# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 04:12:16 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 5-{[ethyl(methyl)amino]methyl}-2-methylpyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(C)Cc1cnc(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
 YF4  YF4  5-{[ethyl(methyl)amino]methyl}-2-methylpyrimidin-4-amine  ligand  29  13  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YF4
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
 YF4  N1'   N  N     0  -0.449   1.5371   0.3565  -1.7234
 YF4  C2'   C  CR6   0   0.345   0.6705   0.1554  -2.7048
 YF4  CM2   C  CH3   0  -0.728   1.2032   0.1158  -4.1039
 YF4  N3'   N  N     0  -0.467  -0.6320  -0.0417  -2.5523
 YF4  C4'   C  CR6   0   0.452  -1.1304  -0.0437  -1.3150
 YF4  N4'   N  NH2   0  -0.833  -2.4652  -0.1881  -1.1999
 YF4  C5'   C  CR6   0  -0.091  -0.2942   0.1404  -0.1909
 YF4  C6'   C  CR16  0  -0.071   1.0327   0.3432  -0.4851
 YF4  C7'   C  CH2   0  -0.309  -0.8331   0.1722   1.2139
 YF4  CM4   C  CH3   0  -0.685   0.8918   0.4354   4.5471
 YF4  C4    C  CH2   0  -0.270  -0.2217   0.4541   3.5141
 YF4  N3    N  NT    0  -0.410   0.1885  -0.0570   2.2146
 YF4  C2    C  CH3   0  -0.536   0.5486  -1.4604   2.2711
 YF4  HM21  H  HCH3  0   0.255   1.4568  -0.9106  -4.3792
 YF4  HM22  H  HCH3  0   0.245   0.4620   0.4704  -4.8176
 YF4  HM23  H  HCH3  0   0.244   2.1081   0.7132  -4.1952
 YF4  H4'1  H  HNH2  0   0.395  -2.9812  -0.4700  -2.0164
 YF4  H4'2  H  HNH2  0   0.404  -2.8899  -0.3999  -0.3142
 YF4  H6'   H  HCR6  0   0.257   1.7355   0.5036   0.3251
 YF4  H7'1  H  HCH2  0   0.203  -1.6586  -0.5546   1.3192
 YF4  H7'2  H  HCH2  0   0.262  -1.2805   1.1553   1.3931
 YF4  HM41  H  HCH3  0   0.235   0.5676   0.9588   5.4468
 YF4  HM42  H  HCH3  0   0.228   1.1737  -0.5738   4.8460
 YF4  HM43  H  HCH3  0   0.224   1.7819   0.9391   4.1678
 YF4  H41   H  HCH2  0   0.189  -1.0936  -0.0971   3.9048
 YF4  H42   H  HCH2  0   0.231  -0.5478   1.4875   3.3749
 YF4  H21   H  HCH3  0   0.240   0.8342  -1.8202   1.2830
 YF4  H22   H  HCH3  0   0.242   1.4013  -1.6165   2.9304
 YF4  H23   H  HCH3  0   0.198  -0.2781  -2.0924   2.6320

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
 YF4  N1'  C2'   aromatic  1.325  0.020  1.325
 YF4  N1'  C6'   aromatic  1.337  0.020  1.337
 YF4  C2'  CM2   single    1.498  0.020  1.498
 YF4  C2'  N3'   aromatic  1.326  0.020  1.326
 YF4  CM2  HM21  single    0.970  0.020  1.090
 YF4  CM2  HM22  single    0.970  0.020  1.090
 YF4  CM2  HM23  single    0.970  0.020  1.090
 YF4  N3'  C4'   aromatic  1.334  0.020  1.334
 YF4  C4'  N4'   single    1.347  0.020  1.347
 YF4  C4'  C5'   aromatic  1.413  0.020  1.413
 YF4  N4'  H4'1  single    0.890  0.020  1.040
 YF4  N4'  H4'2  single    0.890  0.020  1.040
 YF4  C5'  C6'   aromatic  1.374  0.020  1.374
 YF4  C5'  C7'   single    1.505  0.020  1.505
 YF4  C6'  H6'   single    0.930  0.020  1.080
 YF4  C7'  N3    single    1.448  0.020  1.448
 YF4  C7'  H7'1  single    0.970  0.020  1.090
 YF4  C7'  H7'2  single    0.970  0.020  1.090
 YF4  CM4  C4    single    1.519  0.020  1.519
 YF4  CM4  HM41  single    0.970  0.020  1.090
 YF4  CM4  HM42  single    0.970  0.020  1.090
 YF4  CM4  HM43  single    0.970  0.020  1.090
 YF4  C4   N3    single    1.455  0.020  1.455
 YF4  C4   H41   single    0.970  0.020  1.090
 YF4  C4   H42   single    0.970  0.020  1.090
 YF4  N3   C2    single    1.450  0.020  1.450
 YF4  C2   H21   single    0.970  0.020  1.090
 YF4  C2   H22   single    0.970  0.020  1.090
 YF4  C2   H23   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
 YF4  C6'   N1'  C2'   115.97  3.000
 YF4  N3'   C2'  CM2   116.93  3.000
 YF4  N3'   C2'  N1'   125.44  3.000
 YF4  CM2   C2'  N1'   117.62  3.000
 YF4  HM23  CM2  HM22  109.42  3.000
 YF4  HM23  CM2  HM21  107.55  3.000
 YF4  HM22  CM2  HM21  107.40  3.000
 YF4  HM23  CM2  C2'   111.08  3.000
 YF4  HM22  CM2  C2'   111.21  3.000
 YF4  HM21  CM2  C2'   110.05  3.000
 YF4  C4'   N3'  C2'   118.29  3.000
 YF4  C5'   C4'  N4'   122.15  3.000
 YF4  C5'   C4'  N3'   121.10  3.000
 YF4  N4'   C4'  N3'   116.71  3.000
 YF4  H4'2  N4'  H4'1  116.07  3.000
 YF4  H4'2  N4'  C4'   121.10  3.000
 YF4  H4'1  N4'  C4'   117.95  3.000
 YF4  C7'   C5'  C6'   122.86  3.000
 YF4  C7'   C5'  C4'   122.24  3.000
 YF4  C6'   C5'  C4'   114.85  3.000
 YF4  H6'   C6'  C5'   119.18  3.000
 YF4  H6'   C6'  N1'   116.49  3.000
 YF4  C5'   C6'  N1'   124.33  3.000
 YF4  H7'2  C7'  H7'1  105.64  3.000
 YF4  H7'2  C7'  N3    108.50  3.000
 YF4  H7'1  C7'  N3    110.92  3.000
 YF4  H7'2  C7'  C5'   108.55  3.000
 YF4  H7'1  C7'  C5'   110.04  3.000
 YF4  N3    C7'  C5'   112.90  3.000
 YF4  HM43  CM4  HM42  108.18  3.000
 YF4  HM43  CM4  HM41  107.93  3.000
 YF4  HM42  CM4  HM41  107.17  3.000
 YF4  HM43  CM4  C4    110.85  3.000
 YF4  HM42  CM4  C4    112.81  3.000
 YF4  HM41  CM4  C4    109.71  3.000
 YF4  H42   C4   H41   106.37  3.000
 YF4  H42   C4   N3    107.61  3.000
 YF4  H41   C4   N3    111.32  3.000
 YF4  H42   C4   CM4   108.49  3.000
 YF4  H41   C4   CM4   109.41  3.000
 YF4  N3    C4   CM4   113.35  3.000
 YF4  C2    N3   C4    112.03  3.000
 YF4  C2    N3   C7'   110.81  3.000
 YF4  C4    N3   C7'   111.26  3.000
 YF4  H23   C2   H22   107.88  3.000
 YF4  H23   C2   H21   107.72  3.000
 YF4  H22   C2   H21   107.24  3.000
 YF4  H23   C2   N3    112.44  3.000
 YF4  H22   C2   N3    110.90  3.000
 YF4  H21   C2   N3    110.45  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
 YF4  CONST_01  C4'   N3'  C2'  N1'     0.00   0.0  0
 YF4  CONST_02  C4'   C5'  C6'  N1'     0.00   0.0  0
 YF4  CONST_03  C5'   C6'  N1'  C2'     0.00   0.0  0
 YF4  CONST_04  C5'   C4'  N3'  C2'     0.00   0.0  0
 YF4  CONST_05  C6'   N1'  C2'  N3'     0.00   0.0  0
 YF4  CONST_06  C6'   C5'  C4'  N3'     0.00   0.0  0
 YF4  CONST_07  C7'   C5'  C6'  N1'   180.00   0.0  0
 YF4  CONST_08  N4'   C4'  N3'  C2'   180.00   0.0  0
 YF4  CONST_09  C6'   N1'  C2'  CM2   180.00   0.0  0
 YF4  CONST_10  C4'   N3'  C2'  CM2   180.00   0.0  0
 YF4  CONST_11  C7'   C5'  C4'  N3'   180.00   0.0  0
 YF4  CONST_12  C6'   C5'  C4'  N4'   180.00   0.0  0
 YF4  CONST_13  H6'   C6'  N1'  C2'   180.00   0.0  0
 YF4  CONST_14  H4'1  N4'  C4'  N3'     0.00   0.0  0
 YF4  CONST_15  H4'2  N4'  C4'  N3'   180.00   0.0  0
 YF4  Var_01    N3    C7'  C5'  C4'   161.50  30.0  2
 YF4  Var_02    HM21  CM2  C2'  N1'    91.28  30.0  2
 YF4  Var_03    C4    N3   C7'  C5'   158.85  30.0  3
 YF4  Var_04    CM4   C4   N3   C7'  -171.05  30.0  2
 YF4  Var_05    H21   C2   N3   C7'    54.10  30.0  3
 YF4  Var_06    HM41  CM4  C4   N3    171.86  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
 YF4  plan-1  N1'   0.020
 YF4  plan-1  C2'   0.020
 YF4  plan-1  CM2   0.020
 YF4  plan-1  N3'   0.020
 YF4  plan-1  C4'   0.020
 YF4  plan-1  N4'   0.020
 YF4  plan-1  C5'   0.020
 YF4  plan-1  C6'   0.020
 YF4  plan-1  C7'   0.020
 YF4  plan-1  H6'   0.020
 YF4  plan-2  C4'   0.020
 YF4  plan-2  N4'   0.020
 YF4  plan-2  H4'1  0.020
 YF4  plan-2  H4'2  0.020

