# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 16:15:19 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: ~{N}-[3-(azepan-1-ylsulfonyl)-4-methyl-phenyl]-2-[4,4-dimethyl-2,5-bis(oxidanylidene)imidazolidin-1-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(NC(=O)CN2C(=O)NC(C)(C)C2=O)cc1[S](=O)(=O)N3CCCCCC3
#
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
 KVT  KVT  ~{N}-[3-(azepan-1-ylsulfonyl)-4-methyl-phenyl]-2-[4,4-dimethyl-2,5-bis(oxidanylidene)imidazolidin-1-yl]ethanamide  ligand  58  30  .  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_KVT
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
 KVT  C10  C  CR6   0   0.386  -0.1063   2.2112  -0.5333
 KVT  C13  C  C     0   0.547  -2.2523   0.9709  -0.3985
 KVT  C15  C  CH2   0  -0.460  -3.7037   1.1312  -0.8388
 KVT  C24  C  CH3   0  -0.629  -4.5527  -3.2159   0.4894
 KVT  C28  C  CH3   0  -0.628  -6.7932  -2.4165  -0.3577
 KVT  C01  C  CH3   0  -0.757   4.1140   3.0974  -0.0678
 KVT  C05  C  CR6   0   0.146   2.6588   2.7567  -0.1957
 KVT  C06  C  CR16  0  -0.294   1.7970   3.6645  -0.8063
 KVT  C08  C  CR16  0  -0.315   0.4498   3.4088  -0.9759
 KVT  N11  N  NH1   0  -0.751  -1.4754   2.0237  -0.7397
 KVT  O14  O  O     0  -0.448  -1.8725  -0.0234   0.1852
 KVT  N18  N  NR5   0  -0.534  -4.5059   0.0873  -0.2855
 KVT  C19  C  CR5   0   0.707  -4.9339   0.1009   1.0483
 KVT  O20  O  O     0  -0.481  -4.7922   1.0429   1.7965
 KVT  N21  N  NR15  0  -0.666  -5.5090  -1.0890   1.2761
 KVT  C23  C  CR5   0  -0.038  -5.4181  -2.0030   0.1560
 KVT  C32  C  CR5   0   0.576  -4.7042  -1.1296  -0.8665
 KVT  O33  O  O     0  -0.432  -4.3746  -1.4497  -1.9829
 KVT  C34  C  CR16  0  -0.302   0.7252   1.2803   0.0828
 KVT  C36  C  CR6   0  -0.249   2.0765   1.5623   0.2402
 KVT  S37  S  S     0   1.396   3.0519   0.3133   1.0650
 KVT  O38  O  OS    0  -0.658   3.7629   0.9169   2.1843
 KVT  O39  O  OS    0  -0.643   2.1495  -0.7934   1.3599
 KVT  N40  N  N     0  -0.585   4.1529  -0.1151  -0.0588
 KVT  C41  C  CH2   0  -0.307   5.5854  -0.1258   0.2245
 KVT  C44  C  CH2   0  -0.425   6.1147  -1.4454   0.7576
 KVT  C47  C  CH2   0  -0.447   5.7860  -2.6639  -0.1024
 KVT  C50  C  CH2   0  -0.436   4.3009  -3.0367  -0.0959
 KVT  C53  C  CH2   0  -0.429   3.4231  -2.3079  -1.1114
 KVT  C56  C  CH2   0  -0.315   3.6870  -0.8066  -1.2541
 KVT  H1   H  HCH2  0   0.314  -4.0960   2.1025  -0.5351
 KVT  H2   H  HCH2  0   0.323  -3.7617   1.0871  -1.9279
 KVT  H3   H  HCH3  0   0.246  -4.4552  -3.8665  -0.3787
 KVT  H4   H  HCH3  0   0.246  -3.5564  -2.9143   0.8133
 KVT  H5   H  HCH3  0   0.253  -5.0154  -3.7908   1.2921
 KVT  H6   H  HCH3  0   0.252  -7.3174  -2.9916   0.4059
 KVT  H7   H  HCH3  0   0.248  -7.4015  -1.5481  -0.6107
 KVT  H8   H  HCH3  0   0.245  -6.6970  -3.0426  -1.2439
 KVT  H9   H  HCH3  0   0.264   4.7345   2.4346  -0.6720
 KVT  H10  H  HCH3  0   0.260   4.2909   4.1145  -0.4118
 KVT  H11  H  HCH3  0   0.257   4.4660   3.0262   0.9599
 KVT  H12  H  HCR6  0   0.269   2.1953   4.6053  -1.1644
 KVT  H13  H  HCR6  0   0.284  -0.1739   4.1505  -1.4608
 KVT  H14  H  HNH1  0   0.426  -1.9396   2.7862  -1.2118
 KVT  H15  H  HNR5  0   0.414  -5.8629  -1.3516   2.1822
 KVT  H16  H  HCR6  0   0.306   0.3304   0.3429   0.4353
 KVT  H17  H  HCH2  0   0.247   6.0775   0.1182  -0.7208
 KVT  H18  H  HCH2  0   0.269   5.8233   0.6822   0.9138
 KVT  H19  H  HCH2  0   0.235   7.1995  -1.3436   0.8522
 KVT  H20  H  HCH2  0   0.222   5.7316  -1.6082   1.7702
 KVT  H21  H  HCH2  0   0.218   6.1413  -2.5110  -1.1278
 KVT  H22  H  HCH2  0   0.237   6.3584  -3.5092   0.2866
 KVT  H23  H  HCH2  0   0.233   4.1939  -4.1084  -0.2795
 KVT  H24  H  HCH2  0   0.219   3.9079  -2.8701   0.9106
 KVT  H25  H  HCH2  0   0.229   3.5675  -2.7468  -2.1022
 KVT  H26  H  HCH2  0   0.232   2.3771  -2.4795  -0.8535
 KVT  H27  H  HCH2  0   0.267   2.7961  -0.3035  -1.6390
 KVT  H28  H  HCH2  0   0.259   4.4637  -0.6357  -2.0010

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
 KVT  O33  C32  double    1.207  0.020  1.207
 KVT  C28  C23  single    1.525  0.020  1.525
 KVT  C32  C23  single    1.522  0.020  1.522
 KVT  C32  N18  single    1.363  0.020  1.363
 KVT  C23  C24  single    1.527  0.020  1.527
 KVT  C23  N21  single    1.449  0.020  1.449
 KVT  C15  N18  single    1.428  0.020  1.428
 KVT  C15  C13  single    1.525  0.020  1.525
 KVT  N18  C19  single    1.401  0.020  1.401
 KVT  N11  C13  single    1.352  0.020  1.352
 KVT  N11  C10  single    1.397  0.020  1.397
 KVT  C13  O14  double    1.214  0.020  1.214
 KVT  C08  C10  aromatic  1.393  0.020  1.393
 KVT  C08  C06  aromatic  1.382  0.020  1.382
 KVT  N21  C19  single    1.341  0.020  1.341
 KVT  C10  C34  aromatic  1.392  0.020  1.392
 KVT  C06  C05  aromatic  1.393  0.020  1.393
 KVT  C19  O20  double    1.211  0.020  1.211
 KVT  C34  C36  aromatic  1.389  0.020  1.389
 KVT  C05  C36  aromatic  1.398  0.020  1.398
 KVT  C05  C01  single    1.500  0.020  1.500
 KVT  C36  S37  single    1.787  0.020  1.787
 KVT  O39  S37  double    1.458  0.020  1.458
 KVT  C56  C53  single    1.531  0.020  1.531
 KVT  C56  N40  single    1.457  0.020  1.457
 KVT  C53  C50  single    1.527  0.020  1.527
 KVT  S37  N40  single    1.630  0.020  1.630
 KVT  S37  O38  double    1.457  0.020  1.457
 KVT  N40  C41  single    1.460  0.020  1.460
 KVT  C50  C47  single    1.531  0.020  1.531
 KVT  C41  C44  single    1.519  0.020  1.519
 KVT  C44  C47  single    1.527  0.020  1.527
 KVT  C15  H1   single    0.970  0.020  1.090
 KVT  C15  H2   single    0.970  0.020  1.090
 KVT  C24  H3   single    0.970  0.020  1.090
 KVT  C24  H4   single    0.970  0.020  1.090
 KVT  C24  H5   single    0.970  0.020  1.090
 KVT  C28  H6   single    0.970  0.020  1.090
 KVT  C28  H7   single    0.970  0.020  1.090
 KVT  C28  H8   single    0.970  0.020  1.090
 KVT  C01  H9   single    0.970  0.020  1.090
 KVT  C01  H10  single    0.970  0.020  1.090
 KVT  C01  H11  single    0.970  0.020  1.090
 KVT  C06  H12  single    0.930  0.020  1.080
 KVT  C08  H13  single    0.930  0.020  1.080
 KVT  N11  H14  single    0.860  0.020  1.020
 KVT  N21  H15  single    0.860  0.020  1.020
 KVT  C34  H16  single    0.930  0.020  1.080
 KVT  C41  H17  single    0.970  0.020  1.090
 KVT  C41  H18  single    0.970  0.020  1.090
 KVT  C44  H19  single    0.970  0.020  1.090
 KVT  C44  H20  single    0.970  0.020  1.090
 KVT  C47  H21  single    0.970  0.020  1.090
 KVT  C47  H22  single    0.970  0.020  1.090
 KVT  C50  H23  single    0.970  0.020  1.090
 KVT  C50  H24  single    0.970  0.020  1.090
 KVT  C53  H25  single    0.970  0.020  1.090
 KVT  C53  H26  single    0.970  0.020  1.090
 KVT  C56  H27  single    0.970  0.020  1.090
 KVT  C56  H28  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
 KVT  C34  C10  N11  124.12  3.000
 KVT  C34  C10  C08  118.51  3.000
 KVT  N11  C10  C08  117.37  3.000
 KVT  O14  C13  N11  125.40  3.000
 KVT  O14  C13  C15  121.50  3.000
 KVT  N11  C13  C15  113.09  3.000
 KVT  H2   C15  H1   107.14  3.000
 KVT  H2   C15  N18  109.10  3.000
 KVT  H1   C15  N18  109.94  3.000
 KVT  H2   C15  C13  109.54  3.000
 KVT  H1   C15  C13  110.82  3.000
 KVT  N18  C15  C13  110.24  3.000
 KVT  H5   C24  H4   108.36  3.000
 KVT  H5   C24  H3   108.05  3.000
 KVT  H4   C24  H3   108.68  3.000
 KVT  H5   C24  C23  109.82  3.000
 KVT  H4   C24  C23  111.29  3.000
 KVT  H3   C24  C23  110.56  3.000
 KVT  H8   C28  H7   108.56  3.000
 KVT  H8   C28  H6   108.01  3.000
 KVT  H7   C28  H6   108.33  3.000
 KVT  H8   C28  C23  110.50  3.000
 KVT  H7   C28  C23  111.43  3.000
 KVT  H6   C28  C23  109.91  3.000
 KVT  H11  C01  H10  107.88  3.000
 KVT  H11  C01  H9   107.42  3.000
 KVT  H10  C01  H9   107.48  3.000
 KVT  H11  C01  C05  112.29  3.000
 KVT  H10  C01  C05  110.06  3.000
 KVT  H9   C01  C05  111.52  3.000
 KVT  C36  C05  C06  115.84  3.000
 KVT  C36  C05  C01  124.84  3.000
 KVT  C06  C05  C01  119.32  3.000
 KVT  H12  C06  C08  118.62  3.000
 KVT  H12  C06  C05  118.94  3.000
 KVT  C08  C06  C05  122.45  3.000
 KVT  H13  C08  C06  119.30  3.000
 KVT  H13  C08  C10  120.07  3.000
 KVT  C06  C08  C10  120.63  3.000
 KVT  H14  N11  C13  116.21  3.000
 KVT  H14  N11  C10  114.72  3.000
 KVT  C13  N11  C10  129.07  3.000
 KVT  C32  N18  C19  111.72  3.000
 KVT  C19  N18  C15  122.24  3.000
 KVT  C32  N18  C15  124.70  3.000
 KVT  N21  C19  O20  129.44  3.000
 KVT  O20  C19  N18  124.05  3.000
 KVT  N21  C19  N18  106.51  3.000
 KVT  H15  N21  C23  123.57  3.000
 KVT  H15  N21  C19  122.32  3.000
 KVT  C23  N21  C19  113.68  3.000
 KVT  C32  C23  N21  100.77  3.000
 KVT  N21  C23  C28  112.02  3.000
 KVT  C32  C23  C28  110.62  3.000
 KVT  N21  C23  C24  111.59  3.000
 KVT  C32  C23  C24  109.67  3.000
 KVT  C28  C23  C24  111.67  3.000
 KVT  O33  C32  C23  126.66  3.000
 KVT  C23  C32  N18  107.11  3.000
 KVT  O33  C32  N18  126.24  3.000
 KVT  H16  C34  C36  119.76  3.000
 KVT  H16  C34  C10  120.54  3.000
 KVT  C36  C34  C10  119.69  3.000
 KVT  S37  C36  C34  116.19  3.000
 KVT  S37  C36  C05  120.91  3.000
 KVT  C34  C36  C05  122.89  3.000
 KVT  N40  S37  O39  110.97  3.000
 KVT  N40  S37  O38  107.99  3.000
 KVT  O39  S37  O38  117.46  3.000
 KVT  O38  S37  C36  109.36  3.000
 KVT  N40  S37  C36  103.54  3.000
 KVT  O39  S37  C36  106.62  3.000
 KVT  C56  N40  C41  117.98  3.000
 KVT  C41  N40  S37  122.05  3.000
 KVT  C56  N40  S37  118.30  3.000
 KVT  H18  C41  H17  106.48  3.000
 KVT  H18  C41  C44  110.28  3.000
 KVT  H17  C41  C44  109.91  3.000
 KVT  H18  C41  N40  109.38  3.000
 KVT  H17  C41  N40  105.79  3.000
 KVT  C44  C41  N40  114.61  3.000
 KVT  H20  C44  H19  106.32  3.000
 KVT  H20  C44  C47  109.08  3.000
 KVT  H19  C44  C47  109.66  3.000
 KVT  H20  C44  C41  109.39  3.000
 KVT  H19  C44  C41  107.17  3.000
 KVT  C47  C44  C41  114.88  3.000
 KVT  H22  C47  H21  105.74  3.000
 KVT  H22  C47  C50  108.56  3.000
 KVT  H21  C47  C50  110.63  3.000
 KVT  H22  C47  C44  107.70  3.000
 KVT  H21  C47  C44  110.23  3.000
 KVT  C50  C47  C44  113.62  3.000
 KVT  H24  C50  H23  105.61  3.000
 KVT  H24  C50  C53  109.43  3.000
 KVT  H23  C50  C53  107.46  3.000
 KVT  H24  C50  C47  108.39  3.000
 KVT  H23  C50  C47  109.46  3.000
 KVT  C53  C50  C47  116.00  3.000
 KVT  H26  C53  H25  106.13  3.000
 KVT  H26  C53  C56  109.97  3.000
 KVT  H25  C53  C56  106.64  3.000
 KVT  H26  C53  C50  108.59  3.000
 KVT  H25  C53  C50  109.58  3.000
 KVT  C56  C53  C50  115.52  3.000
 KVT  H28  C56  H27  105.49  3.000
 KVT  H28  C56  C53  109.89  3.000
 KVT  H27  C56  C53  110.10  3.000
 KVT  H28  C56  N40  105.04  3.000
 KVT  H27  C56  N40  109.32  3.000
 KVT  C53  C56  N40  116.36  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
 KVT  CONST_01  C05  C06  C08  C10     0.00   0.0  0
 KVT  CONST_02  C05  C36  C34  C10     0.00   0.0  0
 KVT  CONST_03  C34  C10  C08  C06     0.00   0.0  0
 KVT  CONST_04  C34  C36  C05  C06     0.00   0.0  0
 KVT  CONST_05  C36  C34  C10  C08     0.00   0.0  0
 KVT  CONST_06  C36  C05  C06  C08     0.00   0.0  0
 KVT  CONST_07  N21  C23  C32  N18     0.00   0.0  0
 KVT  CONST_08  C23  N21  C19  N18     0.00   0.0  0
 KVT  CONST_09  C23  C32  N18  C19     0.00   0.0  0
 KVT  CONST_10  C32  C23  N21  C19     0.00   0.0  0
 KVT  CONST_11  C32  N18  C19  N21     0.00   0.0  0
 KVT  CONST_12  S37  C36  C34  C10   180.00   0.0  0
 KVT  CONST_13  C08  C06  C05  C01   180.00   0.0  0
 KVT  CONST_14  C34  C36  C05  C01   180.00   0.0  0
 KVT  CONST_15  N11  C10  C08  C06   180.00   0.0  0
 KVT  CONST_16  S37  C36  C05  C06   180.00   0.0  0
 KVT  CONST_17  C36  C34  C10  N11   180.00   0.0  0
 KVT  CONST_18  C23  C32  N18  C15   180.00   0.0  0
 KVT  CONST_19  N21  C19  N18  C15   180.00   0.0  0
 KVT  CONST_20  C32  N18  C19  O20   180.00   0.0  0
 KVT  CONST_21  C23  N21  C19  O20   180.00   0.0  0
 KVT  CONST_22  H12  C06  C08  C10   180.00   0.0  0
 KVT  CONST_23  H13  C08  C06  C05   180.00   0.0  0
 KVT  CONST_24  H16  C34  C36  C05   180.00   0.0  0
 KVT  CONST_25  H15  N21  C19  N18   180.00   0.0  0
 KVT  CONST_26  C08  C10  N11  C13   180.00   0.0  0
 KVT  CONST_27  C34  C10  N11  C13     0.00   0.0  0
 KVT  CONST_28  O20  C19  N18  C15     0.00   0.0  0
 KVT  CONST_29  H14  N11  C10  C08     0.00   0.0  0
 KVT  CONST_30  C15  C13  N11  C10   180.00   0.0  0
 KVT  CONST_31  O14  C13  N11  C10     0.00   0.0  0
 KVT  Var_01    N18  C32  C23  C24  -118.88  30.0  1
 KVT  Var_02    C19  N21  C23  C24   114.35  30.0  1
 KVT  Var_03    N40  S37  C36  C05   -61.98  30.0  2
 KVT  Var_04    C32  N18  C15  C13   -87.83  30.0  3
 KVT  Var_05    H9   C01  C05  C06  -113.67  30.0  2
 KVT  Var_06    H6   C28  C23  N21   -65.12  30.0  3
 KVT  Var_07    H3   C24  C23  N21  -177.19  30.0  3
 KVT  Var_08    N18  C15  C13  N11  -171.67  30.0  2

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
 KVT  plan-1  C10  0.020
 KVT  plan-1  C01  0.020
 KVT  plan-1  C05  0.020
 KVT  plan-1  C06  0.020
 KVT  plan-1  C08  0.020
 KVT  plan-1  N11  0.020
 KVT  plan-1  C34  0.020
 KVT  plan-1  C36  0.020
 KVT  plan-1  S37  0.020
 KVT  plan-1  H12  0.020
 KVT  plan-1  H13  0.020
 KVT  plan-1  H16  0.020
 KVT  plan-2  C10  0.020
 KVT  plan-2  C13  0.020
 KVT  plan-2  C15  0.020
 KVT  plan-2  N11  0.020
 KVT  plan-2  O14  0.020
 KVT  plan-2  H14  0.020
 KVT  plan-3  C15  0.020
 KVT  plan-3  N18  0.020
 KVT  plan-3  C19  0.020
 KVT  plan-3  O20  0.020
 KVT  plan-3  N21  0.020
 KVT  plan-3  C23  0.020
 KVT  plan-3  C32  0.020
 KVT  plan-3  O33  0.020
 KVT  plan-3  H15  0.020

