# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:21:55 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 5'-deoxy-5'-(dimethylamino)-8-methyladenosine
#   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)n2c(C)nc3c(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
 N8M  N8M  5'-deoxy-5'-(dimethylamino)-8-methyladenosine  ligand  42  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N8M
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
 N8M  CG    C  CH3   0  -0.520   5.4092   1.9441   0.6411
 N8M  N2    N  NT    0  -0.412   4.1965   1.2487   1.0186
 N8M  CE    C  CH3   0  -0.524   3.3100   2.1276   1.7534
 N8M  C5'   C  CH2   0  -0.289   3.5776   0.6321  -0.1356
 N8M  C4'   C  CR15  0   0.029   2.5140  -0.3987   0.1898
 N8M  O4'   O  O     0  -0.496   1.2530   0.2097   0.4283
 N8M  C1'   C  CR15  0   0.198   0.2345  -0.7385   0.2347
 N8M  N9    N  NR5   0  -0.579  -0.9324  -0.0699  -0.2828
 N8M  C4    C  CR56  0   0.491  -2.1464  -0.0602   0.3499
 N8M  N3    N  N     0  -0.463  -2.4832  -0.6522   1.4924
 N8M  C2    C  CR16  0   0.042  -3.7497  -0.4335   1.8039
 N8M  N1    N  N     0  -0.473  -4.6556   0.2688   1.1303
 N8M  C6    C  CR6   0   0.448  -4.2993   0.8583  -0.0175
 N8M  N6    N  NH2   0  -0.819  -5.2041   1.5688  -0.6940
 N8M  C5    C  CR56  0  -0.003  -2.9727   0.7016  -0.4546
 N8M  N7    N  N     0  -0.465  -2.2917   1.1588  -1.5514
 N8M  C8    C  CR5   0   0.454  -1.0828   0.6885  -1.4274
 N8M  C2'   C  CR15  0  -0.059   0.8151  -1.8663  -0.6436
 N8M  O2'   O  OH1   0  -0.666   0.8706  -3.0338   0.1296
 N8M  C3'   C  CR15  0  -0.015   2.2285  -1.3490  -0.9707
 N8M  O3'   O  OH1   0  -0.659   3.1907  -2.3649  -1.0285
 N8M  C9    C  CH3   0  -0.780   0.0044   0.9414  -2.4034
 N8M  HG    H  HCH3  0   0.193   5.2359   2.7793  -0.0552
 N8M  HGA   H  HCH3  0   0.233   5.8960   2.3500   1.5290
 N8M  HGB   H  HCH3  0   0.233   6.1072   1.2541   0.1644
 N8M  HE    H  HCH3  0   0.190   2.9463   2.9764   1.1530
 N8M  HEA   H  HCH3  0   0.241   2.4421   1.5878   2.1268
 N8M  HEB   H  HCH3  0   0.231   3.8388   2.5357   2.6155
 N8M  H5'   H  HCH2  0   0.202   3.1545   1.3721  -0.8389
 N8M  H5'A  H  HCH2  0   0.249   4.3622   0.1018  -0.6828
 N8M  H4'   H  HCR5  0   0.236   2.8367  -0.9788   1.0665
 N8M  H1'   H  HCR5  0   0.267  -0.0825  -1.1782   1.1861
 N8M  H2    H  HCR6  0   0.251  -4.0998  -0.8847   2.7261
 N8M  HN6   H  HNH2  0   0.403  -6.1524   1.6260  -0.3659
 N8M  HN6A  H  HNH2  0   0.410  -4.9781   1.9931  -1.5760
 N8M  H2'   H  HCR5  0   0.248   0.2147  -2.0222  -1.5485
 N8M  HO2'  H  HOH1  0   0.450   1.6431  -3.5343  -0.1634
 N8M  H3'   H  HCR5  0   0.244   2.2045  -0.7756  -1.9045
 N8M  HO3'  H  HOH1  0   0.470   3.2618  -2.6786  -1.9354
 N8M  H9    H  HCH3  0   0.263   0.3740   0.0186  -2.8522
 N8M  H9A   H  HCH3  0   0.280  -0.3845   1.5642  -3.2051
 N8M  H9B   H  HCH3  0   0.267   0.8489   1.4572  -1.9475

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
 N8M  N2   CG    single    1.448  0.020  1.448
 N8M  CG   HG    single    0.970  0.020  1.090
 N8M  CG   HGA   single    0.970  0.020  1.090
 N8M  CG   HGB   single    0.970  0.020  1.090
 N8M  CE   N2    single    1.449  0.020  1.449
 N8M  N2   C5'   single    1.448  0.020  1.448
 N8M  CE   HE    single    0.970  0.020  1.090
 N8M  CE   HEA   single    0.970  0.020  1.090
 N8M  CE   HEB   single    0.970  0.020  1.090
 N8M  C4'  C5'   single    1.516  0.020  1.516
 N8M  C5'  H5'   single    0.970  0.020  1.090
 N8M  C5'  H5'A  single    0.970  0.020  1.090
 N8M  O4'  C4'   single    1.420  0.020  1.420
 N8M  C4'  C3'   single    1.527  0.020  1.527
 N8M  C4'  H4'   single    0.970  0.020  1.090
 N8M  C1'  O4'   single    1.405  0.020  1.405
 N8M  N9   C1'   single    1.441  0.020  1.441
 N8M  C1'  C2'   single    1.543  0.020  1.543
 N8M  C1'  H1'   single    0.970  0.020  1.090
 N8M  C8   N9    aromatic  1.381  0.020  1.381
 N8M  N9   C4    aromatic  1.369  0.020  1.369
 N8M  C5   C4    aromatic  1.382  0.020  1.382
 N8M  C4   N3    aromatic  1.330  0.020  1.330
 N8M  N3   C2    aromatic  1.322  0.020  1.322
 N8M  N1   C2    aromatic  1.329  0.020  1.329
 N8M  C2   H2    single    0.930  0.020  1.080
 N8M  C6   N1    aromatic  1.339  0.020  1.339
 N8M  C5   C6    aromatic  1.406  0.020  1.406
 N8M  N6   C6    single    1.335  0.020  1.335
 N8M  N6   HN6   single    0.860  0.020  1.020
 N8M  N6   HN6A  single    0.860  0.020  1.020
 N8M  N7   C5    aromatic  1.370  0.020  1.370
 N8M  C8   N7    aromatic  1.303  0.020  1.303
 N8M  C9   C8    single    1.483  0.020  1.483
 N8M  O2'  C2'   single    1.401  0.020  1.401
 N8M  C2'  C3'   single    1.540  0.020  1.540
 N8M  C2'  H2'   single    0.970  0.020  1.090
 N8M  O2'  HO2'  single    0.850  0.020  0.980
 N8M  O3'  C3'   single    1.400  0.020  1.400
 N8M  C3'  H3'   single    0.970  0.020  1.090
 N8M  O3'  HO3'  single    0.850  0.020  0.980
 N8M  C9   H9    single    0.970  0.020  1.090
 N8M  C9   H9A   single    0.970  0.020  1.090
 N8M  C9   H9B   single    0.970  0.020  1.090

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
 N8M  HGB   CG   HGA  107.78  3.000
 N8M  HGB   CG   HG   107.70  3.000
 N8M  HGA   CG   HG   107.62  3.000
 N8M  HGB   CG   N2   110.24  3.000
 N8M  HGA   CG   N2   109.89  3.000
 N8M  HG    CG   N2   113.41  3.000
 N8M  C5'   N2   CE   113.65  3.000
 N8M  C5'   N2   CG   110.78  3.000
 N8M  CE    N2   CG   110.69  3.000
 N8M  HEB   CE   HEA  107.52  3.000
 N8M  HEB   CE   HE   107.62  3.000
 N8M  HEA   CE   HE   107.82  3.000
 N8M  HEB   CE   N2   109.34  3.000
 N8M  HEA   CE   N2   111.17  3.000
 N8M  HE    CE   N2   113.15  3.000
 N8M  H5'A  C5'  H5'  106.32  3.000
 N8M  H5'A  C5'  C4'  106.32  3.000
 N8M  H5'   C5'  C4'  108.86  3.000
 N8M  H5'A  C5'  N2   107.37  3.000
 N8M  H5'   C5'  N2   112.70  3.000
 N8M  C4'   C5'  N2   114.73  3.000
 N8M  H4'   C4'  C3'  109.42  3.000
 N8M  H4'   C4'  O4'  110.65  3.000
 N8M  C3'   C4'  O4'  103.20  3.000
 N8M  H4'   C4'  C5'  108.90  3.000
 N8M  C3'   C4'  C5'  113.02  3.000
 N8M  O4'   C4'  C5'  111.57  3.000
 N8M  C1'   O4'  C4'  109.35  3.000
 N8M  H1'   C1'  C2'  108.06  3.000
 N8M  H1'   C1'  N9   105.30  3.000
 N8M  C2'   C1'  N9   116.07  3.000
 N8M  H1'   C1'  O4'  111.17  3.000
 N8M  C2'   C1'  O4'  107.40  3.000
 N8M  N9    C1'  O4'  108.87  3.000
 N8M  C8    N9   C4   106.41  3.000
 N8M  C4    N9   C1'  123.74  3.000
 N8M  C8    N9   C1'  129.83  3.000
 N8M  C5    C4   N3   126.43  3.000
 N8M  N3    C4   N9   128.20  3.000
 N8M  C5    C4   N9   105.37  3.000
 N8M  C2    N3   C4   111.79  3.000
 N8M  H2    C2   N1   115.51  3.000
 N8M  H2    C2   N3   116.14  3.000
 N8M  N1    C2   N3   128.36  3.000
 N8M  C6    N1   C2   119.06  3.000
 N8M  C5    C6   N6   122.79  3.000
 N8M  N6    C6   N1   119.26  3.000
 N8M  C5    C6   N1   117.95  3.000
 N8M  HN6A  N6   HN6  118.35  3.000
 N8M  HN6A  N6   C6   121.16  3.000
 N8M  HN6   N6   C6   120.30  3.000
 N8M  N7    C5   C6   132.93  3.000
 N8M  N7    C5   C4   110.66  3.000
 N8M  C6    C5   C4   116.41  3.000
 N8M  C8    N7   C5   105.35  3.000
 N8M  C9    C8   N7   123.78  3.000
 N8M  C9    C8   N9   124.01  3.000
 N8M  N7    C8   N9   112.21  3.000
 N8M  H2'   C2'  C3'  112.01  3.000
 N8M  H2'   C2'  O2'  111.00  3.000
 N8M  C3'   C2'  O2'  111.14  3.000
 N8M  H2'   C2'  C1'  111.55  3.000
 N8M  C3'   C2'  C1'  102.75  3.000
 N8M  O2'   C2'  C1'  108.04  3.000
 N8M  HO2'  O2'  C2'  107.21  3.000
 N8M  H3'   C3'  O3'  111.07  3.000
 N8M  H3'   C3'  C2'  109.66  3.000
 N8M  O3'   C3'  C2'  113.30  3.000
 N8M  H3'   C3'  C4'  109.03  3.000
 N8M  O3'   C3'  C4'  110.76  3.000
 N8M  C2'   C3'  C4'  102.66  3.000
 N8M  HO3'  O3'  C3'  109.04  3.000
 N8M  H9B   C9   H9A  108.34  3.000
 N8M  H9B   C9   H9   108.06  3.000
 N8M  H9A   C9   H9   107.61  3.000
 N8M  H9B   C9   C8   111.94  3.000
 N8M  H9A   C9   C8   108.71  3.000
 N8M  H9    C9   C8   112.03  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
 N8M  CONST_01  C5    N7   C8  N9     0.00   0.0  0
 N8M  CONST_02  C6    C5   C4  N9   180.00   0.0  0
 N8M  CONST_03  N7    C5   C4  N9     0.00   0.0  0
 N8M  CONST_04  C2    N3   C4  N9   180.00   0.0  0
 N8M  CONST_05  N7    C8   N9  C4     0.00   0.0  0
 N8M  CONST_06  N1    C6   C5  C4     0.00   0.0  0
 N8M  CONST_07  C8    N7   C5  C4     0.00   0.0  0
 N8M  CONST_08  N1    C2   N3  C4     0.00   0.0  0
 N8M  CONST_09  C8    N9   C4  N3   180.00   0.0  0
 N8M  CONST_10  C6    C5   C4  N3     0.00   0.0  0
 N8M  CONST_11  N7    C5   C4  N3   180.00   0.0  0
 N8M  CONST_12  C6    N1   C2  N3     0.00   0.0  0
 N8M  CONST_13  C5    C4   N3  C2     0.00   0.0  0
 N8M  CONST_14  C5    C6   N1  C2     0.00   0.0  0
 N8M  CONST_15  N7    C5   C6  N1   180.00   0.0  0
 N8M  CONST_16  C8    N7   C5  C6   180.00   0.0  0
 N8M  CONST_17  C8    N9   C4  C5     0.00   0.0  0
 N8M  CONST_18  N7    C8   N9  C1'  180.00   0.0  0
 N8M  CONST_19  C5    C4   N9  C1'  180.00   0.0  0
 N8M  CONST_20  N3    C4   N9  C1'    0.00   0.0  0
 N8M  CONST_21  C9    C8   N9  C1'    0.00   0.0  0
 N8M  CONST_22  C9    C8   N9  C4   180.00   0.0  0
 N8M  CONST_23  N6    C6   C5  C4   180.00   0.0  0
 N8M  CONST_24  N6    C6   N1  C2   180.00   0.0  0
 N8M  CONST_25  N7    C5   C6  N6     0.00   0.0  0
 N8M  CONST_26  C9    C8   N7  C5   180.00   0.0  0
 N8M  CONST_27  H2    C2   N3  C4   180.00   0.0  0
 N8M  CONST_28  HN6   N6   C6  N1     0.00   0.0  0
 N8M  CONST_29  HN6A  N6   C6  N1   180.00   0.0  0
 N8M  Var_01    H9    C9   C8  N9    61.20  30.0  2
 N8M  Var_02    C4'   C5'  N2  CG   165.29  30.0  3
 N8M  Var_03    HE    CE   N2  CG    64.18  30.0  3
 N8M  Var_04    HG    CG   N2  CE   -64.01  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
 N8M  chir_01  C4'  C5'  O4'  C3'  negativ
 N8M  chir_02  C1'  O4'  N9   C2'  negativ
 N8M  chir_03  C2'  O2'  C1'  C3'  negativ
 N8M  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
 N8M  plan-1  C1'   0.020
 N8M  plan-1  N9    0.020
 N8M  plan-1  C4    0.020
 N8M  plan-1  N3    0.020
 N8M  plan-1  C2    0.020
 N8M  plan-1  N1    0.020
 N8M  plan-1  C6    0.020
 N8M  plan-1  N6    0.020
 N8M  plan-1  C5    0.020
 N8M  plan-1  N7    0.020
 N8M  plan-1  C8    0.020
 N8M  plan-1  C9    0.020
 N8M  plan-1  H2    0.020
 N8M  plan-2  C6    0.020
 N8M  plan-2  N6    0.020
 N8M  plan-2  HN6   0.020
 N8M  plan-2  HN6A  0.020

