# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 07:23:34 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 3-amino-6-{3-[(methylsulfonyl)amino]phenyl}-N-(piperidin-4-ylmethyl)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)Nc1cccc(c1)c2cnc(N)c(n2)C(=O)NCC3CCNCC3
#
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
 0K0  0K0  3-amino-6-{3-[(methylsulfonyl)amino]phenyl}-N-(piperidin-4-ylmethyl)pyrazine-2-carboxamide  ligand  52  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0K0
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
 0K0  C1   C  CR6   0   0.082  -1.3369  -0.0563   0.1495
 0K0  C2   C  CR16  0  -0.361  -2.6628  -0.1935   0.5561
 0K0  C3   C  CR16  0  -0.291  -0.8139   1.2266  -0.0135
 0K0  C4   C  CR6   0   0.300  -3.4495   0.9262   0.7978
 0K0  C5   C  CR16  0  -0.243  -1.6047   2.3400   0.2208
 0K0  C6   C  CR16  0  -0.263  -2.9223   2.2011   0.6315
 0K0  C7   C  CR6   0   0.157  -0.5049  -1.2400  -0.1186
 0K0  C8   C  CR16  0  -0.094  -1.0313  -2.4485  -0.5824
 0K0  N10  N  N     0  -0.412  -0.2832  -3.4961  -0.8440
 0K0  C11  C  CR6   0  -0.010   1.5899  -2.1774  -0.1986
 0K0  C12  C  CR6   0   0.474   1.0412  -3.4056  -0.6605
 0K0  O14  O  O     0  -0.506   3.8658  -2.8715  -0.2492
 0K0  C16  C  CH2   0  -0.235   4.7395  -0.4016   0.8637
 0K0  C17  C  CH1   0  -0.279   4.9750   1.0688   0.5352
 0K0  C18  C  CH2   0  -0.429   6.3910   1.4751   0.9379
 0K0  C19  C  CH2   0  -0.420   4.7437   1.3842  -0.9410
 0K0  C21  C  CH2   0  -0.315   5.0887   2.8401  -1.2484
 0K0  N22  N  NH1   0  -0.576   6.4278   3.2325  -0.8395
 0K0  O26  O  OS    0  -0.664  -7.2541   0.7887   0.9609
 0K0  C27  C  CH3   0  -0.797  -5.9054  -0.3102  -1.0147
 0K0  O28  O  OS    0  -0.654  -5.8181   2.2572  -0.4897
 0K0  S25  S  S     0   1.317  -6.0412   0.9918   0.1874
 0K0  N24  N  NC1   0  -0.822  -4.7846   0.7729   1.2557
 0K0  N9   N  N     0  -0.408   0.8056  -1.1490   0.0508
 0K0  N23  N  NH2   0  -0.832   1.7668  -4.4960  -0.9199
 0K0  C13  C  C     0   0.561   3.0542  -1.9905   0.0328
 0K0  N15  N  NH1   0  -0.644   3.3878  -0.8119   0.5625
 0K0  C20  C  CH2   0  -0.314   6.6746   2.9273   0.5609
 0K0  H1   H  HCR6  0   0.268  -3.0877  -1.1773   0.7176
 0K0  H2   H  HCR6  0   0.255   0.2130   1.3521  -0.3306
 0K0  H3   H  HCR6  0   0.266  -1.1883   3.3297   0.0884
 0K0  H4   H  HCR6  0   0.270  -3.5277   3.0717   0.8405
 0K0  H5   H  HCR6  0   0.270  -2.0943  -2.5606  -0.7658
 0K0  H6   H  HCH2  0   0.237   5.4270  -1.0232   0.2889
 0K0  H7   H  HCH2  0   0.242   4.9578  -0.5777   1.9226
 0K0  H8   H  HCH1  0   0.224   4.2722   1.6700   1.1292
 0K0  H9   H  HCH2  0   0.229   6.5367   1.3342   2.0130
 0K0  H10  H  HCH2  0   0.214   7.1142   0.8241   0.4321
 0K0  H11  H  HCH2  0   0.211   5.3719   0.7267  -1.5538
 0K0  H12  H  HCH2  0   0.226   3.7075   1.1837  -1.2266
 0K0  H13  H  HCH2  0   0.234   4.9789   3.0339  -2.3174
 0K0  H14  H  HCH2  0   0.213   4.3723   3.4946  -0.7389
 0K0  H15  H  HNH1  0   0.337   7.1028   2.7320  -1.4073
 0K0  H17  H  HCH3  0   0.311  -6.7289  -0.1989  -1.7180
 0K0  H18  H  HCH3  0   0.292  -4.9581  -0.2228  -1.5423
 0K0  H19  H  HCH3  0   0.297  -5.9726  -1.2720  -0.5115
 0K0  H20  H  HNC1  0   0.421  -4.9373  -0.0350   1.8515
 0K0  H21  H  HNH2  0   0.416   2.7710  -4.4539  -0.8747
 0K0  H22  H  HNH2  0   0.397   1.3114  -5.3052  -1.3055
 0K0  H23  H  HNH1  0   0.402   2.6303  -0.1791   0.7771
 0K0  H24  H  HCH2  0   0.213   6.0429   3.5858   1.1672
 0K0  H25  H  HCH2  0   0.234   7.7087   3.1837   0.7992

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
 0K0  O28  S25  double    1.452  0.020  1.452
 0K0  C21  C19  single    1.528  0.020  1.528
 0K0  C21  N22  single    1.454  0.020  1.454
 0K0  C19  C17  single    1.527  0.020  1.527
 0K0  O26  S25  double    1.453  0.020  1.453
 0K0  S25  N24  single    1.664  0.020  1.664
 0K0  S25  C27  single    1.777  0.020  1.777
 0K0  C16  C17  single    1.525  0.020  1.525
 0K0  C16  N15  single    1.444  0.020  1.444
 0K0  C17  C18  single    1.527  0.020  1.527
 0K0  N24  C4   single    1.420  0.020  1.420
 0K0  N22  C20  single    1.454  0.020  1.454
 0K0  N15  C13  single    1.335  0.020  1.335
 0K0  C4   C2   aromatic  1.390  0.020  1.390
 0K0  C4   C6   aromatic  1.390  0.020  1.390
 0K0  C18  C20  single    1.527  0.020  1.527
 0K0  C2   C1   aromatic  1.394  0.020  1.394
 0K0  C13  O14  double    1.231  0.020  1.231
 0K0  C13  C11  single    1.494  0.020  1.494
 0K0  C6   C5   aromatic  1.387  0.020  1.387
 0K0  N9   C11  aromatic  1.317  0.020  1.317
 0K0  N9   C7   aromatic  1.324  0.020  1.324
 0K0  C11  C12  aromatic  1.422  0.020  1.422
 0K0  C1   C7   single    1.471  0.020  1.471
 0K0  C1   C3   aromatic  1.395  0.020  1.395
 0K0  C5   C3   aromatic  1.386  0.020  1.386
 0K0  C7   C8   aromatic  1.397  0.020  1.397
 0K0  C12  N23  single    1.335  0.020  1.335
 0K0  C12  N10  aromatic  1.340  0.020  1.340
 0K0  C8   N10  aromatic  1.314  0.020  1.314
 0K0  C2   H1   single    0.930  0.020  1.080
 0K0  C3   H2   single    0.930  0.020  1.080
 0K0  C5   H3   single    0.930  0.020  1.080
 0K0  C6   H4   single    0.930  0.020  1.080
 0K0  C8   H5   single    0.930  0.020  1.080
 0K0  C16  H6   single    0.970  0.020  1.090
 0K0  C16  H7   single    0.970  0.020  1.090
 0K0  C17  H8   single    0.970  0.020  1.090
 0K0  C18  H9   single    0.970  0.020  1.090
 0K0  C18  H10  single    0.970  0.020  1.090
 0K0  C19  H11  single    0.970  0.020  1.090
 0K0  C19  H12  single    0.970  0.020  1.090
 0K0  C21  H13  single    0.970  0.020  1.090
 0K0  C21  H14  single    0.970  0.020  1.090
 0K0  N22  H15  single    0.890  0.020  1.040
 0K0  C27  H17  single    0.970  0.020  1.090
 0K0  C27  H18  single    0.970  0.020  1.090
 0K0  C27  H19  single    0.970  0.020  1.090
 0K0  N24  H20  single    0.890  0.020  1.040
 0K0  N23  H21  single    0.860  0.020  1.020
 0K0  N23  H22  single    0.860  0.020  1.020
 0K0  N15  H23  single    0.860  0.020  1.020
 0K0  C20  H24  single    0.970  0.020  1.090
 0K0  C20  H25  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
 0K0  C7   C1   C3   120.43  3.000
 0K0  C3   C1   C2   118.77  3.000
 0K0  C7   C1   C2   120.79  3.000
 0K0  H1   C2   C4   118.92  3.000
 0K0  H1   C2   C1   120.39  3.000
 0K0  C4   C2   C1   120.67  3.000
 0K0  H2   C3   C5   119.86  3.000
 0K0  H2   C3   C1   119.79  3.000
 0K0  C5   C3   C1   120.35  3.000
 0K0  N24  C4   C6   119.63  3.000
 0K0  C6   C4   C2   120.24  3.000
 0K0  N24  C4   C2   120.10  3.000
 0K0  H3   C5   C6   119.57  3.000
 0K0  H3   C5   C3   119.65  3.000
 0K0  C6   C5   C3   120.78  3.000
 0K0  H4   C6   C5   120.57  3.000
 0K0  H4   C6   C4   120.23  3.000
 0K0  C5   C6   C4   119.19  3.000
 0K0  N9   C7   C8   118.33  3.000
 0K0  C8   C7   C1   122.90  3.000
 0K0  N9   C7   C1   118.75  3.000
 0K0  H5   C8   N10  116.24  3.000
 0K0  H5   C8   C7   120.98  3.000
 0K0  N10  C8   C7   122.77  3.000
 0K0  C12  N10  C8   118.80  3.000
 0K0  C13  C11  N9   117.17  3.000
 0K0  N9   C11  C12  120.40  3.000
 0K0  C13  C11  C12  122.43  3.000
 0K0  N23  C12  C11  123.97  3.000
 0K0  N23  C12  N10  117.08  3.000
 0K0  C11  C12  N10  118.95  3.000
 0K0  H7   C16  H6   106.99  3.000
 0K0  H7   C16  N15  110.03  3.000
 0K0  H6   C16  N15  108.55  3.000
 0K0  H7   C16  C17  109.42  3.000
 0K0  H6   C16  C17  109.79  3.000
 0K0  N15  C16  C17  111.93  3.000
 0K0  H8   C17  C19  108.21  3.000
 0K0  H8   C17  C18  107.75  3.000
 0K0  C19  C17  C18  109.90  3.000
 0K0  H8   C17  C16  108.19  3.000
 0K0  C18  C17  C16  110.06  3.000
 0K0  C19  C17  C16  112.58  3.000
 0K0  H10  C18  H9   106.79  3.000
 0K0  H10  C18  C20  109.16  3.000
 0K0  H9   C18  C20  109.90  3.000
 0K0  H10  C18  C17  109.38  3.000
 0K0  H9   C18  C17  110.39  3.000
 0K0  C20  C18  C17  111.11  3.000
 0K0  H12  C19  H11  106.68  3.000
 0K0  H12  C19  C21  109.65  3.000
 0K0  H11  C19  C21  109.25  3.000
 0K0  H12  C19  C17  110.99  3.000
 0K0  H11  C19  C17  109.24  3.000
 0K0  C21  C19  C17  110.93  3.000
 0K0  H14  C21  H13  106.47  3.000
 0K0  H14  C21  N22  108.07  3.000
 0K0  H13  C21  N22  108.66  3.000
 0K0  H14  C21  C19  109.15  3.000
 0K0  H13  C21  C19  110.09  3.000
 0K0  N22  C21  C19  114.12  3.000
 0K0  H15  N22  C20  108.82  3.000
 0K0  H15  N22  C21  108.80  3.000
 0K0  C20  N22  C21  111.74  3.000
 0K0  H19  C27  H18  110.44  3.000
 0K0  H19  C27  H17  110.04  3.000
 0K0  H18  C27  H17  109.70  3.000
 0K0  H19  C27  S25  109.28  3.000
 0K0  H18  C27  S25  109.62  3.000
 0K0  H17  C27  S25  107.72  3.000
 0K0  N24  S25  O28  107.34  3.000
 0K0  N24  S25  C27  106.27  3.000
 0K0  O28  S25  C27  108.14  3.000
 0K0  C27  S25  O26  108.75  3.000
 0K0  N24  S25  O26  105.68  3.000
 0K0  O28  S25  O26  119.88  3.000
 0K0  H20  N24  S25  111.58  3.000
 0K0  H20  N24  C4   114.62  3.000
 0K0  S25  N24  C4   119.27  3.000
 0K0  C11  N9   C7   120.75  3.000
 0K0  H22  N23  H21  120.21  3.000
 0K0  H22  N23  C12  119.05  3.000
 0K0  H21  N23  C12  119.96  3.000
 0K0  N15  C13  O14  123.94  3.000
 0K0  O14  C13  C11  121.42  3.000
 0K0  N15  C13  C11  114.64  3.000
 0K0  H23  N15  C13  116.75  3.000
 0K0  H23  N15  C16  118.66  3.000
 0K0  C13  N15  C16  124.58  3.000
 0K0  H25  C20  H24  106.51  3.000
 0K0  H25  C20  N22  108.77  3.000
 0K0  H24  C20  N22  108.00  3.000
 0K0  H25  C20  C18  110.20  3.000
 0K0  H24  C20  C18  109.14  3.000
 0K0  N22  C20  C18  113.94  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
 0K0  CONST_01  C6   C4   C2   C1      0.00   0.0  0
 0K0  CONST_02  C11  N9   C7   C1    180.00   0.0  0
 0K0  CONST_03  N10  C8   C7   C1    180.00   0.0  0
 0K0  CONST_04  C6   C5   C3   C1      0.00   0.0  0
 0K0  CONST_05  C5   C6   C4   C2      0.00   0.0  0
 0K0  CONST_08  C5   C3   C1   C2      0.00   0.0  0
 0K0  CONST_09  C4   C2   C1   C3      0.00   0.0  0
 0K0  CONST_12  C4   C6   C5   C3      0.00   0.0  0
 0K0  CONST_13  C7   C1   C2   C4    180.00   0.0  0
 0K0  CONST_14  C7   C1   C3   C5    180.00   0.0  0
 0K0  CONST_15  C12  C11  N9   C7      0.00   0.0  0
 0K0  CONST_16  C12  N10  C8   C7      0.00   0.0  0
 0K0  CONST_17  C11  N9   C7   C8      0.00   0.0  0
 0K0  CONST_18  C11  C12  N10  C8      0.00   0.0  0
 0K0  CONST_19  N9   C11  C12  N10     0.00   0.0  0
 0K0  CONST_20  N9   C7   C8   N10     0.00   0.0  0
 0K0  CONST_21  N24  C4   C2   C1    180.00   0.0  0
 0K0  CONST_22  N24  C4   C6   C5    180.00   0.0  0
 0K0  CONST_23  C13  C11  N9   C7    180.00   0.0  0
 0K0  CONST_24  N23  C12  N10  C8    180.00   0.0  0
 0K0  CONST_25  C13  C11  C12  N10   180.00   0.0  0
 0K0  CONST_26  N23  C12  C11  N9    180.00   0.0  0
 0K0  CONST_27  H5   C8   C7   C1      0.00   0.0  0
 0K0  CONST_28  H3   C5   C3   C1    180.00   0.0  0
 0K0  CONST_29  H4   C6   C4   C2    180.00   0.0  0
 0K0  CONST_30  H2   C3   C1   C2    180.00   0.0  0
 0K0  CONST_31  H1   C2   C1   C3    180.00   0.0  0
 0K0  CONST_35  H21  N23  C12  N10   180.00   0.0  0
 0K0  CONST_36  H22  N23  C12  N10     0.00   0.0  0
 0K0  CONST_37  C16  N15  C13  C11   180.00   0.0  0
 0K0  CONST_38  H23  N15  C13  C11     0.00   0.0  0
 0K0  CONST_39  C16  N15  C13  O14     0.00   0.0  0
 0K0  Var_01    N22  C21  C19  C17    53.96  30.0  1
 0K0  Var_02    N22  C20  C18  C17   -53.97  30.0  1
 0K0  Var_03    C21  N22  C20  C18    53.19  30.0  1
 0K0  Var_04    C20  N22  C21  C19   -53.29  30.0  1
 0K0  Var_05    N15  C13  C11  C12  -175.13  30.0  2
 0K0  Var_06    O28  S25  N24  C4    -50.06  30.0  2
 0K0  Var_07    C13  N15  C16  C17   140.90  30.0  3
 0K0  Var_08    H17  C27  S25  O26    65.71  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
 0K0  chir_01  C17  C19  C16  C18  negativ

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
 0K0  plan-1  C1   0.020
 0K0  plan-1  C2   0.020
 0K0  plan-1  C3   0.020
 0K0  plan-1  C4   0.020
 0K0  plan-1  C5   0.020
 0K0  plan-1  C6   0.020
 0K0  plan-1  C7   0.020
 0K0  plan-1  N24  0.020
 0K0  plan-1  H1   0.020
 0K0  plan-1  H2   0.020
 0K0  plan-1  H3   0.020
 0K0  plan-1  H4   0.020
 0K0  plan-2  C1   0.020
 0K0  plan-2  C7   0.020
 0K0  plan-2  C8   0.020
 0K0  plan-2  N10  0.020
 0K0  plan-2  C11  0.020
 0K0  plan-2  C12  0.020
 0K0  plan-2  N9   0.020
 0K0  plan-2  N23  0.020
 0K0  plan-2  C13  0.020
 0K0  plan-2  H5   0.020
 0K0  plan-3  C4   0.020
 0K0  plan-3  S25  0.020
 0K0  plan-3  N24  0.020
 0K0  plan-3  H20  0.020
 0K0  plan-4  C12  0.020
 0K0  plan-4  N23  0.020
 0K0  plan-4  H21  0.020
 0K0  plan-4  H22  0.020
 0K0  plan-5  C11  0.020
 0K0  plan-5  O14  0.020
 0K0  plan-5  C16  0.020
 0K0  plan-5  C13  0.020
 0K0  plan-5  N15  0.020
 0K0  plan-5  H23  0.020

