# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:58:15 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 6-ethenyl-N,N-dimethyl-2-(methylsulfonyl)pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cc(C=C)nc(n1)[S](C)(=O)=O
#
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
 EDM  EDM  6-ethenyl-N,N-dimethyl-2-(methylsulfonyl)pyrimidin-4-amine  ligand  28  15  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EDM
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
 EDM  C23   C  CH3   0  -0.544   4.0102   0.6995  -0.1353
 EDM  N21   N  NT    0  -0.477   2.6368   1.1587  -0.1882
 EDM  C25   C  CH3   0  -0.521   2.3510   2.5817  -0.2145
 EDM  C1    C  CR6   0   0.589   1.6312   0.2847  -0.0862
 EDM  C2    C  CR16  0  -0.413   1.8299  -1.1154   0.0042
 EDM  N6    N  N     0  -0.446   0.3789   0.7688  -0.0677
 EDM  C5    C  CR6   0   0.138  -0.5792  -0.1205   0.0083
 EDM  S17   S  S     0   1.207  -2.2320   0.6206   0.0443
 EDM  C29   C  CH3   0  -0.799  -2.3236   1.4621  -1.5186
 EDM  O27   O  OS    0  -0.666  -3.2226  -0.4483   0.0692
 EDM  O19   O  OS    0  -0.674  -2.2401   1.6152   1.1144
 EDM  N4    N  N     0  -0.436  -0.5306  -1.4178   0.0757
 EDM  C3    C  CR6   0   0.286   0.7214  -1.9284   0.0797
 EDM  C13   C  C1    0  -0.251   0.8716  -3.3821   0.1628
 EDM  C15   C  C2    0  -0.498  -0.1513  -4.2315   0.2212
 EDM  H23   H  HCH3  0   0.251   4.2578   0.2644   0.8353
 EDM  H23A  H  HCH3  0   0.254   4.2121  -0.0430  -0.9083
 EDM  H23B  H  HCH3  0   0.270   4.6729   1.5418  -0.3060
 EDM  H25   H  HCH3  0   0.251   3.2650   3.1161  -0.4555
 EDM  H25A  H  HCH3  0   0.252   1.6055   2.8194  -0.9710
 EDM  H25B  H  HCH3  0   0.245   1.9843   2.9413   0.7487
 EDM  H2    H  HCR6  0   0.292   2.8182  -1.5502   0.0123
 EDM  H29   H  HCH3  0   0.297  -2.2225   0.7384  -2.3242
 EDM  H29A  H  HCH3  0   0.314  -3.3019   1.9399  -1.5674
 EDM  H29B  H  HCH3  0   0.296  -1.5384   2.2112  -1.5755
 EDM  H13   H  H     0   0.266   1.8895  -3.7549   0.1725
 EDM  H15   H  H     0   0.259   0.0159  -5.2979   0.2781
 EDM  H15A  H  H     0   0.260  -1.1777  -3.8901   0.2124

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
 EDM  C23  N21   single    1.449  0.020  1.449
 EDM  N21  C25   single    1.452  0.020  1.452
 EDM  N21  C1    single    1.336  0.020  1.336
 EDM  C1   C2    aromatic  1.417  0.020  1.417
 EDM  C1   N6    aromatic  1.343  0.020  1.343
 EDM  C2   C3    aromatic  1.377  0.020  1.377
 EDM  N6   C5    aromatic  1.309  0.020  1.309
 EDM  C5   S17   single    1.812  0.020  1.812
 EDM  C5   N4    aromatic  1.300  0.020  1.300
 EDM  S17  C29   single    1.777  0.020  1.777
 EDM  S17  O27   double    1.458  0.020  1.458
 EDM  S17  O19   double    1.461  0.020  1.461
 EDM  N4   C3    aromatic  1.352  0.020  1.352
 EDM  C3   C13   single    1.464  0.020  1.464
 EDM  C13  C15   double    1.331  0.020  1.331
 EDM  C23  H23   single    0.970  0.020  1.090
 EDM  C23  H23A  single    0.970  0.020  1.090
 EDM  C23  H23B  single    0.970  0.020  1.090
 EDM  C25  H25   single    0.970  0.020  1.090
 EDM  C25  H25A  single    0.970  0.020  1.090
 EDM  C25  H25B  single    0.970  0.020  1.090
 EDM  C2   H2    single    0.930  0.020  1.080
 EDM  C29  H29   single    0.970  0.020  1.090
 EDM  C29  H29A  single    0.970  0.020  1.090
 EDM  C29  H29B  single    0.970  0.020  1.090
 EDM  C13  H13   single    0.930  0.020  1.080
 EDM  C15  H15   single    0.930  0.020  1.080
 EDM  C15  H15A  single    0.930  0.020  1.080

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
 EDM  H23B  C23  H23A  107.69  3.000
 EDM  H23B  C23  H23   108.09  3.000
 EDM  H23A  C23  H23   108.47  3.000
 EDM  H23B  C23  N21   109.09  3.000
 EDM  H23A  C23  N21   111.43  3.000
 EDM  H23   C23  N21   111.94  3.000
 EDM  C1    N21  C25   119.63  3.000
 EDM  C1    N21  C23   120.21  3.000
 EDM  C25   N21  C23   119.86  3.000
 EDM  H25B  C25  H25A  108.14  3.000
 EDM  H25B  C25  H25   108.46  3.000
 EDM  H25A  C25  H25   108.35  3.000
 EDM  H25B  C25  N21   111.91  3.000
 EDM  H25A  C25  N21   111.19  3.000
 EDM  H25   C25  N21   108.71  3.000
 EDM  N6    C1   C2    119.09  3.000
 EDM  N6    C1   N21   117.84  3.000
 EDM  C2    C1   N21   123.07  3.000
 EDM  H2    C2   C3    119.92  3.000
 EDM  H2    C2   C1    121.78  3.000
 EDM  C3    C2   C1    118.29  3.000
 EDM  C5    N6   C1    115.99  3.000
 EDM  N4    C5   S17   116.19  3.000
 EDM  N4    C5   N6    130.81  3.000
 EDM  S17   C5   N6    113.00  3.000
 EDM  O19   S17  O27   118.88  3.000
 EDM  O19   S17  C29   108.75  3.000
 EDM  O27   S17  C29   109.10  3.000
 EDM  O19   S17  C5    107.34  3.000
 EDM  O27   S17  C5    108.68  3.000
 EDM  C29   S17  C5    102.90  3.000
 EDM  H29B  C29  H29A  110.13  3.000
 EDM  H29B  C29  H29   110.65  3.000
 EDM  H29A  C29  H29   110.00  3.000
 EDM  H29B  C29  S17   109.59  3.000
 EDM  H29A  C29  S17   107.05  3.000
 EDM  H29   C29  S17   109.36  3.000
 EDM  C3    N4   C5    114.31  3.000
 EDM  C13   C3   N4    118.05  3.000
 EDM  C13   C3   C2    120.45  3.000
 EDM  N4    C3   C2    121.49  3.000
 EDM  H13   C13  C15   120.12  3.000
 EDM  H13   C13  C3    116.00  3.000
 EDM  C15   C13  C3    123.88  3.000
 EDM  H15A  C15  H15   117.29  3.000
 EDM  H15A  C15  C13   121.84  3.000
 EDM  H15   C15  C13   120.87  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
 EDM  CONST_01  N4   C3   C2   C1      0.00   0.0  0
 EDM  CONST_02  N4   C5   N6   C1      0.00   0.0  0
 EDM  CONST_03  C5   N6   C1   C2      0.00   0.0  0
 EDM  CONST_04  C5   N4   C3   C2      0.00   0.0  0
 EDM  CONST_05  C3   C2   C1   N6      0.00   0.0  0
 EDM  CONST_06  C3   N4   C5   N6      0.00   0.0  0
 EDM  CONST_07  C3   C2   C1   N21   180.00   0.0  0
 EDM  CONST_08  C5   N6   C1   N21   180.00   0.0  0
 EDM  CONST_09  C13  C3   C2   C1    180.00   0.0  0
 EDM  CONST_10  S17  C5   N6   C1    180.00   0.0  0
 EDM  CONST_11  C13  C3   N4   C5    180.00   0.0  0
 EDM  CONST_12  C3   N4   C5   S17   180.00   0.0  0
 EDM  CONST_13  H2   C2   C1   N6    180.00   0.0  0
 EDM  CONST_14  C2   C1   N21  C23     0.00   0.0  0
 EDM  CONST_15  N6   C1   N21  C23   180.00   0.0  0
 EDM  CONST_16  C2   C1   N21  C25   180.00   0.0  0
 EDM  CONST_17  N6   C1   N21  C25     0.00   0.0  0
 EDM  Var_01    C15  C13  C3   C2   -179.11  30.0  2
 EDM  Var_02    C29  S17  C5   N6     61.94  30.0  2
 EDM  Var_03    H15  C15  C13  C3    179.77   0.0  2
 EDM  Var_04    H23  C23  N21  C1    -64.45  30.0  3
 EDM  Var_05    H25  C25  N21  C1   -171.25  30.0  3
 EDM  Var_06    H29  C29  S17  C5     61.01  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
 EDM  plan-1  N21   0.020
 EDM  plan-1  C1    0.020
 EDM  plan-1  C2    0.020
 EDM  plan-1  N6    0.020
 EDM  plan-1  C5    0.020
 EDM  plan-1  S17   0.020
 EDM  plan-1  N4    0.020
 EDM  plan-1  C3    0.020
 EDM  plan-1  C13   0.020
 EDM  plan-1  H2    0.020
 EDM  plan-2  C23   0.020
 EDM  plan-2  N21   0.020
 EDM  plan-2  C25   0.020
 EDM  plan-2  C1    0.020
 EDM  plan-3  C3    0.020
 EDM  plan-3  C13   0.020
 EDM  plan-3  C15   0.020
 EDM  plan-3  H13   0.020
 EDM  plan-3  H15   0.020
 EDM  plan-3  H15A  0.020

