# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:26:11 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-{[(5-butylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCc1cnc(SCC(=O)c2ccc(cc2)[S](N)(=O)=O)nc1
#
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
 E2I  E2I  4-{[(5-butylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide  ligand  43  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E2I
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
 E2I  N1    N  N     0  -0.400  -2.7952  -0.0670  -0.4567
 E2I  C2    C  CR16  0  -0.038  -3.8939  -0.7609  -0.7355
 E2I  C3    C  CR6   0  -0.011  -5.1684  -0.2193  -0.6762
 E2I  C4    C  CR16  0  -0.047  -5.2141   1.1202  -0.3006
 E2I  N5    N  N     0  -0.411  -4.1331   1.8291  -0.0191
 E2I  C6    C  CR6   0   0.241  -2.9711   1.1940  -0.1103
 E2I  C13   C  CH2   0  -0.510  -6.4022  -1.0224  -0.9445
 E2I  C15   C  CH2   0  -0.406  -7.0268  -1.5632   0.3427
 E2I  C17   C  CH2   0  -0.424  -8.2844  -2.3830   0.0857
 E2I  C19   C  CH3   0  -0.662  -8.9105  -2.9108   1.3688
 E2I  S21   S  S2    0   0.082  -1.5936   2.2111   0.2807
 E2I  C23   C  CH2   0  -0.710  -0.2344   1.0426   0.0577
 E2I  C25   C  C     0   0.399   1.0585   1.7605   0.3415
 E2I  O27   O  O     0  -0.371   1.0655   2.9236   0.6741
 E2I  C29   C  CR6   0   0.010   2.3273   0.9905   0.2041
 E2I  C31   C  CR16  0  -0.248   3.5319   1.6294   0.5047
 E2I  C32   C  CR16  0  -0.207   4.7303   0.9536   0.3863
 E2I  C33   C  CR6   0  -0.202   4.7197  -0.3694  -0.0397
 E2I  C34   C  CR16  0  -0.213   3.5382  -1.0220  -0.3463
 E2I  C35   C  CR16  0  -0.277   2.3399  -0.3355  -0.2175
 E2I  S42   S  S     0   1.368   6.2676  -1.2240  -0.2092
 E2I  O44   O  OS    0  -0.645   6.0255  -2.4223  -0.9987
 E2I  O46   O  OS    0  -0.660   7.2802  -0.2822  -0.6601
 E2I  N48   N  NC2   0  -0.888   6.6142  -1.5518   1.3681
 E2I  H2    H  HCR6  0   0.274  -3.7483  -1.7977  -1.0227
 E2I  H4    H  HCR6  0   0.275  -6.1647   1.6402  -0.2273
 E2I  H13   H  HCH2  0   0.249  -7.1349  -0.4069  -1.4731
 E2I  H13A  H  HCH2  0   0.248  -6.1567  -1.8543  -1.6100
 E2I  H15   H  HCH2  0   0.224  -6.2894  -2.1744   0.8732
 E2I  H15A  H  HCH2  0   0.223  -7.2644  -0.7266   1.0079
 E2I  H17   H  HCH2  0   0.216  -9.0118  -1.7696  -0.4547
 E2I  H17A  H  HCH2  0   0.216  -8.0406  -3.2187  -0.5772
 E2I  H19   H  HCH3  0   0.218  -8.2128  -3.5490   1.9139
 E2I  H19A  H  HCH3  0   0.218  -9.1961  -2.0928   2.0330
 E2I  H19B  H  HCH3  0   0.228  -9.8064  -3.4976   1.1642
 E2I  H23   H  HCH2  0   0.323  -0.3438   0.1923   0.7343
 E2I  H23A  H  HCH2  0   0.322  -0.2353   0.6459  -0.9594
 E2I  H31   H  HCR6  0   0.281   3.5336   2.6600   0.8318
 E2I  H32   H  HCR6  0   0.293   5.6583   1.4568   0.6214
 E2I  H34   H  HCR6  0   0.294   3.5360  -2.0490  -0.6828
 E2I  H35   H  HCR6  0   0.285   1.4223  -0.8549  -0.4576
 E2I  HN48  H  HNC2  0   0.420   6.0765  -2.3284   1.7391
 E2I  HN4A  H  HNC2  0   0.424   7.6081  -1.7032   1.5124

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
 E2I  C6   N1    aromatic  1.320  0.020  1.320
 E2I  N1   C2    aromatic  1.329  0.020  1.329
 E2I  C3   C2    aromatic  1.386  0.020  1.386
 E2I  C2   H2    single    0.930  0.020  1.080
 E2I  C4   C3    aromatic  1.392  0.020  1.392
 E2I  C3   C13   single    1.496  0.020  1.496
 E2I  N5   C4    aromatic  1.323  0.020  1.323
 E2I  C4   H4    single    0.930  0.020  1.080
 E2I  N5   C6    aromatic  1.327  0.020  1.327
 E2I  S21  C6    single    1.756  0.020  1.756
 E2I  C15  C13   single    1.529  0.020  1.529
 E2I  C13  H13   single    0.970  0.020  1.090
 E2I  C13  H13A  single    0.970  0.020  1.090
 E2I  C15  C17   single    1.523  0.020  1.523
 E2I  C15  H15   single    0.970  0.020  1.090
 E2I  C15  H15A  single    0.970  0.020  1.090
 E2I  C17  C19   single    1.522  0.020  1.522
 E2I  C17  H17   single    0.970  0.020  1.090
 E2I  C17  H17A  single    0.970  0.020  1.090
 E2I  C19  H19   single    0.970  0.020  1.090
 E2I  C19  H19A  single    0.970  0.020  1.090
 E2I  C19  H19B  single    0.970  0.020  1.090
 E2I  S21  C23   single    1.806  0.020  1.806
 E2I  C25  C23   single    1.506  0.020  1.506
 E2I  C23  H23   single    0.970  0.020  1.090
 E2I  C23  H23A  single    0.970  0.020  1.090
 E2I  O27  C25   double    1.210  0.020  1.210
 E2I  C25  C29   single    1.490  0.020  1.490
 E2I  C29  C31   aromatic  1.396  0.020  1.396
 E2I  C29  C35   aromatic  1.392  0.020  1.392
 E2I  C31  C32   aromatic  1.381  0.020  1.381
 E2I  C31  H31   single    0.930  0.020  1.080
 E2I  C32  C33   aromatic  1.390  0.020  1.390
 E2I  C32  H32   single    0.930  0.020  1.080
 E2I  C34  C33   aromatic  1.384  0.020  1.384
 E2I  C33  S42   single    1.776  0.020  1.776
 E2I  C35  C34   aromatic  1.387  0.020  1.387
 E2I  C34  H34   single    0.930  0.020  1.080
 E2I  C35  H35   single    0.930  0.020  1.080
 E2I  N48  S42   single    1.648  0.020  1.648
 E2I  O46  S42   double    1.455  0.020  1.455
 E2I  S42  O44   double    1.455  0.020  1.455
 E2I  N48  HN48  single    0.890  0.020  1.040
 E2I  N48  HN4A  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
 E2I  C6    N1   C2    116.34  3.000
 E2I  H2    C2   C3    120.52  3.000
 E2I  H2    C2   N1    116.31  3.000
 E2I  C3    C2   N1    123.17  3.000
 E2I  C13   C3   C4    122.53  3.000
 E2I  C13   C3   C2    122.74  3.000
 E2I  C4    C3   C2    114.69  3.000
 E2I  H4    C4   N5    116.38  3.000
 E2I  H4    C4   C3    120.52  3.000
 E2I  N5    C4   C3    123.11  3.000
 E2I  C6    N5   C4    116.38  3.000
 E2I  S21   C6   N5    113.22  3.000
 E2I  S21   C6   N1    120.48  3.000
 E2I  N5    C6   N1    126.30  3.000
 E2I  H13A  C13  H13   106.53  3.000
 E2I  H13A  C13  C15   109.57  3.000
 E2I  H13   C13  C15   109.41  3.000
 E2I  H13A  C13  C3    109.41  3.000
 E2I  H13   C13  C3    109.70  3.000
 E2I  C15   C13  C3    112.06  3.000
 E2I  H15A  C15  H15   106.16  3.000
 E2I  H15A  C15  C17   109.55  3.000
 E2I  H15   C15  C17   109.71  3.000
 E2I  H15A  C15  C13   109.26  3.000
 E2I  H15   C15  C13   109.28  3.000
 E2I  C17   C15  C13   112.67  3.000
 E2I  H17A  C17  H17   106.09  3.000
 E2I  H17A  C17  C19   109.72  3.000
 E2I  H17   C17  C19   109.71  3.000
 E2I  H17A  C17  C15   109.23  3.000
 E2I  H17   C17  C15   109.30  3.000
 E2I  C19   C17  C15   112.58  3.000
 E2I  H19B  C19  H19A  107.60  3.000
 E2I  H19B  C19  H19   107.71  3.000
 E2I  H19A  C19  H19   107.54  3.000
 E2I  H19B  C19  C17   111.50  3.000
 E2I  H19A  C19  C17   111.15  3.000
 E2I  H19   C19  C17   111.15  3.000
 E2I  C23   S21  C6    100.84  3.000
 E2I  H23A  C23  H23   107.11  3.000
 E2I  H23A  C23  C25   110.45  3.000
 E2I  H23   C23  C25   109.90  3.000
 E2I  H23A  C23  S21   110.46  3.000
 E2I  H23   C23  S21   110.60  3.000
 E2I  C25   C23  S21   108.33  3.000
 E2I  C29   C25  O27   121.14  3.000
 E2I  C29   C25  C23   117.86  3.000
 E2I  O27   C25  C23   121.01  3.000
 E2I  C35   C29  C31   119.57  3.000
 E2I  C35   C29  C25   121.87  3.000
 E2I  C31   C29  C25   118.57  3.000
 E2I  H31   C31  C32   119.41  3.000
 E2I  H31   C31  C29   120.17  3.000
 E2I  C32   C31  C29   120.42  3.000
 E2I  H32   C32  C33   121.07  3.000
 E2I  H32   C32  C31   119.89  3.000
 E2I  C33   C32  C31   119.04  3.000
 E2I  S42   C33  C34   119.73  3.000
 E2I  S42   C33  C32   118.72  3.000
 E2I  C34   C33  C32   121.55  3.000
 E2I  H34   C34  C35   119.83  3.000
 E2I  H34   C34  C33   121.25  3.000
 E2I  C35   C34  C33   118.92  3.000
 E2I  H35   C35  C34   118.35  3.000
 E2I  H35   C35  C29   121.15  3.000
 E2I  C34   C35  C29   120.50  3.000
 E2I  N48   S42  O46   106.21  3.000
 E2I  O46   S42  O44   118.74  3.000
 E2I  N48   S42  O44   112.98  3.000
 E2I  O44   S42  C33   107.64  3.000
 E2I  O46   S42  C33   108.95  3.000
 E2I  N48   S42  C33   100.82  3.000
 E2I  HN4A  N48  HN48  110.64  3.000
 E2I  HN4A  N48  S42   111.81  3.000
 E2I  HN48  N48  S42   113.00  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
 E2I  CONST_01  C4    N5   C6   N1      0.00   0.0  0
 E2I  CONST_02  C4    C3   C2   N1      0.00   0.0  0
 E2I  CONST_03  N5    C6   N1   C2      0.00   0.0  0
 E2I  CONST_04  N5    C4   C3   C2      0.00   0.0  0
 E2I  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 E2I  CONST_06  C6    N5   C4   C3      0.00   0.0  0
 E2I  CONST_07  C33   C32  C31  C29     0.00   0.0  0
 E2I  CONST_08  C33   C34  C35  C29     0.00   0.0  0
 E2I  CONST_09  C34   C35  C29  C31     0.00   0.0  0
 E2I  CONST_10  C34   C33  C32  C31     0.00   0.0  0
 E2I  CONST_11  C35   C29  C31  C32     0.00   0.0  0
 E2I  CONST_12  C35   C34  C33  C32     0.00   0.0  0
 E2I  CONST_13  C13   C3   C2   N1    180.00   0.0  0
 E2I  CONST_14  S21   C6   N1   C2    180.00   0.0  0
 E2I  CONST_15  S21   C6   N5   C4    180.00   0.0  0
 E2I  CONST_16  C13   C3   C4   N5    180.00   0.0  0
 E2I  CONST_17  C32   C31  C29  C25   180.00   0.0  0
 E2I  CONST_18  C34   C35  C29  C25   180.00   0.0  0
 E2I  CONST_19  S42   C33  C32  C31   180.00   0.0  0
 E2I  CONST_20  S42   C33  C34  C35   180.00   0.0  0
 E2I  CONST_21  H4    C4   C3   C2    180.00   0.0  0
 E2I  CONST_22  H2    C2   C3   C4    180.00   0.0  0
 E2I  CONST_23  H32   C32  C31  C29   180.00   0.0  0
 E2I  CONST_24  H34   C34  C35  C29   180.00   0.0  0
 E2I  CONST_25  H35   C35  C29  C31   180.00   0.0  0
 E2I  CONST_26  H31   C31  C32  C33   180.00   0.0  0
 E2I  Var_01    C15   C13  C3   C2     95.17  30.0  2
 E2I  Var_02    C31   C29  C25  C23  -178.00  30.0  2
 E2I  Var_03    N48   S42  C33  C32    76.86  30.0  2
 E2I  Var_04    C17   C15  C13  C3    179.99  30.0  2
 E2I  Var_05    C25   C23  S21  C6    179.36  30.0  3
 E2I  Var_06    C29   C25  C23  S21  -179.32  30.0  1
 E2I  Var_07    HN48  N48  S42  C33    77.11  30.0  3
 E2I  Var_08    C19   C17  C15  C13  -179.54  30.0  3
 E2I  Var_09    H19   C19  C17  C15   -59.59  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
 E2I  plan-1  N1   0.020
 E2I  plan-1  C2   0.020
 E2I  plan-1  C3   0.020
 E2I  plan-1  C4   0.020
 E2I  plan-1  N5   0.020
 E2I  plan-1  C6   0.020
 E2I  plan-1  C13  0.020
 E2I  plan-1  S21  0.020
 E2I  plan-1  H2   0.020
 E2I  plan-1  H4   0.020
 E2I  plan-2  C25  0.020
 E2I  plan-2  C29  0.020
 E2I  plan-2  C31  0.020
 E2I  plan-2  C32  0.020
 E2I  plan-2  C33  0.020
 E2I  plan-2  C34  0.020
 E2I  plan-2  C35  0.020
 E2I  plan-2  S42  0.020
 E2I  plan-2  H31  0.020
 E2I  plan-2  H32  0.020
 E2I  plan-2  H34  0.020
 E2I  plan-2  H35  0.020
 E2I  plan-3  C23  0.020
 E2I  plan-3  C25  0.020
 E2I  plan-3  O27  0.020
 E2I  plan-3  C29  0.020

