# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:46:07 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-[(2-hydroxyethoxy)methyl]-5-methyl-6-(phenylsulfanyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(Sc2ccccc2)N(COCCO)C(=O)NC1=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
 HEF  HEF  1-[(2-hydroxyethoxy)methyl]-5-methyl-6-(phenylsulfanyl)pyrimidine-2,4(1H,3H)-dione  ligand  37  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HEF
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
 HEF  N1    N  NR6   0  -0.569   0.1575  -0.8140  -0.6265
 HEF  C2    C  CR6   0   0.715   0.8978  -1.6727  -1.4175
 HEF  O2    O  O     0  -0.473   0.4698  -2.7222  -1.8504
 HEF  N3    N  NR16  0  -0.719   2.1664  -1.2499  -1.7014
 HEF  C4    C  CR6   0   0.571   2.7740  -0.0813  -1.3042
 HEF  O4    O  O     0  -0.443   3.8990   0.1867  -1.6783
 HEF  C5    C  CR6   0  -0.129   1.9786   0.7489  -0.4056
 HEF  C6    C  CR6   0   0.160   0.7162   0.3543  -0.1249
 HEF  CM5   C  CH3   0  -0.710   2.6262   1.9852   0.1360
 HEF  CM    C  CH2   0  -0.066  -1.2842  -1.0747  -0.5180
 HEF  OM    O  O2    0  -0.460  -2.0414  -0.1955  -1.2690
 HEF  CE1   C  CH2   0  -0.182  -1.9572  -0.3789  -2.6698
 HEF  CE2   C  CH2   0  -0.181  -3.0181   0.4488  -3.3476
 HEF  OE    O  OH1   0  -0.668  -2.7562   1.8164  -3.1364
 HEF  S'    S  S2    0   0.131  -0.2922   1.3903   0.8905
 HEF  C1'   C  CR6   0  -0.165  -0.5131   0.3781   2.3308
 HEF  C2'   C  CR16  0  -0.240  -1.7218   0.4937   3.0112
 HEF  C3'   C  CR16  0  -0.244  -1.9237  -0.2280   4.1792
 HEF  C4'   C  CR16  0  -0.255  -0.9341  -1.0768   4.6569
 HEF  C5'   C  CR16  0  -0.244   0.2663  -1.1922   3.9680
 HEF  C6'   C  CR16  0  -0.213   0.4891  -0.4566   2.8129
 HEF  HN3   H  HNR6  0   0.430   2.7042  -1.8632  -2.3021
 HEF  HM51  H  HCH3  0   0.257   3.7084   1.8767   0.1404
 HEF  HM52  H  HCH3  0   0.258   2.3906   2.8564  -0.4783
 HEF  HM53  H  HCH3  0   0.256   2.2975   2.1993   1.1498
 HEF  HM1   H  HCH2  0   0.270  -1.4329  -2.1129  -0.8159
 HEF  HM2   H  HCH2  0   0.275  -1.5916  -0.9746   0.5197
 HEF  HE11  H  HCH2  0   0.216  -0.9686  -0.0890  -3.0481
 HEF  HE12  H  HCH2  0   0.220  -2.1164  -1.4312  -2.9343
 HEF  HE21  H  HCH2  0   0.205  -2.9988   0.1872  -4.4130
 HEF  HE22  H  HCH2  0   0.203  -4.0049   0.1563  -2.9660
 HEF  HOE   H  HOH1  0   0.456  -3.4357   2.3220  -3.5908
 HEF  H2'   H  HCR6  0   0.274  -2.5063   1.1351   2.6293
 HEF  H3'   H  HCR6  0   0.267  -2.8643  -0.1363   4.7060
 HEF  H4'   H  HCR6  0   0.264  -1.0980  -1.6466   5.5611
 HEF  H5'   H  HCR6  0   0.267   1.0430  -1.8491   4.3367
 HEF  H6'   H  HCR6  0   0.269   1.4380  -0.5381   2.2975

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
 HEF  N1   C2    single    1.382  0.020  1.382
 HEF  N1   C6    single    1.389  0.020  1.389
 HEF  N1   CM    single    1.469  0.020  1.469
 HEF  C2   O2    double    1.213  0.020  1.213
 HEF  C2   N3    single    1.367  0.020  1.367
 HEF  N3   C4    single    1.376  0.020  1.376
 HEF  N3   HN3   single    0.860  0.020  1.020
 HEF  C4   O4    double    1.216  0.020  1.216
 HEF  C4   C5    single    1.459  0.020  1.459
 HEF  C5   C6    double    1.352  0.020  1.352
 HEF  C5   CM5   single    1.497  0.020  1.497
 HEF  C6   S'    single    1.767  0.020  1.767
 HEF  CM5  HM51  single    0.970  0.020  1.090
 HEF  CM5  HM52  single    0.970  0.020  1.090
 HEF  CM5  HM53  single    0.970  0.020  1.090
 HEF  CM   OM    single    1.382  0.020  1.382
 HEF  CM   HM1   single    0.970  0.020  1.090
 HEF  CM   HM2   single    0.970  0.020  1.090
 HEF  OM   CE1   single    1.415  0.020  1.415
 HEF  CE1  CE2   single    1.507  0.020  1.507
 HEF  CE1  HE11  single    0.970  0.020  1.090
 HEF  CE1  HE12  single    0.970  0.020  1.090
 HEF  CE2  OE    single    1.408  0.020  1.408
 HEF  CE2  HE21  single    0.970  0.020  1.090
 HEF  CE2  HE22  single    0.970  0.020  1.090
 HEF  OE   HOE   single    0.850  0.020  0.980
 HEF  S'   C1'   single    1.774  0.020  1.774
 HEF  C1'  C2'   aromatic  1.392  0.020  1.392
 HEF  C1'  C6'   aromatic  1.390  0.020  1.390
 HEF  C2'  C3'   aromatic  1.388  0.020  1.388
 HEF  C2'  H2'   single    0.930  0.020  1.080
 HEF  C3'  C4'   aromatic  1.388  0.020  1.388
 HEF  C3'  H3'   single    0.930  0.020  1.080
 HEF  C4'  C5'   aromatic  1.389  0.020  1.389
 HEF  C4'  H4'   single    0.930  0.020  1.080
 HEF  C5'  C6'   aromatic  1.388  0.020  1.388
 HEF  C5'  H5'   single    0.930  0.020  1.080
 HEF  C6'  H6'   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
 HEF  CM    N1   C6    121.16  3.000
 HEF  CM    N1   C2    117.23  3.000
 HEF  C6    N1   C2    120.92  3.000
 HEF  N3    C2   O2    121.39  3.000
 HEF  N3    C2   N1    115.07  3.000
 HEF  O2    C2   N1    123.54  3.000
 HEF  HN3   N3   C4    116.81  3.000
 HEF  HN3   N3   C2    115.38  3.000
 HEF  C4    N3   C2    127.77  3.000
 HEF  C5    C4   O4    124.65  3.000
 HEF  C5    C4   N3    114.86  3.000
 HEF  O4    C4   N3    120.47  3.000
 HEF  CM5   C5   C6    124.74  3.000
 HEF  CM5   C5   C4    117.19  3.000
 HEF  C6    C5   C4    118.08  3.000
 HEF  S'    C6   C5    118.76  3.000
 HEF  S'    C6   N1    118.12  3.000
 HEF  C5    C6   N1    123.10  3.000
 HEF  HM53  CM5  HM52  107.60  3.000
 HEF  HM53  CM5  HM51  108.47  3.000
 HEF  HM52  CM5  HM51  107.25  3.000
 HEF  HM53  CM5  C5    111.67  3.000
 HEF  HM52  CM5  C5    111.23  3.000
 HEF  HM51  CM5  C5    110.46  3.000
 HEF  HM2   CM   HM1   108.06  3.000
 HEF  HM2   CM   OM    107.78  3.000
 HEF  HM1   CM   OM    112.49  3.000
 HEF  HM2   CM   N1    109.37  3.000
 HEF  HM1   CM   N1    106.42  3.000
 HEF  OM    CM   N1    112.62  3.000
 HEF  CE1   OM   CM    115.01  3.000
 HEF  HE12  CE1  HE11  107.52  3.000
 HEF  HE12  CE1  CE2   108.45  3.000
 HEF  HE11  CE1  CE2   109.52  3.000
 HEF  HE12  CE1  OM    110.76  3.000
 HEF  HE11  CE1  OM    111.13  3.000
 HEF  CE2   CE1  OM    109.40  3.000
 HEF  HE22  CE2  HE21  106.85  3.000
 HEF  HE22  CE2  OE    111.95  3.000
 HEF  HE21  CE2  OE    111.96  3.000
 HEF  HE22  CE2  CE1   109.28  3.000
 HEF  HE21  CE2  CE1   107.07  3.000
 HEF  OE    CE2  CE1   109.58  3.000
 HEF  HOE   OE   CE2   107.96  3.000
 HEF  C1'   S'   C6    101.72  3.000
 HEF  C6'   C1'  C2'   120.42  3.000
 HEF  C6'   C1'  S'    122.29  3.000
 HEF  C2'   C1'  S'    117.23  3.000
 HEF  H2'   C2'  C3'   119.97  3.000
 HEF  H2'   C2'  C1'   120.39  3.000
 HEF  C3'   C2'  C1'   119.64  3.000
 HEF  H3'   C3'  C4'   120.26  3.000
 HEF  H3'   C3'  C2'   119.48  3.000
 HEF  C4'   C3'  C2'   120.25  3.000
 HEF  H4'   C4'  C5'   120.13  3.000
 HEF  H4'   C4'  C3'   120.12  3.000
 HEF  C5'   C4'  C3'   119.75  3.000
 HEF  H5'   C5'  C6'   119.36  3.000
 HEF  H5'   C5'  C4'   120.13  3.000
 HEF  C6'   C5'  C4'   120.51  3.000
 HEF  H6'   C6'  C5'   119.80  3.000
 HEF  H6'   C6'  C1'   120.78  3.000
 HEF  C5'   C6'  C1'   119.41  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
 HEF  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 HEF  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 HEF  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 HEF  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 HEF  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 HEF  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 HEF  CONST_07  C4    N3   C2   N1      0.00   0.0  0
 HEF  CONST_08  C5    C4   N3   C2      0.00   0.0  0
 HEF  CONST_09  C6    N1   C2   N3      0.00   0.0  0
 HEF  CONST_10  C3'   C2'  C1'  S'    180.00   0.0  0
 HEF  CONST_11  C5'   C6'  C1'  S'    180.00   0.0  0
 HEF  CONST_12  O4    C4   N3   C2    180.00   0.0  0
 HEF  CONST_13  C6    N1   C2   O2    180.00   0.0  0
 HEF  CONST_14  C4    N3   C2   O2    180.00   0.0  0
 HEF  CONST_15  CM    N1   C2   N3    180.00   0.0  0
 HEF  CONST_16  H3'   C3'  C2'  C1'   180.00   0.0  0
 HEF  CONST_17  H5'   C5'  C6'  C1'   180.00   0.0  0
 HEF  CONST_18  H6'   C6'  C1'  C2'   180.00   0.0  0
 HEF  CONST_19  H4'   C4'  C3'  C2'   180.00   0.0  0
 HEF  CONST_20  H2'   C2'  C3'  C4'   180.00   0.0  0
 HEF  CONST_21  HN3   N3   C2   N1    180.00   0.0  0
 HEF  CONST_22  CM    N1   C2   O2      0.00   0.0  0
 HEF  Var_01    C2'   C1'  S'   C6   -147.27  30.0  2
 HEF  Var_02    OM    CM   N1   C2   -104.22  30.0  3
 HEF  Var_03    HM51  CM5  C5   C4    -24.85  30.0  3
 HEF  Var_04    CE2   CE1  OM   CM    169.05  30.0  3
 HEF  Var_05    OE    CE2  CE1  OM     65.07  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
 HEF  plan-1  N1   0.020
 HEF  plan-1  C2   0.020
 HEF  plan-1  O2   0.020
 HEF  plan-1  N3   0.020
 HEF  plan-1  C4   0.020
 HEF  plan-1  O4   0.020
 HEF  plan-1  C5   0.020
 HEF  plan-1  C6   0.020
 HEF  plan-1  CM5  0.020
 HEF  plan-1  CM   0.020
 HEF  plan-1  S'   0.020
 HEF  plan-1  HN3  0.020
 HEF  plan-2  S'   0.020
 HEF  plan-2  C1'  0.020
 HEF  plan-2  C2'  0.020
 HEF  plan-2  C3'  0.020
 HEF  plan-2  C4'  0.020
 HEF  plan-2  C5'  0.020
 HEF  plan-2  C6'  0.020
 HEF  plan-2  H2'  0.020
 HEF  plan-2  H3'  0.020
 HEF  plan-2  H4'  0.020
 HEF  plan-2  H5'  0.020
 HEF  plan-2  H6'  0.020

