# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 28 07:02:11 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 3'-deoxy-3'-[(O-methyl-L-tyrosyl)amino]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO)n3cnc4c(N)ncnc34)cc1
#
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
 3NZ  3NZ  3'-deoxy-3'-[(O-methyl-L-tyrosyl)amino]adenosine  ligand  57  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3NZ
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
 3NZ  O    O  O     0  -0.495   1.7194  -2.9620   1.0780
 3NZ  C    C  C     0   0.542   1.7208  -1.7388   1.0731
 3NZ  CA   C  CH1   0  -0.215   3.0199  -0.9366   1.0817
 3NZ  CB   C  CH2   0  -0.523   3.5871  -0.9450  -0.3485
 3NZ  CG   C  CR6   0   0.131   4.7375   0.0044  -0.5107
 3NZ  CD2  C  CR16  0  -0.290   6.0497  -0.3930  -0.2938
 3NZ  CE2  C  CR16  0  -0.373   7.1143   0.4944  -0.4124
 3NZ  CZ   C  CR6   0   0.363   6.8719   1.8227  -0.7519
 3NZ  OM   O  O2    0  -0.473   7.8289   2.7635  -0.8887
 3NZ  CMZ  C  CH3   0  -0.435   9.1736   2.3940  -0.6646
 3NZ  CE1  C  CR16  0  -0.329   5.5580   2.2383  -0.9749
 3NZ  CD1  C  CR16  0  -0.296   4.5152   1.3377  -0.8545
 3NZ  N    N  NH2   0  -0.767   4.0000  -1.4441   2.0132
 3NZ  N3'  N  NH1   0  -0.647   0.5913  -1.0131   1.0114
 3NZ  C3'  C  CR15  0  -0.134  -0.7125  -1.6312   1.0005
 3NZ  C4'  C  CR15  0  -0.040  -1.0468  -2.2505  -0.3592
 3NZ  C5'  C  CH2   0  -0.149  -2.1003  -3.3386  -0.2699
 3NZ  O5'  O  OH1   0  -0.664  -2.4215  -3.7412  -1.5772
 3NZ  C2'  C  CR15  0  -0.049  -1.8063  -0.5686   1.1167
 3NZ  O2'  O  OH1   0  -0.672  -1.4551   0.4840   1.9566
 3NZ  C1'  C  CR15  0   0.211  -2.0112  -0.1494  -0.3581
 3NZ  O4'  O  O     0  -0.482  -1.4920  -1.1529  -1.1584
 3NZ  N9   N  NR5   0  -0.547  -3.4270   0.0419  -0.6526
 3NZ  C8   C  CR15  0   0.112  -4.2004  -0.5204  -1.6291
 3NZ  N7   N  N     0  -0.454  -5.4225  -0.0680  -1.6362
 3NZ  C5   C  CR56  0   0.001  -5.4577   0.8438  -0.6140
 3NZ  C4   C  CR56  0   0.524  -4.2243   0.9208   0.0095
 3NZ  C6   C  CR6   0   0.465  -6.4644   1.6794  -0.0933
 3NZ  N6   N  NH2   0  -0.813  -7.6991   1.7200  -0.5889
 3NZ  N1   N  N     0  -0.476  -6.1537   2.4620   0.9493
 3NZ  C2   C  CR16  0   0.067  -4.9275   2.4237   1.4557
 3NZ  N3   N  N     0  -0.517  -3.9023   1.6890   1.0538
 3NZ  H1   H  HCH1  0   0.262   2.8006   0.1009   1.3533
 3NZ  H2   H  HCH2  0   0.253   3.8949  -1.9653  -0.5940
 3NZ  H3   H  HCH2  0   0.258   2.7900  -0.6817  -1.0490
 3NZ  H4   H  HCR6  0   0.245   6.2603  -1.4218  -0.0297
 3NZ  H5   H  HCR6  0   0.274   8.1174   0.1307  -0.2345
 3NZ  H6   H  HCH3  0   0.227   9.3386   2.0492   0.3598
 3NZ  H7   H  HCH3  0   0.226   9.5051   1.6134  -1.3544
 3NZ  H8   H  HCH3  0   0.258   9.7727   3.2856  -0.8340
 3NZ  H9   H  HCR6  0   0.258   5.3618   3.2687  -1.2449
 3NZ  H10  H  HCR6  0   0.245   3.5033   1.6819  -1.0367
 3NZ  H11  H  HNH2  0   0.353   3.6524  -1.3712   2.9613
 3NZ  H12  H  HNH2  0   0.342   4.1557  -2.4302   1.8406
 3NZ  H14  H  HNH1  0   0.404   0.6482  -0.0147   1.1422
 3NZ  H15  H  HCR5  0   0.292  -0.7888  -2.3673   1.8051
 3NZ  H16  H  HCR5  0   0.272  -0.1593  -2.6584  -0.8458
 3NZ  H17  H  HCH2  0   0.219  -1.6795  -4.1600   0.3246
 3NZ  H18  H  HCH2  0   0.201  -2.9868  -2.9792   0.2706
 3NZ  H19  H  HOH1  0   0.460  -3.1175  -4.4023  -1.5261
 3NZ  H20  H  HCR5  0   0.262  -2.7172  -1.0723   1.4667
 3NZ  H21  H  HOH1  0   0.464  -2.1879   1.1270   1.9076
 3NZ  H22  H  HCR5  0   0.276  -1.5033   0.7988  -0.5682
 3NZ  H23  H  HCR5  0   0.294  -3.8097  -1.2725  -2.2965
 3NZ  H24  H  HNH2  0   0.414  -7.9622   1.1605  -1.3812
 3NZ  H25  H  HNH2  0   0.406  -8.3804   2.3512  -0.2032
 3NZ  H26  H  HCR6  0   0.261  -4.7468   3.0745   2.3038

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
 3NZ  N6   C6   single    1.331  0.020  1.331
 3NZ  N7   C5   aromatic  1.370  0.020  1.370
 3NZ  N7   C8   aromatic  1.303  0.020  1.303
 3NZ  C6   C5   aromatic  1.408  0.020  1.408
 3NZ  C6   N1   aromatic  1.340  0.020  1.340
 3NZ  C5   C4   aromatic  1.384  0.020  1.384
 3NZ  C8   N9   aromatic  1.367  0.020  1.367
 3NZ  N1   C2   aromatic  1.327  0.020  1.327
 3NZ  C4   N9   aromatic  1.359  0.020  1.359
 3NZ  C4   N3   aromatic  1.336  0.020  1.336
 3NZ  N9   C1'  single    1.459  0.020  1.459
 3NZ  C2   N3   aromatic  1.324  0.020  1.324
 3NZ  O4'  C1'  single    1.385  0.020  1.385
 3NZ  O4'  C4'  single    1.429  0.020  1.429
 3NZ  C1'  C2'  single    1.547  0.020  1.547
 3NZ  C4'  C5'  single    1.517  0.020  1.517
 3NZ  C4'  C3'  single    1.531  0.020  1.531
 3NZ  C5'  O5'  single    1.405  0.020  1.405
 3NZ  C2'  O2'  single    1.392  0.020  1.392
 3NZ  C2'  C3'  single    1.529  0.020  1.529
 3NZ  C3'  N3'  single    1.443  0.020  1.443
 3NZ  O    C    double    1.223  0.020  1.223
 3NZ  CMZ  OM   single    1.412  0.020  1.412
 3NZ  N3'  C    single    1.344  0.020  1.344
 3NZ  C    CA   single    1.527  0.020  1.527
 3NZ  OM   CZ   single    1.349  0.020  1.349
 3NZ  CZ   CE1  aromatic  1.396  0.020  1.396
 3NZ  CZ   CE2  aromatic  1.392  0.020  1.392
 3NZ  CE1  CD1  aromatic  1.383  0.020  1.383
 3NZ  CE2  CD2  aromatic  1.391  0.020  1.391
 3NZ  CD1  CG   aromatic  1.395  0.020  1.395
 3NZ  CD2  CG   aromatic  1.388  0.020  1.388
 3NZ  CG   CB   single    1.500  0.020  1.500
 3NZ  CA   CB   single    1.539  0.020  1.539
 3NZ  CA   N    single    1.444  0.020  1.444
 3NZ  CA   H1   single    0.970  0.020  1.090
 3NZ  CB   H2   single    0.970  0.020  1.090
 3NZ  CB   H3   single    0.970  0.020  1.090
 3NZ  CD2  H4   single    0.930  0.020  1.080
 3NZ  CE2  H5   single    0.930  0.020  1.080
 3NZ  CMZ  H6   single    0.970  0.020  1.090
 3NZ  CMZ  H7   single    0.970  0.020  1.090
 3NZ  CMZ  H8   single    0.970  0.020  1.090
 3NZ  CE1  H9   single    0.930  0.020  1.080
 3NZ  CD1  H10  single    0.930  0.020  1.080
 3NZ  N    H11  single    0.890  0.020  1.040
 3NZ  N    H12  single    0.890  0.020  1.040
 3NZ  N3'  H14  single    0.860  0.020  1.020
 3NZ  C3'  H15  single    0.970  0.020  1.090
 3NZ  C4'  H16  single    0.970  0.020  1.090
 3NZ  C5'  H17  single    0.970  0.020  1.090
 3NZ  C5'  H18  single    0.970  0.020  1.090
 3NZ  O5'  H19  single    0.850  0.020  0.980
 3NZ  C2'  H20  single    0.970  0.020  1.090
 3NZ  O2'  H21  single    0.850  0.020  0.980
 3NZ  C1'  H22  single    0.970  0.020  1.090
 3NZ  C8   H23  single    0.930  0.020  1.080
 3NZ  N6   H24  single    0.860  0.020  1.020
 3NZ  N6   H25  single    0.860  0.020  1.020
 3NZ  C2   H26  single    0.930  0.020  1.080

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
 3NZ  N3'  C    CA   115.57  3.000
 3NZ  CA   C    O    121.76  3.000
 3NZ  N3'  C    O    122.63  3.000
 3NZ  H1   CA   N    108.00  3.000
 3NZ  H1   CA   CB   108.03  3.000
 3NZ  N    CA   CB   110.33  3.000
 3NZ  H1   CA   C    109.21  3.000
 3NZ  N    CA   C    113.35  3.000
 3NZ  CB   CA   C    107.79  3.000
 3NZ  H3   CB   H2   106.62  3.000
 3NZ  H3   CB   CG   109.72  3.000
 3NZ  H2   CB   CG   110.51  3.000
 3NZ  H3   CB   CA   108.99  3.000
 3NZ  H2   CB   CA   108.51  3.000
 3NZ  CG   CB   CA   112.32  3.000
 3NZ  CD1  CG   CD2  117.57  3.000
 3NZ  CD2  CG   CB   121.79  3.000
 3NZ  CD1  CG   CB   120.62  3.000
 3NZ  H4   CD2  CE2  118.56  3.000
 3NZ  H4   CD2  CG   119.60  3.000
 3NZ  CE2  CD2  CG   121.84  3.000
 3NZ  H5   CE2  CZ   121.49  3.000
 3NZ  H5   CE2  CD2  118.77  3.000
 3NZ  CZ   CE2  CD2  119.75  3.000
 3NZ  CE1  CZ   OM   116.35  3.000
 3NZ  CE1  CZ   CE2  119.13  3.000
 3NZ  OM   CZ   CE2  124.52  3.000
 3NZ  CMZ  OM   CZ   118.48  3.000
 3NZ  H8   CMZ  H7   108.67  3.000
 3NZ  H8   CMZ  H6   108.75  3.000
 3NZ  H7   CMZ  H6   108.68  3.000
 3NZ  H8   CMZ  OM   106.58  3.000
 3NZ  H7   CMZ  OM   112.05  3.000
 3NZ  H6   CMZ  OM   112.01  3.000
 3NZ  H9   CE1  CD1  120.30  3.000
 3NZ  H9   CE1  CZ   119.57  3.000
 3NZ  CD1  CE1  CZ   120.13  3.000
 3NZ  H10  CD1  CE1  118.84  3.000
 3NZ  H10  CD1  CG   119.58  3.000
 3NZ  CE1  CD1  CG   121.58  3.000
 3NZ  H12  N    H11  106.40  3.000
 3NZ  H12  N    CA   109.66  3.000
 3NZ  H11  N    CA   110.22  3.000
 3NZ  H14  N3'  C3'  118.43  3.000
 3NZ  H14  N3'  C    118.76  3.000
 3NZ  C3'  N3'  C    121.90  3.000
 3NZ  H15  C3'  C2'  111.22  3.000
 3NZ  H15  C3'  C4'  111.47  3.000
 3NZ  C2'  C3'  C4'  101.09  3.000
 3NZ  H15  C3'  N3'  110.24  3.000
 3NZ  C2'  C3'  N3'  110.36  3.000
 3NZ  C4'  C3'  N3'  112.17  3.000
 3NZ  H16  C4'  O4'  106.92  3.000
 3NZ  H16  C4'  C5'  108.84  3.000
 3NZ  O4'  C4'  C5'  111.56  3.000
 3NZ  H16  C4'  C3'  111.69  3.000
 3NZ  C5'  C4'  C3'  112.92  3.000
 3NZ  O4'  C4'  C3'  104.72  3.000
 3NZ  H18  C5'  H17  106.71  3.000
 3NZ  H18  C5'  O5'  111.53  3.000
 3NZ  H17  C5'  O5'  112.15  3.000
 3NZ  H18  C5'  C4'  110.77  3.000
 3NZ  H17  C5'  C4'  107.60  3.000
 3NZ  O5'  C5'  C4'  108.03  3.000
 3NZ  H19  O5'  C5'  108.25  3.000
 3NZ  H20  C2'  C1'  108.56  3.000
 3NZ  H20  C2'  O2'  111.34  3.000
 3NZ  C1'  C2'  O2'  113.82  3.000
 3NZ  H20  C2'  C3'  107.39  3.000
 3NZ  O2'  C2'  C3'  113.01  3.000
 3NZ  C1'  C2'  C3'  102.15  3.000
 3NZ  H21  O2'  C2'  106.17  3.000
 3NZ  H22  C1'  N9   107.32  3.000
 3NZ  H22  C1'  O4'  110.03  3.000
 3NZ  N9   C1'  O4'  110.02  3.000
 3NZ  H22  C1'  C2'  110.84  3.000
 3NZ  O4'  C1'  C2'  107.76  3.000
 3NZ  N9   C1'  C2'  110.89  3.000
 3NZ  C1'  O4'  C4'  110.50  3.000
 3NZ  C4   N9   C8   106.39  3.000
 3NZ  C4   N9   C1'  123.78  3.000
 3NZ  C8   N9   C1'  129.76  3.000
 3NZ  H23  C8   N7   125.33  3.000
 3NZ  H23  C8   N9   121.59  3.000
 3NZ  N7   C8   N9   113.07  3.000
 3NZ  C5   N7   C8   104.54  3.000
 3NZ  C6   C5   C4   115.94  3.000
 3NZ  C4   C5   N7   110.50  3.000
 3NZ  C6   C5   N7   133.55  3.000
 3NZ  N3   C4   C5   126.80  3.000
 3NZ  N3   C4   N9   127.69  3.000
 3NZ  C5   C4   N9   105.51  3.000
 3NZ  N1   C6   N6   119.14  3.000
 3NZ  N1   C6   C5   117.93  3.000
 3NZ  N6   C6   C5   122.93  3.000
 3NZ  H25  N6   H24  118.33  3.000
 3NZ  H25  N6   C6   120.31  3.000
 3NZ  H24  N6   C6   121.29  3.000
 3NZ  C2   N1   C6   119.62  3.000
 3NZ  H26  C2   N3   116.21  3.000
 3NZ  H26  C2   N1   115.79  3.000
 3NZ  N3   C2   N1   128.00  3.000
 3NZ  C2   N3   C4   111.71  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
 3NZ  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 3NZ  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 3NZ  CONST_03  CE1  CZ   CE2  CD2    0.00   0.0  0
 3NZ  CONST_04  CE1  CD1  CG   CD2    0.00   0.0  0
 3NZ  CONST_05  CD1  CE1  CZ   CE2    0.00   0.0  0
 3NZ  CONST_06  CD1  CG   CD2  CE2    0.00   0.0  0
 3NZ  CONST_07  C5   N7   C8   N9     0.00   0.0  0
 3NZ  CONST_08  N7   C5   C4   N9     0.00   0.0  0
 3NZ  CONST_09  C6   C5   C4   N9   180.00   0.0  0
 3NZ  CONST_10  C2   N3   C4   N9   180.00   0.0  0
 3NZ  CONST_11  C6   C5   N7   C8   180.00   0.0  0
 3NZ  CONST_12  C4   C5   N7   C8     0.00   0.0  0
 3NZ  CONST_13  C5   C4   N9   C8     0.00   0.0  0
 3NZ  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 3NZ  CONST_15  N1   C6   C5   N7   180.00   0.0  0
 3NZ  CONST_16  N3   C4   C5   N7   180.00   0.0  0
 3NZ  CONST_17  C4   N9   C8   N7     0.00   0.0  0
 3NZ  CONST_18  C2   N1   C6   C5     0.00   0.0  0
 3NZ  CONST_19  C2   N3   C4   C5     0.00   0.0  0
 3NZ  CONST_20  N1   C6   C5   C4     0.00   0.0  0
 3NZ  CONST_21  N1   C2   N3   C4     0.00   0.0  0
 3NZ  CONST_22  N3   C4   C5   C6     0.00   0.0  0
 3NZ  CONST_23  N3   C2   N1   C6     0.00   0.0  0
 3NZ  CONST_24  N7   C8   N9   C1'  180.00   0.0  0
 3NZ  CONST_25  C5   C4   N9   C1'  180.00   0.0  0
 3NZ  CONST_26  N3   C4   N9   C1'    0.00   0.0  0
 3NZ  CONST_27  CE1  CD1  CG   CB   180.00   0.0  0
 3NZ  CONST_28  CE2  CD2  CG   CB   180.00   0.0  0
 3NZ  CONST_29  OM   CZ   CE2  CD2  180.00   0.0  0
 3NZ  CONST_30  CD1  CE1  CZ   OM   180.00   0.0  0
 3NZ  CONST_31  N6   C6   C5   N7     0.00   0.0  0
 3NZ  CONST_32  N6   C6   C5   C4   180.00   0.0  0
 3NZ  CONST_33  C2   N1   C6   N6   180.00   0.0  0
 3NZ  CONST_34  H9   CE1  CD1  CG   180.00   0.0  0
 3NZ  CONST_35  H5   CE2  CD2  CG   180.00   0.0  0
 3NZ  CONST_36  H10  CD1  CG   CD2  180.00   0.0  0
 3NZ  CONST_37  H4   CD2  CE2  CZ   180.00   0.0  0
 3NZ  CONST_38  H23  C8   N9   C1'    0.00   0.0  0
 3NZ  CONST_39  H26  C2   N3   C4   180.00   0.0  0
 3NZ  CONST_40  H24  N6   C6   C5     0.00   0.0  0
 3NZ  CONST_41  H25  N6   C6   C5   180.00   0.0  0
 3NZ  CONST_42  C3'  N3'  C    O      0.00   0.0  0
 3NZ  CONST_43  C3'  N3'  C    CA   180.00   0.0  0
 3NZ  CONST_44  H14  N3'  C    O    180.00   0.0  0
 3NZ  Var_01    CD1  CG   CB   CA   -87.96  30.0  2
 3NZ  Var_02    CE1  CZ   OM   CMZ  179.59  30.0  2
 3NZ  Var_03    H6   CMZ  OM   CZ   -61.68  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
 3NZ  chir_01  CA   C    CB   N    positiv
 3NZ  chir_02  C3'  N3'  C4'  C2'  positiv
 3NZ  chir_03  C4'  O4'  C3'  C5'  negativ
 3NZ  chir_04  C2'  O2'  C3'  C1'  positiv
 3NZ  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
 3NZ  plan-1  CB   0.020
 3NZ  plan-1  CG   0.020
 3NZ  plan-1  CD2  0.020
 3NZ  plan-1  CE2  0.020
 3NZ  plan-1  CZ   0.020
 3NZ  plan-1  OM   0.020
 3NZ  plan-1  CE1  0.020
 3NZ  plan-1  CD1  0.020
 3NZ  plan-1  H4   0.020
 3NZ  plan-1  H5   0.020
 3NZ  plan-1  H9   0.020
 3NZ  plan-1  H10  0.020
 3NZ  plan-2  C1'  0.020
 3NZ  plan-2  N9   0.020
 3NZ  plan-2  C8   0.020
 3NZ  plan-2  N7   0.020
 3NZ  plan-2  C5   0.020
 3NZ  plan-2  C4   0.020
 3NZ  plan-2  C6   0.020
 3NZ  plan-2  N6   0.020
 3NZ  plan-2  N1   0.020
 3NZ  plan-2  C2   0.020
 3NZ  plan-2  N3   0.020
 3NZ  plan-2  H23  0.020
 3NZ  plan-2  H26  0.020
 3NZ  plan-3  C6   0.020
 3NZ  plan-3  N6   0.020
 3NZ  plan-3  H24  0.020
 3NZ  plan-3  H25  0.020
 3NZ  plan-4  O    0.020
 3NZ  plan-4  C    0.020
 3NZ  plan-4  CA   0.020
 3NZ  plan-4  N3'  0.020
 3NZ  plan-4  C3'  0.020
 3NZ  plan-4  H14  0.020

