# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:38:54 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (2S)-2-{[(4-amino-2-methylpyrimidin-5-yl)methyl]amino}propane-1-thiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CS)NCc1cnc(C)nc1N
#
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
 YF3  YF3  (2S)-2-{[(4-amino-2-methylpyrimidin-5-yl)methyl]amino}propane-1-thiol  ligand  30  14  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YF3
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
 YF3  N1'   N  N     0  -0.450   1.4213   0.7820   2.3321
 YF3  C2'   C  CR6   0   0.344   0.7945   0.2232   3.3538
 YF3  CM2   C  CH3   0  -0.728   1.4285   0.3195   4.7068
 YF3  N3'   N  N     0  -0.467  -0.3633  -0.4255   3.2881
 YF3  C4'   C  CR6   0   0.461  -0.9594  -0.5278   2.1021
 YF3  N4'   N  NH2   0  -0.835  -2.1517  -1.1488   2.0651
 YF3  C5'   C  CR6   0  -0.089  -0.3734   0.0228   0.9367
 YF3  C6'   C  CR16  0  -0.087   0.8207   0.6678   1.1398
 YF3  C7'   C  CH2   0  -0.314  -1.0426  -0.0900  -0.4030
 YF3  N3    N  NH1   0  -0.607  -0.1707   0.3210  -1.4825
 YF3  C4    C  CH1   0  -0.039  -0.8105   0.3173  -2.7893
 YF3  CM4   C  CH3   0  -0.661  -1.7622   1.4979  -2.9397
 YF3  C2    C  CH2   0  -0.580   0.2487   0.4078  -3.8809
 YF3  HM21  H  HCH3  0   0.250   0.7475   0.7889   5.4178
 YF3  HM22  H  HCH3  0   0.251   1.6599  -0.6734   5.0951
 YF3  HM23  H  HCH3  0   0.243   2.3473   0.8997   4.6674
 YF3  H4'1  H  HNH2  0   0.396  -2.4606  -1.6497   2.8808
 YF3  H4'2  H  HNH2  0   0.409  -2.5899  -1.3904   1.1941
 YF3  H6'   H  HCR6  0   0.255   1.3306   1.1250   0.2990
 YF3  H7'1  H  HCH2  0   0.254  -1.9361   0.5422  -0.3987
 YF3  H7'2  H  HCH2  0   0.215  -1.4111  -1.1207  -0.5450
 YF3  HN3   H  HNH1  0   0.339   0.6037  -0.3349  -1.5106
 YF3  H4    H  HCH1  0   0.206  -1.3809  -0.6121  -2.9516
 YF3  HM41  H  HCH3  0   0.224  -1.2234   2.4420  -2.8431
 YF3  HM42  H  HCH3  0   0.232  -2.2407   1.4787  -3.9195
 YF3  HM43  H  HCH3  0   0.239  -2.5572   1.4854  -2.1943
 YF3  HS1   H  HSH1  0   0.226   2.3699  -0.4788  -3.1448
 YF3  H21   H  HCH2  0   0.284  -0.2393   0.4194  -4.8553
 YF3  H22   H  HCH2  0   0.279   0.8217   1.3316  -3.7917
 YF3  S1    S  S2    0  -0.250   1.4135  -0.9963  -3.9232

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
 YF3  N1'  C2'   aromatic  1.322  0.020  1.322
 YF3  N1'  C6'   aromatic  1.340  0.020  1.340
 YF3  C2'  CM2   single    1.497  0.020  1.497
 YF3  C2'  N3'   aromatic  1.329  0.020  1.329
 YF3  CM2  HM21  single    0.970  0.020  1.090
 YF3  CM2  HM22  single    0.970  0.020  1.090
 YF3  CM2  HM23  single    0.970  0.020  1.090
 YF3  N3'  C4'   aromatic  1.331  0.020  1.331
 YF3  C4'  N4'   single    1.345  0.020  1.345
 YF3  C4'  C5'   aromatic  1.416  0.020  1.416
 YF3  N4'  H4'1  single    0.890  0.020  1.040
 YF3  N4'  H4'2  single    0.890  0.020  1.040
 YF3  C5'  C6'   aromatic  1.372  0.020  1.372
 YF3  C5'  C7'   single    1.502  0.020  1.502
 YF3  C6'  H6'   single    0.930  0.020  1.080
 YF3  C7'  N3    single    1.447  0.020  1.447
 YF3  C7'  H7'1  single    0.970  0.020  1.090
 YF3  C7'  H7'2  single    0.970  0.020  1.090
 YF3  N3   C4    single    1.455  0.020  1.455
 YF3  N3   HN3   single    0.890  0.020  1.040
 YF3  C4   CM4   single    1.524  0.020  1.524
 YF3  C4   C2    single    1.524  0.020  1.524
 YF3  C4   H4    single    0.970  0.020  1.090
 YF3  CM4  HM41  single    0.970  0.020  1.090
 YF3  CM4  HM42  single    0.970  0.020  1.090
 YF3  CM4  HM43  single    0.970  0.020  1.090
 YF3  S1   C2    single    1.825  0.020  1.825
 YF3  S1   HS1   single    1.200  0.020  1.300
 YF3  C2   H21   single    0.970  0.020  1.090
 YF3  C2   H22   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
 YF3  C6'   N1'  C2'   116.04  3.000
 YF3  N3'   C2'  CM2   116.43  3.000
 YF3  N3'   C2'  N1'   125.52  3.000
 YF3  CM2   C2'  N1'   118.05  3.000
 YF3  HM23  CM2  HM22  108.62  3.000
 YF3  HM23  CM2  HM21  108.76  3.000
 YF3  HM22  CM2  HM21  106.99  3.000
 YF3  HM23  CM2  C2'   111.06  3.000
 YF3  HM22  CM2  C2'   110.66  3.000
 YF3  HM21  CM2  C2'   110.63  3.000
 YF3  C4'   N3'  C2'   118.15  3.000
 YF3  C5'   C4'  N4'   121.59  3.000
 YF3  C5'   C4'  N3'   121.19  3.000
 YF3  N4'   C4'  N3'   117.20  3.000
 YF3  H4'2  N4'  H4'1  116.72  3.000
 YF3  H4'2  N4'  C4'   121.44  3.000
 YF3  H4'1  N4'  C4'   118.68  3.000
 YF3  C7'   C5'  C6'   123.71  3.000
 YF3  C7'   C5'  C4'   121.37  3.000
 YF3  C6'   C5'  C4'   114.91  3.000
 YF3  H6'   C6'  C5'   119.51  3.000
 YF3  H6'   C6'  N1'   116.31  3.000
 YF3  C5'   C6'  N1'   124.17  3.000
 YF3  H7'2  C7'  H7'1  105.51  3.000
 YF3  H7'2  C7'  N3    111.74  3.000
 YF3  H7'1  C7'  N3    109.30  3.000
 YF3  H7'2  C7'  C5'   109.50  3.000
 YF3  H7'1  C7'  C5'   108.48  3.000
 YF3  N3    C7'  C5'   112.06  3.000
 YF3  HN3   N3   C4    107.99  3.000
 YF3  HN3   N3   C7'   107.26  3.000
 YF3  C4    N3   C7'   113.85  3.000
 YF3  H4    C4   C2    107.71  3.000
 YF3  H4    C4   CM4   108.39  3.000
 YF3  C2    C4   CM4   108.51  3.000
 YF3  H4    C4   N3    111.21  3.000
 YF3  C2    C4   N3    109.73  3.000
 YF3  CM4   C4   N3    111.18  3.000
 YF3  HM43  CM4  HM42  107.11  3.000
 YF3  HM43  CM4  HM41  108.03  3.000
 YF3  HM42  CM4  HM41  108.14  3.000
 YF3  HM43  CM4  C4    112.28  3.000
 YF3  HM42  CM4  C4    110.43  3.000
 YF3  HM41  CM4  C4    110.68  3.000
 YF3  H22   C2   H21   107.43  3.000
 YF3  H22   C2   S1    108.56  3.000
 YF3  H21   C2   S1    105.86  3.000
 YF3  H22   C2   C4    110.91  3.000
 YF3  H21   C2   C4    109.26  3.000
 YF3  S1    C2   C4    114.49  3.000
 YF3  HS1   S1   C2     98.35  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
 YF3  CONST_01  C4'   N3'  C2'  N1'     0.00   0.0  0
 YF3  CONST_02  C4'   C5'  C6'  N1'     0.00   0.0  0
 YF3  CONST_03  C5'   C6'  N1'  C2'     0.00   0.0  0
 YF3  CONST_04  C5'   C4'  N3'  C2'     0.00   0.0  0
 YF3  CONST_05  C6'   N1'  C2'  N3'     0.00   0.0  0
 YF3  CONST_06  C6'   C5'  C4'  N3'     0.00   0.0  0
 YF3  CONST_07  C7'   C5'  C6'  N1'   180.00   0.0  0
 YF3  CONST_08  N4'   C4'  N3'  C2'   180.00   0.0  0
 YF3  CONST_09  C6'   N1'  C2'  CM2   180.00   0.0  0
 YF3  CONST_10  C4'   N3'  C2'  CM2   180.00   0.0  0
 YF3  CONST_11  C7'   C5'  C4'  N3'   180.00   0.0  0
 YF3  CONST_12  C6'   C5'  C4'  N4'   180.00   0.0  0
 YF3  CONST_13  H6'   C6'  N1'  C2'   180.00   0.0  0
 YF3  CONST_14  H4'1  N4'  C4'  N3'     0.00   0.0  0
 YF3  CONST_15  H4'2  N4'  C4'  N3'   180.00   0.0  0
 YF3  Var_01    N3    C7'  C5'  C4'  -169.57  30.0  2
 YF3  Var_02    HM21  CM2  C2'  N1'   123.17  30.0  2
 YF3  Var_03    C4    N3   C7'  C5'  -175.89  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 YF3  chir_01  C4  N3  CM4  C2  negativ

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
 YF3  plan-1  N1'   0.020
 YF3  plan-1  C2'   0.020
 YF3  plan-1  CM2   0.020
 YF3  plan-1  N3'   0.020
 YF3  plan-1  C4'   0.020
 YF3  plan-1  N4'   0.020
 YF3  plan-1  C5'   0.020
 YF3  plan-1  C6'   0.020
 YF3  plan-1  C7'   0.020
 YF3  plan-1  H6'   0.020
 YF3  plan-2  C4'   0.020
 YF3  plan-2  N4'   0.020
 YF3  plan-2  H4'1  0.020
 YF3  plan-2  H4'2  0.020

