# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 10:57:59 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: methyl (2R)-2-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}propanoate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](C)N[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)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
 9ZD  9ZD  'methyl (2R)-2-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}propanoate (non-preferred name)'  ligand  50  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9ZD
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
 9ZD  O3P  O  OH1   0  -0.739   2.8037  -3.4463  -0.9521
 9ZD  P    P  P     0   1.427   2.8402  -2.5396   0.3653
 9ZD  O2P  O  O     0  -0.705   2.8134  -3.3767   1.5819
 9ZD  O5'  O  O2    0  -0.598   1.5602  -1.6050   0.0885
 9ZD  C5'  C  CH2   0  -0.187   1.2462  -0.5474   0.9932
 9ZD  C4'  C  CH1   0  -0.039   0.7699   0.6452   0.1919
 9ZD  C3'  C  CH1   0  -0.031   0.4466   1.8458   1.0738
 9ZD  O3'  O  OH1   0  -0.660   0.6504   3.0116   0.3206
 9ZD  C2'  C  CH1   0  -0.047  -1.0425   1.6175   1.3432
 9ZD  O2'  O  OH1   0  -0.651  -1.7700   2.7623   1.6666
 9ZD  C1'  C  CH1   0   0.210  -1.5078   1.0753  -0.0089
 9ZD  O4'  O  O2    0  -0.488  -0.4314   0.3329  -0.5135
 9ZD  N9   N  NR5   0  -0.539  -2.6722   0.2335   0.0717
 9ZD  C4   C  CR56  0   0.493  -3.8999   0.4888  -0.4705
 9ZD  C5   C  CR56  0  -0.012  -4.6823  -0.6005  -0.1230
 9ZD  N7   N  N     0  -0.448  -3.9585  -1.5086   0.6067
 9ZD  C8   C  CR15  0   0.112  -2.7765  -0.9791   0.7005
 9ZD  N3   N  N     0  -0.457  -4.2847   1.5439  -1.1836
 9ZD  C2   C  CR16  0   0.047  -5.5516   1.4507  -1.5493
 9ZD  N1   N  N     0  -0.474  -6.4185   0.4761  -1.2881
 9ZD  C6   C  CR6   0   0.461  -6.0166  -0.5782  -0.5690
 9ZD  N6   N  NH2   0  -0.816  -6.8824  -1.5563  -0.3033
 9ZD  N2   N  NH1   0  -0.767   4.1275  -1.5118   0.3403
 9ZD  C3   C  CH1   0  -0.238   4.4196  -0.5569  -0.7012
 9ZD  C7   C  C     0   0.608   4.3607   0.8640  -0.1524
 9ZD  C9   C  CH3   0  -0.651   5.7789  -0.8277  -1.3476
 9ZD  O10  O  O     0  -0.434   4.3411   1.1498   1.0166
 9ZD  O11  O  O2    0  -0.452   4.3397   1.7485  -1.1343
 9ZD  C12  C  CH3   0  -0.431   4.2696   3.1330  -0.7796
 9ZD  H1   H  HOH1  0   0.493   2.7365  -2.9944  -1.8028
 9ZD  H2   H  HCH2  0   0.253   0.4814  -0.8934   1.6934
 9ZD  H3   H  HCH2  0   0.253   2.1203  -0.2515   1.5781
 9ZD  H4   H  HCH1  0   0.258   1.5359   0.9073  -0.5449
 9ZD  H5   H  HCH1  0   0.259   1.0384   1.8493   1.9980
 9ZD  H6   H  HOH1  0   0.453   0.1559   3.7278   0.7362
 9ZD  H7   H  HCH1  0   0.254  -1.1521   0.8402   2.1115
 9ZD  H8   H  HOH1  0   0.471  -1.6911   2.9264   2.6119
 9ZD  H9   H  HCH1  0   0.266  -1.7745   1.9022  -0.6761
 9ZD  H10  H  HCR5  0   0.295  -1.9373  -1.4327   1.2064
 9ZD  H11  H  HCR6  0   0.253  -5.9401   2.2741  -2.1390
 9ZD  H12  H  HNH2  0   0.404  -7.8250  -1.5076  -0.6490
 9ZD  H13  H  HNH2  0   0.412  -6.6097  -2.3636   0.2290
 9ZD  H14  H  HNH1  0   0.412   4.8754  -1.7094   0.9902
 9ZD  H15  H  HCH1  0   0.284   3.6580  -0.6302  -1.4832
 9ZD  H16  H  HCH3  0   0.242   6.5816  -0.7489  -0.6136
 9ZD  H17  H  HCH3  0   0.256   5.7882  -1.8363  -1.7579
 9ZD  H18  H  HCH3  0   0.252   5.9825  -0.1284  -2.1560
 9ZD  H19  H  HCH3  0   0.242   3.3237   3.3582  -0.2873
 9ZD  H20  H  HCH3  0   0.243   5.0971   3.4232  -0.1336
 9ZD  H21  H  HCH3  0   0.254   4.3306   3.6820  -1.7144

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
 9ZD  N6   C6   single    1.333  0.020  1.333
 9ZD  C6   N1   aromatic  1.338  0.020  1.338
 9ZD  C6   C5   aromatic  1.407  0.020  1.407
 9ZD  N1   C2   aromatic  1.330  0.020  1.330
 9ZD  C5   N7   aromatic  1.372  0.020  1.372
 9ZD  C5   C4   aromatic  1.386  0.020  1.386
 9ZD  C2   N3   aromatic  1.322  0.020  1.322
 9ZD  N7   C8   aromatic  1.299  0.020  1.299
 9ZD  C4   N3   aromatic  1.330  0.020  1.330
 9ZD  C4   N9   aromatic  1.366  0.020  1.366
 9ZD  C8   N9   aromatic  1.370  0.020  1.370
 9ZD  N9   C1'  single    1.439  0.020  1.439
 9ZD  C1'  C2'  single    1.529  0.020  1.529
 9ZD  C1'  O4'  single    1.402  0.020  1.402
 9ZD  O2'  C2'  single    1.394  0.020  1.394
 9ZD  C2'  C3'  single    1.530  0.020  1.530
 9ZD  O4'  C4'  single    1.428  0.020  1.428
 9ZD  C3'  C4'  single    1.524  0.020  1.524
 9ZD  C3'  O3'  single    1.403  0.020  1.403
 9ZD  C4'  C5'  single    1.514  0.020  1.514
 9ZD  C5'  O5'  single    1.427  0.020  1.427
 9ZD  O11  C7   single    1.322  0.020  1.322
 9ZD  O11  C12  single    1.431  0.020  1.431
 9ZD  O10  C7   double    1.204  0.020  1.204
 9ZD  O5'  P    single    1.609  0.020  1.609
 9ZD  C7   C3   single    1.524  0.020  1.524
 9ZD  O2P  P    double    1.477  0.020  1.477
 9ZD  N2   P    single    1.647  0.020  1.647
 9ZD  N2   C3   single    1.443  0.020  1.443
 9ZD  P    O3P  single    1.600  0.020  1.600
 9ZD  C3   C9   single    1.529  0.020  1.529
 9ZD  O3P  H1   single    0.850  0.020  0.980
 9ZD  C5'  H2   single    0.970  0.020  1.090
 9ZD  C5'  H3   single    0.970  0.020  1.090
 9ZD  C4'  H4   single    0.970  0.020  1.090
 9ZD  C3'  H5   single    0.970  0.020  1.090
 9ZD  O3'  H6   single    0.850  0.020  0.980
 9ZD  C2'  H7   single    0.970  0.020  1.090
 9ZD  O2'  H8   single    0.850  0.020  0.980
 9ZD  C1'  H9   single    0.970  0.020  1.090
 9ZD  C8   H10  single    0.930  0.020  1.080
 9ZD  C2   H11  single    0.930  0.020  1.080
 9ZD  N6   H12  single    0.860  0.020  1.020
 9ZD  N6   H13  single    0.860  0.020  1.020
 9ZD  N2   H14  single    0.860  0.020  1.020
 9ZD  C3   H15  single    0.970  0.020  1.090
 9ZD  C9   H16  single    0.970  0.020  1.090
 9ZD  C9   H17  single    0.970  0.020  1.090
 9ZD  C9   H18  single    0.970  0.020  1.090
 9ZD  C12  H19  single    0.970  0.020  1.090
 9ZD  C12  H20  single    0.970  0.020  1.090
 9ZD  C12  H21  single    0.970  0.020  1.090

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
 9ZD  H1   O3P  P    117.51  3.000
 9ZD  N2   P    O5'  104.87  3.000
 9ZD  N2   P    O2P  112.35  3.000
 9ZD  O5'  P    O2P  117.16  3.000
 9ZD  N2   P    O3P  111.04  3.000
 9ZD  O2P  P    O3P  110.90  3.000
 9ZD  O5'  P    O3P   99.75  3.000
 9ZD  C5'  O5'  P    119.77  3.000
 9ZD  H3   C5'  H2   107.62  3.000
 9ZD  H3   C5'  C4'  108.77  3.000
 9ZD  H2   C5'  C4'  111.61  3.000
 9ZD  H3   C5'  O5'  111.35  3.000
 9ZD  H2   C5'  O5'  108.99  3.000
 9ZD  C4'  C5'  O5'  108.52  3.000
 9ZD  H4   C4'  O4'  107.97  3.000
 9ZD  H4   C4'  C3'  110.44  3.000
 9ZD  O4'  C4'  C3'  106.24  3.000
 9ZD  H4   C4'  C5'  108.95  3.000
 9ZD  C3'  C4'  C5'  112.40  3.000
 9ZD  O4'  C4'  C5'  110.73  3.000
 9ZD  H5   C3'  C2'  112.15  3.000
 9ZD  H5   C3'  O3'  111.79  3.000
 9ZD  C2'  C3'  O3'  111.09  3.000
 9ZD  H5   C3'  C4'  112.04  3.000
 9ZD  O3'  C3'  C4'  108.24  3.000
 9ZD  C2'  C3'  C4'  100.99  3.000
 9ZD  H6   O3'  C3'  108.13  3.000
 9ZD  H7   C2'  C1'  109.70  3.000
 9ZD  H7   C2'  O2'  111.51  3.000
 9ZD  C1'  C2'  O2'  109.72  3.000
 9ZD  H7   C2'  C3'  109.02  3.000
 9ZD  O2'  C2'  C3'  115.21  3.000
 9ZD  C1'  C2'  C3'  101.15  3.000
 9ZD  H8   O2'  C2'  108.96  3.000
 9ZD  H9   C1'  N9   106.18  3.000
 9ZD  H9   C1'  O4'  111.56  3.000
 9ZD  N9   C1'  O4'  109.37  3.000
 9ZD  H9   C1'  C2'  110.18  3.000
 9ZD  O4'  C1'  C2'  105.81  3.000
 9ZD  N9   C1'  C2'  113.83  3.000
 9ZD  C1'  O4'  C4'  110.64  3.000
 9ZD  C8   N9   C4   106.21  3.000
 9ZD  C8   N9   C1'  127.24  3.000
 9ZD  C4   N9   C1'  126.55  3.000
 9ZD  N3   C4   C5   126.49  3.000
 9ZD  N3   C4   N9   128.38  3.000
 9ZD  C5   C4   N9   105.13  3.000
 9ZD  C6   C5   N7   132.81  3.000
 9ZD  N7   C5   C4   110.85  3.000
 9ZD  C6   C5   C4   116.34  3.000
 9ZD  C8   N7   C5   104.40  3.000
 9ZD  H10  C8   N7   124.74  3.000
 9ZD  H10  C8   N9   121.85  3.000
 9ZD  N7   C8   N9   113.40  3.000
 9ZD  C2   N3   C4   111.69  3.000
 9ZD  H11  C2   N1   115.44  3.000
 9ZD  H11  C2   N3   116.11  3.000
 9ZD  N1   C2   N3   128.45  3.000
 9ZD  C6   N1   C2   119.15  3.000
 9ZD  N6   C6   N1   119.36  3.000
 9ZD  N1   C6   C5   117.88  3.000
 9ZD  N6   C6   C5   122.76  3.000
 9ZD  H13  N6   H12  118.40  3.000
 9ZD  H13  N6   C6   121.26  3.000
 9ZD  H12  N6   C6   120.33  3.000
 9ZD  H14  N2   C3   116.35  3.000
 9ZD  H14  N2   P    116.53  3.000
 9ZD  C3   N2   P    125.59  3.000
 9ZD  H15  C3   C9   107.75  3.000
 9ZD  H15  C3   C7   107.03  3.000
 9ZD  C9   C3   C7   110.58  3.000
 9ZD  H15  C3   N2   109.31  3.000
 9ZD  C9   C3   N2   111.58  3.000
 9ZD  C7   C3   N2   110.44  3.000
 9ZD  O11  C7   O10  124.22  3.000
 9ZD  O10  C7   C3   124.86  3.000
 9ZD  O11  C7   C3   110.92  3.000
 9ZD  H18  C9   H17  108.28  3.000
 9ZD  H18  C9   H16  108.41  3.000
 9ZD  H17  C9   H16  108.32  3.000
 9ZD  H18  C9   C3   111.50  3.000
 9ZD  H17  C9   C3   109.33  3.000
 9ZD  H16  C9   C3   110.91  3.000
 9ZD  C12  O11  C7   117.65  3.000
 9ZD  H21  C12  H20  109.46  3.000
 9ZD  H21  C12  H19  109.46  3.000
 9ZD  H20  C12  H19  109.66  3.000
 9ZD  H21  C12  O11  105.85  3.000
 9ZD  H20  C12  O11  111.57  3.000
 9ZD  H19  C12  O11  110.76  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
 9ZD  CONST_01  C6   C5   C4   N9   180.00   0.0  0
 9ZD  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 9ZD  CONST_03  C2   N3   C4   N9   180.00   0.0  0
 9ZD  CONST_04  C5   N7   C8   N9     0.00   0.0  0
 9ZD  CONST_05  N1   C6   C5   C4     0.00   0.0  0
 9ZD  CONST_06  C8   N7   C5   C4     0.00   0.0  0
 9ZD  CONST_07  N1   C2   N3   C4     0.00   0.0  0
 9ZD  CONST_08  N7   C8   N9   C4     0.00   0.0  0
 9ZD  CONST_09  C2   N1   C6   C5     0.00   0.0  0
 9ZD  CONST_10  C2   N3   C4   C5     0.00   0.0  0
 9ZD  CONST_11  C8   N9   C4   C5     0.00   0.0  0
 9ZD  CONST_12  N1   C6   C5   N7   180.00   0.0  0
 9ZD  CONST_13  N3   C4   C5   N7   180.00   0.0  0
 9ZD  CONST_14  C6   C5   N7   C8   180.00   0.0  0
 9ZD  CONST_15  N3   C4   N9   C8   180.00   0.0  0
 9ZD  CONST_16  C6   N1   C2   N3     0.00   0.0  0
 9ZD  CONST_17  C6   C5   C4   N3     0.00   0.0  0
 9ZD  CONST_18  C5   C4   N9   C1'  180.00   0.0  0
 9ZD  CONST_19  N3   C4   N9   C1'    0.00   0.0  0
 9ZD  CONST_20  N7   C8   N9   C1'  180.00   0.0  0
 9ZD  CONST_21  N6   C6   C5   C4   180.00   0.0  0
 9ZD  CONST_22  N6   C6   C5   N7     0.00   0.0  0
 9ZD  CONST_23  N6   C6   N1   C2   180.00   0.0  0
 9ZD  CONST_24  H10  C8   N9   C1'    0.00   0.0  0
 9ZD  CONST_25  H11  C2   N3   C4   180.00   0.0  0
 9ZD  CONST_26  H12  N6   C6   C5   180.00   0.0  0
 9ZD  CONST_27  H13  N6   C6   C5     0.00   0.0  0
 9ZD  Var_01    C4'  C5'  O5'  P    141.19  30.0  1
 9ZD  Var_02    C3   N2   P    O3P   56.07  30.0  1
 9ZD  Var_03    N2   P    O5'  C5'  -60.87  30.0  3
 9ZD  Var_04    H19  C12  O11  C7   -65.16  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
 9ZD  chir_02  C4'  O4'  C3'  C5'  negativ
 9ZD  chir_03  C3'  O3'  C4'  C2'  positiv
 9ZD  chir_04  C2'  O2'  C3'  C1'  positiv
 9ZD  chir_05  C1'  O4'  N9   C2'  negativ
 9ZD  chir_06  C3   C7   N2   C9   positiv
 9ZD  chir_07  P    O2P  N2   O3P  both

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
 9ZD  plan-1  C1'  0.020
 9ZD  plan-1  N9   0.020
 9ZD  plan-1  C4   0.020
 9ZD  plan-1  C5   0.020
 9ZD  plan-1  N7   0.020
 9ZD  plan-1  C8   0.020
 9ZD  plan-1  N3   0.020
 9ZD  plan-1  C2   0.020
 9ZD  plan-1  N1   0.020
 9ZD  plan-1  C6   0.020
 9ZD  plan-1  N6   0.020
 9ZD  plan-1  H10  0.020
 9ZD  plan-1  H11  0.020
 9ZD  plan-2  C6   0.020
 9ZD  plan-2  N6   0.020
 9ZD  plan-2  H12  0.020
 9ZD  plan-2  H13  0.020
 9ZD  plan-3  C3   0.020
 9ZD  plan-3  C7   0.020
 9ZD  plan-3  O10  0.020
 9ZD  plan-3  O11  0.020

