# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:01:49 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 3'-deoxy-3'-(glycylamino)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO)n2cnc3c(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
 A3G  A3G  3'-deoxy-3'-(glycylamino)adenosine  ligand  40  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_A3G
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
 A3G  C     C  C     0   0.541  -4.2529   0.9185   0.0942
 A3G  N     N  NH2   0  -0.793  -6.3841   2.0153   0.5711
 A3G  O     O  O     0  -0.493  -4.8365  -0.0145  -0.4343
 A3G  N1    N  N     0  -0.476   4.6567   1.2287  -0.6029
 A3G  C2    C  CR16  0   0.065   3.5274   1.9265  -0.6060
 A3G  N3    N  N     0  -0.511   2.3164   1.5195  -0.2599
 A3G  C4    C  CR56  0   0.519   2.3180   0.2413   0.1269
 A3G  C5    C  CR56  0   0.002   3.4059  -0.6141   0.1618
 A3G  C6    C  CR6   0   0.463   4.6400  -0.0564  -0.2234
 A3G  N6    N  NH2   0  -0.813   5.7756  -0.7522  -0.2391
 A3G  N7    N  N     0  -0.454   3.0225  -1.8615   0.5793
 A3G  C8    C  CR15  0   0.110   1.7407  -1.7559   0.7911
 A3G  N8    N  NH1   0  -0.649  -2.9121   1.0442   0.0654
 A3G  N9    N  NR5   0  -0.546   1.2575  -0.5034   0.5351
 A3G  CA    C  CH2   0  -0.408  -4.9728   1.9951   0.8846
 A3G  C1'   C  CH1   0   0.207  -0.0917   0.0274   0.6925
 A3G  C2'   C  CH1   0  -0.048  -0.6224   0.5979  -0.6443
 A3G  O2'   O  OH1   0  -0.671  -0.5140   1.9825  -0.7442
 A3G  C3'   C  CH1   0  -0.129  -2.0734   0.1130  -0.6486
 A3G  C4'   C  CH1   0  -0.043  -1.9345  -1.2247   0.0840
 A3G  O4'   O  O2    0  -0.481  -0.9543  -0.9782   1.0951
 A3G  C5'   C  CH2   0  -0.151  -1.5224  -2.3558  -0.8401
 A3G  O5'   O  OH1   0  -0.665  -1.2935  -3.5016  -0.0596
 A3G  HN    H  HNH2  0   0.345  -6.8130   1.1475   0.8648
 A3G  HNA   H  HNH2  0   0.355  -6.8273   2.7437   1.1149
 A3G  HN6   H  HNH2  0   0.405   6.6433  -0.2965  -0.4640
 A3G  HN6A  H  HNH2  0   0.413   5.8104  -1.6949   0.1071
 A3G  H8    H  HCR5  0   0.294   1.0961  -2.5530   1.1265
 A3G  HN8   H  HNH1  0   0.404  -2.4953   1.8963   0.4074
 A3G  HA    H  HCH2  0   0.243  -4.7379   1.8199   1.9454
 A3G  HAA   H  HCH2  0   0.254  -4.5391   2.9677   0.6395
 A3G  H1'   H  HCH1  0   0.277  -0.0460   0.8125   1.4559
 A3G  H2'   H  HCH1  0   0.263  -0.1016   0.1001  -1.4726
 A3G  HO2'  H  HOH1  0   0.464   0.4357   2.1900  -0.6761
 A3G  H3'   H  HCH1  0   0.290  -2.4390  -0.0262  -1.6696
 A3G  H4'   H  HCH1  0   0.274  -2.8546  -1.5070   0.5978
 A3G  H5'   H  HCH2  0   0.219  -2.3372  -2.5041  -1.5615
 A3G  H5'A  H  HCH2  0   0.203  -0.6338  -2.0794  -1.4219
 A3G  HO5'  H  HOH1  0   0.461  -0.8921  -4.1718  -0.6196
 A3G  H2    H  HCR6  0   0.260   3.6102   2.9560  -0.9357

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
 A3G  C    O     double    1.221  0.020  1.221
 A3G  C    N8    single    1.347  0.020  1.347
 A3G  C    CA    single    1.517  0.020  1.517
 A3G  N    CA    single    1.446  0.020  1.446
 A3G  N1   C2    aromatic  1.328  0.020  1.328
 A3G  N1   C6    aromatic  1.340  0.020  1.340
 A3G  C2   N3    aromatic  1.324  0.020  1.324
 A3G  N3   C4    aromatic  1.335  0.020  1.335
 A3G  C4   C5    aromatic  1.384  0.020  1.384
 A3G  C4   N9    aromatic  1.359  0.020  1.359
 A3G  C5   C6    aromatic  1.408  0.020  1.408
 A3G  C5   N7    aromatic  1.370  0.020  1.370
 A3G  C6   N6    single    1.332  0.020  1.332
 A3G  N7   C8    aromatic  1.304  0.020  1.304
 A3G  C8   N9    aromatic  1.367  0.020  1.367
 A3G  N8   C3'   single    1.442  0.020  1.442
 A3G  N9   C1'   single    1.458  0.020  1.458
 A3G  C1'  C2'   single    1.547  0.020  1.547
 A3G  C1'  O4'   single    1.385  0.020  1.385
 A3G  C2'  O2'   single    1.392  0.020  1.392
 A3G  C2'  C3'   single    1.530  0.020  1.530
 A3G  C3'  C4'   single    1.531  0.020  1.531
 A3G  C4'  O4'   single    1.430  0.020  1.430
 A3G  C4'  C5'   single    1.518  0.020  1.518
 A3G  C5'  O5'   single    1.405  0.020  1.405
 A3G  N    HN    single    0.890  0.020  1.040
 A3G  N    HNA   single    0.890  0.020  1.040
 A3G  C2   H2    single    0.930  0.020  1.080
 A3G  N6   HN6   single    0.860  0.020  1.020
 A3G  N6   HN6A  single    0.860  0.020  1.020
 A3G  C8   H8    single    0.930  0.020  1.080
 A3G  N8   HN8   single    0.860  0.020  1.020
 A3G  CA   HA    single    0.970  0.020  1.090
 A3G  CA   HAA   single    0.970  0.020  1.090
 A3G  C1'  H1'   single    0.970  0.020  1.090
 A3G  C2'  H2'   single    0.970  0.020  1.090
 A3G  O2'  HO2'  single    0.850  0.020  0.980
 A3G  C3'  H3'   single    0.970  0.020  1.090
 A3G  C4'  H4'   single    0.970  0.020  1.090
 A3G  C5'  H5'   single    0.970  0.020  1.090
 A3G  C5'  H5'A  single    0.970  0.020  1.090
 A3G  O5'  HO5'  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
 A3G  CA    C    N8   114.66  3.000
 A3G  CA    C    O    122.75  3.000
 A3G  N8    C    O    122.54  3.000
 A3G  HNA   N    HN   106.01  3.000
 A3G  HNA   N    CA   108.73  3.000
 A3G  HN    N    CA   109.81  3.000
 A3G  C6    N1   C2   119.61  3.000
 A3G  H2    C2   N3   116.19  3.000
 A3G  H2    C2   N1   115.77  3.000
 A3G  N3    C2   N1   128.04  3.000
 A3G  C4    N3   C2   111.65  3.000
 A3G  N9    C4   C5   105.49  3.000
 A3G  N9    C4   N3   127.64  3.000
 A3G  C5    C4   N3   126.85  3.000
 A3G  N7    C5   C6   133.57  3.000
 A3G  N7    C5   C4   110.51  3.000
 A3G  C6    C5   C4   115.92  3.000
 A3G  N6    C6   C5   122.93  3.000
 A3G  N6    C6   N1   119.14  3.000
 A3G  C5    C6   N1   117.92  3.000
 A3G  HN6A  N6   HN6  118.19  3.000
 A3G  HN6A  N6   C6   121.03  3.000
 A3G  HN6   N6   C6   120.11  3.000
 A3G  C8    N7   C5   104.53  3.000
 A3G  H8    C8   N9   121.62  3.000
 A3G  H8    C8   N7   125.33  3.000
 A3G  N9    C8   N7   113.04  3.000
 A3G  HN8   N8   C3'  118.24  3.000
 A3G  HN8   N8   C    118.88  3.000
 A3G  C3'   N8   C    121.95  3.000
 A3G  C1'   N9   C8   129.82  3.000
 A3G  C1'   N9   C4   123.71  3.000
 A3G  C8    N9   C4   106.42  3.000
 A3G  HAA   CA   HA   105.86  3.000
 A3G  HAA   CA   N    109.04  3.000
 A3G  HA    CA   N    114.81  3.000
 A3G  HAA   CA   C    109.05  3.000
 A3G  HA    CA   C    106.73  3.000
 A3G  N     CA   C    111.11  3.000
 A3G  H1'   C1'  O4'  110.10  3.000
 A3G  H1'   C1'  C2'  110.61  3.000
 A3G  O4'   C1'  C2'  107.78  3.000
 A3G  H1'   C1'  N9   107.29  3.000
 A3G  O4'   C1'  N9   110.08  3.000
 A3G  C2'   C1'  N9   110.99  3.000
 A3G  H2'   C2'  C3'  107.70  3.000
 A3G  H2'   C2'  O2'  111.09  3.000
 A3G  C3'   C2'  O2'  112.89  3.000
 A3G  H2'   C2'  C1'  108.78  3.000
 A3G  C3'   C2'  C1'  102.17  3.000
 A3G  O2'   C2'  C1'  113.70  3.000
 A3G  HO2'  O2'  C2'  106.42  3.000
 A3G  H3'   C3'  C4'  111.46  3.000
 A3G  H3'   C3'  C2'  111.11  3.000
 A3G  C4'   C3'  C2'  100.93  3.000
 A3G  H3'   C3'  N8   110.48  3.000
 A3G  C4'   C3'  N8   112.32  3.000
 A3G  C2'   C3'  N8   110.21  3.000
 A3G  H4'   C4'  C5'  108.84  3.000
 A3G  H4'   C4'  O4'  106.85  3.000
 A3G  C5'   C4'  O4'  111.90  3.000
 A3G  H4'   C4'  C3'  112.01  3.000
 A3G  C5'   C4'  C3'  112.60  3.000
 A3G  O4'   C4'  C3'  104.47  3.000
 A3G  C4'   O4'  C1'  110.29  3.000
 A3G  H5'A  C5'  H5'  106.65  3.000
 A3G  H5'A  C5'  O5'  111.58  3.000
 A3G  H5'   C5'  O5'  112.06  3.000
 A3G  H5'A  C5'  C4'  110.79  3.000
 A3G  H5'   C5'  C4'  107.41  3.000
 A3G  O5'   C5'  C4'  108.28  3.000
 A3G  HO5'  O5'  C5'  108.24  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
 A3G  CONST_01  C4    N3  C2  N1    0.00   0.0  0
 A3G  CONST_02  C4    C5  C6  N1    0.00   0.0  0
 A3G  CONST_03  N7    C5  C6  N1  180.00   0.0  0
 A3G  CONST_04  C5    C6  N1  C2    0.00   0.0  0
 A3G  CONST_05  C5    C4  N3  C2    0.00   0.0  0
 A3G  CONST_06  N9    C4  N3  C2  180.00   0.0  0
 A3G  CONST_07  C6    N1  C2  N3    0.00   0.0  0
 A3G  CONST_08  C6    C5  C4  N3    0.00   0.0  0
 A3G  CONST_09  N7    C5  C4  N3  180.00   0.0  0
 A3G  CONST_10  C8    N9  C4  N3  180.00   0.0  0
 A3G  CONST_11  C8    N7  C5  C4    0.00   0.0  0
 A3G  CONST_12  N7    C8  N9  C4    0.00   0.0  0
 A3G  CONST_13  C8    N9  C4  C5    0.00   0.0  0
 A3G  CONST_14  N9    C8  N7  C5    0.00   0.0  0
 A3G  CONST_15  N9    C4  C5  C6  180.00   0.0  0
 A3G  CONST_16  C8    N7  C5  C6  180.00   0.0  0
 A3G  CONST_17  N9    C4  C5  N7    0.00   0.0  0
 A3G  CONST_18  C1'   N9  C4  N3    0.00   0.0  0
 A3G  CONST_19  C1'   N9  C4  C5  180.00   0.0  0
 A3G  CONST_20  C1'   N9  C8  N7  180.00   0.0  0
 A3G  CONST_21  N6    C6  N1  C2  180.00   0.0  0
 A3G  CONST_22  N6    C6  C5  C4  180.00   0.0  0
 A3G  CONST_23  N7    C5  C6  N6    0.00   0.0  0
 A3G  CONST_24  H2    C2  N3  C4  180.00   0.0  0
 A3G  CONST_25  H8    C8  N9  C4  180.00   0.0  0
 A3G  CONST_26  HN6   N6  C6  N1    0.00   0.0  0
 A3G  CONST_27  HN6A  N6  C6  N1  180.00   0.0  0
 A3G  CONST_28  C3'   N8  C   O     0.00   0.0  0
 A3G  CONST_29  C3'   N8  C   CA  180.00   0.0  0
 A3G  CONST_30  HN8   N8  C   O   180.00   0.0  0
 A3G  Var_01    O     C   CA  N   -18.37  30.0  2
 A3G  Var_02    HN    N   CA  C    64.47  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
 A3G  chir_01  C1'  N9   C2'  O4'  negativ
 A3G  chir_02  C2'  O2'  C3'  C1'  positiv
 A3G  chir_03  C3'  N8   C4'  C2'  positiv
 A3G  chir_04  C4'  O4'  C3'  C5'  negativ

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
 A3G  plan-1  N1    0.020
 A3G  plan-1  C2    0.020
 A3G  plan-1  N3    0.020
 A3G  plan-1  C4    0.020
 A3G  plan-1  C5    0.020
 A3G  plan-1  C6    0.020
 A3G  plan-1  N6    0.020
 A3G  plan-1  N7    0.020
 A3G  plan-1  C8    0.020
 A3G  plan-1  N9    0.020
 A3G  plan-1  C1'   0.020
 A3G  plan-1  H8    0.020
 A3G  plan-1  H2    0.020
 A3G  plan-2  C6    0.020
 A3G  plan-2  N6    0.020
 A3G  plan-2  HN6   0.020
 A3G  plan-2  HN6A  0.020
 A3G  plan-3  C     0.020
 A3G  plan-3  O     0.020
 A3G  plan-3  N8    0.020
 A3G  plan-3  CA    0.020
 A3G  plan-3  C3'   0.020
 A3G  plan-3  HN8   0.020

