# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 06:37:14 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 3-amino-N-(3-methoxypropyl)-6-{4-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCCNC(=O)c1nc(cnc1N)c2ccc(cc2)[S](=O)(=O)N3CCN(C)CC3
#
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
 KDI  KDI  3-amino-N-(3-methoxypropyl)-6-{4-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}pyrazine-2-carboxamide  ligand  59  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KDI
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
 KDI  C1    C  CH3   0  -0.517  -3.3426  -1.4273  -3.5560
 KDI  N2    N  NT    0  -0.413  -4.0606  -1.6371  -2.3195
 KDI  C3    C  CH2   0  -0.281  -4.6223  -0.4017  -1.8124
 KDI  C4    C  CH2   0  -0.281  -3.2290  -2.2695  -1.3161
 KDI  C5    C  CH2   0  -0.328  -4.0385  -2.5771  -0.0685
 KDI  N6    N  N     0  -0.561  -4.7159  -1.3905   0.4505
 KDI  S7    S  S     0   1.378  -4.1266  -0.6102   1.7663
 KDI  O8    O  OS    0  -0.654  -5.1293   0.3657   2.1632
 KDI  O9    O  OS    0  -0.654  -3.7052  -1.6320   2.7115
 KDI  C10   C  CR6   0  -0.216  -2.6783   0.2858   1.2788
 KDI  C11   C  CR16  0  -0.213  -2.8086   1.5606   0.7447
 KDI  C12   C  CR16  0  -0.323  -1.6821   2.2369   0.3116
 KDI  C13   C  CR6   0   0.086  -0.4133   1.6620   0.4156
 KDI  C14   C  CR16  0  -0.284  -0.3077   0.3801   0.9604
 KDI  C15   C  CR16  0  -0.216  -1.4274  -0.3071   1.3917
 KDI  C16   C  CR6   0   0.176   0.7953   2.3743  -0.0262
 KDI  C17   C  CR16  0  -0.094   0.8418   3.7521  -0.2596
 KDI  N18   N  N     0  -0.413   1.9345   4.3717  -0.6431
 KDI  C19   C  CR6   0   0.482   3.0563   3.6593  -0.8174
 KDI  C20   C  CR6   0  -0.002   3.0272   2.2587  -0.5649
 KDI  N21   N  N     0  -0.417   1.9117   1.6770  -0.1839
 KDI  C22   C  C     0   0.568   4.2342   1.3904  -0.7083
 KDI  O23   O  O     0  -0.504   5.3225   1.8431  -1.0604
 KDI  N24   N  NH1   0  -0.650   4.0379   0.1029  -0.4218
 KDI  C25   C  CH2   0  -0.241   5.0872  -0.8897  -0.4919
 KDI  C27   C  CH3   0  -0.398   6.1415  -5.4921   0.5655
 KDI  C30   C  CH2   0  -0.520   4.5898  -2.2158   0.0605
 KDI  N31   N  NH2   0  -0.829   4.1415   4.3199  -1.2205
 KDI  C6    C  CH2   0  -0.329  -5.4615  -0.6629  -0.5743
 KDI  C28   C  CH2   0  -0.120   5.6787  -3.2695   0.0124
 KDI  O29   O  O2    0  -0.486   5.1849  -4.4640   0.5633
 KDI  H11C  H  HCH3  0   0.194  -2.4846  -0.7454  -3.4509
 KDI  H12C  H  HCH3  0   0.236  -2.9674  -2.3788  -3.9350
 KDI  H13C  H  HCH3  0   0.236  -4.0117  -1.0063  -4.3081
 KDI  H31C  H  HCH2  0   0.202  -3.8392   0.3438  -1.5917
 KDI  H32C  H  HCH2  0   0.251  -5.2681   0.0391  -2.5755
 KDI  H41C  H  HCH2  0   0.252  -2.8409  -3.2106  -1.7128
 KDI  H42C  H  HCH2  0   0.200  -2.3549  -1.6494  -1.0504
 KDI  H61C  H  HCH2  0   0.276  -5.8517   0.2700  -0.1733
 KDI  H62C  H  HCH2  0   0.261  -6.3235  -1.2794  -0.8428
 KDI  H51C  H  HCH2  0   0.260  -4.8142  -3.3097  -0.3061
 KDI  H52C  H  HCH2  0   0.276  -3.4069  -3.0236   0.6966
 KDI  H11   H  HCR6  0   0.288  -3.7769   2.0338   0.6530
 KDI  H15   H  HCR6  0   0.285  -1.3116  -1.2935   1.8200
 KDI  H12   H  HCR6  0   0.265  -1.8137   3.2208  -0.1173
 KDI  H14   H  HCR6  0   0.268   0.6637  -0.0828   1.0648
 KDI  H17   H  HCR6  0   0.276  -0.0314   4.3779  -0.1159
 KDI  H311  H  HNH2  0   0.400   4.0944   5.3174  -1.3397
 KDI  H312  H  HNH2  0   0.418   5.0176   3.8368  -1.3296
 KDI  H24   H  HNH1  0   0.408   3.1044  -0.1793  -0.1644
 KDI  H251  H  HCH2  0   0.238   5.4201  -1.0134  -1.5269
 KDI  H252  H  HCH2  0   0.239   5.9535  -0.5480   0.0805
 KDI  H301  H  HCH2  0   0.243   4.2599  -2.0797   1.0942
 KDI  H302  H  HCH2  0   0.243   3.7260  -2.5564  -0.5178
 KDI  H271  H  HCH3  0   0.234   5.6970  -6.3670   1.0387
 KDI  H272  H  HCH3  0   0.204   6.4531  -5.7686  -0.4488
 KDI  H273  H  HCH3  0   0.203   7.0411  -5.2151   1.1286
 KDI  H281  H  HCH2  0   0.199   6.0048  -3.4254  -1.0265
 KDI  H282  H  HCH2  0   0.198   6.5613  -2.9226   0.5703

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
 KDI  C1   N2    single    1.445  0.020  1.445
 KDI  N2   C3    single    1.449  0.020  1.449
 KDI  N2   C4    single    1.448  0.020  1.448
 KDI  C3   C6    single    1.518  0.020  1.518
 KDI  C4   C5    single    1.519  0.020  1.519
 KDI  C5   N6    single    1.462  0.020  1.462
 KDI  N6   S7    single    1.639  0.020  1.639
 KDI  N6   C6    single    1.461  0.020  1.461
 KDI  S7   O8    double    1.454  0.020  1.454
 KDI  S7   O9    double    1.454  0.020  1.454
 KDI  S7   C10   single    1.771  0.020  1.771
 KDI  C10  C11   aromatic  1.388  0.020  1.388
 KDI  C10  C15   aromatic  1.389  0.020  1.389
 KDI  C11  C12   aromatic  1.383  0.020  1.383
 KDI  C12  C13   aromatic  1.397  0.020  1.397
 KDI  C13  C14   aromatic  1.397  0.020  1.397
 KDI  C13  C16   single    1.471  0.020  1.471
 KDI  C14  C15   aromatic  1.383  0.020  1.383
 KDI  C16  C17   aromatic  1.398  0.020  1.398
 KDI  C16  N21   aromatic  1.326  0.020  1.326
 KDI  C17  N18   aromatic  1.313  0.020  1.313
 KDI  N18  C19   aromatic  1.340  0.020  1.340
 KDI  C19  C20   aromatic  1.423  0.020  1.423
 KDI  C19  N31   single    1.333  0.020  1.333
 KDI  C20  N21   aromatic  1.314  0.020  1.314
 KDI  C20  C22   single    1.494  0.020  1.494
 KDI  C22  O23   double    1.230  0.020  1.230
 KDI  C22  N24   single    1.333  0.020  1.333
 KDI  N24  C25   single    1.446  0.020  1.446
 KDI  C25  C30   single    1.520  0.020  1.520
 KDI  C27  O29   single    1.404  0.020  1.404
 KDI  C30  C28   single    1.516  0.020  1.516
 KDI  C28  O29   single    1.405  0.020  1.405
 KDI  C1   H11C  single    0.970  0.020  1.090
 KDI  C1   H12C  single    0.970  0.020  1.090
 KDI  C1   H13C  single    0.970  0.020  1.090
 KDI  C3   H31C  single    0.970  0.020  1.090
 KDI  C3   H32C  single    0.970  0.020  1.090
 KDI  C4   H41C  single    0.970  0.020  1.090
 KDI  C4   H42C  single    0.970  0.020  1.090
 KDI  C6   H61C  single    0.970  0.020  1.090
 KDI  C6   H62C  single    0.970  0.020  1.090
 KDI  C5   H51C  single    0.970  0.020  1.090
 KDI  C5   H52C  single    0.970  0.020  1.090
 KDI  C11  H11   single    0.930  0.020  1.080
 KDI  C15  H15   single    0.930  0.020  1.080
 KDI  C12  H12   single    0.930  0.020  1.080
 KDI  C14  H14   single    0.930  0.020  1.080
 KDI  C17  H17   single    0.930  0.020  1.080
 KDI  N31  H311  single    0.860  0.020  1.020
 KDI  N31  H312  single    0.860  0.020  1.020
 KDI  N24  H24   single    0.860  0.020  1.020
 KDI  C25  H251  single    0.970  0.020  1.090
 KDI  C25  H252  single    0.970  0.020  1.090
 KDI  C30  H301  single    0.970  0.020  1.090
 KDI  C30  H302  single    0.970  0.020  1.090
 KDI  C27  H271  single    0.970  0.020  1.090
 KDI  C27  H272  single    0.970  0.020  1.090
 KDI  C27  H273  single    0.970  0.020  1.090
 KDI  C28  H281  single    0.970  0.020  1.090
 KDI  C28  H282  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
 KDI  H13C  C1   H12C  107.94  3.000
 KDI  H13C  C1   H11C  107.74  3.000
 KDI  H12C  C1   H11C  107.78  3.000
 KDI  H13C  C1   N2    109.95  3.000
 KDI  H12C  C1   N2    109.97  3.000
 KDI  H11C  C1   N2    113.29  3.000
 KDI  C4    N2   C3    110.64  3.000
 KDI  C4    N2   C1    111.77  3.000
 KDI  C3    N2   C1    111.61  3.000
 KDI  H32C  C3   H31C  106.65  3.000
 KDI  H32C  C3   C6    108.20  3.000
 KDI  H31C  C3   C6    110.20  3.000
 KDI  H32C  C3   N2    109.20  3.000
 KDI  H31C  C3   N2    111.77  3.000
 KDI  C6    C3   N2    110.68  3.000
 KDI  H42C  C4   H41C  106.85  3.000
 KDI  H42C  C4   C5    109.76  3.000
 KDI  H41C  C4   C5    108.25  3.000
 KDI  H42C  C4   N2    112.09  3.000
 KDI  H41C  C4   N2    109.18  3.000
 KDI  C5    C4   N2    110.58  3.000
 KDI  H52C  C5   H51C  106.84  3.000
 KDI  H52C  C5   N6    110.64  3.000
 KDI  H51C  C5   N6    107.00  3.000
 KDI  H52C  C5   C4    110.57  3.000
 KDI  H51C  C5   C4    109.60  3.000
 KDI  N6    C5   C4    111.98  3.000
 KDI  C6    N6   S7    120.62  3.000
 KDI  C6    N6   C5    113.06  3.000
 KDI  S7    N6   C5    120.32  3.000
 KDI  C10   S7   O9    107.30  3.000
 KDI  C10   S7   O8    107.42  3.000
 KDI  O9    S7   O8    119.59  3.000
 KDI  C10   S7   N6    108.29  3.000
 KDI  O9    S7   N6    106.94  3.000
 KDI  O8    S7   N6    106.89  3.000
 KDI  C15   C10  C11   120.52  3.000
 KDI  C15   C10  S7    119.87  3.000
 KDI  C11   C10  S7    119.58  3.000
 KDI  H11   C11  C12   119.24  3.000
 KDI  H11   C11  C10   121.23  3.000
 KDI  C12   C11  C10   119.53  3.000
 KDI  H12   C12  C13   120.97  3.000
 KDI  H12   C12  C11   118.03  3.000
 KDI  C13   C12  C11   121.01  3.000
 KDI  C16   C13  C14   119.96  3.000
 KDI  C16   C13  C12   121.65  3.000
 KDI  C14   C13  C12   118.39  3.000
 KDI  H14   C14  C15   118.99  3.000
 KDI  H14   C14  C13   119.90  3.000
 KDI  C15   C14  C13   121.10  3.000
 KDI  H15   C15  C14   119.34  3.000
 KDI  H15   C15  C10   121.19  3.000
 KDI  C14   C15  C10   119.46  3.000
 KDI  N21   C16  C17   118.06  3.000
 KDI  N21   C16  C13   118.23  3.000
 KDI  C17   C16  C13   123.69  3.000
 KDI  H17   C17  N18   115.89  3.000
 KDI  H17   C17  C16   121.34  3.000
 KDI  N18   C17  C16   122.77  3.000
 KDI  C19   N18  C17   118.92  3.000
 KDI  N31   C19  C20   123.91  3.000
 KDI  N31   C19  N18   117.22  3.000
 KDI  C20   C19  N18   118.87  3.000
 KDI  C22   C20  N21   117.15  3.000
 KDI  C22   C20  C19   122.57  3.000
 KDI  N21   C20  C19   120.28  3.000
 KDI  C20   N21  C16   121.09  3.000
 KDI  N24   C22  O23   123.17  3.000
 KDI  N24   C22  C20   114.94  3.000
 KDI  O23   C22  C20   121.90  3.000
 KDI  H24   N24  C25   119.46  3.000
 KDI  H24   N24  C22   117.47  3.000
 KDI  C25   N24  C22   123.06  3.000
 KDI  H252  C25  H251  106.83  3.000
 KDI  H252  C25  C30   109.98  3.000
 KDI  H251  C25  C30   110.15  3.000
 KDI  H252  C25  N24   109.58  3.000
 KDI  H251  C25  N24   110.13  3.000
 KDI  C30   C25  N24   110.11  3.000
 KDI  H273  C27  H272  107.79  3.000
 KDI  H273  C27  H271  108.33  3.000
 KDI  H272  C27  H271  108.37  3.000
 KDI  H273  C27  O29   112.00  3.000
 KDI  H272  C27  O29   112.13  3.000
 KDI  H271  C27  O29   108.10  3.000
 KDI  H302  C30  H301  107.47  3.000
 KDI  H302  C30  C28   109.51  3.000
 KDI  H301  C30  C28   109.46  3.000
 KDI  H302  C30  C25   109.75  3.000
 KDI  H301  C30  C25   109.48  3.000
 KDI  C28   C30  C25   111.09  3.000
 KDI  H312  N31  H311  120.26  3.000
 KDI  H312  N31  C19   120.24  3.000
 KDI  H311  N31  C19   119.30  3.000
 KDI  H62C  C6   H61C  106.94  3.000
 KDI  H62C  C6   N6    107.08  3.000
 KDI  H61C  C6   N6    110.58  3.000
 KDI  H62C  C6   C3    109.42  3.000
 KDI  H61C  C6   C3    110.57  3.000
 KDI  N6    C6   C3    112.06  3.000
 KDI  H282  C28  H281  106.61  3.000
 KDI  H282  C28  O29   110.55  3.000
 KDI  H281  C28  O29   110.73  3.000
 KDI  H282  C28  C30   109.93  3.000
 KDI  H281  C28  C30   109.96  3.000
 KDI  O29   C28  C30   109.03  3.000
 KDI  C28   O29  C27   112.56  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
 KDI  CONST_01  C13   C12  C11  C10     0.00   0.0  0
 KDI  CONST_02  C13   C14  C15  C10     0.00   0.0  0
 KDI  CONST_03  C14   C15  C10  C11     0.00   0.0  0
 KDI  CONST_04  C14   C13  C12  C11     0.00   0.0  0
 KDI  CONST_05  C16   C13  C12  C11   180.00   0.0  0
 KDI  CONST_06  C15   C10  C11  C12     0.00   0.0  0
 KDI  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 KDI  CONST_10  N18   C17  C16  C13   180.00   0.0  0
 KDI  CONST_11  C20   N21  C16  C13   180.00   0.0  0
 KDI  CONST_14  C16   C13  C14  C15   180.00   0.0  0
 KDI  CONST_15  C19   N18  C17  C16     0.00   0.0  0
 KDI  CONST_16  C19   C20  N21  C16     0.00   0.0  0
 KDI  CONST_17  C20   N21  C16  C17     0.00   0.0  0
 KDI  CONST_18  C20   C19  N18  C17     0.00   0.0  0
 KDI  CONST_19  N21   C16  C17  N18     0.00   0.0  0
 KDI  CONST_20  N21   C20  C19  N18     0.00   0.0  0
 KDI  CONST_21  C12   C11  C10  S7    180.00   0.0  0
 KDI  CONST_22  C14   C15  C10  S7    180.00   0.0  0
 KDI  CONST_23  C22   C20  N21  C16   180.00   0.0  0
 KDI  CONST_24  N31   C19  N18  C17   180.00   0.0  0
 KDI  CONST_25  C22   C20  C19  N18   180.00   0.0  0
 KDI  CONST_26  N31   C19  C20  N21   180.00   0.0  0
 KDI  CONST_27  H12   C12  C11  C10   180.00   0.0  0
 KDI  CONST_28  H14   C14  C15  C10   180.00   0.0  0
 KDI  CONST_29  H15   C15  C10  C11   180.00   0.0  0
 KDI  CONST_30  H11   C11  C12  C13   180.00   0.0  0
 KDI  CONST_31  H17   C17  C16  C13     0.00   0.0  0
 KDI  CONST_32  H311  N31  C19  N18     0.00   0.0  0
 KDI  CONST_33  H312  N31  C19  N18   180.00   0.0  0
 KDI  CONST_34  C25   N24  C22  C20   180.00   0.0  0
 KDI  CONST_35  H24   N24  C22  C20     0.00   0.0  0
 KDI  CONST_36  C25   N24  C22  O23     0.00   0.0  0
 KDI  Var_01    N6    C6   C3   N2     54.01  30.0  1
 KDI  Var_02    N6    C5   C4   N2    -54.34  30.0  1
 KDI  Var_03    C5    C4   N2   C3     59.45  30.0  1
 KDI  Var_04    C5    N6   C6   C3    -49.56  30.0  1
 KDI  Var_05    C6    C3   N2   C4    -59.29  30.0  1
 KDI  Var_06    C6    N6   C5   C4     49.72  30.0  1
 KDI  Var_07    C10   S7   N6   C5     74.11  30.0  3
 KDI  Var_08    C11   C10  S7   N6     85.81  30.0  2
 KDI  Var_09    O23   C22  C20  C19    -0.33  30.0  2
 KDI  Var_10    H11C  C1   N2   C3     61.69  30.0  3
 KDI  Var_11    C30   C25  N24  C22   172.85  30.0  3
 KDI  Var_12    C28   C30  C25  N24  -179.34  30.0  3
 KDI  Var_13    O29   C28  C30  C25   178.48  30.0  3
 KDI  Var_14    C30   C28  O29  C27  -179.52  30.0  1
 KDI  Var_15    H271  C27  O29  C28   177.93  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
 KDI  plan-1  S7    0.020
 KDI  plan-1  C10   0.020
 KDI  plan-1  C11   0.020
 KDI  plan-1  C12   0.020
 KDI  plan-1  C13   0.020
 KDI  plan-1  C14   0.020
 KDI  plan-1  C15   0.020
 KDI  plan-1  C16   0.020
 KDI  plan-1  H11   0.020
 KDI  plan-1  H15   0.020
 KDI  plan-1  H12   0.020
 KDI  plan-1  H14   0.020
 KDI  plan-2  C13   0.020
 KDI  plan-2  C16   0.020
 KDI  plan-2  C17   0.020
 KDI  plan-2  N18   0.020
 KDI  plan-2  C19   0.020
 KDI  plan-2  C20   0.020
 KDI  plan-2  N21   0.020
 KDI  plan-2  C22   0.020
 KDI  plan-2  N31   0.020
 KDI  plan-2  H17   0.020
 KDI  plan-3  C19   0.020
 KDI  plan-3  N31   0.020
 KDI  plan-3  H311  0.020
 KDI  plan-3  H312  0.020
 KDI  plan-4  C20   0.020
 KDI  plan-4  C22   0.020
 KDI  plan-4  O23   0.020
 KDI  plan-4  N24   0.020
 KDI  plan-4  C25   0.020
 KDI  plan-4  H24   0.020

