# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:09:53 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 5'-O-(2-amino-2-oxoethyl)-8-(methylamino)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc2c(N)ncnc2n1[C@@H]3O[C@H](COCC(N)=O)[C@@H](O)[C@H]3O
#
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
 3F5  3F5  5'-O-(2-amino-2-oxoethyl)-8-(methylamino)adenosine  ligand  44  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3F5
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
 3F5  N1    N  N     0  -0.469  -4.9851   0.9428   1.5141
 3F5  C2    C  CR16  0   0.035  -4.1630   0.1714   2.2142
 3F5  N3    N  N     0  -0.459  -2.9528  -0.2490   1.8759
 3F5  C4    C  CR6   0   0.427  -4.5982   1.3832   0.3092
 3F5  N5    N  NR5   0  -0.609  -1.4143  -0.0405   0.0111
 3F5  C6    C  CR5   0   0.690  -1.5168   0.6419  -1.1869
 3F5  N7    N  N     0  -0.511  -2.6480   1.2792  -1.3185
 3F5  C8    C  CR56  0   0.024  -3.3352   1.0027  -0.1609
 3F5  C9    C  CR56  0   0.485  -2.5901   0.1975   0.6809
 3F5  N10   N  NH2   0  -0.822  -5.4184   2.1885  -0.3847
 3F5  C11   C  CH1   0   0.184  -0.4091  -0.9763   0.4349
 3F5  O12   O  O2    0  -0.502   0.8553  -0.3602   0.3457
 3F5  C13   C  CH1   0  -0.023   1.8175  -1.3399  -0.0085
 3F5  C14   C  CH1   0  -0.016   1.0749  -2.2435  -0.9886
 3F5  C15   C  CH1   0  -0.050  -0.3405  -2.2875  -0.3808
 3F5  C16   C  CH2   0  -0.141   3.0371  -0.6828  -0.6004
 3F5  O17   O  O2    0  -0.477   3.6781   0.0763   0.3892
 3F5  O18   O  OH1   0  -0.668  -0.4761  -3.3657   0.5030
 3F5  O19   O  OH1   0  -0.657   1.6852  -3.5014  -1.0607
 3F5  N20   N  NH1   0  -0.688  -0.5304   0.5931  -2.1170
 3F5  C21   C  CH3   0  -0.524  -0.6978   1.3678  -3.3289
 3F5  C22   C  CH2   0  -0.249   4.8492   0.6783  -0.0697
 3F5  C23   C  C     0   0.464   5.4010   1.5737   1.0271
 3F5  O24   O  O     0  -0.479   4.7308   1.9149   1.9858
 3F5  N25   N  NH2   0  -0.802   6.6648   1.9673   0.8192
 3F5  H2    H  HCR6  0   0.248  -4.5305  -0.1551   3.1809
 3F5  HN10  H  HNH2  0   0.397  -6.3707   2.2967  -0.0804
 3F5  HN1A  H  HNH2  0   0.404  -5.2194   2.3941  -1.3482
 3F5  H11   H  HCH1  0   0.272  -0.6542  -1.2260   1.4723
 3F5  H13   H  HCH1  0   0.253   2.1129  -1.9238   0.8753
 3F5  H14   H  HCH1  0   0.243   1.0280  -1.7634  -1.9724
 3F5  H15   H  HCH1  0   0.253  -1.1139  -2.3119  -1.1575
 3F5  H16   H  HCH2  0   0.225   3.6926  -1.4747  -0.9885
 3F5  H16A  H  HCH2  0   0.207   2.7531  -0.0548  -1.4589
 3F5  HO18  H  HOH1  0   0.450   0.1219  -4.0620   0.1995
 3F5  HO19  H  HOH1  0   0.473   1.5098  -3.8871  -1.9247
 3F5  HN20  H  HNH1  0   0.392   0.4023   0.6075  -1.7346
 3F5  H21   H  HCH3  0   0.250   0.1679   1.1999  -3.9640
 3F5  H21A  H  HCH3  0   0.244  -1.5837   1.0359  -3.8665
 3F5  H21B  H  HCH3  0   0.229  -0.7929   2.4404  -3.1425
 3F5  H22   H  HCH2  0   0.238   5.6015  -0.0660  -0.3659
 3F5  H22A  H  HCH2  0   0.246   4.6654   1.3042  -0.9561
 3F5  HN25  H  HNH2  0   0.410   7.2034   1.6454   0.0333
 3F5  HN2A  H  HNH2  0   0.405   7.1071   2.6188   1.4465

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
 3F5  N1   C2    aromatic  1.327  0.020  1.327
 3F5  N1   C4    aromatic  1.340  0.020  1.340
 3F5  C2   N3    aromatic  1.325  0.020  1.325
 3F5  N3   C9    aromatic  1.326  0.020  1.326
 3F5  C4   C8    aromatic  1.400  0.020  1.400
 3F5  C4   N10   single    1.343  0.020  1.343
 3F5  N5   C6    aromatic  1.383  0.020  1.383
 3F5  N5   C9    aromatic  1.374  0.020  1.374
 3F5  N5   C11   single    1.437  0.020  1.437
 3F5  C6   N7    aromatic  1.305  0.020  1.305
 3F5  C6   N20   single    1.357  0.020  1.357
 3F5  N7   C8    aromatic  1.374  0.020  1.374
 3F5  C8   C9    aromatic  1.383  0.020  1.383
 3F5  C11  O12   single    1.409  0.020  1.409
 3F5  C11  C15   single    1.546  0.020  1.546
 3F5  O12  C13   single    1.418  0.020  1.418
 3F5  C13  C14   single    1.526  0.020  1.526
 3F5  C13  C16   single    1.506  0.020  1.506
 3F5  C14  C15   single    1.541  0.020  1.541
 3F5  C14  O19   single    1.400  0.020  1.400
 3F5  C15  O18   single    1.401  0.020  1.401
 3F5  C16  O17   single    1.402  0.020  1.402
 3F5  O17  C22   single    1.394  0.020  1.394
 3F5  N20  C21   single    1.448  0.020  1.448
 3F5  C22  C23   single    1.520  0.020  1.520
 3F5  C23  O24   double    1.218  0.020  1.218
 3F5  C23  N25   single    1.340  0.020  1.340
 3F5  C2   H2    single    0.930  0.020  1.080
 3F5  N10  HN10  single    0.890  0.020  1.040
 3F5  N10  HN1A  single    0.890  0.020  1.040
 3F5  C11  H11   single    0.970  0.020  1.090
 3F5  C13  H13   single    0.970  0.020  1.090
 3F5  C14  H14   single    0.970  0.020  1.090
 3F5  C15  H15   single    0.970  0.020  1.090
 3F5  C16  H16   single    0.970  0.020  1.090
 3F5  C16  H16A  single    0.970  0.020  1.090
 3F5  O18  HO18  single    0.850  0.020  0.980
 3F5  O19  HO19  single    0.850  0.020  0.980
 3F5  N20  HN20  single    0.890  0.020  1.040
 3F5  C21  H21   single    0.970  0.020  1.090
 3F5  C21  H21A  single    0.970  0.020  1.090
 3F5  C21  H21B  single    0.970  0.020  1.090
 3F5  C22  H22   single    0.970  0.020  1.090
 3F5  C22  H22A  single    0.970  0.020  1.090
 3F5  N25  HN25  single    0.860  0.020  1.020
 3F5  N25  HN2A  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
 3F5  C4    N1   C2    119.12  3.000
 3F5  H2    C2   N3    116.20  3.000
 3F5  H2    C2   N1    115.81  3.000
 3F5  N3    C2   N1    127.99  3.000
 3F5  C9    N3   C2    111.90  3.000
 3F5  N10   C4   C8    122.71  3.000
 3F5  N10   C4   N1    119.04  3.000
 3F5  C8    C4   N1    118.23  3.000
 3F5  C11   N5   C9    124.58  3.000
 3F5  C11   N5   C6    128.96  3.000
 3F5  C9    N5   C6    105.87  3.000
 3F5  N20   C6   N7    125.36  3.000
 3F5  N20   C6   N5    121.49  3.000
 3F5  N7    C6   N5    113.12  3.000
 3F5  C8    N7   C6    104.49  3.000
 3F5  C9    C8   N7    111.13  3.000
 3F5  C9    C8   C4    116.09  3.000
 3F5  N7    C8   C4    132.78  3.000
 3F5  C8    C9   N5    105.38  3.000
 3F5  C8    C9   N3    126.67  3.000
 3F5  N5    C9   N3    127.95  3.000
 3F5  HN1A  N10  HN10  117.10  3.000
 3F5  HN1A  N10  C4    119.81  3.000
 3F5  HN10  N10  C4    119.12  3.000
 3F5  H11   C11  C15   108.45  3.000
 3F5  H11   C11  O12   111.13  3.000
 3F5  C15   C11  O12   107.31  3.000
 3F5  H11   C11  N5    105.74  3.000
 3F5  C15   C11  N5    115.32  3.000
 3F5  O12   C11  N5    108.91  3.000
 3F5  C13   O12  C11   108.81  3.000
 3F5  H13   C13  C16   109.27  3.000
 3F5  H13   C13  C14   109.42  3.000
 3F5  C16   C13  C14   113.57  3.000
 3F5  H13   C13  O12   110.38  3.000
 3F5  C16   C13  O12   110.25  3.000
 3F5  C14   C13  O12   103.84  3.000
 3F5  H14   C14  O19   111.47  3.000
 3F5  H14   C14  C15   109.11  3.000
 3F5  O19   C14  C15   113.27  3.000
 3F5  H14   C14  C13   109.76  3.000
 3F5  O19   C14  C13   110.67  3.000
 3F5  C15   C14  C13   102.16  3.000
 3F5  H15   C15  O18   111.19  3.000
 3F5  H15   C15  C14   111.66  3.000
 3F5  O18   C15  C14   111.09  3.000
 3F5  H15   C15  C11   111.19  3.000
 3F5  O18   C15  C11   108.40  3.000
 3F5  C14   C15  C11   102.99  3.000
 3F5  H16A  C16  H16   106.83  3.000
 3F5  H16A  C16  O17   111.06  3.000
 3F5  H16   C16  O17   111.51  3.000
 3F5  H16A  C16  C13   110.27  3.000
 3F5  H16   C16  C13   107.91  3.000
 3F5  O17   C16  C13   109.20  3.000
 3F5  C22   O17  C16   112.67  3.000
 3F5  HO18  O18  C15   107.24  3.000
 3F5  HO19  O19  C14   109.08  3.000
 3F5  HN20  N20  C21   114.63  3.000
 3F5  HN20  N20  C6    114.33  3.000
 3F5  C21   N20  C6    118.06  3.000
 3F5  H21B  C21  H21A  108.23  3.000
 3F5  H21B  C21  H21   108.70  3.000
 3F5  H21A  C21  H21   108.22  3.000
 3F5  H21B  C21  N20   113.11  3.000
 3F5  H21A  C21  N20   110.14  3.000
 3F5  H21   C21  N20   108.32  3.000
 3F5  H22A  C22  H22   106.40  3.000
 3F5  H22A  C22  C23   107.87  3.000
 3F5  H22   C22  C23   110.18  3.000
 3F5  H22A  C22  O17   111.74  3.000
 3F5  H22   C22  O17   111.80  3.000
 3F5  C23   C22  O17   108.77  3.000
 3F5  N25   C23  O24   123.96  3.000
 3F5  N25   C23  C22   113.81  3.000
 3F5  O24   C23  C22   122.22  3.000
 3F5  HN2A  N25  HN25  117.31  3.000
 3F5  HN2A  N25  C23   120.52  3.000
 3F5  HN25  N25  C23   122.17  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
 3F5  CONST_01  C9    N3   C2   N1      0.00   0.0  0
 3F5  CONST_02  N7    C8   C4   N1    180.00   0.0  0
 3F5  CONST_03  C9    C8   C4   N1      0.00   0.0  0
 3F5  CONST_04  C8    C4   N1   C2      0.00   0.0  0
 3F5  CONST_05  N5    C9   N3   C2    180.00   0.0  0
 3F5  CONST_06  C8    C9   N3   C2      0.00   0.0  0
 3F5  CONST_07  C4    N1   C2   N3      0.00   0.0  0
 3F5  CONST_08  C6    N5   C9   N3    180.00   0.0  0
 3F5  CONST_09  C4    C8   C9   N3      0.00   0.0  0
 3F5  CONST_10  N7    C8   C9   N3    180.00   0.0  0
 3F5  CONST_11  C6    N7   C8   C4    180.00   0.0  0
 3F5  CONST_12  N5    C9   C8   C4    180.00   0.0  0
 3F5  CONST_13  C8    N7   C6   N5      0.00   0.0  0
 3F5  CONST_14  N7    C8   C9   N5      0.00   0.0  0
 3F5  CONST_15  C8    C9   N5   C6      0.00   0.0  0
 3F5  CONST_16  C9    C8   N7   C6      0.00   0.0  0
 3F5  CONST_17  C9    N5   C6   N7      0.00   0.0  0
 3F5  CONST_18  C11   N5   C9   N3      0.00   0.0  0
 3F5  CONST_19  C11   N5   C6   N7    180.00   0.0  0
 3F5  CONST_20  C11   N5   C9   C8    180.00   0.0  0
 3F5  CONST_21  N10   C4   N1   C2    180.00   0.0  0
 3F5  CONST_22  N10   C4   C8   N7      0.00   0.0  0
 3F5  CONST_23  N20   C6   N7   C8    180.00   0.0  0
 3F5  CONST_24  N20   C6   N5   C9    180.00   0.0  0
 3F5  CONST_25  N10   C4   C8   C9    180.00   0.0  0
 3F5  CONST_26  N20   C6   N5   C11     0.00   0.0  0
 3F5  CONST_27  H2    C2   N1   C4    180.00   0.0  0
 3F5  CONST_28  C21   N20  C6   N5    180.00   0.0  0
 3F5  CONST_29  C21   N20  C6   N7      0.00   0.0  0
 3F5  CONST_30  HN10  N10  C4   N1      0.00   0.0  0
 3F5  CONST_31  HN1A  N10  C4   N1    180.00   0.0  0
 3F5  CONST_33  HN25  N25  C23  C22     0.00   0.0  0
 3F5  CONST_34  HN2A  N25  C23  C22   180.00   0.0  0
 3F5  Var_01    H21   C21  N20  C6   -178.97  30.0  3
 3F5  Var_02    C23   C22  O17  C16   174.96  30.0  3
 3F5  Var_03    O24   C23  C22  O17   -15.59  30.0  3
 3F5  Var_04    H16   C16  O17  C22    58.59  30.0  2

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
 3F5  chir_01  C11  N5   O12  C15  positiv
 3F5  chir_02  C13  O12  C14  C16  negativ
 3F5  chir_03  C14  O19  C13  C15  positiv
 3F5  chir_04  C15  O18  C14  C11  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
 3F5  plan-1  N1    0.020
 3F5  plan-1  C2    0.020
 3F5  plan-1  N3    0.020
 3F5  plan-1  C4    0.020
 3F5  plan-1  N5    0.020
 3F5  plan-1  C6    0.020
 3F5  plan-1  N7    0.020
 3F5  plan-1  C8    0.020
 3F5  plan-1  C9    0.020
 3F5  plan-1  N10   0.020
 3F5  plan-1  C11   0.020
 3F5  plan-1  N20   0.020
 3F5  plan-1  H2    0.020
 3F5  plan-2  C4    0.020
 3F5  plan-2  N10   0.020
 3F5  plan-2  HN10  0.020
 3F5  plan-2  HN1A  0.020
 3F5  plan-3  C6    0.020
 3F5  plan-3  N20   0.020
 3F5  plan-3  C21   0.020
 3F5  plan-3  HN20  0.020
 3F5  plan-4  C22   0.020
 3F5  plan-4  C23   0.020
 3F5  plan-4  O24   0.020
 3F5  plan-4  N25   0.020
 3F5  plan-4  HN25  0.020
 3F5  plan-4  HN2A  0.020

