# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 04:59:50 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 5'-[(3-aminopropyl)(methyl)amino]-5'-deoxy-8-methyladenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCCN)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
 A8M  A8M  5'-[(3-aminopropyl)(methyl)amino]-5'-deoxy-8-methyladenosine  ligand  50  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A8M
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
 A8M  N1    N  NH2   0  -0.800  -5.7437   3.7072   0.1756
 A8M  C2    C  CH2   0  -0.272  -5.3716   2.4141   0.7310
 A8M  C4    C  CH2   0  -0.457  -4.5769   1.5977  -0.2771
 A8M  C5    C  CH2   0  -0.265  -4.1747   0.2465   0.2970
 A8M  N2    N  NT    0  -0.413  -3.2323  -0.4852  -0.5339
 A8M  C6    C  CH3   0  -0.541  -3.8166  -0.9072  -1.7904
 A8M  C5'   C  CH2   0  -0.282  -2.6564  -1.5944   0.1929
 A8M  C4'   C  CH1   0  -0.023  -1.4396  -2.2156  -0.4827
 A8M  O4'   O  O2    0  -0.490  -0.5003  -1.2143  -0.8935
 A8M  C1'   C  CH1   0   0.231   0.7024  -1.3624  -0.1954
 A8M  N5    N  NR5   0  -0.583   1.3113  -0.0763   0.0380
 A8M  C11   C  CR56  0   0.488   2.6107   0.2094  -0.2851
 A8M  N4    N  N     0  -0.462   3.5164  -0.5917  -0.8402
 A8M  C10   C  CR16  0   0.041   4.6758   0.0206  -1.0101
 A8M  N3    N  N     0  -0.474   5.0023   1.2717  -0.6996
 A8M  C9    C  CR6   0   0.446   4.0778   2.0657  -0.1454
 A8M  N7    N  NH2   0  -0.819   4.3960   3.3264   0.1571
 A8M  C12   C  CR56  0  -0.003   2.8002   1.5274   0.0858
 A8M  N6    N  N     0  -0.467   1.6515   2.0482   0.6192
 A8M  C7    C  CR5   0   0.457   0.7811   1.0784   0.5826
 A8M  C2'   C  CH1   0  -0.052   0.3511  -2.1608   1.0558
 A8M  O2'   O  OH1   0  -0.653   1.4974  -2.7670   1.5736
 A8M  C3'   C  CH1   0  -0.029  -0.6894  -3.1290   0.4820
 A8M  O3'   O  OH1   0  -0.670  -0.0667  -4.1594  -0.2414
 A8M  C8    C  CH3   0  -0.792  -0.6181   1.2111   1.0555
 A8M  HN1   H  HNH2  0   0.337  -6.4203   3.5700  -0.5654
 A8M  HN1A  H  HNH2  0   0.346  -6.2228   4.2510   0.8819
 A8M  H2    H  HCH2  0   0.213  -4.7528   2.5883   1.6157
 A8M  H2A   H  HCH2  0   0.190  -6.2327   1.8217   1.0739
 A8M  H4    H  HCH2  0   0.223  -5.1781   1.4737  -1.1830
 A8M  H4A   H  HCH2  0   0.221  -3.6773   2.1494  -0.5652
 A8M  H5    H  HCH2  0   0.225  -3.6921   0.4227   1.2639
 A8M  H5A   H  HCH2  0   0.199  -5.0795  -0.3493   0.5108
 A8M  H6    H  HCH3  0   0.244  -4.2131  -0.0522  -2.3357
 A8M  H6A   H  HCH3  0   0.243  -3.0653  -1.3675  -2.4316
 A8M  H6B   H  HCH3  0   0.193  -4.6347  -1.6322  -1.6579
 A8M  H5'   H  HCH2  0   0.233  -2.3721  -1.2378   1.1868
 A8M  H5'A  H  HCH2  0   0.218  -3.3833  -2.4096   0.3581
 A8M  H4'   H  HCH1  0   0.259  -1.7464  -2.7777  -1.3694
 A8M  H1'   H  HCH1  0   0.255   1.4414  -1.9217  -0.7817
 A8M  H10   H  HCR6  0   0.249   5.4670  -0.5706  -1.4591
 A8M  HN7   H  HNH2  0   0.402   5.3352   3.6593   0.0230
 A8M  HN7A  H  HNH2  0   0.409   3.7342   3.9343   0.6065
 A8M  H2'   H  HCH1  0   0.247  -0.1335  -1.5117   1.7950
 A8M  HO2'  H  HOH1  0   0.469   1.3239  -3.0351   2.4817
 A8M  H3'   H  HCH1  0   0.249  -1.3534  -3.5278   1.2605
 A8M  HO3'  H  HOH1  0   0.448   0.6647  -4.4950   0.2909
 A8M  H8    H  HCH3  0   0.255  -0.8236   0.5549   1.9025
 A8M  H8A   H  HCH3  0   0.271  -0.7783   2.2357   1.3825
 A8M  H8B   H  HCH3  0   0.284  -1.3358   0.9736   0.2695

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
 A8M  N1   C2    single    1.456  0.020  1.456
 A8M  C2   C4    single    1.521  0.020  1.521
 A8M  C4   C5    single    1.522  0.020  1.522
 A8M  C5   N2    single    1.454  0.020  1.454
 A8M  N2   C6    single    1.449  0.020  1.449
 A8M  N2   C5'   single    1.446  0.020  1.446
 A8M  C5'  C4'   single    1.524  0.020  1.524
 A8M  C4'  O4'   single    1.433  0.020  1.433
 A8M  C4'  C3'   single    1.526  0.020  1.526
 A8M  O4'  C1'   single    1.398  0.020  1.398
 A8M  C1'  N5    single    1.442  0.020  1.442
 A8M  C1'  C2'   single    1.525  0.020  1.525
 A8M  N5   C11   aromatic  1.369  0.020  1.369
 A8M  N5   C7    aromatic  1.382  0.020  1.382
 A8M  C11  N4    aromatic  1.330  0.020  1.330
 A8M  C11  C12   aromatic  1.382  0.020  1.382
 A8M  N4   C10   aromatic  1.322  0.020  1.322
 A8M  C10  N3    aromatic  1.330  0.020  1.330
 A8M  N3   C9    aromatic  1.339  0.020  1.339
 A8M  C9   N7    single    1.335  0.020  1.335
 A8M  C9   C12   aromatic  1.405  0.020  1.405
 A8M  C12  N6    aromatic  1.369  0.020  1.369
 A8M  N6   C7    aromatic  1.304  0.020  1.304
 A8M  C7   C8    single    1.483  0.020  1.483
 A8M  C2'  O2'   single    1.396  0.020  1.396
 A8M  C2'  C3'   single    1.533  0.020  1.533
 A8M  C3'  O3'   single    1.405  0.020  1.405
 A8M  N1   HN1   single    0.890  0.020  1.040
 A8M  N1   HN1A  single    0.890  0.020  1.040
 A8M  C2   H2    single    0.970  0.020  1.090
 A8M  C2   H2A   single    0.970  0.020  1.090
 A8M  C4   H4    single    0.970  0.020  1.090
 A8M  C4   H4A   single    0.970  0.020  1.090
 A8M  C5   H5    single    0.970  0.020  1.090
 A8M  C5   H5A   single    0.970  0.020  1.090
 A8M  C6   H6    single    0.970  0.020  1.090
 A8M  C6   H6A   single    0.970  0.020  1.090
 A8M  C6   H6B   single    0.970  0.020  1.090
 A8M  C5'  H5'   single    0.970  0.020  1.090
 A8M  C5'  H5'A  single    0.970  0.020  1.090
 A8M  C4'  H4'   single    0.970  0.020  1.090
 A8M  C1'  H1'   single    0.970  0.020  1.090
 A8M  C10  H10   single    0.930  0.020  1.080
 A8M  N7   HN7   single    0.860  0.020  1.020
 A8M  N7   HN7A  single    0.860  0.020  1.020
 A8M  C2'  H2'   single    0.970  0.020  1.090
 A8M  O2'  HO2'  single    0.850  0.020  0.980
 A8M  C3'  H3'   single    0.970  0.020  1.090
 A8M  O3'  HO3'  single    0.850  0.020  0.980
 A8M  C8   H8    single    0.970  0.020  1.090
 A8M  C8   H8A   single    0.970  0.020  1.090
 A8M  C8   H8B   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
 A8M  HN1A  N1   HN1  105.49  3.000
 A8M  HN1A  N1   C2   109.39  3.000
 A8M  HN1   N1   C2   109.24  3.000
 A8M  H2A   C2   H2   106.05  3.000
 A8M  H2A   C2   C4   109.05  3.000
 A8M  H2    C2   C4   109.02  3.000
 A8M  H2A   C2   N1   113.41  3.000
 A8M  H2    C2   N1   108.17  3.000
 A8M  C4    C2   N1   110.94  3.000
 A8M  H4A   C4   H4   106.91  3.000
 A8M  H4A   C4   C5   109.25  3.000
 A8M  H4    C4   C5   110.91  3.000
 A8M  H4A   C4   C2   109.47  3.000
 A8M  H4    C4   C2   108.81  3.000
 A8M  C5    C4   C2   111.38  3.000
 A8M  H5A   C5   H5   106.08  3.000
 A8M  H5A   C5   N2   111.74  3.000
 A8M  H5    C5   N2   107.46  3.000
 A8M  H5A   C5   C4   109.60  3.000
 A8M  H5    C5   C4   107.86  3.000
 A8M  N2    C5   C4   113.73  3.000
 A8M  C5'   N2   C6   111.92  3.000
 A8M  C5'   N2   C5   110.92  3.000
 A8M  C6    N2   C5   112.39  3.000
 A8M  H6B   C6   H6A  107.75  3.000
 A8M  H6B   C6   H6   107.86  3.000
 A8M  H6A   C6   H6   106.74  3.000
 A8M  H6B   C6   N2   112.78  3.000
 A8M  H6A   C6   N2   110.81  3.000
 A8M  H6    C6   N2   110.64  3.000
 A8M  H5'A  C5'  H5'  106.01  3.000
 A8M  H5'A  C5'  C4'  106.91  3.000
 A8M  H5'   C5'  C4'  109.16  3.000
 A8M  H5'A  C5'  N2   112.29  3.000
 A8M  H5'   C5'  N2   108.08  3.000
 A8M  C4'   C5'  N2   114.07  3.000
 A8M  H4'   C4'  C3'  110.05  3.000
 A8M  H4'   C4'  O4'  108.09  3.000
 A8M  C3'   C4'  O4'  106.09  3.000
 A8M  H4'   C4'  C5'  110.18  3.000
 A8M  C3'   C4'  C5'  110.87  3.000
 A8M  O4'   C4'  C5'  111.44  3.000
 A8M  C1'   O4'  C4'  110.28  3.000
 A8M  H1'   C1'  C2'  109.08  3.000
 A8M  H1'   C1'  N5   104.88  3.000
 A8M  C2'   C1'  N5   115.55  3.000
 A8M  H1'   C1'  O4'  111.51  3.000
 A8M  C2'   C1'  O4'  105.48  3.000
 A8M  N5    C1'  O4'  110.46  3.000
 A8M  C7    N5   C11  106.42  3.000
 A8M  C7    N5   C1'  130.30  3.000
 A8M  C11   N5   C1'  123.28  3.000
 A8M  C12   C11  N4   126.35  3.000
 A8M  C12   C11  N5   105.41  3.000
 A8M  N4    C11  N5   128.24  3.000
 A8M  C10   N4   C11  111.83  3.000
 A8M  H10   C10  N3   115.49  3.000
 A8M  H10   C10  N4   116.13  3.000
 A8M  N3    C10  N4   128.39  3.000
 A8M  C9    N3   C10  119.02  3.000
 A8M  C12   C9   N7   122.75  3.000
 A8M  C12   C9   N3   117.95  3.000
 A8M  N7    C9   N3   119.30  3.000
 A8M  HN7A  N7   HN7  118.33  3.000
 A8M  HN7A  N7   C9   121.05  3.000
 A8M  HN7   N7   C9   120.33  3.000
 A8M  N6    C12  C9   132.91  3.000
 A8M  N6    C12  C11  110.62  3.000
 A8M  C9    C12  C11  116.47  3.000
 A8M  C7    N6   C12  105.44  3.000
 A8M  C8    C7   N6   123.67  3.000
 A8M  C8    C7   N5   124.21  3.000
 A8M  N6    C7   N5   112.11  3.000
 A8M  H2'   C2'  C3'  109.04  3.000
 A8M  H2'   C2'  O2'  111.70  3.000
 A8M  C3'   C2'  O2'  114.95  3.000
 A8M  H2'   C2'  C1'  110.18  3.000
 A8M  C3'   C2'  C1'  100.36  3.000
 A8M  O2'   C2'  C1'  110.02  3.000
 A8M  HO2'  O2'  C2'  108.83  3.000
 A8M  H3'   C3'  O3'  111.51  3.000
 A8M  H3'   C3'  C2'  111.99  3.000
 A8M  O3'   C3'  C2'  110.81  3.000
 A8M  H3'   C3'  C4'  111.61  3.000
 A8M  O3'   C3'  C4'  109.36  3.000
 A8M  C2'   C3'  C4'  101.09  3.000
 A8M  HO3'  O3'  C3'  107.89  3.000
 A8M  H8B   C8   H8A  108.97  3.000
 A8M  H8B   C8   H8   107.74  3.000
 A8M  H8A   C8   H8   107.80  3.000
 A8M  H8B   C8   C7   111.81  3.000
 A8M  H8A   C8   C7   108.61  3.000
 A8M  H8    C8   C7   111.81  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
 A8M  CONST_01  C10   N4   C11  N5    180.00   0.0  0
 A8M  CONST_02  C9    C12  C11  N5    180.00   0.0  0
 A8M  CONST_03  N6    C12  C11  N5      0.00   0.0  0
 A8M  CONST_04  C12   N6   C7   N5      0.00   0.0  0
 A8M  CONST_05  N6    C7   N5   C11     0.00   0.0  0
 A8M  CONST_06  N3    C10  N4   C11     0.00   0.0  0
 A8M  CONST_07  N3    C9   C12  C11     0.00   0.0  0
 A8M  CONST_08  C7    N6   C12  C11     0.00   0.0  0
 A8M  CONST_09  C7    N5   C11  N4    180.00   0.0  0
 A8M  CONST_10  C9    C12  C11  N4      0.00   0.0  0
 A8M  CONST_11  N6    C12  C11  N4    180.00   0.0  0
 A8M  CONST_12  C9    N3   C10  N4      0.00   0.0  0
 A8M  CONST_13  C12   C11  N4   C10     0.00   0.0  0
 A8M  CONST_14  C12   C9   N3   C10     0.00   0.0  0
 A8M  CONST_15  N6    C12  C9   N3    180.00   0.0  0
 A8M  CONST_16  C7    N6   C12  C9    180.00   0.0  0
 A8M  CONST_17  C7    N5   C11  C12     0.00   0.0  0
 A8M  CONST_18  N4    C11  N5   C1'     0.00   0.0  0
 A8M  CONST_19  C12   C11  N5   C1'   180.00   0.0  0
 A8M  CONST_20  N6    C7   N5   C1'   180.00   0.0  0
 A8M  CONST_21  C8    C7   N5   C1'     0.00   0.0  0
 A8M  CONST_22  C8    C7   N5   C11   180.00   0.0  0
 A8M  CONST_23  N7    C9   C12  C11   180.00   0.0  0
 A8M  CONST_24  N7    C9   N3   C10   180.00   0.0  0
 A8M  CONST_25  N6    C12  C9   N7      0.00   0.0  0
 A8M  CONST_26  C8    C7   N6   C12   180.00   0.0  0
 A8M  CONST_27  H10   C10  N4   C11   180.00   0.0  0
 A8M  CONST_28  HN7   N7   C9   N3      0.00   0.0  0
 A8M  CONST_29  HN7A  N7   C9   N3    180.00   0.0  0
 A8M  Var_01    H8    C8   C7   N5     64.27  30.0  2
 A8M  Var_02    C4'   C5'  N2   C5   -166.80  30.0  3
 A8M  Var_03    C5    C4   C2   N1    179.63  30.0  3
 A8M  Var_04    N2    C5   C4   C2   -170.46  30.0  3
 A8M  Var_05    C6    N2   C5   C4    -67.17  30.0  3
 A8M  Var_06    HN1   N1   C2   C4     68.29  30.0  3
 A8M  Var_07    H6    C6   N2   C5     56.37  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
 A8M  chir_01  C4'  C5'  O4'  C3'  negativ
 A8M  chir_02  C1'  O4'  N5   C2'  negativ
 A8M  chir_03  C2'  O2'  C1'  C3'  negativ
 A8M  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
 A8M  plan-1  C1'   0.020
 A8M  plan-1  N5    0.020
 A8M  plan-1  C11   0.020
 A8M  plan-1  N4    0.020
 A8M  plan-1  C10   0.020
 A8M  plan-1  N3    0.020
 A8M  plan-1  C9    0.020
 A8M  plan-1  N7    0.020
 A8M  plan-1  C12   0.020
 A8M  plan-1  N6    0.020
 A8M  plan-1  C7    0.020
 A8M  plan-1  C8    0.020
 A8M  plan-1  H10   0.020
 A8M  plan-2  C9    0.020
 A8M  plan-2  N7    0.020
 A8M  plan-2  HN7   0.020
 A8M  plan-2  HN7A  0.020

