# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:55:21 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: N,N-dimethyladenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
#
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
 26A  26A  'N,N-dimethyladenosine    '  ligand  38  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_26A
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
 26A  C10   C  CH3   0  -0.516   5.5582  -0.3265  -0.2625
 26A  N6    N  NT    0  -0.467   4.2021  -0.8410  -0.2466
 26A  C9    C  CH3   0  -0.541   4.0649  -2.2811  -0.3176
 26A  C6    C  CR6   0   0.517   3.1912  -0.0260   0.0932
 26A  C5    C  CR56  0   0.006   1.8274  -0.3988   0.2183
 26A  C4    C  CR56  0   0.478   0.9488   0.6290   0.5495
 26A  N3    N  N     0  -0.459   1.2420   1.9093   0.7647
 26A  C2    C  CR16  0   0.039   2.5362   2.1320   0.6289
 26A  N1    N  N     0  -0.494   3.4888   1.2627   0.3211
 26A  N7    N  N     0  -0.463   1.1306  -1.5749   0.0806
 26A  C8    C  CR15  0   0.107  -0.1099  -1.2648   0.3169
 26A  N9    N  NR5   0  -0.535  -0.2867   0.0571   0.6041
 26A  C1'   C  CH1   0   0.172  -1.5218   0.7722   0.9097
 26A  O4'   O  O2    0  -0.496  -2.5273  -0.1502   1.1977
 26A  C4'   C  CH1   0   0.007  -3.5192  -0.1707   0.1693
 26A  C5'   C  CH2   0  -0.155  -3.9196  -1.5867  -0.1611
 26A  O5'   O  OH1   0  -0.668  -4.5254  -2.1683   0.9660
 26A  C2'   C  CH1   0  -0.039  -2.0012   1.5925  -0.2858
 26A  O2'   O  OH1   0  -0.664  -2.7698   2.6544   0.2081
 26A  C3'   C  CH1   0  -0.043  -2.8813   0.5654  -1.0060
 26A  O3'   O  OH1   0  -0.656  -3.8718   1.1325  -1.8151
 26A  H101  H  HCH3  0   0.252   5.6102   0.6284  -0.7785
 26A  H102  H  HCH3  0   0.236   5.9596  -0.1927   0.7453
 26A  H103  H  HCH3  0   0.242   6.1883  -1.0392  -0.7893
 26A  H91   H  HCH3  0   0.236   4.3615  -2.7588   0.6206
 26A  H92   H  HCH3  0   0.275   3.0440  -2.5692  -0.5398
 26A  H93   H  HCH3  0   0.246   4.7083  -2.6619  -1.1094
 26A  H2    H  HCR6  0   0.249   2.8682   3.1522   0.7909
 26A  H8    H  HCR5  0   0.299  -0.9289  -1.9659   0.3055
 26A  H1'   H  HCH1  0   0.284  -1.3208   1.4070   1.7768
 26A  H4'   H  HCH1  0   0.247  -4.4021   0.3838   0.5117
 26A  H5'1  H  HCH2  0   0.216  -4.6032  -1.5390  -1.0184
 26A  H5'2  H  HCH2  0   0.198  -3.0362  -2.1510  -0.4917
 26A  H5'   H  HOH1  0   0.460  -4.8265  -3.0490   0.7248
 26A  H2'   H  HCH1  0   0.261  -1.1674   1.9453  -0.9042
 26A  HO'2  H  HOH1  0   0.452  -3.4358   2.8677  -0.4573
 26A  H3'   H  HCH1  0   0.244  -2.2409  -0.1216  -1.5755
 26A  HO'3  H  HOH1  0   0.469  -3.4919   1.3415  -2.6745

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
 26A  C10  N6    single    1.450  0.020  1.450
 26A  C10  H101  single    0.970  0.020  1.090
 26A  C10  H102  single    0.970  0.020  1.090
 26A  C10  H103  single    0.970  0.020  1.090
 26A  N6   C9    single    1.448  0.020  1.448
 26A  N6   C6    single    1.342  0.020  1.342
 26A  C9   H91   single    0.970  0.020  1.090
 26A  C9   H92   single    0.970  0.020  1.090
 26A  C9   H93   single    0.970  0.020  1.090
 26A  C6   C5    aromatic  1.419  0.020  1.419
 26A  C6   N1    aromatic  1.342  0.020  1.342
 26A  C5   C4    aromatic  1.392  0.020  1.392
 26A  C5   N7    aromatic  1.374  0.020  1.374
 26A  C4   N3    aromatic  1.331  0.020  1.331
 26A  C4   N9    aromatic  1.362  0.020  1.362
 26A  N3   C2    aromatic  1.320  0.020  1.320
 26A  C2   N1    aromatic  1.326  0.020  1.326
 26A  C2   H2    single    0.930  0.020  1.080
 26A  N7   C8    aromatic  1.300  0.020  1.300
 26A  C8   N9    aromatic  1.364  0.020  1.364
 26A  C8   H8    single    0.930  0.020  1.080
 26A  N9   C1'   single    1.460  0.020  1.460
 26A  C1'  O4'   single    1.395  0.020  1.395
 26A  C1'  C2'   single    1.527  0.020  1.527
 26A  C1'  H1'   single    0.970  0.020  1.090
 26A  O4'  C4'   single    1.429  0.020  1.429
 26A  C4'  C5'   single    1.508  0.020  1.508
 26A  C4'  C3'   single    1.526  0.020  1.526
 26A  C4'  H4'   single    0.970  0.020  1.090
 26A  C5'  O5'   single    1.406  0.020  1.406
 26A  C5'  H5'1  single    0.970  0.020  1.090
 26A  C5'  H5'2  single    0.970  0.020  1.090
 26A  O5'  H5'   single    0.850  0.020  0.980
 26A  C2'  O2'   single    1.401  0.020  1.401
 26A  C2'  C3'   single    1.532  0.020  1.532
 26A  C2'  H2'   single    0.970  0.020  1.090
 26A  O2'  HO'2  single    0.850  0.020  0.980
 26A  C3'  O3'   single    1.399  0.020  1.399
 26A  C3'  H3'   single    0.970  0.020  1.090
 26A  O3'  HO'3  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
 26A  H103  C10  H102  108.31  3.000
 26A  H103  C10  H101  108.55  3.000
 26A  H102  C10  H101  108.22  3.000
 26A  H103  C10  N6    108.34  3.000
 26A  H102  C10  N6    112.13  3.000
 26A  H101  C10  N6    111.20  3.000
 26A  C6    N6   C9    123.01  3.000
 26A  C6    N6   C10   119.44  3.000
 26A  C9    N6   C10   116.15  3.000
 26A  H93   C9   H92   108.33  3.000
 26A  H93   C9   H91   108.10  3.000
 26A  H92   C9   H91   108.38  3.000
 26A  H93   C9   N6    109.11  3.000
 26A  H92   C9   N6    111.32  3.000
 26A  H91   C9   N6    111.50  3.000
 26A  N1    C6   C5    116.76  3.000
 26A  N1    C6   N6    117.33  3.000
 26A  C5    C6   N6    125.91  3.000
 26A  N7    C5   C4    109.62  3.000
 26A  N7    C5   C6    134.69  3.000
 26A  C4    C5   C6    115.69  3.000
 26A  N9    C4   N3    126.66  3.000
 26A  N9    C4   C5    105.78  3.000
 26A  N3    C4   C5    127.56  3.000
 26A  C2    N3   C4    111.20  3.000
 26A  H2    C2   N1    115.55  3.000
 26A  H2    C2   N3    116.31  3.000
 26A  N1    C2   N3    128.14  3.000
 26A  C2    N1   C6    120.64  3.000
 26A  C8    N7   C5    105.15  3.000
 26A  H8    C8   N9    122.27  3.000
 26A  H8    C8   N7    124.59  3.000
 26A  N9    C8   N7    113.14  3.000
 26A  C1'   N9   C8    128.94  3.000
 26A  C1'   N9   C4    124.76  3.000
 26A  C8    N9   C4    106.30  3.000
 26A  H1'   C1'  C2'   111.51  3.000
 26A  H1'   C1'  O4'   110.67  3.000
 26A  C2'   C1'  O4'   106.90  3.000
 26A  H1'   C1'  N9    107.15  3.000
 26A  C2'   C1'  N9    111.40  3.000
 26A  O4'   C1'  N9    109.23  3.000
 26A  C4'   O4'  C1'   111.18  3.000
 26A  H4'   C4'  C3'   109.44  3.000
 26A  H4'   C4'  C5'   109.22  3.000
 26A  C3'   C4'  C5'   113.26  3.000
 26A  H4'   C4'  O4'   109.07  3.000
 26A  C3'   C4'  O4'   104.90  3.000
 26A  C5'   C4'  O4'   110.82  3.000
 26A  H5'2  C5'  H5'1  106.73  3.000
 26A  H5'2  C5'  O5'   112.03  3.000
 26A  H5'1  C5'  O5'   112.07  3.000
 26A  H5'2  C5'  C4'   109.55  3.000
 26A  H5'1  C5'  C4'   107.20  3.000
 26A  O5'   C5'  C4'   109.11  3.000
 26A  H5'   O5'  C5'   108.24  3.000
 26A  H2'   C2'  C3'   112.80  3.000
 26A  H2'   C2'  O2'   111.85  3.000
 26A  C3'   C2'  O2'   111.02  3.000
 26A  H2'   C2'  C1'   112.07  3.000
 26A  C3'   C2'  C1'   100.85  3.000
 26A  O2'   C2'  C1'   107.66  3.000
 26A  HO'2  O2'  C2'   107.63  3.000
 26A  H3'   C3'  O3'   111.50  3.000
 26A  H3'   C3'  C2'   109.15  3.000
 26A  O3'   C3'  C2'   114.00  3.000
 26A  H3'   C3'  C4'   109.95  3.000
 26A  O3'   C3'  C4'   110.18  3.000
 26A  C2'   C3'  C4'   101.61  3.000
 26A  HO'3  O3'  C3'   108.96  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
 26A  CONST_01  N3    C4   C5  C6     0.00   0.0  0
 26A  CONST_02  N9    C4   C5  C6   180.00   0.0  0
 26A  CONST_03  C8    N7   C5  C6   180.00   0.0  0
 26A  CONST_04  N3    C2   N1  C6     0.00   0.0  0
 26A  CONST_05  C2    N1   C6  C5     0.00   0.0  0
 26A  CONST_06  C2    N3   C4  C5     0.00   0.0  0
 26A  CONST_07  C8    N9   C4  C5     0.00   0.0  0
 26A  CONST_08  N9    C8   N7  C5     0.00   0.0  0
 26A  CONST_09  N1    C6   C5  C4     0.00   0.0  0
 26A  CONST_10  C8    N7   C5  C4     0.00   0.0  0
 26A  CONST_11  N1    C2   N3  C4     0.00   0.0  0
 26A  CONST_12  N7    C8   N9  C4     0.00   0.0  0
 26A  CONST_13  N7    C5   C4  N3   180.00   0.0  0
 26A  CONST_14  C8    N9   C4  N3   180.00   0.0  0
 26A  CONST_15  N9    C4   N3  C2   180.00   0.0  0
 26A  CONST_16  N7    C5   C6  N1   180.00   0.0  0
 26A  CONST_17  N9    C4   C5  N7     0.00   0.0  0
 26A  CONST_18  C1'   N9   C4  C5   180.00   0.0  0
 26A  CONST_19  C1'   N9   C4  N3     0.00   0.0  0
 26A  CONST_20  C1'   N9   C8  N7   180.00   0.0  0
 26A  CONST_21  C4    C5   C6  N6   180.00   0.0  0
 26A  CONST_22  N7    C5   C6  N6     0.00   0.0  0
 26A  CONST_23  C2    N1   C6  N6   180.00   0.0  0
 26A  CONST_24  H2    C2   N1  C6   180.00   0.0  0
 26A  CONST_25  H8    C8   N7  C5   180.00   0.0  0
 26A  CONST_26  C5    C6   N6  C10  180.00   0.0  0
 26A  CONST_27  N1    C6   N6  C10    0.00   0.0  0
 26A  CONST_28  C5    C6   N6  C9     0.00   0.0  0
 26A  CONST_29  N1    C6   N6  C9   180.00   0.0  0
 26A  Var_01    H101  C10  N6  C6   -46.87  30.0  3
 26A  Var_02    H91   C9   N6  C6   -93.87  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
 26A  chir_01  C1'  N9   O4'  C2'  positiv
 26A  chir_02  C4'  O4'  C5'  C3'  positiv
 26A  chir_03  C2'  O2'  C3'  C1'  positiv
 26A  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
 26A  plan-1  N6   0.020
 26A  plan-1  C6   0.020
 26A  plan-1  C5   0.020
 26A  plan-1  C4   0.020
 26A  plan-1  N3   0.020
 26A  plan-1  C2   0.020
 26A  plan-1  N1   0.020
 26A  plan-1  N7   0.020
 26A  plan-1  C8   0.020
 26A  plan-1  N9   0.020
 26A  plan-1  C1'  0.020
 26A  plan-1  H2   0.020
 26A  plan-1  H8   0.020
 26A  plan-2  C10  0.020
 26A  plan-2  N6   0.020
 26A  plan-2  C9   0.020
 26A  plan-2  C6   0.020

