  3.000
 KRE  N27   C26  C23   122.80  3.000
 KRE  H281  C28  H282  107.53  3.000
 KRE  H281  C28  N27   109.36  3.000
 KRE  H282  C28  N27   111.81  3.000
 KRE  H281  C28  C29   108.45  3.000
 KRE  H282  C28  C29   109.40  3.000
 KRE  N27   C28  C29   110.21  3.000
 KRE  H292  C29  H291  107.30  3.000
 KRE  H292  C29  N30   109.56  3.000
 KRE  H291  C29  N30   112.71  3.000
 KRE  H292  C29  C28   108.71  3.000
 KRE  H291  C29  C28   108.57  3.000
 KRE  N30   C29  C28   109.89  3.000
 KRE  H312  C31  H311  107.36  3.000
 KRE  H312  C31  N30   112.88  3.000
 KRE  H311  C31  N30   109.54  3.000
 KRE  H312  C31  C32   108.64  3.000
 KRE  H311  C31  C32   108.81  3.000
 KRE  N30   C31  C32   109.51  3.000
 KRE  H321  C32  H322  107.23  3.000
 KRE  H321  C32  N27   110.32  3.000
 KRE  H322  C32  N27   110.21  3.000
 KRE  H321  C32  C31   109.50  3.000
 KRE  H322  C32  C31   108.80  3.000
 KRE  N27   C32  C31   110.71  3.000
 KRE  H071  N07  S08   111.15  3.000
 KRE  H071  N07  C06   114.17  3.000
 KRE  S08   N07  C06   119.83  3.000
 KRE  C02   N18  C19   119.38  3.000
 KRE  C32   N27  C28   112.11  3.000
 KRE  C32   N27  C26   116.75  3.000
 KRE  C28   N27  C26   117.78  3.000
 KRE  H301  N30  C31   109.89  3.000
 KRE  H301  N30  C29   109.86  3.000
 KRE  C31   N30  C29   110.15  3.000
 KRE  C13   O14  C15   118.71  3.000
 KRE  O09   S08  N07   105.59  3.000
 KRE  N07   S08  C10   105.95  3.000
 KRE  O09   S08  C10   109.06  3.000
 KRE  N07   S08  O11   107.48  3.000
 KRE  O09   S08  O11   119.71  3.000
 KRE  C10   S08  O11   108.23  3.000
 KRE  H012  N01  H011  115.05  3.000
 KRE  H012  N01  C02   116.59  3.000
 KRE  H011  N01  C02   119.55  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
 KRE  CONST_03  C03   C17  C20  C19     0.00   0.0  0
 KRE  CONST_04  C03   C02  N18  C19     0.00   0.0  0
 KRE  CONST_05  C04   C16  C13  C12     0.00   0.0  0
 KRE  CONST_06  C04   C05  C06  C12     0.00   0.0  0
 KRE  CONST_07  C03   C04  C16  C13   180.00   0.0  0
 KRE  CONST_08  C05   C04  C16  C13     0.00   0.0  0
 KRE  CONST_09  C05   C06  C12  C13     0.00   0.0  0
 KRE  CONST_12  C06   C05  C04  C16     0.00   0.0  0
 KRE  CONST_13  C06   C12  C13  C16     0.00   0.0  0
 KRE  CONST_16  N18   C19  C20  C17     0.00   0.0  0
 KRE  CONST_17  N18   C02  C03  C17     0.00   0.0  0
 KRE  CONST_19  C20   C19  N18  C02     0.00   0.0  0
 KRE  CONST_20  C20   C17  C03  C02     0.00   0.0  0
 KRE  CONST_22  C21   C20  C17  C03   180.00   0.0  0
 KRE  CONST_23  C06   C05  C04  C03   180.00   0.0  0
 KRE  CONST_24  C20   C17  C03  C04   180.00   0.0  0
 KRE  CONST_25  N18   C02  C03  C04   180.00   0.0  0
 KRE  CONST_26  C25   C24  C21  C20   180.00   0.0  0
 KRE  CONST_27  C23   C22  C21  C20   180.00   0.0  0
 KRE  CONST_28  C26   C25  C24  C21     0.00   0.0  0
 KRE  CONST_29  C26   C23  C22  C21     0.00   0.0  0
 KRE  CONST_30  N18   C19  C20  C21   180.00   0.0  0
 KRE  CONST_31  C25   C26  C23  C22     0.00   0.0  0
 KRE  CONST_32  C25   C24  C21  C22     0.00   0.0  0
 KRE  CONST_33  C24   C25  C26  C23     0.00   0.0  0
 KRE  CONST_34  C24   C21  C22  C23     0.00   0.0  0
 KRE  CONST_35  N27   C26  C23  C22   180.00   0.0  0
 KRE  CONST_36  N27   C26  C25  C24   180.00   0.0  0
 KRE  CONST_37  N01   C02  N18  C19   180.00   0.0  0
 KRE  CONST_38  N07   C06  C12  C13   180.00   0.0  0
 KRE  CONST_39  N01   C02  C03  C17   180.00   0.0  0
 KRE  CONST_40  N01   C02  C03  C04     0.00   0.0  0
 KRE  CONST_41  O14   C13  C16  C04   180.00   0.0  0
 KRE  CONST_42  N07   C06  C05  C04   180.00   0.0  0
 KRE  CONST_43  O14   C13  C12  C06   180.00   0.0  0
 KRE  CONST_44  H171  C17  C20  C19   180.00   0.0  0
 KRE  CONST_45  H161  C16  C13  C12   180.00   0.0  0
 KRE  CONST_46  H051  C05  C06  C12   180.00   0.0  0
 KRE  CONST_47  H121  C12  C13  C16   180.00   0.0  0
 KRE  CONST_48  H191  C19  C20  C17   180.00   0.0  0
 KRE  CONST_49  H241  C24  C21  C20     0.00   0.0  0
 KRE  CONST_50  H221  C22  C21  C20     0.00   0.0  0
 KRE  CONST_51  H251  C25  C24  C21   180.00   0.0  0
 KRE  CONST_52  H231  C23  C22  C21   180.00   0.0  0
 KRE  Var_01    C28   N27  C26  C23    -7.32  30.0  1
 KRE  Var_02    C29   C28  N27  C26  -165.64  30.0  1
 KRE  Var_03    C31   C32  N27  C26   165.10  30.0  1
 KRE  Var_04    C31   N30  C29  C28    60.91  30.0  1
 KRE  Var_05    C32   C31  N30  C29   -60.50  30.0  1
 KRE  Var_06    N30   C29  C28  N27   -57.29  30.0  1
 KRE  Var_07    N30   C31  C32  N27    56.82  30.0  1
 KRE  Var_08    C16   C13  O14  C15  -179.70  30.0  2
 KRE  Var_09    C06   N07  S08  O11   -50.73  30.0  1
 KRE  Var_10    H153  C15  O14  C13  -179.48  30.0  3
 KRE  Var_11    H101  C10  S08  O11   177.68  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
 KRE  plan-1  C19   0.020
 KRE  plan-1  C17   0.020
 KRE  plan-1  C02   0.020
 KRE  plan-1  C03   0.020
 KRE  plan-1  C04   0.020
 KRE  plan-1  C20   0.020
 KRE  plan-1  C21   0.020
 KRE  plan-1  N18   0.020
 KRE  plan-1  H191  0.020
 KRE  plan-1  H171  0.020
 KRE  plan-1  N01   0.020
 KRE  plan-2  C12   0.020
 KRE  plan-2  C13   0.020
 KRE  plan-2  C16   0.020
 KRE  plan-2  C03   0.020
 KRE  plan-2  C04   0.020
 KRE  plan-2  C05   0.020
 KRE  plan-2  C06   0.020
 KRE  plan-2  N07   0.020
 KRE  plan-2  O14   0.020
 KRE  plan-2  H121  0.020
 KRE  plan-2  H161  0.020
 KRE  plan-2  H051  0.020
 KRE  plan-3  C20   0.020
 KRE  plan-3  C21   0.020
 KRE  plan-3  C22   0.020
 KRE  plan-3  C23   0.020
 KRE  plan-3  C24   0.020
 KRE  plan-3  C25   0.020
 KRE  plan-3  C26   0.020
 KRE  plan-3  N27   0.020
 KRE  plan-3  H221  0.020
 KRE  plan-3  H231  0.020
 KRE  plan-3  H241  0.020
 KRE  plan-3  H251  0.020
 KRE  plan-4  C06   0.020
 KRE  plan-4  N07   0.020
 KRE  plan-4  S08   0.020
 KRE  plan-4  H071  0.020
 KRE  plan-5  C02   0.020
 KRE  plan-5  H011  0.020
 KRE  plan-5  H012  0.020
 KRE  plan-5  N01   0.020

