# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 22:58:50 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxy-8-methyladenosine
#   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)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
 M8M  M8M  5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxy-8-methyladenosine  ligand  48  25  .  2022-07-25  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_M8M
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
 M8M  N1    N  NH2   0  -0.544  -2.8865   3.9793   1.0271
 M8M  O2    O  O2    0  -0.428  -3.3137   2.9910   0.1181
 M8M  C4    C  CH2   0  -0.131  -4.0128   1.9815   0.8103
 M8M  C5    C  CH2   0  -0.327  -4.5060   0.9644  -0.1978
 M8M  N2    N  NT    0  -0.404  -3.4608   0.1432  -0.7938
 M8M  C6    C  CH3   0  -0.540  -3.8893  -0.3887  -2.0736
 M8M  C5'   C  CH2   0  -0.286  -3.0644  -0.9067   0.1216
 M8M  C4'   C  CH1   0  -0.018  -1.9383  -1.8000  -0.3759
 M8M  O4'   O  O2    0  -0.492  -0.8115  -1.0302  -0.8098
 M8M  C1'   C  CH1   0   0.225   0.3285  -1.4040  -0.0921
 M8M  N5    N  NR5   0  -0.581   1.2283  -0.2865   0.0255
 M8M  C11   C  CR56  0   0.487   2.5566  -0.3442  -0.2990
 M8M  N4    N  N     0  -0.460   3.2453  -1.3797  -0.7715
 M8M  C10   C  CR16  0   0.041   4.5150  -1.0728  -0.9763
 M8M  N3    N  N     0  -0.473   5.1276   0.0891  -0.7680
 M8M  C9    C  CR6   0   0.444   4.4192   1.1209  -0.2938
 M8M  N7    N  NH2   0  -0.819   5.0310   2.2874  -0.0741
 M8M  C12   C  CR56  0  -0.003   3.0522   0.9194  -0.0371
 M8M  N6    N  N     0  -0.467   2.0606   1.7399   0.4312
 M8M  C7    C  CR5   0   0.461   0.9868   1.0015   0.4618
 M8M  C2'   C  CH1   0  -0.040  -0.1955  -1.9674   1.2250
 M8M  O2'   O  OH1   0  -0.653   0.7824  -2.7594   1.8293
 M8M  C3'   C  CH1   0  -0.035  -1.4292  -2.7280   0.7284
 M8M  O3'   O  OH1   0  -0.669  -1.0623  -3.9580   0.1587
 M8M  C8    C  CH3   0  -0.790  -0.3420   1.4960   0.8954
 M8M  HN1   H  HNH2  0   0.364  -1.9227   4.1638   0.7702
 M8M  HN1A  H  HNH2  0   0.361  -3.3979   4.8186   0.7695
 M8M  H4    H  HCH2  0   0.200  -3.3789   1.5199   1.5765
 M8M  H4A   H  HCH2  0   0.211  -4.8864   2.3982   1.3274
 M8M  H5    H  HCH2  0   0.208  -5.2754   0.3468   0.2937
 M8M  H5A   H  HCH2  0   0.241  -5.0222   1.5060  -0.9941
 M8M  H6    H  HCH3  0   0.241  -4.2450   0.4235  -2.7073
 M8M  H6A   H  HCH3  0   0.241  -3.0607  -0.8614  -2.6006
 M8M  H6B   H  HCH3  0   0.196  -4.6999  -1.1286  -1.9891
 M8M  H5'   H  HCH2  0   0.236  -2.7722  -0.4562   1.0740
 M8M  H5'A  H  HCH2  0   0.215  -3.9116  -1.5804   0.3487
 M8M  H4'   H  HCH1  0   0.257  -2.2915  -2.4028  -1.2178
 M8M  H1'   H  HCH1  0   0.256   0.9013  -2.1807  -0.6133
 M8M  H10   H  HCR6  0   0.250   5.1427  -1.8684  -1.3636
 M8M  HN7   H  HNH2  0   0.402   5.9959   2.4085  -0.3287
 M8M  HN7A  H  HNH2  0   0.409   4.5111   3.0970   0.2143
 M8M  H2'   H  HCH1  0   0.246  -0.5182  -1.1513   1.8815
 M8M  HO2'  H  HOH1  0   0.469   0.5691  -2.8607   2.7622
 M8M  H3'   H  HCH1  0   0.248  -2.1776  -2.8583   1.5211
 M8M  HO3'  H  HOH1  0   0.448  -0.4380  -4.3879   0.7553
 M8M  H8    H  HCH3  0   0.254  -0.7085   0.9598   1.7715
 M8M  H8A   H  HCH3  0   0.265  -0.2447   2.5431   1.1699
 M8M  H8B   H  HCH3  0   0.283  -1.0920   1.3984   0.1120

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
 M8M  N1   O2    single    1.409  0.020  1.409
 M8M  O2   C4    single    1.410  0.020  1.410
 M8M  C4   C5    single    1.515  0.020  1.515
 M8M  C5   N2    single    1.457  0.020  1.457
 M8M  N2   C6    single    1.451  0.020  1.451
 M8M  N2   C5'   single    1.448  0.020  1.448
 M8M  C5'  C4'   single    1.521  0.020  1.521
 M8M  C4'  O4'   single    1.432  0.020  1.432
 M8M  C4'  C3'   single    1.530  0.020  1.530
 M8M  O4'  C1'   single    1.398  0.020  1.398
 M8M  C1'  N5    single    1.440  0.020  1.440
 M8M  C1'  C2'   single    1.525  0.020  1.525
 M8M  N5   C11   aromatic  1.369  0.020  1.369
 M8M  N5   C7    aromatic  1.381  0.020  1.381
 M8M  C11  N4    aromatic  1.330  0.020  1.330
 M8M  C11  C12   aromatic  1.382  0.020  1.382
 M8M  N4   C10   aromatic  1.322  0.020  1.322
 M8M  C10  N3    aromatic  1.330  0.020  1.330
 M8M  N3   C9    aromatic  1.338  0.020  1.338
 M8M  C9   N7    single    1.335  0.020  1.335
 M8M  C9   C12   aromatic  1.405  0.020  1.405
 M8M  C12  N6    aromatic  1.370  0.020  1.370
 M8M  N6   C7    aromatic  1.304  0.020  1.304
 M8M  C7   C8    single    1.483  0.020  1.483
 M8M  C2'  O2'   single    1.396  0.020  1.396
 M8M  C2'  C3'   single    1.532  0.020  1.532
 M8M  C3'  O3'   single    1.404  0.020  1.404
 M8M  N1   HN1   single    0.890  0.020  1.040
 M8M  N1   HN1A  single    0.890  0.020  1.040
 M8M  C4   H4    single    0.970  0.020  1.090
 M8M  C4   H4A   single    0.970  0.020  1.090
 M8M  C5   H5    single    0.970  0.020  1.090
 M8M  C5   H5A   single    0.970  0.020  1.090
 M8M  C6   H6    single    0.970  0.020  1.090
 M8M  C6   H6A   single    0.970  0.020  1.090
 M8M  C6   H6B   single    0.970  0.020  1.090
 M8M  C5'  H5'   single    0.970  0.020  1.090
 M8M  C5'  H5'A  single    0.970  0.020  1.090
 M8M  C4'  H4'   single    0.970  0.020  1.090
 M8M  C1'  H1'   single    0.970  0.020  1.090
 M8M  C10  H10   single    0.930  0.020  1.080
 M8M  N7   HN7   single    0.860  0.020  1.020
 M8M  N7   HN7A  single    0.860  0.020  1.020
 M8M  C2'  H2'   single    0.970  0.020  1.090
 M8M  O2'  HO2'  single    0.850  0.020  0.980
 M8M  C3'  H3'   single    0.970  0.020  1.090
 M8M  O3'  HO3'  single    0.850  0.020  0.980
 M8M  C8   H8    single    0.970  0.020  1.090
 M8M  C8   H8A   single    0.970  0.020  1.090
 M8M  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
 M8M  HN1A  N1   HN1  105.29  3.000
 M8M  HN1A  N1   O2   105.26  3.000
 M8M  HN1   N1   O2   104.61  3.000
 M8M  C4    O2   N1   109.62  3.000
 M8M  H4A   C4   H4   106.91  3.000
 M8M  H4A   C4   C5   108.02  3.000
 M8M  H4    C4   C5   111.76  3.000
 M8M  H4A   C4   O2   110.76  3.000
 M8M  H4    C4   O2   110.97  3.000
 M8M  C5    C4   O2   108.40  3.000
 M8M  H5A   C5   H5   105.84  3.000
 M8M  H5A   C5   N2   108.67  3.000
 M8M  H5    C5   N2   111.56  3.000
 M8M  H5A   C5   C4   107.82  3.000
 M8M  H5    C5   C4   107.87  3.000
 M8M  N2    C5   C4   114.66  3.000
 M8M  C5'   N2   C6   111.88  3.000
 M8M  C5'   N2   C5   110.27  3.000
 M8M  C6    N2   C5   110.84  3.000
 M8M  H6B   C6   H6A  107.79  3.000
 M8M  H6B   C6   H6   107.77  3.000
 M8M  H6A   C6   H6   106.87  3.000
 M8M  H6B   C6   N2   113.34  3.000
 M8M  H6A   C6   N2   111.16  3.000
 M8M  H6    C6   N2   109.64  3.000
 M8M  H5'A  C5'  H5'  106.07  3.000
 M8M  H5'A  C5'  C4'  106.06  3.000
 M8M  H5'   C5'  C4'  109.21  3.000
 M8M  H5'A  C5'  N2   111.21  3.000
 M8M  H5'   C5'  N2   108.96  3.000
 M8M  C4'   C5'  N2   114.94  3.000
 M8M  H4'   C4'  C3'  109.19  3.000
 M8M  H4'   C4'  O4'  108.48  3.000
 M8M  C3'   C4'  O4'  106.44  3.000
 M8M  H4'   C4'  C5'  109.65  3.000
 M8M  C3'   C4'  C5'  111.51  3.000
 M8M  O4'   C4'  C5'  111.47  3.000
 M8M  C1'   O4'  C4'  110.02  3.000
 M8M  H1'   C1'  C2'  109.16  3.000
 M8M  H1'   C1'  N5   105.19  3.000
 M8M  C2'   C1'  N5   115.52  3.000
 M8M  H1'   C1'  O4'  111.79  3.000
 M8M  C2'   C1'  O4'  105.18  3.000
 M8M  N5    C1'  O4'  110.12  3.000
 M8M  C7    N5   C11  106.50  3.000
 M8M  C7    N5   C1'  129.83  3.000
 M8M  C11   N5   C1'  123.68  3.000
 M8M  C12   C11  N4   126.38  3.000
 M8M  C12   C11  N5   105.33  3.000
 M8M  N4    C11  N5   128.28  3.000
 M8M  C10   N4   C11  111.81  3.000
 M8M  H10   C10  N3   115.48  3.000
 M8M  H10   C10  N4   116.15  3.000
 M8M  N3    C10  N4   128.37  3.000
 M8M  C9    N3   C10  119.03  3.000
 M8M  C12   C9   N7   122.74  3.000
 M8M  C12   C9   N3   117.97  3.000
 M8M  N7    C9   N3   119.29  3.000
 M8M  HN7A  N7   HN7  118.19  3.000
 M8M  HN7A  N7   C9   120.94  3.000
 M8M  HN7   N7   C9   120.23  3.000
 M8M  N6    C12  C9   132.91  3.000
 M8M  N6    C12  C11  110.66  3.000
 M8M  C9    C12  C11  116.43  3.000
 M8M  C7    N6   C12  105.37  3.000
 M8M  C8    C7   N6   123.79  3.000
 M8M  C8    C7   N5   124.07  3.000
 M8M  N6    C7   N5   112.13  3.000
 M8M  H2'   C2'  C3'  109.07  3.000
 M8M  H2'   C2'  O2'  111.68  3.000
 M8M  C3'   C2'  O2'  115.01  3.000
 M8M  H2'   C2'  C1'  110.08  3.000
 M8M  C3'   C2'  C1'  100.38  3.000
 M8M  O2'   C2'  C1'  110.04  3.000
 M8M  HO2'  O2'  C2'  108.92  3.000
 M8M  H3'   C3'  O3'  111.53  3.000
 M8M  H3'   C3'  C2'  111.95  3.000
 M8M  O3'   C3'  C2'  110.85  3.000
 M8M  H3'   C3'  C4'  111.49  3.000
 M8M  O3'   C3'  C4'  109.00  3.000
 M8M  C2'   C3'  C4'  101.58  3.000
 M8M  HO3'  O3'  C3'  107.97  3.000
 M8M  H8B   C8   H8A  109.26  3.000
 M8M  H8B   C8   H8   107.60  3.000
 M8M  H8A   C8   H8   107.51  3.000
 M8M  H8B   C8   C7   112.15  3.000
 M8M  H8A   C8   C7   108.36  3.000
 M8M  H8    C8   C7   111.84  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
 M8M  CONST_01  C10   N4   C11  N5    180.00   0.0  0
 M8M  CONST_02  C9    C12  C11  N5    180.00   0.0  0
 M8M  CONST_03  N6    C12  C11  N5      0.00   0.0  0
 M8M  CONST_04  C12   N6   C7   N5      0.00   0.0  0
 M8M  CONST_05  N6    C7   N5   C11     0.00   0.0  0
 M8M  CONST_06  N3    C10  N4   C11     0.00   0.0  0
 M8M  CONST_07  N3    C9   C12  C11     0.00   0.0  0
 M8M  CONST_08  C7    N6   C12  C11     0.00   0.0  0
 M8M  CONST_09  C7    N5   C11  N4    180.00   0.0  0
 M8M  CONST_10  C9    C12  C11  N4      0.00   0.0  0
 M8M  CONST_11  N6    C12  C11  N4    180.00   0.0  0
 M8M  CONST_12  C9    N3   C10  N4      0.00   0.0  0
 M8M  CONST_13  C12   C11  N4   C10     0.00   0.0  0
 M8M  CONST_14  C12   C9   N3   C10     0.00   0.0  0
 M8M  CONST_15  N6    C12  C9   N3    180.00   0.0  0
 M8M  CONST_16  C7    N6   C12  C9    180.00   0.0  0
 M8M  CONST_17  C7    N5   C11  C12     0.00   0.0  0
 M8M  CONST_18  N4    C11  N5   C1'     0.00   0.0  0
 M8M  CONST_19  C12   C11  N5   C1'   180.00   0.0  0
 M8M  CONST_20  N6    C7   N5   C1'   180.00   0.0  0
 M8M  CONST_21  C8    C7   N5   C1'     0.00   0.0  0
 M8M  CONST_22  C8    C7   N5   C11   180.00   0.0  0
 M8M  CONST_23  N7    C9   C12  C11   180.00   0.0  0
 M8M  CONST_24  N7    C9   N3   C10   180.00   0.0  0
 M8M  CONST_25  N6    C12  C9   N7      0.00   0.0  0
 M8M  CONST_26  C8    C7   N6   C12   180.00   0.0  0
 M8M  CONST_27  H10   C10  N4   C11   180.00   0.0  0
 M8M  CONST_28  HN7   N7   C9   N3      0.00   0.0  0
 M8M  CONST_29  HN7A  N7   C9   N3    180.00   0.0  0
 M8M  Var_01    H8    C8   C7   N5     62.55  30.0  2
 M8M  Var_02    C4'   C5'  N2   C5   -177.87  30.0  3
 M8M  Var_03    C5    C4   O2   N1    177.77  30.0  3
 M8M  Var_04    N2    C5   C4   O2     70.71  30.0  3
 M8M  Var_05    C6    N2   C5   C4   -156.89  30.0  3
 M8M  Var_06    HN1   N1   O2   C4    134.71  30.0  3
 M8M  Var_07    H6    C6   N2   C5     52.49  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
 M8M  chir_01  C4'  C5'  O4'  C3'  negativ
 M8M  chir_02  C1'  O4'  N5   C2'  negativ
 M8M  chir_03  C2'  O2'  C1'  C3'  negativ
 M8M  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
 M8M  plan-1  C1'   0.020
 M8M  plan-1  N5    0.020
 M8M  plan-1  C11   0.020
 M8M  plan-1  N4    0.020
 M8M  plan-1  C10   0.020
 M8M  plan-1  N3    0.020
 M8M  plan-1  C9    0.020
 M8M  plan-1  N7    0.020
 M8M  plan-1  C12   0.020
 M8M  plan-1  N6    0.020
 M8M  plan-1  C7    0.020
 M8M  plan-1  C8    0.020
 M8M  plan-1  H10   0.020
 M8M  plan-2  C9    0.020
 M8M  plan-2  N7    0.020
 M8M  plan-2  HN7   0.020
 M8M  plan-2  HN7A  0.020

