# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 20:59:56 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-[{[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)amino]propanamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCC(N)=O)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
 C8M  C8M  '3-[{[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)amino]propanamide (non-preferred name)'  ligand  49  26  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C8M
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
 C8M  N1    N  NH2   0  -0.805  -5.6007   3.3771   0.0574
 C8M  C1    C  C     0   0.530  -5.3598   2.1146   0.4459
 C8M  C4    C  CH2   0  -0.603  -4.3212   1.3880  -0.3844
 C8M  C5    C  CH2   0  -0.259  -3.9824   0.0113   0.1648
 C8M  N2    N  NT    0  -0.416  -2.9150  -0.6323  -0.5852
 C8M  C6    C  CH3   0  -0.543  -3.3585  -1.0703  -1.8940
 C8M  C5'   C  CH2   0  -0.284  -2.3393  -1.7143   0.1843
 C8M  C4'   C  CH1   0  -0.027  -1.0878  -2.3255  -0.4322
 C8M  O4'   O  O2    0  -0.490  -0.1613  -1.3171  -0.8497
 C8M  C1'   C  CH1   0   0.229   1.0259  -1.4123  -0.1163
 C8M  N5    N  NR5   0  -0.583   1.5941  -0.1023   0.0840
 C8M  C11   C  CR56  0   0.489   2.8774   0.2221  -0.2658
 C8M  N4    N  N     0  -0.461   3.8080  -0.5626  -0.8015
 C8M  C10   C  CR16  0   0.041   4.9366   0.0904  -1.0204
 C8M  N3    N  N     0  -0.472   5.2115   1.3679  -0.7735
 C8M  C9    C  CR6   0   0.440   4.2633   2.1438  -0.2358
 C8M  N7    N  NH2   0  -0.817   4.5403   3.4258   0.0287
 C8M  C12   C  CR56  0  -0.001   3.0161   1.5619   0.0458
 C8M  N6    N  N     0  -0.467   1.8515   2.0584   0.5683
 C8M  C7    C  CR5   0   0.459   1.0214   1.0535   0.5824
 C8M  C2'   C  CH1   0  -0.052   0.6622  -2.1795   1.1513
 C8M  O2'   O  OH1   0  -0.654   1.8085  -2.7493   1.7096
 C8M  C3'   C  CH1   0  -0.028  -0.3453  -3.1868   0.5851
 C8M  O3'   O  OH1   0  -0.670   0.3151  -4.2288  -0.0862
 C8M  C8    C  CH3   0  -0.798  -0.3776   1.1491   1.0658
 C8M  O1    O  O     0  -0.496  -5.9363   1.5921   1.3894
 C8M  HN1   H  HNH2  0   0.406  -5.1138   3.7979  -0.7148
 C8M  HN1A  H  HNH2  0   0.397  -6.2880   3.9369   0.5345
 C8M  H4    H  HCH2  0   0.274  -4.6982   1.3287  -1.4091
 C8M  H4A   H  HCH2  0   0.267  -3.4127   1.9954  -0.4342
 C8M  H5    H  HCH2  0   0.236  -3.6452   0.1244   1.1973
 C8M  H5A   H  HCH2  0   0.210  -4.8857  -0.6176   0.2001
 C8M  H6    H  HCH3  0   0.244  -3.7731  -0.2356  -2.4577
 C8M  H6A   H  HCH3  0   0.245  -2.5253  -1.4560  -2.4805
 C8M  H6B   H  HCH3  0   0.197  -4.1283  -1.8550  -1.8413
 C8M  H5'   H  HCH2  0   0.235  -2.0987  -1.3272   1.1790
 C8M  H5'A  H  HCH2  0   0.222  -3.0536  -2.5425   0.3400
 C8M  H4'   H  HCH1  0   0.260  -1.3540  -2.9276  -1.3058
 C8M  H1'   H  HCH1  0   0.256   1.7929  -1.9722  -0.6645
 C8M  H10   H  HCR6  0   0.250   5.7448  -0.4854  -1.4585
 C8M  HN7   H  HNH2  0   0.400   5.3958   3.8276  -0.3149
 C8M  HN7A  H  HNH2  0   0.408   3.8062   4.0579   0.2972
 C8M  H2'   H  HCH1  0   0.250   0.1512  -1.5196   1.8624
 C8M  HO2'  H  HOH1  0   0.469   1.6268  -2.9795   2.6263
 C8M  H3'   H  HCH1  0   0.250  -1.0209  -3.5727   1.3600
 C8M  HO3'  H  HOH1  0   0.448   1.0380  -4.5329   0.4759
 C8M  H8    H  HCH3  0   0.258  -0.5344   0.5541   1.9675
 C8M  H8A   H  HCH3  0   0.272  -0.5916   2.1864   1.3114
 C8M  H8B   H  HCH3  0   0.284  -1.0900   0.8065   0.3141

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
 C8M  N1   C1    single    1.343  0.020  1.343
 C8M  C1   C4    single    1.515  0.020  1.515
 C8M  C1   O1    double    1.223  0.020  1.223
 C8M  C4   C5    single    1.520  0.020  1.520
 C8M  C5   N2    single    1.455  0.020  1.455
 C8M  N2   C6    single    1.450  0.020  1.450
 C8M  N2   C5'   single    1.447  0.020  1.447
 C8M  C5'  C4'   single    1.523  0.020  1.523
 C8M  C4'  O4'   single    1.432  0.020  1.432
 C8M  C4'  C3'   single    1.526  0.020  1.526
 C8M  O4'  C1'   single    1.399  0.020  1.399
 C8M  C1'  N5    single    1.442  0.020  1.442
 C8M  C1'  C2'   single    1.526  0.020  1.526
 C8M  N5   C11   aromatic  1.369  0.020  1.369
 C8M  N5   C7    aromatic  1.383  0.020  1.383
 C8M  C11  N4    aromatic  1.330  0.020  1.330
 C8M  C11  C12   aromatic  1.383  0.020  1.383
 C8M  N4   C10   aromatic  1.322  0.020  1.322
 C8M  C10  N3    aromatic  1.330  0.020  1.330
 C8M  N3   C9    aromatic  1.338  0.020  1.338
 C8M  C9   N7    single    1.338  0.020  1.338
 C8M  C9   C12   aromatic  1.405  0.020  1.405
 C8M  C12  N6    aromatic  1.370  0.020  1.370
 C8M  N6   C7    aromatic  1.304  0.020  1.304
 C8M  C7   C8    single    1.483  0.020  1.483
 C8M  C2'  O2'   single    1.397  0.020  1.397
 C8M  C2'  C3'   single    1.533  0.020  1.533
 C8M  C3'  O3'   single    1.404  0.020  1.404
 C8M  N1   HN1   single    0.860  0.020  1.020
 C8M  N1   HN1A  single    0.860  0.020  1.020
 C8M  C4   H4    single    0.970  0.020  1.090
 C8M  C4   H4A   single    0.970  0.020  1.090
 C8M  C5   H5    single    0.970  0.020  1.090
 C8M  C5   H5A   single    0.970  0.020  1.090
 C8M  C6   H6    single    0.970  0.020  1.090
 C8M  C6   H6A   single    0.970  0.020  1.090
 C8M  C6   H6B   single    0.970  0.020  1.090
 C8M  C5'  H5'   single    0.970  0.020  1.090
 C8M  C5'  H5'A  single    0.970  0.020  1.090
 C8M  C4'  H4'   single    0.970  0.020  1.090
 C8M  C1'  H1'   single    0.970  0.020  1.090
 C8M  C10  H10   single    0.930  0.020  1.080
 C8M  N7   HN7   single    0.860  0.020  1.020
 C8M  N7   HN7A  single    0.860  0.020  1.020
 C8M  C2'  H2'   single    0.970  0.020  1.090
 C8M  O2'  HO2'  single    0.850  0.020  0.980
 C8M  C3'  H3'   single    0.970  0.020  1.090
 C8M  O3'  HO3'  single    0.850  0.020  0.980
 C8M  C8   H8    single    0.970  0.020  1.090
 C8M  C8   H8A   single    0.970  0.020  1.090
 C8M  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
 C8M  HN1A  N1   HN1  117.51  3.000
 C8M  HN1A  N1   C1   120.55  3.000
 C8M  HN1   N1   C1   121.94  3.000
 C8M  O1    C1   C4   122.75  3.000
 C8M  O1    C1   N1   122.71  3.000
 C8M  C4    C1   N1   114.54  3.000
 C8M  H4A   C4   H4   105.89  3.000
 C8M  H4A   C4   C5   109.52  3.000
 C8M  H4    C4   C5   111.48  3.000
 C8M  H4A   C4   C1   109.15  3.000
 C8M  H4    C4   C1   107.64  3.000
 C8M  C5    C4   C1   112.89  3.000
 C8M  H5A   C5   H5   106.39  3.000
 C8M  H5A   C5   N2   111.45  3.000
 C8M  H5    C5   N2   107.86  3.000
 C8M  H5A   C5   C4   110.24  3.000
 C8M  H5    C5   C4   108.45  3.000
 C8M  N2    C5   C4   112.20  3.000
 C8M  C5'   N2   C6   112.08  3.000
 C8M  C5'   N2   C5   110.40  3.000
 C8M  C6    N2   C5   112.00  3.000
 C8M  H6B   C6   H6A  107.95  3.000
 C8M  H6B   C6   H6   107.75  3.000
 C8M  H6A   C6   H6   106.49  3.000
 C8M  H6B   C6   N2   112.72  3.000
 C8M  H6A   C6   N2   111.04  3.000
 C8M  H6    C6   N2   110.62  3.000
 C8M  H5'A  C5'  H5'  106.22  3.000
 C8M  H5'A  C5'  C4'  106.71  3.000
 C8M  H5'   C5'  C4'  109.23  3.000
 C8M  H5'A  C5'  N2   112.23  3.000
 C8M  H5'   C5'  N2   107.84  3.000
 C8M  C4'   C5'  N2   114.31  3.000
 C8M  H4'   C4'  C3'  109.88  3.000
 C8M  H4'   C4'  O4'  108.20  3.000
 C8M  C3'   C4'  O4'  106.09  3.000
 C8M  H4'   C4'  C5'  110.13  3.000
 C8M  C3'   C4'  C5'  110.88  3.000
 C8M  O4'   C4'  C5'  111.54  3.000
 C8M  C1'   O4'  C4'  110.39  3.000
 C8M  H1'   C1'  C2'  108.99  3.000
 C8M  H1'   C1'  N5   104.93  3.000
 C8M  C2'   C1'  N5   115.81  3.000
 C8M  H1'   C1'  O4'  111.49  3.000
 C8M  C2'   C1'  O4'  105.52  3.000
 C8M  N5    C1'  O4'  110.21  3.000
 C8M  C7    N5   C11  106.39  3.000
 C8M  C7    N5   C1'  130.25  3.000
 C8M  C11   N5   C1'  123.31  3.000
 C8M  C12   C11  N4   126.33  3.000
 C8M  C12   C11  N5   105.43  3.000
 C8M  N4    C11  N5   128.24  3.000
 C8M  C10   N4   C11  111.87  3.000
 C8M  H10   C10  N3   115.52  3.000
 C8M  H10   C10  N4   116.15  3.000
 C8M  N3    C10  N4   128.33  3.000
 C8M  C9    N3   C10  119.02  3.000
 C8M  C12   C9   N7   122.75  3.000
 C8M  C12   C9   N3   118.01  3.000
 C8M  N7    C9   N3   119.23  3.000
 C8M  HN7A  N7   HN7  117.47  3.000
 C8M  HN7A  N7   C9   120.27  3.000
 C8M  HN7   N7   C9   119.43  3.000
 C8M  N6    C12  C9   132.95  3.000
 C8M  N6    C12  C11  110.61  3.000
 C8M  C9    C12  C11  116.44  3.000
 C8M  C7    N6   C12  105.44  3.000
 C8M  C8    C7   N6   123.67  3.000
 C8M  C8    C7   N5   124.19  3.000
 C8M  N6    C7   N5   112.13  3.000
 C8M  H2'   C2'  C3'  109.19  3.000
 C8M  H2'   C2'  O2'  111.64  3.000
 C8M  C3'   C2'  O2'  114.77  3.000
 C8M  H2'   C2'  C1'  110.32  3.000
 C8M  C3'   C2'  C1'  100.38  3.000
 C8M  O2'   C2'  C1'  109.98  3.000
 C8M  HO2'  O2'  C2'  108.87  3.000
 C8M  H3'   C3'  O3'  111.46  3.000
 C8M  H3'   C3'  C2'  112.00  3.000
 C8M  O3'   C3'  C2'  110.79  3.000
 C8M  H3'   C3'  C4'  111.69  3.000
 C8M  O3'   C3'  C4'  109.20  3.000
 C8M  C2'   C3'  C4'  101.25  3.000
 C8M  HO3'  O3'  C3'  107.92  3.000
 C8M  H8B   C8   H8A  109.07  3.000
 C8M  H8B   C8   H8   107.71  3.000
 C8M  H8A   C8   H8   107.76  3.000
 C8M  H8B   C8   C7   111.79  3.000
 C8M  H8A   C8   C7   108.71  3.000
 C8M  H8    C8   C7   111.69  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
 C8M  CONST_01  C10   N4   C11  N5    180.00   0.0  0
 C8M  CONST_02  C9    C12  C11  N5    180.00   0.0  0
 C8M  CONST_03  N6    C12  C11  N5      0.00   0.0  0
 C8M  CONST_04  C12   N6   C7   N5      0.00   0.0  0
 C8M  CONST_05  N6    C7   N5   C11     0.00   0.0  0
 C8M  CONST_06  N3    C10  N4   C11     0.00   0.0  0
 C8M  CONST_07  N3    C9   C12  C11     0.00   0.0  0
 C8M  CONST_08  C7    N6   C12  C11     0.00   0.0  0
 C8M  CONST_09  C7    N5   C11  N4    180.00   0.0  0
 C8M  CONST_10  C9    C12  C11  N4      0.00   0.0  0
 C8M  CONST_11  N6    C12  C11  N4    180.00   0.0  0
 C8M  CONST_12  C9    N3   C10  N4      0.00   0.0  0
 C8M  CONST_13  C12   C11  N4   C10     0.00   0.0  0
 C8M  CONST_14  C12   C9   N3   C10     0.00   0.0  0
 C8M  CONST_15  N6    C12  C9   N3    180.00   0.0  0
 C8M  CONST_16  C7    N6   C12  C9    180.00   0.0  0
 C8M  CONST_17  C7    N5   C11  C12     0.00   0.0  0
 C8M  CONST_18  N4    C11  N5   C1'     0.00   0.0  0
 C8M  CONST_19  C12   C11  N5   C1'   180.00   0.0  0
 C8M  CONST_20  N6    C7   N5   C1'   180.00   0.0  0
 C8M  CONST_21  C8    C7   N5   C1'     0.00   0.0  0
 C8M  CONST_22  C8    C7   N5   C11   180.00   0.0  0
 C8M  CONST_23  N7    C9   C12  C11   180.00   0.0  0
 C8M  CONST_24  N7    C9   N3   C10   180.00   0.0  0
 C8M  CONST_25  N6    C12  C9   N7      0.00   0.0  0
 C8M  CONST_26  C8    C7   N6   C12   180.00   0.0  0
 C8M  CONST_27  H10   C10  N4   C11   180.00   0.0  0
 C8M  CONST_28  HN7   N7   C9   N3      0.00   0.0  0
 C8M  CONST_29  HN7A  N7   C9   N3    180.00   0.0  0
 C8M  CONST_30  HN1   N1   C1   C4      0.00   0.0  0
 C8M  CONST_31  HN1A  N1   C1   C4    180.00   0.0  0
 C8M  Var_01    H8    C8   C7   N5     66.54  30.0  2
 C8M  Var_02    C4'   C5'  N2   C5   -171.90  30.0  3
 C8M  Var_03    C5    C4   C1   N1    174.60  30.0  3
 C8M  Var_04    N2    C5   C4   C1   -175.79  30.0  3
 C8M  Var_05    C6    N2   C5   C4    -72.21  30.0  3
 C8M  Var_06    H6    C6   N2   C5     56.14  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
 C8M  chir_01  C4'  C5'  O4'  C3'  negativ
 C8M  chir_02  C1'  O4'  N5   C2'  negativ
 C8M  chir_03  C2'  O2'  C1'  C3'  negativ
 C8M  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
 C8M  plan-1  C1'   0.020
 C8M  plan-1  N5    0.020
 C8M  plan-1  C11   0.020
 C8M  plan-1  N4    0.020
 C8M  plan-1  C10   0.020
 C8M  plan-1  N3    0.020
 C8M  plan-1  C9    0.020
 C8M  plan-1  N7    0.020
 C8M  plan-1  C12   0.020
 C8M  plan-1  N6    0.020
 C8M  plan-1  C7    0.020
 C8M  plan-1  C8    0.020
 C8M  plan-1  H10   0.020
 C8M  plan-2  C9    0.020
 C8M  plan-2  N7    0.020
 C8M  plan-2  HN7   0.020
 C8M  plan-2  HN7A  0.020
 C8M  plan-3  N1    0.020
 C8M  plan-3  C1    0.020
 C8M  plan-3  C4    0.020
 C8M  plan-3  O1    0.020
 C8M  plan-3  HN1   0.020
 C8M  plan-3  HN1A  0.020

