# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 13:52:38 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N-[2-({6-[(2-sulfanylethyl)amino]pyrimidin-4-yl}amino)ethyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)NCCNc1cc(NCCS)ncn1
#
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
 SYP  SYP  N-[2-({6-[(2-sulfanylethyl)amino]pyrimidin-4-yl}amino)ethyl]propanamide  ligand  37  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SYP
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
 SYP  C1    C  CR16  0  -0.527   1.2708  -0.9463  -0.0475
 SYP  C2    C  CR6   0   0.525   0.5986  -2.1644  -0.1631
 SYP  N3    N  N     0  -0.487   1.2568  -3.3388  -0.1339
 SYP  C4    C  CR16  0   0.051   2.5654  -3.2617   0.0076
 SYP  N5    N  N     0  -0.486   3.3131  -2.1828   0.1302
 SYP  C6    C  CR6   0   0.527   2.6568  -1.0069   0.1085
 SYP  N7    N  NH1   0  -0.658   3.4169   0.0947   0.2494
 SYP  C8    C  CH2   0  -0.246   2.9071   1.4413   0.1818
 SYP  C9    C  CH2   0  -0.588   4.0272   2.4236   0.4818
 SYP  S10   S  S2    0  -0.244   3.3468   4.1109   0.4051
 SYP  N11   N  NH1   0  -0.660  -0.7387  -2.2384  -0.3059
 SYP  C12   C  CH2   0  -0.263  -1.5837  -1.0891  -0.5171
 SYP  C13   C  CH2   0  -0.322  -3.0430  -1.5224  -0.5997
 SYP  N14   N  NH1   0  -0.635  -3.9209  -0.4053  -0.8388
 SYP  C15   C  C     0   0.557  -4.4310   0.3597   0.1452
 SYP  C16   C  CH2   0  -0.573  -5.3623   1.4596  -0.3204
 SYP  O17   O  O     0  -0.500  -4.1875   0.1596   1.3266
 SYP  C18   C  CH3   0  -0.658  -5.4451   2.6225   0.6541
 SYP  H1    H  HCR6  0   0.279   0.7426  -0.0052  -0.0867
 SYP  H4    H  HCR6  0   0.245   3.0962  -4.2099   0.0247
 SYP  HN7   H  HNH1  0   0.390   4.4144  -0.0481   0.2324
 SYP  H8    H  HCH2  0   0.242   2.4821   1.6557  -0.8058
 SYP  H8A   H  HCH2  0   0.246   2.1042   1.5712   0.9133
 SYP  H9    H  HCH2  0   0.281   4.4348   2.2367   1.4750
 SYP  H9A   H  HCH2  0   0.279   4.8279   2.3191  -0.2509
 SYP  HS10  H  HSH1  0   0.233   4.4673   4.7573   0.7416
 SYP  HN11  H  HNH1  0   0.387  -1.1033  -3.1519  -0.5272
 SYP  H12   H  HCH2  0   0.241  -1.4657  -0.3839   0.3097
 SYP  H12A  H  HCH2  0   0.233  -1.3089  -0.5588  -1.4366
 SYP  H13   H  HCH2  0   0.262  -3.1728  -2.2350  -1.4154
 SYP  H13A  H  HCH2  0   0.254  -3.3358  -2.0244   0.3228
 SYP  HN14  H  HNH1  0   0.402  -4.1219  -0.1625  -1.7947
 SYP  H16   H  HCH2  0   0.252  -5.0597   1.8115  -1.3093
 SYP  H16A  H  HCH2  0   0.271  -6.3526   1.0126  -0.4543
 SYP  H18   H  HCH3  0   0.229  -5.8037   2.3024   1.6309
 SYP  H18A  H  HCH3  0   0.228  -4.4735   3.0976   0.7919
 SYP  H18B  H  HCH3  0   0.234  -6.1330   3.3796   0.2793

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
 SYP  C1   C2    aromatic  1.396  0.020  1.396
 SYP  C1   C6    aromatic  1.396  0.020  1.396
 SYP  C2   N3    aromatic  1.347  0.020  1.347
 SYP  C2   N11   single    1.347  0.020  1.347
 SYP  N3   C4    aromatic  1.319  0.020  1.319
 SYP  C4   N5    aromatic  1.318  0.020  1.318
 SYP  N5   C6    aromatic  1.347  0.020  1.347
 SYP  C6   N7    single    1.346  0.020  1.346
 SYP  N7   C8    single    1.441  0.020  1.441
 SYP  C8   C9    single    1.520  0.020  1.520
 SYP  C9   S10   single    1.821  0.020  1.821
 SYP  N11  C12   single    1.442  0.020  1.442
 SYP  C12  C13   single    1.524  0.020  1.524
 SYP  C13  N14   single    1.441  0.020  1.441
 SYP  N14  C15   single    1.347  0.020  1.347
 SYP  C15  C16   single    1.515  0.020  1.515
 SYP  C15  O17   double    1.223  0.020  1.223
 SYP  C16  C18   single    1.520  0.020  1.520
 SYP  C1   H1    single    0.930  0.020  1.080
 SYP  C4   H4    single    0.930  0.020  1.080
 SYP  N7   HN7   single    0.860  0.020  1.020
 SYP  C8   H8    single    0.970  0.020  1.090
 SYP  C8   H8A   single    0.970  0.020  1.090
 SYP  C9   H9    single    0.970  0.020  1.090
 SYP  C9   H9A   single    0.970  0.020  1.090
 SYP  S10  HS10  single    1.200  0.020  1.300
 SYP  N11  HN11  single    0.860  0.020  1.020
 SYP  C12  H12   single    0.970  0.020  1.090
 SYP  C12  H12A  single    0.970  0.020  1.090
 SYP  C13  H13   single    0.970  0.020  1.090
 SYP  C13  H13A  single    0.970  0.020  1.090
 SYP  N14  HN14  single    0.860  0.020  1.020
 SYP  C16  H16   single    0.970  0.020  1.090
 SYP  C16  H16A  single    0.970  0.020  1.090
 SYP  C18  H18   single    0.970  0.020  1.090
 SYP  C18  H18A  single    0.970  0.020  1.090
 SYP  C18  H18B  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
 SYP  H1    C1   C6    121.84  3.000
 SYP  H1    C1   C2    121.45  3.000
 SYP  C6    C1   C2    116.71  3.000
 SYP  N11   C2   N3    116.09  3.000
 SYP  N11   C2   C1    122.33  3.000
 SYP  N3    C2   C1    121.58  3.000
 SYP  C4    N3   C2    115.88  3.000
 SYP  H4    C4   N5    115.83  3.000
 SYP  H4    C4   N3    115.80  3.000
 SYP  N5    C4   N3    128.37  3.000
 SYP  C6    N5   C4    115.89  3.000
 SYP  N7    C6   N5    115.96  3.000
 SYP  N7    C6   C1    122.47  3.000
 SYP  N5    C6   C1    121.57  3.000
 SYP  HN7   N7   C8    118.80  3.000
 SYP  HN7   N7   C6    116.18  3.000
 SYP  C8    N7   C6    124.06  3.000
 SYP  H8A   C8   H8    107.14  3.000
 SYP  H8A   C8   C9    109.40  3.000
 SYP  H8    C8   C9    109.70  3.000
 SYP  H8A   C8   N7    109.82  3.000
 SYP  H8    C8   N7    111.23  3.000
 SYP  C9    C8   N7    109.50  3.000
 SYP  H9A   C9   H9    108.75  3.000
 SYP  H9A   C9   S10   109.56  3.000
 SYP  H9    C9   S10   109.70  3.000
 SYP  H9A   C9   C8    110.28  3.000
 SYP  H9    C9   C8    110.17  3.000
 SYP  S10   C9   C8    108.38  3.000
 SYP  HS10  S10  C9     97.14  3.000
 SYP  HN11  N11  C12   118.56  3.000
 SYP  HN11  N11  C2    115.60  3.000
 SYP  C12   N11  C2    123.61  3.000
 SYP  H12A  C12  H12   107.17  3.000
 SYP  H12A  C12  C13   109.39  3.000
 SYP  H12   C12  C13   109.13  3.000
 SYP  H12A  C12  N11   111.19  3.000
 SYP  H12   C12  N11   109.89  3.000
 SYP  C13   C12  N11   110.02  3.000
 SYP  H13A  C13  H13   107.45  3.000
 SYP  H13A  C13  N14   109.50  3.000
 SYP  H13   C13  N14   108.05  3.000
 SYP  H13A  C13  C12   110.01  3.000
 SYP  H13   C13  C12   109.88  3.000
 SYP  N14   C13  C12   111.83  3.000
 SYP  HN14  N14  C15   118.77  3.000
 SYP  HN14  N14  C13   117.79  3.000
 SYP  C15   N14  C13   123.37  3.000
 SYP  O17   C15  C16   122.57  3.000
 SYP  O17   C15  N14   122.52  3.000
 SYP  C16   C15  N14   114.89  3.000
 SYP  H16A  C16  H16   105.74  3.000
 SYP  H16A  C16  C18   109.98  3.000
 SYP  H16   C16  C18   110.43  3.000
 SYP  H16A  C16  C15   107.30  3.000
 SYP  H16   C16  C15   110.00  3.000
 SYP  C18   C16  C15   113.09  3.000
 SYP  H18B  C18  H18A  107.66  3.000
 SYP  H18B  C18  H18   107.76  3.000
 SYP  H18A  C18  H18   107.96  3.000
 SYP  H18B  C18  C16   110.22  3.000
 SYP  H18A  C18  C16   111.47  3.000
 SYP  H18   C18  C16   111.61  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
 SYP  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 SYP  CONST_02  C4    N5   C6   C1      0.00   0.0  0
 SYP  CONST_03  N5    C6   C1   C2      0.00   0.0  0
 SYP  CONST_04  N5    C4   N3   C2      0.00   0.0  0
 SYP  CONST_05  C6    C1   C2   N3      0.00   0.0  0
 SYP  CONST_06  C6    N5   C4   N3      0.00   0.0  0
 SYP  CONST_07  N7    C6   C1   C2    180.00   0.0  0
 SYP  CONST_08  N11   C2   N3   C4    180.00   0.0  0
 SYP  CONST_09  N7    C6   N5   C4    180.00   0.0  0
 SYP  CONST_10  N11   C2   C1   C6    180.00   0.0  0
 SYP  CONST_11  H4    C4   N3   C2    180.00   0.0  0
 SYP  CONST_12  H1    C1   C2   N3    180.00   0.0  0
 SYP  CONST_13  C12   N11  C2   C1      0.00   0.0  0
 SYP  CONST_14  C8    N7   C6   C1      0.00   0.0  0
 SYP  CONST_15  C12   N11  C2   N3    180.00   0.0  0
 SYP  CONST_16  C8    N7   C6   N5    180.00   0.0  0
 SYP  CONST_17  HN11  N11  C2   C1    180.00   0.0  0
 SYP  CONST_18  HN7   N7   C6   C1    180.00   0.0  0
 SYP  CONST_19  C16   C15  N14  C13   180.00   0.0  0
 SYP  CONST_20  O17   C15  N14  C13     0.00   0.0  0
 SYP  CONST_21  HN14  N14  C15  C16     0.00   0.0  0
 SYP  Var_01    C13   C12  N11  C2   -178.51  30.0  3
 SYP  Var_02    C9    C8   N7   C6    176.03  30.0  3
 SYP  Var_03    S10   C9   C8   N7   -179.43  30.0  3
 SYP  Var_04    N14   C13  C12  N11  -178.79  30.0  3
 SYP  Var_05    C15   N14  C13  C12   -86.83  30.0  3
 SYP  Var_06    C18   C16  C15  N14  -155.43  30.0  3
 SYP  Var_07    H18   C18  C16  C15   -59.71  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
 SYP  plan-1  C1    0.020
 SYP  plan-1  C2    0.020
 SYP  plan-1  N3    0.020
 SYP  plan-1  C4    0.020
 SYP  plan-1  N5    0.020
 SYP  plan-1  C6    0.020
 SYP  plan-1  N7    0.020
 SYP  plan-1  N11   0.020
 SYP  plan-1  H1    0.020
 SYP  plan-1  H4    0.020
 SYP  plan-2  C13   0.020
 SYP  plan-2  N14   0.020
 SYP  plan-2  C15   0.020
 SYP  plan-2  C16   0.020
 SYP  plan-2  O17   0.020
 SYP  plan-2  HN14  0.020
 SYP  plan-3  C6    0.020
 SYP  plan-3  N7    0.020
 SYP  plan-3  C8    0.020
 SYP  plan-3  HN7   0.020
 SYP  plan-4  C2    0.020
 SYP  plan-4  N11   0.020
 SYP  plan-4  C12   0.020
 SYP  plan-4  HN11  0.020

