# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:26:19 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: [(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylselenonium (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se@@+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 EEM  EEM  '[(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylselenonium (non-preferred name)'  ligand  49  27  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EEM
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
 EEM  C2    C   CR16   0   0.049   5.5632  -0.8134   1.6161
 EEM  N3    N   N      0  -0.458   4.7040   0.1070   1.2118
 EEM  C4    C   CR56   0   0.498   3.8363  -0.3849   0.3329
 EEM  C1'   C   CH1    0   0.212   2.4152   1.6262  -0.0817
 EEM  C2'   C   CH1    0  -0.060   2.2024   2.4368  -1.3618
 EEM  C3'   C   CH1    0  -0.008   1.1698   3.4719  -0.8999
 EEM  C4'   C   CH1    0  -0.014   0.3066   2.6214   0.0256
 EEM  C5'   C   CH2    0  -0.659  -0.8178   1.9242  -0.7306
 EEM  C     C   C      0   0.392  -5.9132  -2.5447  -0.0981
 EEM  OXT   O   OC    -1  -0.616  -5.3158  -3.6271  -0.2639
 EEM  CA    C   CH1    0  -0.217  -5.2270  -1.2953  -0.7137
 EEM  N     N   NH2    0  -0.788  -6.0148  -0.0748  -0.7020
 EEM  CG    C   CH2    0  -0.605  -3.1253   0.0706  -0.6345
 EEM  SE    SE  SE     1   0.624  -1.4167   0.3588   0.2697
 EEM  CE    C   CH3   -1  -0.825  -2.0533   1.2416   1.8710
 EEM  O4'   O   O2     0  -0.492   1.1819   1.6560   0.5995
 EEM  O3'   O   OH1    0  -0.662   1.7735   4.4774  -0.1365
 EEM  O2'   O   OH1    0  -0.649   3.4180   2.9727  -1.7818
 EEM  N9    N   NR5    0  -0.544   2.8145   0.2661  -0.3026
 EEM  C8    C   CR15   0   0.113   2.2036  -0.6705  -1.0970
 EEM  N7    N   N      0  -0.442   2.7542  -1.8430  -1.0287
 EEM  C5    C   CR56   0  -0.010   3.7851  -1.6860  -0.1371
 EEM  N1    N   N      0  -0.473   5.6380  -2.0904   1.2531
 EEM  C6    C   CR6    0   0.464   4.7566  -2.5704   0.3678
 EEM  N6    N   NH2    0  -0.815   4.8258  -3.8504   0.0050
 EEM  H2    H   HCR6   0   0.254   6.3057  -0.4894   2.3377
 EEM  H1'   H   HCH1   0   0.278   3.2002   2.0822   0.5283
 EEM  H2'   H   HCH1   0   0.256   1.7500   1.8098  -2.1398
 EEM  H3'   H   HCH1   0   0.268   0.5910   3.8785  -1.7390
 EEM  H4'   H   HCH1   0   0.298  -0.1186   3.2295   0.8279
 EEM  H5'   H   HCH2   0   0.341  -1.6682   2.5923  -0.8777
 EEM  H5'A  H   HCH2   0   0.320  -0.5070   1.5427  -1.7069
 EEM  HA    H   HCH1   0   0.229  -4.9904  -1.5302  -1.7574
 EEM  HN    H   HNH2   0   0.343  -6.7422  -0.1474  -1.4020
 EEM  HNA   H   HNH2   0   0.329  -6.5114  -0.0346   0.1814
 EEM  HB    H   HCH2   0   0.241  -4.1037  -0.8373   1.0660
 EEM  HBA   H   HCH2   0   0.259  -3.3145  -1.9871  -0.0104
 EEM  HG    H   HCH2   0   0.311  -2.8618  -0.1667  -1.6682
 EEM  HGA   H   HCH2   0   0.312  -3.6824   1.0075  -0.6169
 EEM  HE    H   HCH3   0   0.311  -2.6882   2.0832   1.6017
 EEM  HEA   H   HCH3   0   0.319  -2.6115   0.5127   2.4556
 EEM  HEB   H   HCH3   0   0.316  -1.1928   1.5745   2.4486
 EEM  HO3'  H   HOH1   0   0.455   2.5668   4.7697  -0.6017
 EEM  HO2'  H   HOH1   0   0.474   3.3564   3.1963  -2.7160
 EEM  H8    H   HCR5   0   0.291   1.3512  -0.4292  -1.7150
 EEM  HN6   H   HNH2   0   0.413   4.1970  -4.2330  -0.6790
 EEM  HN6A  H   HNH2   0   0.405   5.5469  -4.4449   0.3755
 EEM  CB    C   CH2    0  -0.440  -3.8962  -1.0650   0.0152
 EEM  O     O   O      0  -0.598  -6.9780  -2.3646   0.5219

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
 EEM  N1   C2    aromatic  1.330  0.020  1.330
 EEM  C2   N3    aromatic  1.322  0.020  1.322
 EEM  C2   H2    single    0.930  0.020  1.080
 EEM  C4   N3    aromatic  1.329  0.020  1.329
 EEM  C5   C4    aromatic  1.384  0.020  1.384
 EEM  N9   C4    aromatic  1.368  0.020  1.368
 EEM  N9   C1'   single    1.435  0.020  1.435
 EEM  C1'  O4'   single    1.409  0.020  1.409
 EEM  C1'  C2'   single    1.530  0.020  1.530
 EEM  C1'  H1'   single    0.970  0.020  1.090
 EEM  O2'  C2'   single    1.393  0.020  1.393
 EEM  C2'  C3'   single    1.533  0.020  1.533
 EEM  C2'  H2'   single    0.970  0.020  1.090
 EEM  C4'  C3'   single    1.525  0.020  1.525
 EEM  O3'  C3'   single    1.399  0.020  1.399
 EEM  C3'  H3'   single    0.970  0.020  1.090
 EEM  O4'  C4'   single    1.424  0.020  1.424
 EEM  C4'  C5'   single    1.524  0.020  1.524
 EEM  C4'  H4'   single    0.970  0.020  1.090
 EEM  C5'  H5'   single    0.970  0.020  1.090
 EEM  C5'  H5'A  single    0.970  0.020  1.090
 EEM  C5'  SE    single    1.952  0.020  1.952
 EEM  C    O     deloc     1.245  0.020  1.245
 EEM  CA   C     single    1.553  0.020  1.553
 EEM  C    OXT   deloc     1.247  0.020  1.247
 EEM  CB   CA    single    1.535  0.020  1.535
 EEM  N    CA    single    1.453  0.020  1.453
 EEM  CA   HA    single    0.970  0.020  1.090
 EEM  N    HN    single    0.890  0.020  1.040
 EEM  N    HNA   single    0.890  0.020  1.040
 EEM  CB   CG    single    1.519  0.020  1.519
 EEM  CB   HB    single    0.970  0.020  1.090
 EEM  CB   HBA   single    0.970  0.020  1.090
 EEM  SE   CG    single    1.954  0.020  1.954
 EEM  CG   HG    single    0.970  0.020  1.090
 EEM  CG   HGA   single    0.970  0.020  1.090
 EEM  SE   CE    single    1.936  0.020  1.936
 EEM  CE   HE    single    0.970  0.020  1.090
 EEM  CE   HEA   single    0.970  0.020  1.090
 EEM  CE   HEB   single    0.970  0.020  1.090
 EEM  O3'  HO3'  single    0.850  0.020  0.980
 EEM  O2'  HO2'  single    0.850  0.020  0.980
 EEM  C8   N9    aromatic  1.372  0.020  1.372
 EEM  N7   C8    aromatic  1.297  0.020  1.297
 EEM  C8   H8    single    0.930  0.020  1.080
 EEM  N7   C5    aromatic  1.372  0.020  1.372
 EEM  C6   C5    aromatic  1.407  0.020  1.407
 EEM  C6   N1    aromatic  1.338  0.020  1.338
 EEM  N6   C6    single    1.332  0.020  1.332
 EEM  N6   HN6   single    0.860  0.020  1.020
 EEM  N6   HN6A  single    0.860  0.020  1.020

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
 EEM  H2    C2   N1   115.46  3.000
 EEM  H2    C2   N3   116.12  3.000
 EEM  N1    C2   N3   128.42  3.000
 EEM  C4    N3   C2   111.64  3.000
 EEM  C5    C4   N9   105.18  3.000
 EEM  N9    C4   N3   128.21  3.000
 EEM  C5    C4   N3   126.61  3.000
 EEM  H1'   C1'  N9   106.34  3.000
 EEM  H1'   C1'  O4'  110.47  3.000
 EEM  N9    C1'  O4'  109.76  3.000
 EEM  H1'   C1'  C2'  110.21  3.000
 EEM  O4'   C1'  C2'  105.75  3.000
 EEM  N9    C1'  C2'  114.34  3.000
 EEM  H2'   C2'  O2'  111.46  3.000
 EEM  H2'   C2'  C3'  108.77  3.000
 EEM  O2'   C2'  C3'  114.75  3.000
 EEM  H2'   C2'  C1'  110.36  3.000
 EEM  C3'   C2'  C1'  101.50  3.000
 EEM  O2'   C2'  C1'  109.55  3.000
 EEM  H3'   C3'  O3'  112.24  3.000
 EEM  H3'   C3'  C4'  111.85  3.000
 EEM  O3'   C3'  C4'  108.29  3.000
 EEM  H3'   C3'  C2'  112.02  3.000
 EEM  O3'   C3'  C2'  111.03  3.000
 EEM  C4'   C3'  C2'  100.81  3.000
 EEM  H4'   C4'  O4'  108.70  3.000
 EEM  H4'   C4'  C5'  109.38  3.000
 EEM  O4'   C4'  C5'  110.09  3.000
 EEM  H4'   C4'  C3'  110.82  3.000
 EEM  C5'   C4'  C3'  111.82  3.000
 EEM  O4'   C4'  C3'  105.95  3.000
 EEM  H5'A  C5'  H5'  108.35  3.000
 EEM  H5'A  C5'  SE   105.37  3.000
 EEM  H5'   C5'  SE   108.72  3.000
 EEM  SE    C5'  C4'  109.82  3.000
 EEM  H5'A  C5'  C4'  113.15  3.000
 EEM  H5'   C5'  C4'  111.21  3.000
 EEM  CA    C    OXT  115.71  3.000
 EEM  OXT   C    O    126.96  3.000
 EEM  CA    C    O    117.32  3.000
 EEM  HA    CA   CB   107.30  3.000
 EEM  HA    CA   N    107.75  3.000
 EEM  CB    CA   N    109.90  3.000
 EEM  HA    CA   C    107.49  3.000
 EEM  N     CA   C    115.67  3.000
 EEM  CB    CA   C    108.40  3.000
 EEM  HNA   N    HN   104.68  3.000
 EEM  HNA   N    CA   107.81  3.000
 EEM  HN    N    CA   108.90  3.000
 EEM  HGA   CG   HG   108.97  3.000
 EEM  HGA   CG   SE   108.21  3.000
 EEM  HG    CG   SE   105.00  3.000
 EEM  HGA   CG   CB   112.11  3.000
 EEM  HG    CG   CB   111.39  3.000
 EEM  SE    CG   CB   110.86  3.000
 EEM  CE    SE   CG    99.35  3.000
 EEM  CE    SE   C5'   99.15  3.000
 EEM  CG    SE   C5'   98.59  3.000
 EEM  HEB   CE   HEA  108.98  3.000
 EEM  HEB   CE   HE   110.86  3.000
 EEM  HEA   CE   HE   110.59  3.000
 EEM  HEB   CE   SE   108.56  3.000
 EEM  HEA   CE   SE   107.90  3.000
 EEM  HE    CE   SE   109.87  3.000
 EEM  C4'   O4'  C1'  110.95  3.000
 EEM  HO3'  O3'  C3'  108.02  3.000
 EEM  HO2'  O2'  C2'  109.03  3.000
 EEM  C8    N9   C1'  127.77  3.000
 EEM  C8    N9   C4   106.07  3.000
 EEM  C1'   N9   C4   125.98  3.000
 EEM  H8    C8   N7   124.55  3.000
 EEM  H8    C8   N9   122.03  3.000
 EEM  N7    C8   N9   113.43  3.000
 EEM  C5    N7   C8   104.46  3.000
 EEM  C6    C5   N7   132.83  3.000
 EEM  C6    C5   C4   116.31  3.000
 EEM  N7    C5   C4   110.85  3.000
 EEM  C6    N1   C2   119.21  3.000
 EEM  N6    C6   N1   119.38  3.000
 EEM  N6    C6   C5   122.81  3.000
 EEM  N1    C6   C5   117.81  3.000
 EEM  HN6A  N6   HN6  118.33  3.000
 EEM  HN6A  N6   C6   120.33  3.000
 EEM  HN6   N6   C6   121.25  3.000
 EEM  HBA   CB   HB   107.42  3.000
 EEM  HBA   CB   CG   110.58  3.000
 EEM  HB    CB   CG   110.56  3.000
 EEM  HBA   CB   CA   108.94  3.000
 EEM  HB    CB   CA   108.82  3.000
 EEM  CG    CB   CA   110.44  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
 EEM  CONST_01  C5    C6  N1  C2      0.00   0.0  0
 EEM  CONST_02  C5    C4  N3  C2      0.00   0.0  0
 EEM  CONST_03  N9    C4  N3  C2    180.00   0.0  0
 EEM  CONST_04  C6    N1  C2  N3      0.00   0.0  0
 EEM  CONST_05  N7    C5  C4  N3    180.00   0.0  0
 EEM  CONST_06  C6    C5  C4  N3      0.00   0.0  0
 EEM  CONST_07  C8    N9  C4  N3    180.00   0.0  0
 EEM  CONST_08  N1    C2  N3  C4      0.00   0.0  0
 EEM  CONST_09  C8    N7  C5  C4      0.00   0.0  0
 EEM  CONST_10  N1    C6  C5  C4      0.00   0.0  0
 EEM  CONST_11  N7    C8  N9  C4      0.00   0.0  0
 EEM  CONST_12  N7    C5  C4  N9      0.00   0.0  0
 EEM  CONST_13  C6    C5  C4  N9    180.00   0.0  0
 EEM  CONST_14  C5    N7  C8  N9      0.00   0.0  0
 EEM  CONST_15  C5    C4  N9  C8      0.00   0.0  0
 EEM  CONST_16  C6    C5  N7  C8    180.00   0.0  0
 EEM  CONST_17  N1    C6  C5  N7    180.00   0.0  0
 EEM  CONST_18  C1'   N9  C4  N3      0.00   0.0  0
 EEM  CONST_19  C5    C4  N9  C1'   180.00   0.0  0
 EEM  CONST_20  N7    C8  N9  C1'   180.00   0.0  0
 EEM  CONST_21  N6    C6  N1  C2    180.00   0.0  0
 EEM  CONST_22  N6    C6  C5  C4    180.00   0.0  0
 EEM  CONST_23  N6    C6  C5  N7      0.00   0.0  0
 EEM  CONST_24  H2    C2  N3  C4    180.00   0.0  0
 EEM  CONST_25  H8    C8  N9  C4    180.00   0.0  0
 EEM  CONST_26  HN6   N6  C6  C5      0.00   0.0  0
 EEM  CONST_27  HN6A  N6  C6  C5    180.00   0.0  0
 EEM  Var_01    SE    CG  CB  CA   -179.24  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
 EEM  chir_01  C1'  N9   O4'  C2'  positiv
 EEM  chir_02  C2'  O2'  C1'  C3'  negativ
 EEM  chir_03  C3'  O3'  C4'  C2'  positiv
 EEM  chir_04  C4'  O4'  C3'  C5'  negativ
 EEM  chir_05  CA   N    C    CB   positiv
 EEM  chir_06  SE   CE   CG   C5'  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
 EEM  plan-1  C2    0.020
 EEM  plan-1  N3    0.020
 EEM  plan-1  C4    0.020
 EEM  plan-1  C1'   0.020
 EEM  plan-1  N9    0.020
 EEM  plan-1  C8    0.020
 EEM  plan-1  N7    0.020
 EEM  plan-1  C5    0.020
 EEM  plan-1  N1    0.020
 EEM  plan-1  C6    0.020
 EEM  plan-1  N6    0.020
 EEM  plan-1  H2    0.020
 EEM  plan-1  H8    0.020
 EEM  plan-2  C6    0.020
 EEM  plan-2  N6    0.020
 EEM  plan-2  HN6   0.020
 EEM  plan-2  HN6A  0.020
 EEM  plan-3  C     0.020
 EEM  plan-3  OXT   0.020
 EEM  plan-3  CA    0.020
 EEM  plan-3  O     0.020

