# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:58:37 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCON)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
 MAO  MAO  5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxyadenosine  ligand  45  24  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MAO
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
 MAO  N     N  NH2   0  -0.562  -3.5553  -0.8490  -1.6667
 MAO  OA    O  O2    0  -0.428  -2.7014  -0.0758  -2.4824
 MAO  CB    C  CH2   0  -0.137  -1.8793  -0.9224  -3.2537
 MAO  CG    C  CH2   0  -0.322  -0.9416  -0.0599  -4.0755
 MAO  ND    N  NT    0  -0.405   0.0737   0.6400  -3.2979
 MAO  CE    C  CH3   0  -0.534   0.5527   1.8124  -4.0056
 MAO  C5'   C  CH2   0  -0.302   1.1546  -0.2557  -2.9437
 MAO  C4'   C  CH1   0  -0.048   2.2224   0.3514  -2.0333
 MAO  O4'   O  O2    0  -0.487   1.6706   1.1191  -0.9610
 MAO  C1'   C  CH1   0   0.227   1.6762   0.3997   0.2308
 MAO  N9    N  NR5   0  -0.539   0.3318   0.4013   0.7764
 MAO  C4    C  CR56  0   0.478  -0.0186   0.2537   2.0863
 MAO  N3    N  N     0  -0.450   0.7741   0.1567   3.1521
 MAO  C2    C  CR16  0   0.038   0.0785   0.0319   4.2683
 MAO  N1    N  N     0  -0.475  -1.2434  -0.0090   4.4213
 MAO  C6    C  CR6   0   0.457  -2.0266   0.0928   3.3421
 MAO  N6    N  NH2   0  -0.818  -3.3520   0.0513   3.4887
 MAO  C5    C  CR56  0   0.012  -1.4056   0.2358   2.0880
 MAO  N7    N  N     0  -0.479  -1.8946   0.3747   0.8154
 MAO  C8    C  CR15  0   0.089  -0.8328   0.4691   0.0648
 MAO  C2'   C  CH1   0  -0.058   2.1849  -1.0078  -0.1099
 MAO  O2'   O  OH1   0  -0.651   2.8915  -1.5403   0.9709
 MAO  C3'   C  CH1   0  -0.004   3.0394  -0.7378  -1.3550
 MAO  O3'   O  OH1   0  -0.669   4.2924  -0.2207  -0.9952
 MAO  HN1   H  HNH2  0   0.368  -3.3516  -0.5366  -0.7201
 MAO  HN2   H  HNH2  0   0.357  -4.4892  -0.5140  -1.8794
 MAO  HB1   H  HCH2  0   0.213  -2.4800  -1.5302  -3.9418
 MAO  HB2   H  HCH2  0   0.199  -1.3289  -1.6224  -2.6127
 MAO  HG1   H  HCH2  0   0.242  -1.5436   0.6824  -4.6055
 MAO  HG2   H  HCH2  0   0.211  -0.4901  -0.6934  -4.8558
 MAO  HE1   H  HCH3  0   0.242   1.2159   2.4050  -3.3766
 MAO  HE2   H  HCH3  0   0.197   1.0933   1.5669  -4.9322
 MAO  HE3   H  HCH3  0   0.241  -0.2904   2.4503  -4.2714
 MAO  H5'1  H  HCH2  0   0.239   0.7279  -1.1415  -2.4651
 MAO  H5'2  H  HCH2  0   0.225   1.6839  -0.6290  -3.8389
 MAO  H4'   H  HCH1  0   0.268   2.8683   1.0192  -2.6083
 MAO  H1'   H  HCH1  0   0.264   2.3226   0.8708   0.9791
 MAO  H2    H  HCR6  0   0.250   0.6550  -0.0501   5.1839
 MAO  HN61  H  HNH2  0   0.403  -3.7597  -0.0356   4.4035
 MAO  HN62  H  HNH2  0   0.410  -3.9653   0.1586   2.7004
 MAO  H8    H  HCR5  0   0.320  -0.8347   0.6079  -1.0083
 MAO  H2'   H  HCH1  0   0.252   1.3332  -1.6425  -0.3824
 MAO  HO2'  H  HOH1  0   0.469   2.9216  -2.4981   0.8811
 MAO  H3'   H  HCH1  0   0.247   3.1311  -1.6310  -1.9869
 MAO  HO3'  H  HOH1  0   0.449   4.6143  -0.7265  -0.2392

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
 MAO  N    OA    single    1.411  0.020  1.411
 MAO  N    HN1   single    0.890  0.020  1.040
 MAO  N    HN2   single    0.890  0.020  1.040
 MAO  OA   CB    single    1.410  0.020  1.410
 MAO  CB   CG    single    1.516  0.020  1.516
 MAO  CB   HB1   single    0.970  0.020  1.090
 MAO  CB   HB2   single    0.970  0.020  1.090
 MAO  CG   ND    single    1.458  0.020  1.458
 MAO  CG   HG1   single    0.970  0.020  1.090
 MAO  CG   HG2   single    0.970  0.020  1.090
 MAO  ND   CE    single    1.451  0.020  1.451
 MAO  ND   C5'   single    1.448  0.020  1.448
 MAO  CE   HE1   single    0.970  0.020  1.090
 MAO  CE   HE2   single    0.970  0.020  1.090
 MAO  CE   HE3   single    0.970  0.020  1.090
 MAO  C5'  C4'   single    1.529  0.020  1.529
 MAO  C5'  H5'1  single    0.970  0.020  1.090
 MAO  C5'  H5'2  single    0.970  0.020  1.090
 MAO  C4'  O4'   single    1.430  0.020  1.430
 MAO  C4'  C3'   single    1.521  0.020  1.521
 MAO  C4'  H4'   single    0.970  0.020  1.090
 MAO  O4'  C1'   single    1.392  0.020  1.392
 MAO  C1'  N9    single    1.451  0.020  1.451
 MAO  C1'  C2'   single    1.535  0.020  1.535
 MAO  C1'  H1'   single    0.970  0.020  1.090
 MAO  N9   C4    aromatic  1.364  0.020  1.364
 MAO  N9   C8    aromatic  1.367  0.020  1.367
 MAO  C4   N3    aromatic  1.332  0.020  1.332
 MAO  C4   C5    aromatic  1.387  0.020  1.387
 MAO  N3   C2    aromatic  1.321  0.020  1.321
 MAO  C2   N1    aromatic  1.331  0.020  1.331
 MAO  C2   H2    single    0.930  0.020  1.080
 MAO  N1   C6    aromatic  1.337  0.020  1.337
 MAO  C6   N6    single    1.334  0.020  1.334
 MAO  C6   C5    aromatic  1.407  0.020  1.407
 MAO  N6   HN61  single    0.860  0.020  1.020
 MAO  N6   HN62  single    0.860  0.020  1.020
 MAO  C5   N7    aromatic  1.370  0.020  1.370
 MAO  N7   C8    aromatic  1.304  0.020  1.304
 MAO  C8   H8    single    0.930  0.020  1.080
 MAO  C2'  O2'   single    1.397  0.020  1.397
 MAO  C2'  C3'   single    1.534  0.020  1.534
 MAO  C2'  H2'   single    0.970  0.020  1.090
 MAO  O2'  HO2'  single    0.850  0.020  0.980
 MAO  C3'  O3'   single    1.403  0.020  1.403
 MAO  C3'  H3'   single    0.970  0.020  1.090
 MAO  O3'  HO3'  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
 MAO  HN2   N    HN1   106.14  3.000
 MAO  HN2   N    OA    104.76  3.000
 MAO  HN1   N    OA    104.38  3.000
 MAO  CB    OA   N     109.88  3.000
 MAO  HB2   CB   HB1   106.71  3.000
 MAO  HB2   CB   CG    111.68  3.000
 MAO  HB1   CB   CG    108.29  3.000
 MAO  HB2   CB   OA    110.85  3.000
 MAO  HB1   CB   OA    110.89  3.000
 MAO  CG    CB   OA    108.40  3.000
 MAO  HG2   CG   HG1   105.84  3.000
 MAO  HG2   CG   ND    111.61  3.000
 MAO  HG1   CG   ND    108.43  3.000
 MAO  HG2   CG   CB    108.07  3.000
 MAO  HG1   CG   CB    107.98  3.000
 MAO  ND    CG   CB    114.50  3.000
 MAO  C5'   ND   CE    111.89  3.000
 MAO  C5'   ND   CG    110.69  3.000
 MAO  CE    ND   CG    110.96  3.000
 MAO  HE3   CE   HE2   107.78  3.000
 MAO  HE3   CE   HE1   107.06  3.000
 MAO  HE2   CE   HE1   107.96  3.000
 MAO  HE3   CE   ND    109.66  3.000
 MAO  HE2   CE   ND    113.12  3.000
 MAO  HE1   CE   ND    111.03  3.000
 MAO  H5'2  C5'  H5'1  105.54  3.000
 MAO  H5'2  C5'  C4'   106.38  3.000
 MAO  H5'1  C5'  C4'   109.48  3.000
 MAO  H5'2  C5'  ND    111.62  3.000
 MAO  H5'1  C5'  ND    108.48  3.000
 MAO  C4'   C5'  ND    114.92  3.000
 MAO  H4'   C4'  C3'   110.78  3.000
 MAO  H4'   C4'  O4'   107.14  3.000
 MAO  C3'   C4'  O4'   104.92  3.000
 MAO  H4'   C4'  C5'   110.01  3.000
 MAO  C3'   C4'  C5'   110.87  3.000
 MAO  O4'   C4'  C5'   112.97  3.000
 MAO  C1'   O4'  C4'   111.29  3.000
 MAO  H1'   C1'  C2'   110.51  3.000
 MAO  H1'   C1'  N9    106.83  3.000
 MAO  C2'   C1'  N9    113.05  3.000
 MAO  H1'   C1'  O4'   111.41  3.000
 MAO  C2'   C1'  O4'   106.57  3.000
 MAO  N9    C1'  O4'   108.52  3.000
 MAO  C8    N9   C4    106.65  3.000
 MAO  C8    N9   C1'   126.44  3.000
 MAO  C4    N9   C1'   126.80  3.000
 MAO  C5    C4   N3    126.39  3.000
 MAO  C5    C4   N9    105.04  3.000
 MAO  N3    C4   N9    128.57  3.000
 MAO  C2    N3   C4    111.69  3.000
 MAO  H2    C2   N1    115.35  3.000
 MAO  H2    C2   N3    116.12  3.000
 MAO  N1    C2   N3    128.52  3.000
 MAO  C6    N1   C2    119.10  3.000
 MAO  C5    C6   N6    122.66  3.000
 MAO  C5    C6   N1    117.95  3.000
 MAO  N6    C6   N1    119.39  3.000
 MAO  HN62  N6   HN61  118.41  3.000
 MAO  HN62  N6   C6    121.13  3.000
 MAO  HN61  N6   C6    120.37  3.000
 MAO  N7    C5   C6    132.90  3.000
 MAO  N7    C5   C4    110.75  3.000
 MAO  C6    C5   C4    116.35  3.000
 MAO  C8    N7   C5    104.56  3.000
 MAO  H8    C8   N7    125.37  3.000
 MAO  H8    C8   N9    121.62  3.000
 MAO  N7    C8   N9    113.00  3.000
 MAO  H2'   C2'  C3'   109.44  3.000
 MAO  H2'   C2'  O2'   111.38  3.000
 MAO  C3'   C2'  O2'   114.42  3.000
 MAO  H2'   C2'  C1'   109.18  3.000
 MAO  C3'   C2'  C1'   101.74  3.000
 MAO  O2'   C2'  C1'   110.21  3.000
 MAO  HO2'  O2'  C2'   108.85  3.000
 MAO  H3'   C3'  O3'   111.90  3.000
 MAO  H3'   C3'  C2'   111.75  3.000
 MAO  O3'   C3'  C2'   110.75  3.000
 MAO  H3'   C3'  C4'   111.76  3.000
 MAO  O3'   C3'  C4'   109.28  3.000
 MAO  C2'   C3'  C4'   100.88  3.000
 MAO  HO3'  O3'  C3'   107.81  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
 MAO  CONST_01  C2    N3   C4  N9    180.00   0.0  0
 MAO  CONST_02  C6    C5   C4  N9    180.00   0.0  0
 MAO  CONST_03  N7    C5   C4  N9      0.00   0.0  0
 MAO  CONST_04  C5    N7   C8  N9      0.00   0.0  0
 MAO  CONST_05  N7    C8   N9  C4      0.00   0.0  0
 MAO  CONST_06  N1    C2   N3  C4      0.00   0.0  0
 MAO  CONST_07  N1    C6   C5  C4      0.00   0.0  0
 MAO  CONST_08  C8    N7   C5  C4      0.00   0.0  0
 MAO  CONST_09  C8    N9   C4  N3    180.00   0.0  0
 MAO  CONST_10  C6    C5   C4  N3      0.00   0.0  0
 MAO  CONST_11  N7    C5   C4  N3    180.00   0.0  0
 MAO  CONST_12  C6    N1   C2  N3      0.00   0.0  0
 MAO  CONST_13  C5    C4   N3  C2      0.00   0.0  0
 MAO  CONST_14  C5    C6   N1  C2      0.00   0.0  0
 MAO  CONST_15  N7    C5   C6  N1    180.00   0.0  0
 MAO  CONST_16  C8    N7   C5  C6    180.00   0.0  0
 MAO  CONST_17  C8    N9   C4  C5      0.00   0.0  0
 MAO  CONST_18  N3    C4   N9  C1'     0.00   0.0  0
 MAO  CONST_19  C5    C4   N9  C1'   180.00   0.0  0
 MAO  CONST_20  N7    C8   N9  C1'   180.00   0.0  0
 MAO  CONST_21  N6    C6   C5  C4    180.00   0.0  0
 MAO  CONST_22  N6    C6   N1  C2    180.00   0.0  0
 MAO  CONST_23  N7    C5   C6  N6      0.00   0.0  0
 MAO  CONST_24  H8    C8   N9  C1'     0.00   0.0  0
 MAO  CONST_25  H2    C2   N3  C4    180.00   0.0  0
 MAO  CONST_26  HN61  N6   C6  N1      0.00   0.0  0
 MAO  CONST_27  HN62  N6   C6  N1    180.00   0.0  0
 MAO  Var_01    C4'   C5'  ND  CG   -175.46  30.0  3
 MAO  Var_02    CG    CB   OA  N    -177.86  30.0  3
 MAO  Var_03    ND    CG   CB  OA     69.32  30.0  3
 MAO  Var_04    CE    ND   CG  CB   -156.62  30.0  3
 MAO  Var_05    HN1   N    OA  CB    122.70  30.0  3
 MAO  Var_06    HE1   CE   ND  CG    172.81  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
 MAO  chir_01  C4'  C5'  O4'  C3'  negativ
 MAO  chir_02  C1'  O4'  N9   C2'  negativ
 MAO  chir_03  C2'  O2'  C1'  C3'  negativ
 MAO  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
 MAO  plan-1  C1'   0.020
 MAO  plan-1  N9    0.020
 MAO  plan-1  C4    0.020
 MAO  plan-1  N3    0.020
 MAO  plan-1  C2    0.020
 MAO  plan-1  N1    0.020
 MAO  plan-1  C6    0.020
 MAO  plan-1  N6    0.020
 MAO  plan-1  C5    0.020
 MAO  plan-1  N7    0.020
 MAO  plan-1  C8    0.020
 MAO  plan-1  H2    0.020
 MAO  plan-1  H8    0.020
 MAO  plan-2  C6    0.020
 MAO  plan-2  N6    0.020
 MAO  plan-2  HN61  0.020
 MAO  plan-2  HN62  0.020

