# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 09:27:56 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl]amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCNC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
#
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
 0Y0  0Y0  5'-{[(3S)-3-amino-3-carboxypropyl]amino}-5'-deoxyadenosine  ligand  47  26  .  2022-07-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0Y0
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
 0Y0  OXT  O  OH1   0  -0.593   4.4637  -3.3981  -0.6417
 0Y0  C    C  C     0   0.521   5.3569  -2.5029  -0.2354
 0Y0  O    O  O     0  -0.440   6.5243  -2.5516  -0.5319
 0Y0  CA   C  CH1   0  -0.208   4.7281  -1.4196   0.6324
 0Y0  N    N  NH2   0  -0.776   5.6917  -0.6388   1.3700
 0Y0  CB   C  CH2   0  -0.459   3.8484  -0.5173  -0.2424
 0Y0  CAS  C  CH2   0  -0.251   3.0513   0.4865   0.5748
 0Y0  NAR  N  NH1   0  -0.608   2.1850   1.2672  -0.2926
 0Y0  CAF  C  CH2   0  -0.284   1.3499   2.1948   0.4358
 0Y0  CAA  C  CH1   0  -0.057   0.3972   2.9411  -0.4890
 0Y0  OAE  O  O2    0  -0.485  -0.3614   2.0594  -1.3219
 0Y0  CAB  C  CH1   0   0.007  -0.6547   3.7201   0.2805
 0Y0  OAH  O  OH1   0  -0.670  -1.1820   4.7197  -0.5495
 0Y0  CAC  C  CH1   0  -0.063  -1.6966   2.6217   0.5401
 0Y0  OAI  O  OH1   0  -0.653  -2.9989   3.1057   0.6932
 0Y0  CAD  C  CH1   0   0.221  -1.5906   1.7695  -0.7392
 0Y0  N9   N  NR5   0  -0.544  -1.6650   0.3379  -0.4764
 0Y0  C8   C  CR15  0   0.083  -0.6210  -0.5398  -0.3540
 0Y0  N7   N  N     0  -0.457  -1.0031  -1.7557  -0.0833
 0Y0  C5   C  CR56  0  -0.008  -2.3691  -1.6795  -0.0241
 0Y0  C4   C  CR56  0   0.483  -2.8028  -0.3848  -0.2705
 0Y0  N3   N  N     0  -0.448  -4.0678   0.0322  -0.3022
 0Y0  C2   C  CR16  0   0.035  -4.9130  -0.9535  -0.0609
 0Y0  N1   N  N     0  -0.474  -4.6446  -2.2313   0.2001
 0Y0  C6   C  CR6   0   0.450  -3.3704  -2.6353   0.2262
 0Y0  N6   N  NH2   0  -0.818  -3.0964  -3.9182   0.4757
 0Y0  H1   H  HOH1  0   0.481   4.8888  -4.0612  -1.2058
 0Y0  H2   H  HCH1  0   0.268   4.0764  -1.9271   1.3520
 0Y0  H3   H  HNH2  0   0.355   6.2539  -1.2367   1.9618
 0Y0  H4   H  HNH2  0   0.344   6.3338  -0.1820   0.7339
 0Y0  H6   H  HCH2  0   0.235   4.4830   0.0096  -0.9645
 0Y0  H7   H  HCH2  0   0.248   3.1522  -1.1276  -0.8207
 0Y0  H8   H  HCH2  0   0.218   2.4179  -0.0550   1.2861
 0Y0  H9   H  HCH2  0   0.216   3.7291   1.1096   1.1713
 0Y0  H10  H  HNH1  0   0.349   2.7563   1.7786  -0.9574
 0Y0  H12  H  HCH2  0   0.226   0.7890   1.6265   1.1862
 0Y0  H13  H  HCH2  0   0.233   1.9224   2.9485   0.9981
 0Y0  H14  H  HCH1  0   0.265   0.9737   3.5896  -1.1551
 0Y0  H15  H  HCH1  0   0.243  -0.2597   4.1336   1.2178
 0Y0  H16  H  HOH1  0   0.448  -2.0819   4.9031  -0.2537
 0Y0  H17  H  HCH1  0   0.260  -1.3881   2.0270   1.4069
 0Y0  H18  H  HOH1  0   0.469  -3.1583   3.2813   1.6253
 0Y0  H19  H  HCH1  0   0.268  -2.4085   2.0066  -1.4269
 0Y0  H20  H  HCR5  0   0.312   0.4040  -0.2183  -0.4962
 0Y0  H21  H  HCR6  0   0.249  -5.9663  -0.6939  -0.0734
 0Y0  H22  H  HNH2  0   0.410  -2.1483  -4.2342   0.5759
 0Y0  H23  H  HNH2  0   0.402  -3.8363  -4.5537   0.7187

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
 0Y0  O    C    double    1.206  0.020  1.206
 0Y0  C    CA   single    1.524  0.020  1.524
 0Y0  C    OXT  single    1.328  0.020  1.328
 0Y0  CA   N    single    1.443  0.020  1.443
 0Y0  CA   CB   single    1.534  0.020  1.534
 0Y0  CB   CAS  single    1.520  0.020  1.520
 0Y0  CAS  NAR  single    1.453  0.020  1.453
 0Y0  NAR  CAF  single    1.445  0.020  1.445
 0Y0  CAF  CAA  single    1.523  0.020  1.523
 0Y0  CAB  CAA  single    1.518  0.020  1.518
 0Y0  CAB  OAH  single    1.402  0.020  1.402
 0Y0  CAB  CAC  single    1.536  0.020  1.536
 0Y0  CAA  OAE  single    1.431  0.020  1.431
 0Y0  CAC  OAI  single    1.398  0.020  1.398
 0Y0  CAC  CAD  single    1.541  0.020  1.541
 0Y0  OAE  CAD  single    1.391  0.020  1.391
 0Y0  CAD  N9   single    1.457  0.020  1.457
 0Y0  C8   N9   aromatic  1.369  0.020  1.369
 0Y0  C8   N7   aromatic  1.303  0.020  1.303
 0Y0  N9   C4   aromatic  1.364  0.020  1.364
 0Y0  N7   C5   aromatic  1.369  0.020  1.369
 0Y0  C4   N3   aromatic  1.332  0.020  1.332
 0Y0  C4   C5   aromatic  1.387  0.020  1.387
 0Y0  N3   C2   aromatic  1.321  0.020  1.321
 0Y0  C5   C6   aromatic  1.407  0.020  1.407
 0Y0  C2   N1   aromatic  1.332  0.020  1.332
 0Y0  C6   N1   aromatic  1.337  0.020  1.337
 0Y0  C6   N6   single    1.335  0.020  1.335
 0Y0  OXT  H1   single    0.850  0.020  0.980
 0Y0  CA   H2   single    0.970  0.020  1.090
 0Y0  N    H3   single    0.890  0.020  1.040
 0Y0  N    H4   single    0.890  0.020  1.040
 0Y0  CB   H6   single    0.970  0.020  1.090
 0Y0  CB   H7   single    0.970  0.020  1.090
 0Y0  CAS  H8   single    0.970  0.020  1.090
 0Y0  CAS  H9   single    0.970  0.020  1.090
 0Y0  NAR  H10  single    0.890  0.020  1.040
 0Y0  CAF  H12  single    0.970  0.020  1.090
 0Y0  CAF  H13  single    0.970  0.020  1.090
 0Y0  CAA  H14  single    0.970  0.020  1.090
 0Y0  CAB  H15  single    0.970  0.020  1.090
 0Y0  OAH  H16  single    0.850  0.020  0.980
 0Y0  CAC  H17  single    0.970  0.020  1.090
 0Y0  OAI  H18  single    0.850  0.020  0.980
 0Y0  CAD  H19  single    0.970  0.020  1.090
 0Y0  C8   H20  single    0.930  0.020  1.080
 0Y0  C2   H21  single    0.930  0.020  1.080
 0Y0  N6   H22  single    0.860  0.020  1.020
 0Y0  N6   H23  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
 0Y0  H1   OXT  C    110.14  3.000
 0Y0  CA   C    O    124.64  3.000
 0Y0  CA   C    OXT  112.08  3.000
 0Y0  O    C    OXT  123.28  3.000
 0Y0  H2   CA   CB   107.82  3.000
 0Y0  H2   CA   N    108.19  3.000
 0Y0  CB   CA   N    110.86  3.000
 0Y0  H2   CA   C    106.87  3.000
 0Y0  CB   CA   C    109.27  3.000
 0Y0  N    CA   C    113.59  3.000
 0Y0  H4   N    H3   106.35  3.000
 0Y0  H4   N    CA   110.27  3.000
 0Y0  H3   N    CA   110.51  3.000
 0Y0  H7   CB   H6   106.80  3.000
 0Y0  H7   CB   CAS  108.63  3.000
 0Y0  H6   CB   CAS  109.89  3.000
 0Y0  H7   CB   CA   109.82  3.000
 0Y0  H6   CB   CA   109.05  3.000
 0Y0  CAS  CB   CA   112.49  3.000
 0Y0  H9   CAS  H8   106.55  3.000
 0Y0  H9   CAS  NAR  112.82  3.000
 0Y0  H8   CAS  NAR  107.96  3.000
 0Y0  H9   CAS  CB   110.09  3.000
 0Y0  H8   CAS  CB   109.01  3.000
 0Y0  NAR  CAS  CB   110.27  3.000
 0Y0  H10  NAR  CAF  109.39  3.000
 0Y0  H10  NAR  CAS  109.03  3.000
 0Y0  CAF  NAR  CAS  112.85  3.000
 0Y0  H13  CAF  H12  105.75  3.000
 0Y0  H13  CAF  CAA  107.45  3.000
 0Y0  H12  CAF  CAA  110.47  3.000
 0Y0  H13  CAF  NAR  113.35  3.000
 0Y0  H12  CAF  NAR  107.94  3.000
 0Y0  CAA  CAF  NAR  111.71  3.000
 0Y0  H14  CAA  CAB  111.69  3.000
 0Y0  H14  CAA  OAE  106.87  3.000
 0Y0  CAB  CAA  OAE  104.11  3.000
 0Y0  H14  CAA  CAF  109.31  3.000
 0Y0  OAE  CAA  CAF  112.53  3.000
 0Y0  CAB  CAA  CAF  112.15  3.000
 0Y0  CAD  OAE  CAA  110.68  3.000
 0Y0  H15  CAB  CAC  111.65  3.000
 0Y0  H15  CAB  OAH  111.84  3.000
 0Y0  CAC  CAB  OAH  110.78  3.000
 0Y0  H15  CAB  CAA  112.12  3.000
 0Y0  CAC  CAB  CAA  100.88  3.000
 0Y0  OAH  CAB  CAA  109.05  3.000
 0Y0  H16  OAH  CAB  107.74  3.000
 0Y0  H17  CAC  CAD  109.72  3.000
 0Y0  H17  CAC  OAI  111.33  3.000
 0Y0  CAD  CAC  OAI  110.27  3.000
 0Y0  H17  CAC  CAB  109.32  3.000
 0Y0  CAD  CAC  CAB  102.03  3.000
 0Y0  OAI  CAC  CAB  113.76  3.000
 0Y0  H18  OAI  CAC  108.89  3.000
 0Y0  H19  CAD  N9   106.73  3.000
 0Y0  H19  CAD  CAC  110.52  3.000
 0Y0  N9   CAD  CAC  112.96  3.000
 0Y0  H19  CAD  OAE  110.61  3.000
 0Y0  N9   CAD  OAE  108.99  3.000
 0Y0  CAC  CAD  OAE  107.06  3.000
 0Y0  C4   N9   C8   106.43  3.000
 0Y0  C4   N9   CAD  126.19  3.000
 0Y0  C8   N9   CAD  127.36  3.000
 0Y0  H20  C8   N7   125.56  3.000
 0Y0  H20  C8   N9   121.28  3.000
 0Y0  N7   C8   N9   113.15  3.000
 0Y0  C5   N7   C8   104.45  3.000
 0Y0  C6   C5   C4   116.30  3.000
 0Y0  C6   C5   N7   132.84  3.000
 0Y0  C4   C5   N7   110.86  3.000
 0Y0  N3   C4   C5   126.38  3.000
 0Y0  C5   C4   N9   105.10  3.000
 0Y0  N3   C4   N9   128.52  3.000
 0Y0  C2   N3   C4   111.70  3.000
 0Y0  H21  C2   N1   115.31  3.000
 0Y0  H21  C2   N3   116.14  3.000
 0Y0  N1   C2   N3   128.54  3.000
 0Y0  C6   N1   C2   119.07  3.000
 0Y0  N6   C6   N1   119.31  3.000
 0Y0  N6   C6   C5   122.68  3.000
 0Y0  N1   C6   C5   118.01  3.000
 0Y0  H23  N6   H22  118.15  3.000
 0Y0  H23  N6   C6   120.10  3.000
 0Y0  H22  N6   C6   120.97  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
 0Y0  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 0Y0  CONST_02  C2   N3   C4   N9    180.00   0.0  0
 0Y0  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 0Y0  CONST_04  C6   C5   C4   N9    180.00   0.0  0
 0Y0  CONST_05  N3   C4   N9   C8    180.00   0.0  0
 0Y0  CONST_06  C5   C4   N9   C8      0.00   0.0  0
 0Y0  CONST_07  C4   C5   N7   C8      0.00   0.0  0
 0Y0  CONST_08  C6   C5   N7   C8    180.00   0.0  0
 0Y0  CONST_09  C4   N9   C8   N7      0.00   0.0  0
 0Y0  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 0Y0  CONST_11  N1   C6   C5   N7    180.00   0.0  0
 0Y0  CONST_12  C2   N3   C4   C5      0.00   0.0  0
 0Y0  CONST_13  C2   N1   C6   C5      0.00   0.0  0
 0Y0  CONST_14  N1   C2   N3   C4      0.00   0.0  0
 0Y0  CONST_15  N1   C6   C5   C4      0.00   0.0  0
 0Y0  CONST_16  C6   C5   C4   N3      0.00   0.0  0
 0Y0  CONST_17  C6   N1   C2   N3      0.00   0.0  0
 0Y0  CONST_18  N7   C8   N9   CAD   180.00   0.0  0
 0Y0  CONST_19  N3   C4   N9   CAD     0.00   0.0  0
 0Y0  CONST_20  C5   C4   N9   CAD   180.00   0.0  0
 0Y0  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 0Y0  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 0Y0  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 0Y0  CONST_24  H20  C8   N9   CAD     0.00   0.0  0
 0Y0  CONST_25  H21  C2   N3   C4    180.00   0.0  0
 0Y0  CONST_26  H22  N6   C6   C5      0.00   0.0  0
 0Y0  CONST_27  H23  N6   C6   C5    180.00   0.0  0
 0Y0  CONST_28  H1   OXT  C    O       0.00   0.0  0
 0Y0  Var_01    CAA  CAF  NAR  CAS  -176.73  30.0  3
 0Y0  Var_02    NAR  CAS  CB   CA   -177.03  30.0  3
 0Y0  Var_03    CAF  NAR  CAS  CB    177.05  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
 0Y0  chir_01  CA   C    N    CB   negativ
 0Y0  chir_02  CAA  CAF  CAB  OAE  positiv
 0Y0  chir_03  CAB  OAH  CAC  CAA  negativ
 0Y0  chir_04  CAC  OAI  CAD  CAB  negativ
 0Y0  chir_05  CAD  OAE  N9   CAC  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
 0Y0  plan-1  CAD  0.020
 0Y0  plan-1  N9   0.020
 0Y0  plan-1  C8   0.020
 0Y0  plan-1  N7   0.020
 0Y0  plan-1  C5   0.020
 0Y0  plan-1  C4   0.020
 0Y0  plan-1  N3   0.020
 0Y0  plan-1  C2   0.020
 0Y0  plan-1  N1   0.020
 0Y0  plan-1  C6   0.020
 0Y0  plan-1  N6   0.020
 0Y0  plan-1  H20  0.020
 0Y0  plan-1  H21  0.020
 0Y0  plan-2  C6   0.020
 0Y0  plan-2  N6   0.020
 0Y0  plan-2  H22  0.020
 0Y0  plan-2  H23  0.020
 0Y0  plan-3  OXT  0.020
 0Y0  plan-3  C    0.020
 0Y0  plan-3  O    0.020
 0Y0  plan-3  CA   0.020
 0Y0  plan-3  H1   0.020

