# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 15:56:59 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(Cc2csc(CCO)c2C)c(N)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
 0YN  0YN  2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethanol  ligand  35  18  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0YN
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
 0YN  C2A  C  CH3   0  -0.729   5.0655   1.6501   1.2394
 0YN  C35  C  CH2   0  -0.623   0.8146  -0.6201  -1.7914
 0YN  C2   C  CR15  0  -0.574  -1.0242  -2.0788  -0.8603
 0YN  S1   S  S2    0   0.203  -2.4703  -2.0006   0.0516
 0YN  C5   C  CR5   0  -0.227  -2.3497  -0.2872   0.2131
 0YN  C4   C  CR5   0   0.133  -1.2382   0.1947  -0.4202
 0YN  C4A  C  CH3   0  -0.747  -0.8711   1.6447  -0.4908
 0YN  C5A  C  CH2   0  -0.541  -3.4262   0.4705   0.9215
 0YN  C5B  C  CH2   0  -0.126  -4.5920   0.7846  -0.0068
 0YN  O5G  O  OH1   0  -0.670  -5.5624   1.5005   0.7218
 0YN  N1'  N  N     0  -0.446   3.4942   1.7434  -0.5925
 0YN  C2'  C  CR6   0   0.350   3.9619   1.0418   0.4309
 0YN  N3'  N  N     0  -0.467   3.5147  -0.1444   0.8185
 0YN  C4'  C  CR6   0   0.451   2.5090  -0.6976   0.1379
 0YN  N4'  N  NH2   0  -0.827   2.1103  -1.9231   0.5281
 0YN  C5'  C  CR6   0  -0.015   1.9282  -0.0351  -0.9677
 0YN  C6'  C  CR16  0  -0.098   2.4869   1.1848  -1.2659
 0YN  C3   C  CR5   0   0.186  -0.4648  -0.8486  -1.0326
 0YN  H1   H  HCH3  0   0.256   4.6473   2.2884   2.0212
 0YN  H2   H  HCH3  0   0.246   5.6651   0.8849   1.7277
 0YN  H3   H  HCH3  0   0.246   5.7085   2.2717   0.6196
 0YN  H4   H  HCH2  0   0.276   0.6214   0.0554  -2.6300
 0YN  H5   H  HCH2  0   0.276   1.1371  -1.5671  -2.2350
 0YN  H6   H  HCR5  0   0.298  -0.6610  -3.0258  -1.2332
 0YN  H7   H  HCH3  0   0.249  -0.0576   1.8909   0.1935
 0YN  H8   H  HCH3  0   0.243  -0.5407   1.9184  -1.4934
 0YN  H9   H  HCH3  0   0.252  -1.7145   2.2875  -0.2421
 0YN  H10  H  HCH2  0   0.259  -3.7884  -0.0998   1.7810
 0YN  H11  H  HCH2  0   0.257  -3.0145   1.4004   1.3191
 0YN  H12  H  HCH2  0   0.199  -4.2193   1.3605  -0.8641
 0YN  H13  H  HCH2  0   0.195  -4.9958  -0.1540  -0.4076
 0YN  H14  H  HOH1  0   0.455  -6.2965   1.6947   0.1323
 0YN  H15  H  HNH2  0   0.393   2.4677  -2.2742   1.4011
 0YN  H16  H  HNH2  0   0.411   1.2125  -2.2782   0.2458
 0YN  H17  H  HCR6  0   0.256   2.0982   1.7534  -2.1069

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
 0YN  O5G  C5B  single    1.409  0.020  1.409
 0YN  C5B  C5A  single    1.523  0.020  1.523
 0YN  C5A  C5   single    1.495  0.020  1.495
 0YN  C5   C4   aromatic  1.367  0.020  1.367
 0YN  C5   S1   aromatic  1.725  0.020  1.725
 0YN  C4A  C4   single    1.497  0.020  1.497
 0YN  C4   C3   aromatic  1.436  0.020  1.436
 0YN  S1   C2   aromatic  1.711  0.020  1.711
 0YN  C3   C2   aromatic  1.362  0.020  1.362
 0YN  C3   C35  single    1.505  0.020  1.505
 0YN  C35  C5'  single    1.504  0.020  1.504
 0YN  C5'  C6'  aromatic  1.375  0.020  1.375
 0YN  C5'  C4'  aromatic  1.414  0.020  1.414
 0YN  C6'  N1'  aromatic  1.334  0.020  1.334
 0YN  N4'  C4'  single    1.346  0.020  1.346
 0YN  C4'  N3'  aromatic  1.334  0.020  1.334
 0YN  N1'  C2'  aromatic  1.326  0.020  1.326
 0YN  N3'  C2'  aromatic  1.326  0.020  1.326
 0YN  C2'  C2A  single    1.497  0.020  1.497
 0YN  C2A  H1   single    0.970  0.020  1.090
 0YN  C2A  H2   single    0.970  0.020  1.090
 0YN  C2A  H3   single    0.970  0.020  1.090
 0YN  C35  H4   single    0.970  0.020  1.090
 0YN  C35  H5   single    0.970  0.020  1.090
 0YN  C2   H6   single    0.930  0.020  1.080
 0YN  C4A  H7   single    0.970  0.020  1.090
 0YN  C4A  H8   single    0.970  0.020  1.090
 0YN  C4A  H9   single    0.970  0.020  1.090
 0YN  C5A  H10  single    0.970  0.020  1.090
 0YN  C5A  H11  single    0.970  0.020  1.090
 0YN  C5B  H12  single    0.970  0.020  1.090
 0YN  C5B  H13  single    0.970  0.020  1.090
 0YN  O5G  H14  single    0.850  0.020  0.980
 0YN  N4'  H15  single    0.890  0.020  1.040
 0YN  N4'  H16  single    0.890  0.020  1.040
 0YN  C6'  H17  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
 0YN  H3   C2A  H2   109.38  3.000
 0YN  H3   C2A  H1   107.46  3.000
 0YN  H2   C2A  H1   107.51  3.000
 0YN  H3   C2A  C2'  111.11  3.000
 0YN  H2   C2A  C2'  111.28  3.000
 0YN  H1   C2A  C2'  109.98  3.000
 0YN  H5   C35  H4   106.00  3.000
 0YN  H5   C35  C3   108.87  3.000
 0YN  H4   C35  C3   109.27  3.000
 0YN  H5   C35  C5'  109.91  3.000
 0YN  H4   C35  C5'  108.09  3.000
 0YN  C3   C35  C5'  114.36  3.000
 0YN  H6   C2   C3   127.57  3.000
 0YN  H6   C2   S1   120.52  3.000
 0YN  C3   C2   S1   111.90  3.000
 0YN  C5   S1   C2    92.08  3.000
 0YN  C5A  C5   C4   128.78  3.000
 0YN  C4   C5   S1   111.32  3.000
 0YN  C5A  C5   S1   119.83  3.000
 0YN  C3   C4   C4A  123.46  3.000
 0YN  C3   C4   C5   112.30  3.000
 0YN  C4A  C4   C5   124.23  3.000
 0YN  H9   C4A  H8   107.24  3.000
 0YN  H9   C4A  H7   107.51  3.000
 0YN  H8   C4A  H7   107.10  3.000
 0YN  H9   C4A  C4   111.77  3.000
 0YN  H8   C4A  C4   111.14  3.000
 0YN  H7   C4A  C4   111.82  3.000
 0YN  H11  C5A  H10  106.44  3.000
 0YN  H11  C5A  C5B  109.56  3.000
 0YN  H10  C5A  C5B  109.46  3.000
 0YN  H11  C5A  C5   109.43  3.000
 0YN  H10  C5A  C5   110.29  3.000
 0YN  C5B  C5A  C5   111.52  3.000
 0YN  H13  C5B  H12  106.76  3.000
 0YN  H13  C5B  O5G  111.72  3.000
 0YN  H12  C5B  O5G  111.78  3.000
 0YN  H13  C5B  C5A  109.13  3.000
 0YN  H12  C5B  C5A  108.92  3.000
 0YN  O5G  C5B  C5A  108.47  3.000
 0YN  H14  O5G  C5B  108.15  3.000
 0YN  C6'  N1'  C2'  115.74  3.000
 0YN  N3'  C2'  N1'  125.46  3.000
 0YN  N3'  C2'  C2A  117.02  3.000
 0YN  N1'  C2'  C2A  117.50  3.000
 0YN  C4'  N3'  C2'  118.43  3.000
 0YN  C5'  C4'  N4'  122.11  3.000
 0YN  N4'  C4'  N3'  116.91  3.000
 0YN  C5'  C4'  N3'  120.94  3.000
 0YN  H16  N4'  H15  115.92  3.000
 0YN  H16  N4'  C4'  120.28  3.000
 0YN  H15  N4'  C4'  117.63  3.000
 0YN  C6'  C5'  C4'  114.75  3.000
 0YN  C4'  C5'  C35  123.39  3.000
 0YN  C6'  C5'  C35  121.83  3.000
 0YN  H17  C6'  C5'  119.13  3.000
 0YN  H17  C6'  N1'  116.20  3.000
 0YN  C5'  C6'  N1'  124.68  3.000
 0YN  C4   C3   C2   112.40  3.000
 0YN  C2   C3   C35  123.36  3.000
 0YN  C4   C3   C35  124.24  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
 0YN  CONST_01  C4   C5   S1   C2      0.00   0.0  0
 0YN  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 0YN  CONST_03  C3   C4   C5   S1      0.00   0.0  0
 0YN  CONST_04  C4   C3   C2   S1      0.00   0.0  0
 0YN  CONST_05  C3   C2   S1   C5      0.00   0.0  0
 0YN  CONST_06  C4'  C5'  C6'  N1'     0.00   0.0  0
 0YN  CONST_07  C4'  N3'  C2'  N1'     0.00   0.0  0
 0YN  CONST_08  C5'  C6'  N1'  C2'     0.00   0.0  0
 0YN  CONST_09  C5'  C4'  N3'  C2'     0.00   0.0  0
 0YN  CONST_10  C6'  C5'  C4'  N3'     0.00   0.0  0
 0YN  CONST_11  C6'  N1'  C2'  N3'     0.00   0.0  0
 0YN  CONST_12  C6'  N1'  C2'  C2A   180.00   0.0  0
 0YN  CONST_13  C4'  N3'  C2'  C2A   180.00   0.0  0
 0YN  CONST_14  C5   C4   C3   C35   180.00   0.0  0
 0YN  CONST_15  S1   C2   C3   C35   180.00   0.0  0
 0YN  CONST_16  N1'  C6'  C5'  C35   180.00   0.0  0
 0YN  CONST_17  N3'  C4'  C5'  C35   180.00   0.0  0
 0YN  CONST_18  C5A  C5   S1   C2    180.00   0.0  0
 0YN  CONST_19  C4A  C4   C3   C2    180.00   0.0  0
 0YN  CONST_20  C4A  C4   C5   S1    180.00   0.0  0
 0YN  CONST_21  C3   C4   C5   C5A   180.00   0.0  0
 0YN  CONST_22  N4'  C4'  N3'  C2'   180.00   0.0  0
 0YN  CONST_23  C6'  C5'  C4'  N4'   180.00   0.0  0
 0YN  CONST_24  H6   C2   S1   C5    180.00   0.0  0
 0YN  CONST_25  H17  C6'  N1'  C2'   180.00   0.0  0
 0YN  CONST_26  H15  N4'  C4'  N3'     0.00   0.0  0
 0YN  Var_01    C5'  C35  C3   C2   -118.18  30.0  2
 0YN  Var_02    C3   C35  C5'  C4'    63.18  30.0  1
 0YN  Var_03    C5B  C5A  C5   S1    -83.73  30.0  1
 0YN  Var_04    H7   C4A  C4   C5    104.03  30.0  2
 0YN  Var_05    H1   C2A  C2'  N1'    86.59  30.0  2
 0YN  Var_06    O5G  C5B  C5A  C5   -179.78  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
 0YN  plan-1  C35  0.020
 0YN  plan-1  C2   0.020
 0YN  plan-1  S1   0.020
 0YN  plan-1  C5   0.020
 0YN  plan-1  C4   0.020
 0YN  plan-1  C4A  0.020
 0YN  plan-1  C5A  0.020
 0YN  plan-1  C3   0.020
 0YN  plan-1  H6   0.020
 0YN  plan-2  C2A  0.020
 0YN  plan-2  C35  0.020
 0YN  plan-2  N1'  0.020
 0YN  plan-2  C2'  0.020
 0YN  plan-2  N3'  0.020
 0YN  plan-2  C4'  0.020
 0YN  plan-2  N4'  0.020
 0YN  plan-2  C5'  0.020
 0YN  plan-2  C6'  0.020
 0YN  plan-2  H17  0.020
 0YN  plan-3  C4'  0.020
 0YN  plan-3  N4'  0.020
 0YN  plan-3  H15  0.020
 0YN  plan-3  H16  0.020

