# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:33:49 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: methyl (2S)-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
 9ZA  9ZA  'methyl (2S)-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_9ZA
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
 9ZA  O3P  O  OH1   0  -0.738   3.8879  -1.9506   0.7863
 9ZA  P    P  P     0   1.445   3.3936  -0.7010   1.6578
 9ZA  O2P  O  O     0  -0.711   4.1125  -0.4216   2.9205
 9ZA  O5'  O  O2    0  -0.594   1.8442  -1.0956   1.8335
 9ZA  C5'  C  CH2   0  -0.192   1.0144  -0.4697   2.8050
 9ZA  C4'  C  CH1   0  -0.049   0.6338   0.9532   2.4268
 9ZA  C3'  C  CH1   0  -0.026  -0.4863   1.4814   3.3152
 9ZA  O3'  O  OH1   0  -0.666  -0.3863   2.8789   3.3799
 9ZA  C2'  C  CH1   0  -0.050  -1.7198   1.0541   2.5126
 9ZA  O2'  O  OH1   0  -0.652  -2.8691   1.8083   2.7499
 9ZA  C1'  C  CH1   0   0.224  -1.2354   1.2821   1.0802
 9ZA  O4'  O  O2    0  -0.480   0.1341   1.0041   1.0910
 9ZA  N9   N  NR5   0  -0.539  -1.8775   0.4401   0.1023
 9ZA  C4   C  CR56  0   0.491  -2.7641   0.8407  -0.8552
 9ZA  C5   C  CR56  0  -0.011  -3.0979  -0.3140  -1.5454
 9ZA  N7   N  N     0  -0.450  -2.4316  -1.3977  -1.0333
 9ZA  C8   C  CR15  0   0.112  -1.7210  -0.9103  -0.0606
 9ZA  N3   N  N     0  -0.456  -3.2198   2.0674  -1.0975
 9ZA  C2   C  CR16  0   0.045  -4.0659   2.0823  -2.1125
 9ZA  N1   N  N     0  -0.475  -4.4787   1.0627  -2.8608
 9ZA  C6   C  CR6   0   0.459  -4.0110  -0.1646  -2.6056
 9ZA  N6   N  NH2   0  -0.816  -4.4271  -1.1893  -3.3508
 9ZA  N2   N  NH1   0  -0.757   3.4363   0.5622   0.5994
 9ZA  C3   C  CH1   0  -0.223   2.8968   0.4847  -0.7402
 9ZA  C7   C  C     0   0.606   3.8919  -0.1444  -1.7048
 9ZA  C9   C  CH3   0  -0.663   2.5261   1.8780  -1.2445
 9ZA  O10  O  O     0  -0.446   5.0880  -0.0644  -1.5940
 9ZA  O11  O  O2    0  -0.450   3.2762  -0.7419  -2.7119
 9ZA  C12  C  CH3   0  -0.425   4.0878  -1.3008  -3.7464
 9ZA  H1   H  HOH1  0   0.496   3.8160  -2.8106   1.2226
 9ZA  H2   H  HCH2  0   0.250   0.1307  -1.1054   2.8825
 9ZA  H3   H  HCH2  0   0.256   1.4984  -0.4591   3.7850
 9ZA  H4   H  HCH1  0   0.270   1.5135   1.5992   2.4859
 9ZA  H5   H  HCH1  0   0.256  -0.4684   1.0245   4.3137
 9ZA  H6   H  HOH1  0   0.451  -1.2493   3.2283   3.6317
 9ZA  H7   H  HCH1  0   0.253  -1.8989  -0.0163   2.6747
 9ZA  H8   H  HOH1  0   0.470  -3.3352   1.4396   3.5070
 9ZA  H9   H  HCH1  0   0.263  -1.4384   2.3140   0.7727
 9ZA  H10  H  HCR5  0   0.295  -1.0531  -1.4851   0.5635
 9ZA  H11  H  HCR6  0   0.252  -4.4820   3.0497  -2.3732
 9ZA  H12  H  HNH2  0   0.404  -5.0384  -1.0301  -4.1329
 9ZA  H13  H  HNH2  0   0.411  -4.0553  -2.1131  -3.2177
 9ZA  H14  H  HNH1  0   0.403   4.2153   1.1966   0.7149
 9ZA  H15  H  HCH1  0   0.281   1.9911  -0.1228  -0.7181
 9ZA  H16  H  HCH3  0   0.235   3.3963   2.5353  -1.2496
 9ZA  H17  H  HCH3  0   0.245   2.1240   1.8359  -2.2560
 9ZA  H18  H  HCH3  0   0.263   1.7684   2.3058  -0.5918
 9ZA  H19  H  HCH3  0   0.241   4.6783  -0.5333  -4.2460
 9ZA  H20  H  HCH3  0   0.240   4.7533  -2.0704  -3.3568
 9ZA  H21  H  HCH3  0   0.253   3.3994  -1.7459  -4.4584

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
 9ZA  N6   C6   single    1.334  0.020  1.334
 9ZA  C6   N1   aromatic  1.338  0.020  1.338
 9ZA  C6   C5   aromatic  1.407  0.020  1.407
 9ZA  N1   C2   aromatic  1.330  0.020  1.330
 9ZA  C5   N7   aromatic  1.371  0.020  1.371
 9ZA  C5   C4   aromatic  1.386  0.020  1.386
 9ZA  C2   N3   aromatic  1.322  0.020  1.322
 9ZA  N7   C8   aromatic  1.300  0.020  1.300
 9ZA  C4   N3   aromatic  1.331  0.020  1.331
 9ZA  C4   N9   aromatic  1.365  0.020  1.365
 9ZA  C8   N9   aromatic  1.369  0.020  1.369
 9ZA  N9   C1'  single    1.441  0.020  1.441
 9ZA  C1'  C2'  single    1.529  0.020  1.529
 9ZA  C1'  O4'  single    1.397  0.020  1.397
 9ZA  O2'  C2'  single    1.395  0.020  1.395
 9ZA  C2'  C3'  single    1.532  0.020  1.532
 9ZA  O4'  C4'  single    1.427  0.020  1.427
 9ZA  C3'  C4'  single    1.524  0.020  1.524
 9ZA  C3'  O3'  single    1.403  0.020  1.403
 9ZA  C4'  C5'  single    1.521  0.020  1.521
 9ZA  C5'  O5'  single    1.423  0.020  1.423
 9ZA  O5'  P    single    1.609  0.020  1.609
 9ZA  O10  C7   double    1.204  0.020  1.204
 9ZA  O2P  P    double    1.480  0.020  1.480
 9ZA  N2   P    single    1.649  0.020  1.649
 9ZA  N2   C3   single    1.446  0.020  1.446
 9ZA  P    O3P  single    1.602  0.020  1.602
 9ZA  C7   C3   single    1.522  0.020  1.522
 9ZA  C7   O11  single    1.323  0.020  1.323
 9ZA  C9   C3   single    1.527  0.020  1.527
 9ZA  C12  O11  single    1.429  0.020  1.429
 9ZA  O3P  H1   single    0.850  0.020  0.980
 9ZA  C5'  H2   single    0.970  0.020  1.090
 9ZA  C5'  H3   single    0.970  0.020  1.090
 9ZA  C4'  H4   single    0.970  0.020  1.090
 9ZA  C3'  H5   single    0.970  0.020  1.090
 9ZA  O3'  H6   single    0.850  0.020  0.980
 9ZA  C2'  H7   single    0.970  0.020  1.090
 9ZA  O2'  H8   single    0.850  0.020  0.980
 9ZA  C1'  H9   single    0.970  0.020  1.090
 9ZA  C8   H10  single    0.930  0.020  1.080
 9ZA  C2   H11  single    0.930  0.020  1.080
 9ZA  N6   H12  single    0.860  0.020  1.020
 9ZA  N6   H13  single    0.860  0.020  1.020
 9ZA  N2   H14  single    0.890  0.020  1.040
 9ZA  C3   H15  single    0.970  0.020  1.090
 9ZA  C9   H16  single    0.970  0.020  1.090
 9ZA  C9   H17  single    0.970  0.020  1.090
 9ZA  C9   H18  single    0.970  0.020  1.090
 9ZA  C12  H19  single    0.970  0.020  1.090
 9ZA  C12  H20  single    0.970  0.020  1.090
 9ZA  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
 9ZA  H1   O3P  P    115.18  3.000
 9ZA  N2   P    O5'  106.44  3.000
 9ZA  N2   P    O2P  112.99  3.000
 9ZA  O5'  P    O2P  114.91  3.000
 9ZA  N2   P    O3P  103.91  3.000
 9ZA  O2P  P    O3P  117.50  3.000
 9ZA  O5'  P    O3P   99.51  3.000
 9ZA  C5'  O5'  P    121.90  3.000
 9ZA  H3   C5'  H2   107.49  3.000
 9ZA  H3   C5'  C4'  108.95  3.000
 9ZA  H2   C5'  C4'  111.10  3.000
 9ZA  H3   C5'  O5'  110.99  3.000
 9ZA  H2   C5'  O5'  105.33  3.000
 9ZA  C4'  C5'  O5'  112.82  3.000
 9ZA  H4   C4'  O4'  108.14  3.000
 9ZA  H4   C4'  C3'  110.80  3.000
 9ZA  O4'  C4'  C3'  106.02  3.000
 9ZA  H4   C4'  C5'  109.76  3.000
 9ZA  C3'  C4'  C5'  111.30  3.000
 9ZA  O4'  C4'  C5'  110.72  3.000
 9ZA  H5   C3'  C2'  111.92  3.000
 9ZA  H5   C3'  O3'  111.80  3.000
 9ZA  C2'  C3'  O3'  111.06  3.000
 9ZA  H5   C3'  C4'  111.96  3.000
 9ZA  O3'  C3'  C4'  108.65  3.000
 9ZA  C2'  C3'  C4'  100.93  3.000
 9ZA  H6   O3'  C3'  108.02  3.000
 9ZA  H7   C2'  C1'  109.60  3.000
 9ZA  H7   C2'  O2'  111.58  3.000
 9ZA  C1'  C2'  O2'  109.86  3.000
 9ZA  H7   C2'  C3'  109.03  3.000
 9ZA  O2'  C2'  C3'  115.05  3.000
 9ZA  C1'  C2'  C3'  101.18  3.000
 9ZA  H8   O2'  C2'  109.01  3.000
 9ZA  H9   C1'  N9   106.09  3.000
 9ZA  H9   C1'  O4'  111.79  3.000
 9ZA  N9   C1'  O4'  109.00  3.000
 9ZA  H9   C1'  C2'  110.15  3.000
 9ZA  O4'  C1'  C2'  105.88  3.000
 9ZA  N9   C1'  C2'  114.03  3.000
 9ZA  C1'  O4'  C4'  110.94  3.000
 9ZA  C8   N9   C4   106.28  3.000
 9ZA  C8   N9   C1'  127.29  3.000
 9ZA  C4   N9   C1'  126.43  3.000
 9ZA  N3   C4   C5   126.50  3.000
 9ZA  N3   C4   N9   128.36  3.000
 9ZA  C5   C4   N9   105.14  3.000
 9ZA  C6   C5   N7   132.89  3.000
 9ZA  N7   C5   C4   110.82  3.000
 9ZA  C6   C5   C4   116.30  3.000
 9ZA  C8   N7   C5   104.41  3.000
 9ZA  H10  C8   N7   124.83  3.000
 9ZA  H10  C8   N9   121.80  3.000
 9ZA  N7   C8   N9   113.36  3.000
 9ZA  C2   N3   C4   111.68  3.000
 9ZA  H11  C2   N1   115.42  3.000
 9ZA  H11  C2   N3   116.12  3.000
 9ZA  N1   C2   N3   128.46  3.000
 9ZA  C6   N1   C2   119.16  3.000
 9ZA  N6   C6   N1   119.28  3.000
 9ZA  N1   C6   C5   117.90  3.000
 9ZA  N6   C6   C5   122.81  3.000
 9ZA  H13  N6   H12  118.27  3.000
 9ZA  H13  N6   C6   121.13  3.000
 9ZA  H12  N6   C6   120.19  3.000
 9ZA  H14  N2   C3   115.26  3.000
 9ZA  H14  N2   P    115.30  3.000
 9ZA  C3   N2   P    122.95  3.000
 9ZA  H15  C3   C9   108.25  3.000
 9ZA  H15  C3   C7   108.99  3.000
 9ZA  C9   C3   C7   109.06  3.000
 9ZA  H15  C3   N2   108.71  3.000
 9ZA  C9   C3   N2   110.33  3.000
 9ZA  C7   C3   N2   111.43  3.000
 9ZA  O11  C7   O10  124.23  3.000
 9ZA  O11  C7   C3   111.40  3.000
 9ZA  O10  C7   C3   124.31  3.000
 9ZA  H18  C9   H17  108.38  3.000
 9ZA  H18  C9   H16  108.76  3.000
 9ZA  H17  C9   H16  108.27  3.000
 9ZA  H18  C9   C3   109.25  3.000
 9ZA  H17  C9   C3   111.16  3.000
 9ZA  H16  C9   C3   110.95  3.000
 9ZA  C12  O11  C7   117.61  3.000
 9ZA  H21  C12  H20  109.40  3.000
 9ZA  H21  C12  H19  109.36  3.000
 9ZA  H20  C12  H19  109.30  3.000
 9ZA  H21  C12  O11  105.96  3.000
 9ZA  H20  C12  O11  111.37  3.000
 9ZA  H19  C12  O11  111.36  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
 9ZA  CONST_01  C6   C5   C4   N9   180.00   0.0  0
 9ZA  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 9ZA  CONST_03  C2   N3   C4   N9   180.00   0.0  0
 9ZA  CONST_04  C5   N7   C8   N9     0.00   0.0  0
 9ZA  CONST_05  N1   C6   C5   C4     0.00   0.0  0
 9ZA  CONST_06  C8   N7   C5   C4     0.00   0.0  0
 9ZA  CONST_07  N1   C2   N3   C4     0.00   0.0  0
 9ZA  CONST_08  N7   C8   N9   C4     0.00   0.0  0
 9ZA  CONST_09  C2   N1   C6   C5     0.00   0.0  0
 9ZA  CONST_10  C2   N3   C4   C5     0.00   0.0  0
 9ZA  CONST_11  C8   N9   C4   C5     0.00   0.0  0
 9ZA  CONST_12  N1   C6   C5   N7   180.00   0.0  0
 9ZA  CONST_13  N3   C4   C5   N7   180.00   0.0  0
 9ZA  CONST_14  C6   C5   N7   C8   180.00   0.0  0
 9ZA  CONST_15  N3   C4   N9   C8   180.00   0.0  0
 9ZA  CONST_16  C6   N1   C2   N3     0.00   0.0  0
 9ZA  CONST_17  C6   C5   C4   N3     0.00   0.0  0
 9ZA  CONST_18  C5   C4   N9   C1'  180.00   0.0  0
 9ZA  CONST_19  N3   C4   N9   C1'    0.00   0.0  0
 9ZA  CONST_20  N7   C8   N9   C1'  180.00   0.0  0
 9ZA  CONST_21  N6   C6   C5   C4   180.00   0.0  0
 9ZA  CONST_22  N6   C6   C5   N7     0.00   0.0  0
 9ZA  CONST_23  N6   C6   N1   C2   180.00   0.0  0
 9ZA  CONST_24  H10  C8   N9   C1'    0.00   0.0  0
 9ZA  CONST_25  H11  C2   N3   C4   180.00   0.0  0
 9ZA  CONST_26  H12  N6   C6   C5   180.00   0.0  0
 9ZA  CONST_27  H13  N6   C6   C5     0.00   0.0  0
 9ZA  Var_01    C4'  C5'  O5'  P     73.64  30.0  1
 9ZA  Var_02    C3   N2   P    O3P   46.42  30.0  1
 9ZA  Var_03    N2   P    O5'  C5'  -87.67  30.0  3
 9ZA  Var_04    H19  C12  O11  C7   -61.79  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
 9ZA  chir_02  C4'  O4'  C3'  C5'  negativ
 9ZA  chir_03  C3'  O3'  C4'  C2'  positiv
 9ZA  chir_04  C2'  O2'  C3'  C1'  positiv
 9ZA  chir_05  C1'  O4'  N9   C2'  negativ
 9ZA  chir_06  C3   N2   C7   C9   positiv
 9ZA  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
 9ZA  plan-1  C1'  0.020
 9ZA  plan-1  N9   0.020
 9ZA  plan-1  C4   0.020
 9ZA  plan-1  C5   0.020
 9ZA  plan-1  N7   0.020
 9ZA  plan-1  C8   0.020
 9ZA  plan-1  N3   0.020
 9ZA  plan-1  C2   0.020
 9ZA  plan-1  N1   0.020
 9ZA  plan-1  C6   0.020
 9ZA  plan-1  N6   0.020
 9ZA  plan-1  H10  0.020
 9ZA  plan-1  H11  0.020
 9ZA  plan-2  C6   0.020
 9ZA  plan-2  N6   0.020
 9ZA  plan-2  H12  0.020
 9ZA  plan-2  H13  0.020
 9ZA  plan-3  C3   0.020
 9ZA  plan-3  C7   0.020
 9ZA  plan-3  O10  0.020
 9ZA  plan-3  O11  0.020

