# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 02:46:43 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 3'-deoxy-3'-(D-tyrosylamino)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc(O)cc1)C(=O)N[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO)n3cnc4c(N)ncnc34
#
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
 D3Y  D3Y  3'-deoxy-3'-(D-tyrosylamino)adenosine  ligand  54  31  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D3Y
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
 D3Y  CD1  C  CR16  0  -0.288  -4.9849   1.8301   0.5925
 D3Y  CE1  C  CR16  0  -0.369  -6.1671   2.4271   1.0036
 D3Y  CZ   C  CR6   0   0.339  -7.3586   2.1369   0.3434
 D3Y  OH   O  OH1   0  -0.634  -8.5403   2.6849   0.6945
 D3Y  CE2  C  CR16  0  -0.325  -7.3456   1.2500  -0.7294
 D3Y  CD2  C  CR16  0  -0.304  -6.1538   0.6621  -1.1245
 D3Y  CG   C  CR6   0   0.108  -4.9514   0.9395  -0.4772
 D3Y  CB   C  CH2   0  -0.528  -3.6753   0.2590  -0.8772
 D3Y  CA   C  CH1   0  -0.223  -3.3952  -0.9969  -0.0164
 D3Y  N    N  NH2   0  -0.783  -4.4190  -2.0167  -0.0533
 D3Y  C    C  C     0   0.564  -2.0824  -1.5986  -0.4940
 D3Y  O    O  O     0  -0.492  -2.0441  -2.3964  -1.4181
 D3Y  N8   N  NH1   0  -0.631  -0.9867  -1.1426   0.1405
 D3Y  C3'  C  CR15  0  -0.165   0.3519  -1.4769  -0.2480
 D3Y  C2'  C  CR15  0   0.004   1.3357  -0.2814  -0.1822
 D3Y  O2'  O  OH1   0  -0.678   0.7452   0.8536   0.3690
 D3Y  C4'  C  CR15  0   0.033   1.0040  -2.5404   0.6532
 D3Y  C5'  C  CH2   0  -0.168   0.7644  -3.9535   0.1901
 D3Y  O5'  O  OH1   0  -0.668   1.3429  -4.8435   1.1116
 D3Y  O4'  O  O     0  -0.501   2.3901  -2.2360   0.6064
 D3Y  C1'  C  CR15  0   0.232   2.4742  -0.8526   0.6935
 D3Y  N9   N  NR5   0  -0.564   3.7882  -0.4411   0.2551
 D3Y  C8   C  CR15  0   0.110   4.9014  -1.1964   0.0051
 D3Y  N7   N  N     0  -0.453   5.9397  -0.4823  -0.3221
 D3Y  C5   C  CR56  0   0.003   5.4944   0.8125  -0.2800
 D3Y  C4   C  CR56  0   0.522   4.1585   0.8564   0.0784
 D3Y  N3   N  N     0  -0.514   3.4039   1.9496   0.2114
 D3Y  C2   C  CR16  0   0.067   4.0904   3.0530  -0.0402
 D3Y  N1   N  N     0  -0.476   5.3663   3.1612  -0.3897
 D3Y  C6   C  CR6   0   0.466   6.1097   2.0549  -0.5256
 D3Y  N6   N  NH2   0  -0.813   7.3877   2.1691  -0.8801
 D3Y  H1   H  HCR6  0   0.250  -4.0684   2.0717   1.1193
 D3Y  H2   H  HCR6  0   0.269  -6.1584   3.1209   1.8369
 D3Y  H3   H  HOH1  0   0.473  -8.4272   3.2738   1.4486
 D3Y  H4   H  HCR6  0   0.261  -8.2669   1.0243  -1.2523
 D3Y  H5   H  HCR6  0   0.251  -6.1628  -0.0222  -1.9651
 D3Y  H6   H  HCH2  0   0.255  -3.7262  -0.0424  -1.9272
 D3Y  H7   H  HCH2  0   0.251  -2.8347   0.9525  -0.7862
 D3Y  H8   H  HCH1  0   0.262  -3.2868  -0.6742   1.0237
 D3Y  H9   H  HNH2  0   0.356  -5.2846  -1.6423   0.3137
 D3Y  H10  H  HNH2  0   0.343  -4.6066  -2.2873  -1.0113
 D3Y  H12  H  HNH1  0   0.403  -1.1070  -0.4947   0.9028
 D3Y  H13  H  HCR5  0   0.285   0.3186  -1.8484  -1.2727
 D3Y  H14  H  HCR5  0   0.253   1.7236  -0.0863  -1.1894
 D3Y  H15  H  HOH1  0   0.463   1.4427   1.5338   0.3964
 D3Y  H16  H  HCR5  0   0.243   0.6316  -2.4190   1.6813
 D3Y  H17  H  HCH2  0   0.215  -0.3203  -4.0939   0.1072
 D3Y  H18  H  HCH2  0   0.205   1.1798  -4.0739  -0.8199
 D3Y  H19  H  HOH1  0   0.460   1.1443  -5.7405   0.8285
 D3Y  H20  H  HCR5  0   0.254   2.3284  -0.5087   1.7286
 D3Y  H21  H  HCR5  0   0.300   4.8883  -2.2721   0.0780
 D3Y  H22  H  HCR6  0   0.260   3.5451   3.9858   0.0489
 D3Y  H23  H  HNH2  0   0.414   7.9623   1.3569  -1.0211
 D3Y  H24  H  HNH2  0   0.406   7.7847   3.0737  -1.0673

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
 D3Y  O4'  C4'  single    1.420  0.020  1.420
 D3Y  O4'  C1'  single    1.389  0.020  1.389
 D3Y  C5'  C4'  single    1.506  0.020  1.506
 D3Y  C5'  O5'  single    1.406  0.020  1.406
 D3Y  C4'  C3'  single    1.539  0.020  1.539
 D3Y  OH   CZ   single    1.349  0.020  1.349
 D3Y  O2'  C2'  single    1.393  0.020  1.393
 D3Y  C1'  C2'  single    1.546  0.020  1.546
 D3Y  C1'  N9   single    1.445  0.020  1.445
 D3Y  N    CA   single    1.446  0.020  1.446
 D3Y  CZ   CE2  aromatic  1.392  0.020  1.392
 D3Y  CZ   CE1  aromatic  1.393  0.020  1.393
 D3Y  CE2  CD2  aromatic  1.386  0.020  1.386
 D3Y  C2'  C3'  single    1.550  0.020  1.550
 D3Y  C3'  N8   single    1.433  0.020  1.433
 D3Y  N8   C    single    1.346  0.020  1.346
 D3Y  C8   N9   aromatic  1.368  0.020  1.368
 D3Y  C8   N7   aromatic  1.302  0.020  1.302
 D3Y  CE1  CD1  aromatic  1.387  0.020  1.387
 D3Y  N9   C4   aromatic  1.361  0.020  1.361
 D3Y  CD2  CG   aromatic  1.393  0.020  1.393
 D3Y  CD1  CG   aromatic  1.392  0.020  1.392
 D3Y  CG   CB   single    1.500  0.020  1.500
 D3Y  CA   C    single    1.521  0.020  1.521
 D3Y  CA   CB   single    1.548  0.020  1.548
 D3Y  N7   C5   aromatic  1.370  0.020  1.370
 D3Y  C    O    double    1.221  0.020  1.221
 D3Y  C4   C5   aromatic  1.384  0.020  1.384
 D3Y  C4   N3   aromatic  1.335  0.020  1.335
 D3Y  C5   C6   aromatic  1.408  0.020  1.408
 D3Y  N3   C2   aromatic  1.324  0.020  1.324
 D3Y  C6   N6   single    1.331  0.020  1.331
 D3Y  C6   N1   aromatic  1.340  0.020  1.340
 D3Y  C2   N1   aromatic  1.327  0.020  1.327
 D3Y  CD1  H1   single    0.930  0.020  1.080
 D3Y  CE1  H2   single    0.930  0.020  1.080
 D3Y  OH   H3   single    0.850  0.020  0.980
 D3Y  CE2  H4   single    0.930  0.020  1.080
 D3Y  CD2  H5   single    0.930  0.020  1.080
 D3Y  CB   H6   single    0.970  0.020  1.090
 D3Y  CB   H7   single    0.970  0.020  1.090
 D3Y  CA   H8   single    0.970  0.020  1.090
 D3Y  N    H9   single    0.890  0.020  1.040
 D3Y  N    H10  single    0.890  0.020  1.040
 D3Y  N8   H12  single    0.860  0.020  1.020
 D3Y  C3'  H13  single    0.970  0.020  1.090
 D3Y  C2'  H14  single    0.970  0.020  1.090
 D3Y  O2'  H15  single    0.850  0.020  0.980
 D3Y  C4'  H16  single    0.970  0.020  1.090
 D3Y  C5'  H17  single    0.970  0.020  1.090
 D3Y  C5'  H18  single    0.970  0.020  1.090
 D3Y  O5'  H19  single    0.850  0.020  0.980
 D3Y  C1'  H20  single    0.970  0.020  1.090
 D3Y  C8   H21  single    0.930  0.020  1.080
 D3Y  C2   H22  single    0.930  0.020  1.080
 D3Y  N6   H23  single    0.860  0.020  1.020
 D3Y  N6   H24  single    0.860  0.020  1.020

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
 D3Y  H1   CD1  CG   119.70  3.000
 D3Y  H1   CD1  CE1  118.73  3.000
 D3Y  CG   CD1  CE1  121.58  3.000
 D3Y  H2   CE1  CZ   120.30  3.000
 D3Y  H2   CE1  CD1  119.76  3.000
 D3Y  CZ   CE1  CD1  119.94  3.000
 D3Y  CE2  CZ   OH   117.88  3.000
 D3Y  CE2  CZ   CE1  119.35  3.000
 D3Y  OH   CZ   CE1  122.77  3.000
 D3Y  H3   OH   CZ   110.44  3.000
 D3Y  H4   CE2  CD2  120.35  3.000
 D3Y  H4   CE2  CZ   119.79  3.000
 D3Y  CD2  CE2  CZ   119.86  3.000
 D3Y  H5   CD2  CG   119.54  3.000
 D3Y  H5   CD2  CE2  118.79  3.000
 D3Y  CG   CD2  CE2  121.66  3.000
 D3Y  CB   CG   CD2  121.31  3.000
 D3Y  CB   CG   CD1  121.02  3.000
 D3Y  CD2  CG   CD1  117.61  3.000
 D3Y  H7   CB   H6   106.89  3.000
 D3Y  H7   CB   CA   109.21  3.000
 D3Y  H6   CB   CA   108.59  3.000
 D3Y  H7   CB   CG   110.12  3.000
 D3Y  H6   CB   CG   109.96  3.000
 D3Y  CA   CB   CG   111.93  3.000
 D3Y  H8   CA   C    109.24  3.000
 D3Y  H8   CA   N    107.60  3.000
 D3Y  C    CA   N    108.91  3.000
 D3Y  H8   CA   CB   107.89  3.000
 D3Y  C    CA   CB   107.61  3.000
 D3Y  N    CA   CB   115.47  3.000
 D3Y  H10  N    H9   106.47  3.000
 D3Y  H10  N    CA   110.11  3.000
 D3Y  H9   N    CA   109.60  3.000
 D3Y  N8   C    O    123.54  3.000
 D3Y  O    C    CA   121.53  3.000
 D3Y  N8   C    CA   114.87  3.000
 D3Y  H12  N8   C3'  117.80  3.000
 D3Y  H12  N8   C    118.52  3.000
 D3Y  C3'  N8   C    123.61  3.000
 D3Y  H13  C3'  C4'  109.14  3.000
 D3Y  H13  C3'  C2'  108.79  3.000
 D3Y  C4'  C3'  C2'  103.84  3.000
 D3Y  H13  C3'  N8   107.79  3.000
 D3Y  C2'  C3'  N8   113.67  3.000
 D3Y  C4'  C3'  N8   113.47  3.000
 D3Y  H14  C2'  C1'  108.99  3.000
 D3Y  H14  C2'  O2'  111.62  3.000
 D3Y  C1'  C2'  O2'  112.90  3.000
 D3Y  H14  C2'  C3'  108.83  3.000
 D3Y  C1'  C2'  C3'  101.92  3.000
 D3Y  O2'  C2'  C3'  112.10  3.000
 D3Y  H15  O2'  C2'  106.05  3.000
 D3Y  H16  C4'  O4'  109.73  3.000
 D3Y  H16  C4'  C5'  109.69  3.000
 D3Y  O4'  C4'  C5'  110.26  3.000
 D3Y  H16  C4'  C3'  109.12  3.000
 D3Y  C5'  C4'  C3'  113.63  3.000
 D3Y  O4'  C4'  C3'  104.26  3.000
 D3Y  H18  C5'  H17  106.89  3.000
 D3Y  H18  C5'  O5'  112.19  3.000
 D3Y  H17  C5'  O5'  112.05  3.000
 D3Y  H18  C5'  C4'  108.98  3.000
 D3Y  H17  C5'  C4'  107.50  3.000
 D3Y  O5'  C5'  C4'  109.09  3.000
 D3Y  H19  O5'  C5'  108.22  3.000
 D3Y  C1'  O4'  C4'  105.70  3.000
 D3Y  H20  C1'  N9   108.47  3.000
 D3Y  H20  C1'  O4'  111.23  3.000
 D3Y  N9   C1'  O4'  108.65  3.000
 D3Y  H20  C1'  C2'  108.65  3.000
 D3Y  N9   C1'  C2'  113.12  3.000
 D3Y  O4'  C1'  C2'  106.74  3.000
 D3Y  C4   N9   C8   106.33  3.000
 D3Y  C4   N9   C1'  123.95  3.000
 D3Y  C8   N9   C1'  129.64  3.000
 D3Y  H21  C8   N7   125.02  3.000
 D3Y  H21  C8   N9   121.90  3.000
 D3Y  N7   C8   N9   113.08  3.000
 D3Y  C5   N7   C8   104.56  3.000
 D3Y  C6   C5   C4   116.04  3.000
 D3Y  C6   C5   N7   133.36  3.000
 D3Y  C4   C5   N7   110.60  3.000
 D3Y  N3   C4   C5   126.69  3.000
 D3Y  N3   C4   N9   127.88  3.000
 D3Y  C5   C4   N9   105.43  3.000
 D3Y  C2   N3   C4   111.74  3.000
 D3Y  H22  C2   N1   115.79  3.000
 D3Y  H22  C2   N3   116.15  3.000
 D3Y  N1   C2   N3   128.06  3.000
 D3Y  C6   N1   C2   119.52  3.000
 D3Y  N6   C6   N1   119.26  3.000
 D3Y  N1   C6   C5   117.93  3.000
 D3Y  N6   C6   C5   122.80  3.000
 D3Y  H24  N6   H23  118.38  3.000
 D3Y  H24  N6   C6   120.39  3.000
 D3Y  H23  N6   C6   121.13  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
 D3Y  CONST_01  CE2  CZ   CE1  CD1    0.00   0.0  0
 D3Y  CONST_02  CE2  CD2  CG   CD1    0.00   0.0  0
 D3Y  CONST_03  CD2  CE2  CZ   CE1    0.00   0.0  0
 D3Y  CONST_04  CD2  CG   CD1  CE1    0.00   0.0  0
 D3Y  CONST_05  CG   CD2  CE2  CZ     0.00   0.0  0
 D3Y  CONST_06  CG   CD1  CE1  CZ     0.00   0.0  0
 D3Y  CONST_07  C5   N7   C8   N9     0.00   0.0  0
 D3Y  CONST_08  N7   C5   C4   N9     0.00   0.0  0
 D3Y  CONST_09  C6   C5   C4   N9   180.00   0.0  0
 D3Y  CONST_10  C2   N3   C4   N9   180.00   0.0  0
 D3Y  CONST_11  C5   C4   N9   C8     0.00   0.0  0
 D3Y  CONST_12  N3   C4   N9   C8   180.00   0.0  0
 D3Y  CONST_13  C4   C5   N7   C8     0.00   0.0  0
 D3Y  CONST_14  C6   C5   N7   C8   180.00   0.0  0
 D3Y  CONST_15  C4   N9   C8   N7     0.00   0.0  0
 D3Y  CONST_16  N3   C4   C5   N7   180.00   0.0  0
 D3Y  CONST_17  N1   C6   C5   N7   180.00   0.0  0
 D3Y  CONST_18  C2   N3   C4   C5     0.00   0.0  0
 D3Y  CONST_19  C2   N1   C6   C5     0.00   0.0  0
 D3Y  CONST_20  N1   C6   C5   C4     0.00   0.0  0
 D3Y  CONST_21  N1   C2   N3   C4     0.00   0.0  0
 D3Y  CONST_22  C6   C5   C4   N3     0.00   0.0  0
 D3Y  CONST_23  C6   N1   C2   N3     0.00   0.0  0
 D3Y  CONST_24  N7   C8   N9   C1'  180.00   0.0  0
 D3Y  CONST_25  C5   C4   N9   C1'  180.00   0.0  0
 D3Y  CONST_26  N3   C4   N9   C1'    0.00   0.0  0
 D3Y  CONST_27  OH   CZ   CE1  CD1  180.00   0.0  0
 D3Y  CONST_28  CB   CG   CD1  CE1  180.00   0.0  0
 D3Y  CONST_29  CD2  CE2  CZ   OH   180.00   0.0  0
 D3Y  CONST_30  CB   CG   CD2  CE2  180.00   0.0  0
 D3Y  CONST_31  N6   C6   C5   N7     0.00   0.0  0
 D3Y  CONST_32  N6   C6   C5   C4   180.00   0.0  0
 D3Y  CONST_33  N6   C6   N1   C2   180.00   0.0  0
 D3Y  CONST_34  H5   CD2  CG   CD1  180.00   0.0  0
 D3Y  CONST_35  H4   CE2  CZ   CE1  180.00   0.0  0
 D3Y  CONST_36  H1   CD1  CE1  CZ   180.00   0.0  0
 D3Y  CONST_37  H2   CE1  CZ   CE2  180.00   0.0  0
 D3Y  CONST_38  H21  C8   N9   C1'    0.00   0.0  0
 D3Y  CONST_39  H22  C2   N3   C4   180.00   0.0  0
 D3Y  CONST_40  H23  N6   C6   C5     0.00   0.0  0
 D3Y  CONST_41  H24  N6   C6   C5   180.00   0.0  0
 D3Y  CONST_42  C3'  N8   C    CA   180.00   0.0  0
 D3Y  CONST_43  C3'  N8   C    O      0.00   0.0  0
 D3Y  CONST_44  H12  N8   C    CA     0.00   0.0  0
 D3Y  Var_01    CA   CB   CG   CD1   83.03  30.0  2

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
 D3Y  chir_01  CA   N    C    CB   negativ
 D3Y  chir_02  C3'  N8   C4'  C2'  positiv
 D3Y  chir_03  C2'  O2'  C3'  C1'  positiv
 D3Y  chir_04  C4'  O4'  C3'  C5'  negativ
 D3Y  chir_05  C1'  O4'  N9   C2'  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
 D3Y  plan-1  CD1  0.020
 D3Y  plan-1  CE1  0.020
 D3Y  plan-1  CZ   0.020
 D3Y  plan-1  OH   0.020
 D3Y  plan-1  CE2  0.020
 D3Y  plan-1  CD2  0.020
 D3Y  plan-1  CG   0.020
 D3Y  plan-1  CB   0.020
 D3Y  plan-1  H1   0.020
 D3Y  plan-1  H2   0.020
 D3Y  plan-1  H4   0.020
 D3Y  plan-1  H5   0.020
 D3Y  plan-2  C1'  0.020
 D3Y  plan-2  N9   0.020
 D3Y  plan-2  C8   0.020
 D3Y  plan-2  N7   0.020
 D3Y  plan-2  C5   0.020
 D3Y  plan-2  C4   0.020
 D3Y  plan-2  N3   0.020
 D3Y  plan-2  C2   0.020
 D3Y  plan-2  N1   0.020
 D3Y  plan-2  C6   0.020
 D3Y  plan-2  N6   0.020
 D3Y  plan-2  H21  0.020
 D3Y  plan-2  H22  0.020
 D3Y  plan-3  C6   0.020
 D3Y  plan-3  N6   0.020
 D3Y  plan-3  H23  0.020
 D3Y  plan-3  H24  0.020
 D3Y  plan-4  CA   0.020
 D3Y  plan-4  C    0.020
 D3Y  plan-4  O    0.020
 D3Y  plan-4  N8   0.020
 D3Y  plan-4  C3'  0.020
 D3Y  plan-4  H12  0.020

