# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 05:15:41 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 5'-deoxy-5'-(dimethylamino)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)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
 EP4  EP4  5'-deoxy-5'-(dimethylamino)adenosine  ligand  39  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EP4
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
 EP4  CG   C  CH3   0  -0.527   4.3076  -1.4631  -1.2706
 EP4  N2   N  NT    0  -0.406   3.3125  -1.4997  -0.2189
 EP4  CE   C  CH3   0  -0.523   3.5361  -2.6233   0.6668
 EP4  C5'  C  CH2   0  -0.291   3.2385  -0.2664   0.5331
 EP4  C4'  C  CR15  0  -0.059   2.8537   0.9501  -0.3038
 EP4  O4'  O  O     0  -0.485   1.7133   0.7068  -1.1311
 EP4  C1'  C  CR15  0   0.223   0.5509   1.1800  -0.5299
 EP4  N9   N  NR5   0  -0.542  -0.3827   0.0761  -0.3810
 EP4  C4   C  CR56  0   0.483  -1.7398   0.1736  -0.2915
 EP4  N3   N  N     0  -0.449  -2.4992   1.2656  -0.3658
 EP4  C2   C  CR16  0   0.037  -3.7826   0.9759  -0.2497
 EP4  N1   N  N     0  -0.475  -4.3516  -0.2148  -0.0737
 EP4  C6   C  CR6   0   0.452  -3.5762  -1.3022  -0.0038
 EP4  N6   N  NH2   0  -0.818  -4.1428  -2.4978   0.1693
 EP4  C5   C  CR56  0  -0.009  -2.1844  -1.1288  -0.1162
 EP4  N7   N  N     0  -0.457  -1.1319  -2.0056  -0.1038
 EP4  C8   C  CR15  0   0.086  -0.0800  -1.2537  -0.2627
 EP4  C2'  C  CR15  0  -0.062   0.9626   1.8088   0.8121
 EP4  O2'  O  OH1   0  -0.652   0.1759   2.9339   1.0752
 EP4  C3'  C  CR15  0   0.006   2.4463   2.1222   0.5743
 EP4  O3'  O  OH1   0  -0.670   2.5938   3.3118  -0.1538
 EP4  H1   H  HCH3  0   0.196   5.3216  -1.2528  -0.8973
 EP4  H2   H  HCH3  0   0.239   4.3337  -2.4263  -1.7807
 EP4  H3   H  HCH3  0   0.241   4.0634  -0.7101  -2.0194
 EP4  H5   H  HCH3  0   0.201   4.4977  -2.5731   1.2006
 EP4  H6   H  HCH3  0   0.234   2.7430  -2.6783   1.4145
 EP4  H7   H  HCH3  0   0.237   3.5221  -3.5531   0.0969
 EP4  H8   H  HCH2  0   0.238   2.5075  -0.4116   1.3349
 EP4  H9   H  HCH2  0   0.226   4.1939  -0.0225   1.0303
 EP4  H10  H  HCR5  0   0.268   3.6785   1.2250  -0.9656
 EP4  H11  H  HCR5  0   0.266   0.0562   1.9246  -1.1621
 EP4  H12  H  HCR6  0   0.249  -4.4688   1.8145  -0.3038
 EP4  H13  H  HNH2  0   0.402  -5.1434  -2.5825   0.2156
 EP4  H14  H  HNH2  0   0.410  -3.5903  -3.3361   0.2043
 EP4  H15  H  HCR5  0   0.311   0.9416  -1.6072  -0.3335
 EP4  H16  H  HCR5  0   0.257   0.8674   1.0654   1.6111
 EP4  H17  H  HOH1  0   0.469   0.2070   3.1195   2.0191
 EP4  H18  H  HCR5  0   0.244   3.0143   2.1455   1.5137
 EP4  H19  H  HOH1  0   0.448   1.9660   3.9537   0.1998

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
 EP4  CE   N2   single    1.448  0.020  1.448
 EP4  CG   N2   single    1.448  0.020  1.448
 EP4  N2   C5'  single    1.446  0.020  1.446
 EP4  C5'  C4'  single    1.526  0.020  1.526
 EP4  C4'  O4'  single    1.430  0.020  1.430
 EP4  C4'  C3'  single    1.520  0.020  1.520
 EP4  O4'  C1'  single    1.392  0.020  1.392
 EP4  C3'  O3'  single    1.403  0.020  1.403
 EP4  C3'  C2'  single    1.535  0.020  1.535
 EP4  C1'  N9   single    1.453  0.020  1.453
 EP4  C1'  C2'  single    1.538  0.020  1.538
 EP4  N3   C2   aromatic  1.321  0.020  1.321
 EP4  N3   C4   aromatic  1.332  0.020  1.332
 EP4  C2   N1   aromatic  1.331  0.020  1.331
 EP4  N9   C4   aromatic  1.364  0.020  1.364
 EP4  N9   C8   aromatic  1.369  0.020  1.369
 EP4  C4   C5   aromatic  1.387  0.020  1.387
 EP4  N1   C6   aromatic  1.337  0.020  1.337
 EP4  C2'  O2'  single    1.398  0.020  1.398
 EP4  C8   N7   aromatic  1.303  0.020  1.303
 EP4  C5   C6   aromatic  1.407  0.020  1.407
 EP4  C5   N7   aromatic  1.370  0.020  1.370
 EP4  C6   N6   single    1.334  0.020  1.334
 EP4  CG   H1   single    0.970  0.020  1.090
 EP4  CG   H2   single    0.970  0.020  1.090
 EP4  CG   H3   single    0.970  0.020  1.090
 EP4  CE   H5   single    0.970  0.020  1.090
 EP4  CE   H6   single    0.970  0.020  1.090
 EP4  CE   H7   single    0.970  0.020  1.090
 EP4  C5'  H8   single    0.970  0.020  1.090
 EP4  C5'  H9   single    0.970  0.020  1.090
 EP4  C4'  H10  single    0.970  0.020  1.090
 EP4  C1'  H11  single    0.970  0.020  1.090
 EP4  C2   H12  single    0.930  0.020  1.080
 EP4  N6   H13  single    0.860  0.020  1.020
 EP4  N6   H14  single    0.860  0.020  1.020
 EP4  C8   H15  single    0.930  0.020  1.080
 EP4  C2'  H16  single    0.970  0.020  1.090
 EP4  O2'  H17  single    0.850  0.020  0.980
 EP4  C3'  H18  single    0.970  0.020  1.090
 EP4  O3'  H19  single    0.850  0.020  0.980

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
 EP4  H3   CG   H2   107.12  3.000
 EP4  H3   CG   H1   107.91  3.000
 EP4  H2   CG   H1   107.78  3.000
 EP4  H3   CG   N2   111.25  3.000
 EP4  H2   CG   N2   109.50  3.000
 EP4  H1   CG   N2   113.05  3.000
 EP4  C5'  N2   CE   110.58  3.000
 EP4  C5'  N2   CG   113.02  3.000
 EP4  CE   N2   CG   110.96  3.000
 EP4  H7   CE   H6   107.80  3.000
 EP4  H7   CE   H5   107.67  3.000
 EP4  H6   CE   H5   107.74  3.000
 EP4  H7   CE   N2   109.87  3.000
 EP4  H6   CE   N2   110.24  3.000
 EP4  H5   CE   N2   113.33  3.000
 EP4  H9   C5'  H8   106.09  3.000
 EP4  H9   C5'  C4'  106.80  3.000
 EP4  H8   C5'  C4'  109.82  3.000
 EP4  H9   C5'  N2   112.22  3.000
 EP4  H8   C5'  N2   107.57  3.000
 EP4  C4'  C5'  N2   114.05  3.000
 EP4  H10  C4'  C3'  110.99  3.000
 EP4  H10  C4'  O4'  107.13  3.000
 EP4  C3'  C4'  O4'  104.58  3.000
 EP4  H10  C4'  C5'  110.02  3.000
 EP4  C3'  C4'  C5'  111.43  3.000
 EP4  O4'  C4'  C5'  112.51  3.000
 EP4  C1'  O4'  C4'  111.00  3.000
 EP4  H11  C1'  C2'  110.28  3.000
 EP4  H11  C1'  N9   106.58  3.000
 EP4  C2'  C1'  N9   113.14  3.000
 EP4  H11  C1'  O4'  111.05  3.000
 EP4  C2'  C1'  O4'  107.00  3.000
 EP4  N9   C1'  O4'  108.82  3.000
 EP4  C8   N9   C4   106.49  3.000
 EP4  C8   N9   C1'  127.20  3.000
 EP4  C4   N9   C1'  126.28  3.000
 EP4  C5   C4   N3   126.43  3.000
 EP4  C5   C4   N9   105.08  3.000
 EP4  N3   C4   N9   128.49  3.000
 EP4  C2   N3   C4   111.67  3.000
 EP4  H12  C2   N1   115.31  3.000
 EP4  H12  C2   N3   116.15  3.000
 EP4  N1   C2   N3   128.54  3.000
 EP4  C6   N1   C2   119.10  3.000
 EP4  C5   C6   N6   122.74  3.000
 EP4  N6   C6   N1   119.28  3.000
 EP4  C5   C6   N1   117.98  3.000
 EP4  H14  N6   H13  118.39  3.000
 EP4  H14  N6   C6   121.24  3.000
 EP4  H13  N6   C6   120.28  3.000
 EP4  N7   C5   C6   132.87  3.000
 EP4  N7   C5   C4   110.84  3.000
 EP4  C6   C5   C4   116.28  3.000
 EP4  C8   N7   C5   104.47  3.000
 EP4  H15  C8   N7   125.53  3.000
 EP4  H15  C8   N9   121.32  3.000
 EP4  N7   C8   N9   113.12  3.000
 EP4  H16  C2'  C3'  109.60  3.000
 EP4  H16  C2'  O2'  111.10  3.000
 EP4  C3'  C2'  O2'  114.13  3.000
 EP4  H16  C2'  C1'  109.61  3.000
 EP4  O2'  C2'  C1'  110.04  3.000
 EP4  C3'  C2'  C1'  101.95  3.000
 EP4  H17  O2'  C2'  108.75  3.000
 EP4  H18  C3'  O3'  111.82  3.000
 EP4  H18  C3'  C2'  111.83  3.000
 EP4  O3'  C3'  C2'  110.81  3.000
 EP4  H18  C3'  C4'  111.84  3.000
 EP4  C2'  C3'  C4'  101.02  3.000
 EP4  O3'  C3'  C4'  109.02  3.000
 EP4  H19  O3'  C3'  107.79  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
 EP4  CONST_01  C2   N3   C4  N9   180.00   0.0  0
 EP4  CONST_02  C6   C5   C4  N9   180.00   0.0  0
 EP4  CONST_03  N7   C5   C4  N9     0.00   0.0  0
 EP4  CONST_04  C5   N7   C8  N9     0.00   0.0  0
 EP4  CONST_05  N1   C2   N3  C4     0.00   0.0  0
 EP4  CONST_06  N7   C8   N9  C4     0.00   0.0  0
 EP4  CONST_07  N1   C6   C5  C4     0.00   0.0  0
 EP4  CONST_08  C8   N7   C5  C4     0.00   0.0  0
 EP4  CONST_09  C6   N1   C2  N3     0.00   0.0  0
 EP4  CONST_10  C8   N9   C4  N3   180.00   0.0  0
 EP4  CONST_11  C6   C5   C4  N3     0.00   0.0  0
 EP4  CONST_12  N7   C5   C4  N3   180.00   0.0  0
 EP4  CONST_13  C5   C4   N3  C2     0.00   0.0  0
 EP4  CONST_14  C5   C6   N1  C2     0.00   0.0  0
 EP4  CONST_15  N7   C5   C6  N1   180.00   0.0  0
 EP4  CONST_16  C8   N7   C5  C6   180.00   0.0  0
 EP4  CONST_17  C8   N9   C4  C5     0.00   0.0  0
 EP4  CONST_18  N3   C4   N9  C1'    0.00   0.0  0
 EP4  CONST_19  C5   C4   N9  C1'  180.00   0.0  0
 EP4  CONST_20  N7   C8   N9  C1'  180.00   0.0  0
 EP4  CONST_21  N6   C6   C5  C4   180.00   0.0  0
 EP4  CONST_22  N6   C6   N1  C2   180.00   0.0  0
 EP4  CONST_23  N7   C5   C6  N6     0.00   0.0  0
 EP4  CONST_24  H15  C8   N9  C1'    0.00   0.0  0
 EP4  CONST_25  H12  C2   N3  C4   180.00   0.0  0
 EP4  CONST_26  H13  N6   C6  N1     0.00   0.0  0
 EP4  CONST_27  H14  N6   C6  N1   180.00   0.0  0
 EP4  Var_01    C4'  C5'  N2  CG    61.22  30.0  3
 EP4  Var_02    H5   CE   N2  CG    62.89  30.0  3
 EP4  Var_03    H1   CG   N2  CE   -66.58  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
 EP4  chir_01  C4'  C5'  O4'  C3'  negativ
 EP4  chir_02  C1'  O4'  N9   C2'  negativ
 EP4  chir_03  C2'  O2'  C1'  C3'  negativ
 EP4  chir_04  C3'  O3'  C4'  C2'  positiv

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
 EP4  plan-1  C1'  0.020
 EP4  plan-1  N9   0.020
 EP4  plan-1  C4   0.020
 EP4  plan-1  N3   0.020
 EP4  plan-1  C2   0.020
 EP4  plan-1  N1   0.020
 EP4  plan-1  C6   0.020
 EP4  plan-1  N6   0.020
 EP4  plan-1  C5   0.020
 EP4  plan-1  N7   0.020
 EP4  plan-1  C8   0.020
 EP4  plan-1  H12  0.020
 EP4  plan-1  H15  0.020
 EP4  plan-2  C6   0.020
 EP4  plan-2  N6   0.020
 EP4  plan-2  H13  0.020
 EP4  plan-2  H14  0.020

