# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 12:19:16 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-({[6-chloro-5-formyl-2-(methylsulfanyl)pyrimidin-4-yl]amino}methyl)benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nc(Cl)c(C=O)c(NCc2ccc(cc2)[S](N)(=O)=O)n1
#
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
 JDR  JDR  4-({[6-chloro-5-formyl-2-(methylsulfanyl)pyrimidin-4-yl]amino}methyl)benzenesulfonamide  ligand  36  23  .  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_JDR
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
 JDR  N1    N   N     0  -0.437  -3.4645  -0.4772  -0.8844
 JDR  C2    C   CR6   0   0.231  -2.4690  -1.1027  -0.2668
 JDR  N3    N   N     0  -0.459  -1.5769  -0.5637   0.5351
 JDR  C4    C   CR6   0   0.599  -1.6588   0.7479   0.7643
 JDR  C5    C   CR6   0  -0.142  -2.6771   1.5430   0.1434
 JDR  C6    C   CR6   0   0.194  -3.5451   0.8147  -0.6667
 JDR  N7    N   NH1   0  -0.697  -0.7446   1.2559   1.5949
 JDR  C8    C   CR6   0  -0.017   1.4436   0.0885   1.3667
 JDR  C9    C   CR16  0  -0.192   2.4021  -0.7769   1.8882
 JDR  C10   C   CR16  0  -0.259   3.5177  -1.1330   1.1509
 JDR  C11   C   CR6   0  -0.174   3.6672  -0.6225  -0.1315
 JDR  C12   C   CR16  0  -0.277   2.7255   0.2415  -0.6708
 JDR  C13   C   CR16  0  -0.185   1.6187   0.5963   0.0843
 JDR  S14   S   S     0   1.346   5.0782  -1.0728  -1.0953
 JDR  O15   O   OS    0  -0.693   5.4205   0.0123  -2.0032
 JDR  O16   O   OS    0  -0.469   6.1040  -1.5587  -0.1822
 JDR  N17   N   NC2   0  -0.942   4.4461  -2.2709  -2.0452
 JDR  C18   C   C1    0   0.160  -2.7395   2.9888   0.3522
 JDR  O19   O   O     0  -0.452  -3.5985   3.7342  -0.0614
 JDR  CL20  CL  CL    0   0.030  -4.8437   1.5773  -1.4956
 JDR  S21   S   S2    0   0.023  -2.2694  -2.8163  -0.5002
 JDR  C22   C   CH3   0  -0.783  -3.6307  -3.2305  -1.6071
 JDR  C23   C   CH2   0  -0.341   0.2670   0.4549   2.2383
 JDR  HN7   H   HNH1  0   0.422  -0.7723   2.2285   1.8446
 JDR  H9    H   HCR6  0   0.281   2.2799  -1.1770   2.8874
 JDR  H10   H   HCR6  0   0.270   4.2548  -1.7985   1.5786
 JDR  H12   H   HCR6  0   0.279   2.8457   0.6442  -1.6675
 JDR  H13   H   HCR6  0   0.277   0.8982   1.2811  -0.3416
 JDR  HN17  H   HNC2  0   0.416   5.0405  -2.4568  -2.8485
 JDR  HN1A  H   HNC2  0   0.420   4.2837  -3.1304  -1.5307
 JDR  H18   H   H     0   0.258  -1.9060   3.4100   0.9352
 JDR  H22   H   HCH3  0   0.274  -3.5407  -4.2989  -1.7992
 JDR  H22A  H   HCH3  0   0.293  -4.5910  -3.0303  -1.1400
 JDR  H22B  H   HCH3  0   0.261  -3.5517  -2.6920  -2.5473
 JDR  H23   H   HCH2  0   0.251   0.6248   1.0259   3.0957
 JDR  H23A  H   HCH2  0   0.233  -0.1813  -0.4560   2.6355

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
 JDR  N1   C2    aromatic  1.328  0.020  1.328
 JDR  N1   C6    aromatic  1.313  0.020  1.313
 JDR  C2   N3    aromatic  1.315  0.020  1.315
 JDR  C2   S21   single    1.741  0.020  1.741
 JDR  N3   C4    aromatic  1.334  0.020  1.334
 JDR  C4   C5    aromatic  1.433  0.020  1.433
 JDR  C4   N7    single    1.336  0.020  1.336
 JDR  C5   C6    aromatic  1.393  0.020  1.393
 JDR  C5   C18   single    1.462  0.020  1.462
 JDR  C6   CL20  single    1.719  0.020  1.719
 JDR  N7   C23   single    1.442  0.020  1.442
 JDR  C8   C9    aromatic  1.393  0.020  1.393
 JDR  C8   C13   aromatic  1.390  0.020  1.390
 JDR  C8   C23   single    1.509  0.020  1.509
 JDR  C9   C10   aromatic  1.384  0.020  1.384
 JDR  C10  C11   aromatic  1.388  0.020  1.388
 JDR  C11  C12   aromatic  1.387  0.020  1.387
 JDR  C11  S14   single    1.767  0.020  1.767
 JDR  C12  C13   aromatic  1.386  0.020  1.386
 JDR  S14  O15   double    1.456  0.020  1.456
 JDR  S14  O16   double    1.457  0.020  1.457
 JDR  S14  N17   single    1.654  0.020  1.654
 JDR  C18  O19   double    1.210  0.020  1.210
 JDR  S21  C22   single    1.803  0.020  1.803
 JDR  N7   HN7   single    0.860  0.020  1.020
 JDR  C9   H9    single    0.930  0.020  1.080
 JDR  C10  H10   single    0.930  0.020  1.080
 JDR  C12  H12   single    0.930  0.020  1.080
 JDR  C13  H13   single    0.930  0.020  1.080
 JDR  N17  HN17  single    0.890  0.020  1.040
 JDR  N17  HN1A  single    0.890  0.020  1.040
 JDR  C18  H18   single    0.930  0.020  1.080
 JDR  C22  H22   single    0.970  0.020  1.090
 JDR  C22  H22A  single    0.970  0.020  1.090
 JDR  C22  H22B  single    0.970  0.020  1.090
 JDR  C23  H23   single    0.970  0.020  1.090
 JDR  C23  H23A  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
 JDR  C6    N1   C2    115.63  3.000
 JDR  S21   C2   N3    114.04  3.000
 JDR  S21   C2   N1    119.16  3.000
 JDR  N3    C2   N1    126.80  3.000
 JDR  C4    N3   C2    117.78  3.000
 JDR  N7    C4   C5    123.00  3.000
 JDR  N7    C4   N3    116.03  3.000
 JDR  C5    C4   N3    120.97  3.000
 JDR  C18   C5   C6    125.00  3.000
 JDR  C18   C5   C4    121.13  3.000
 JDR  C6    C5   C4    113.86  3.000
 JDR  CL20  C6   C5    121.28  3.000
 JDR  CL20  C6   N1    113.77  3.000
 JDR  C5    C6   N1    124.95  3.000
 JDR  HN7   N7   C23   116.50  3.000
 JDR  HN7   N7   C4    120.27  3.000
 JDR  C23   N7   C4    123.13  3.000
 JDR  C23   C8   C13   122.83  3.000
 JDR  C23   C8   C9    118.10  3.000
 JDR  C13   C8   C9    119.06  3.000
 JDR  H9    C9   C10   119.17  3.000
 JDR  H9    C9   C8    119.82  3.000
 JDR  C10   C9   C8    121.01  3.000
 JDR  H10   C10  C11   121.22  3.000
 JDR  H10   C10  C9    119.82  3.000
 JDR  C11   C10  C9    118.96  3.000
 JDR  S14   C11  C12   119.26  3.000
 JDR  S14   C11  C10   119.74  3.000
 JDR  C12   C11  C10   121.00  3.000
 JDR  H12   C12  C13   119.70  3.000
 JDR  H12   C12  C11   120.98  3.000
 JDR  C13   C12  C11   119.33  3.000
 JDR  H13   C13  C12   118.65  3.000
 JDR  H13   C13  C8    120.71  3.000
 JDR  C12   C13  C8    120.63  3.000
 JDR  N17   S14  O16   112.79  3.000
 JDR  N17   S14  O15   105.76  3.000
 JDR  O16   S14  O15   118.29  3.000
 JDR  N17   S14  C11   101.10  3.000
 JDR  O16   S14  C11   107.78  3.000
 JDR  O15   S14  C11   109.76  3.000
 JDR  HN1A  N17  HN17  109.83  3.000
 JDR  HN1A  N17  S14   112.54  3.000
 JDR  HN17  N17  S14   111.27  3.000
 JDR  H18   C18  O19   118.86  3.000
 JDR  H18   C18  C5    114.94  3.000
 JDR  O19   C18  C5    126.19  3.000
 JDR  C22   S21  C2    102.82  3.000
 JDR  H22B  C22  H22A  110.19  3.000
 JDR  H22B  C22  H22   109.12  3.000
 JDR  H22A  C22  H22   109.24  3.000
 JDR  H22B  C22  S21   111.26  3.000
 JDR  H22A  C22  S21   111.17  3.000
 JDR  H22   C22  S21   105.74  3.000
 JDR  H23A  C23  H23   106.62  3.000
 JDR  H23A  C23  C8    109.16  3.000
 JDR  H23   C23  C8    108.99  3.000
 JDR  H23A  C23  N7    109.77  3.000
 JDR  H23   C23  N7    106.87  3.000
 JDR  C8    C23  N7    115.09  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
 JDR  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 JDR  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 JDR  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 JDR  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 JDR  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 JDR  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 JDR  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 JDR  CONST_08  C11   C12  C13  C8      0.00   0.0  0
 JDR  CONST_09  C12   C13  C8   C9      0.00   0.0  0
 JDR  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 JDR  CONST_11  C13   C8   C9   C10     0.00   0.0  0
 JDR  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 JDR  CONST_13  C18   C5   C6   N1    180.00   0.0  0
 JDR  CONST_14  CL20  C6   N1   C2    180.00   0.0  0
 JDR  CONST_15  N7    C4   N3   C2    180.00   0.0  0
 JDR  CONST_16  C18   C5   C4   N3    180.00   0.0  0
 JDR  CONST_17  S21   C2   N3   C4    180.00   0.0  0
 JDR  CONST_18  CL20  C6   C5   C4    180.00   0.0  0
 JDR  CONST_19  S21   C2   N1   C6    180.00   0.0  0
 JDR  CONST_20  N7    C4   C5   C6    180.00   0.0  0
 JDR  CONST_21  S14   C11  C10  C9    180.00   0.0  0
 JDR  CONST_22  C23   C8   C9   C10   180.00   0.0  0
 JDR  CONST_23  C23   C8   C13  C12   180.00   0.0  0
 JDR  CONST_24  S14   C11  C12  C13   180.00   0.0  0
 JDR  CONST_25  H10   C10  C9   C8    180.00   0.0  0
 JDR  CONST_26  H12   C12  C13  C8    180.00   0.0  0
 JDR  CONST_27  H13   C13  C8   C9    180.00   0.0  0
 JDR  CONST_28  H9    C9   C10  C11   180.00   0.0  0
 JDR  CONST_29  C23   N7   C4   N3      0.00   0.0  0
 JDR  CONST_30  C23   N7   C4   C5    180.00   0.0  0
 JDR  CONST_31  HN7   N7   C4   N3    180.00   0.0  0
 JDR  Var_01    O19   C18  C5   C4   -175.48  30.0  2
 JDR  Var_02    C8    C23  N7   C4     78.63  30.0  3
 JDR  Var_03    C9    C8   C23  N7   -174.67  30.0  2
 JDR  Var_04    O15   S14  C11  C10  -150.02  30.0  2
 JDR  Var_05    H22   C22  S21  C2    179.10  30.0  3
 JDR  Var_06    HN17  N17  S14  C11   163.06  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
 JDR  plan-1  N1    0.020
 JDR  plan-1  C2    0.020
 JDR  plan-1  N3    0.020
 JDR  plan-1  C4    0.020
 JDR  plan-1  C5    0.020
 JDR  plan-1  C6    0.020
 JDR  plan-1  N7    0.020
 JDR  plan-1  C18   0.020
 JDR  plan-1  CL20  0.020
 JDR  plan-1  S21   0.020
 JDR  plan-2  C8    0.020
 JDR  plan-2  C9    0.020
 JDR  plan-2  C10   0.020
 JDR  plan-2  C11   0.020
 JDR  plan-2  C12   0.020
 JDR  plan-2  C13   0.020
 JDR  plan-2  S14   0.020
 JDR  plan-2  C23   0.020
 JDR  plan-2  H9    0.020
 JDR  plan-2  H10   0.020
 JDR  plan-2  H12   0.020
 JDR  plan-2  H13   0.020
 JDR  plan-3  C4    0.020
 JDR  plan-3  N7    0.020
 JDR  plan-3  C23   0.020
 JDR  plan-3  HN7   0.020
 JDR  plan-4  C5    0.020
 JDR  plan-4  C18   0.020
 JDR  plan-4  O19   0.020
 JDR  plan-4  H18   0.020

