# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Nov 29 02:15:14 2022
#   Inital geometry file: a 151 line input string
#   Ligand name: ~{N}-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl]-phosphonooxy-phosphonamidic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](N[P](O)(=O)O[P](O)(O)=O)[C@H]3O
#
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
 VE8  VE8  "Non-hydrolasable alarmone analogue"  ligand  59  40  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VE8
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
 VE8  O17  O  O     0  -0.676  59.0944  51.6643  -3.1527
 VE8  P2   P  P     0   1.471  59.8127  50.6891  -2.3246
 VE8  O9   O  OH1   0  -0.660  59.0216  49.4825  -1.6808
 VE8  O10  O  O2    0  -0.639  60.9838  49.8595  -3.0661
 VE8  P3   P  P     0   1.453  61.2284  49.3833  -4.5953
 VE8  O16  O  O     0  -0.591  61.6588  47.9848  -4.6597
 VE8  O15  O  OH1   0  -0.635  59.9541  49.8283  -5.4151
 VE8  O11  O  O2    0  -0.604  62.2581  50.4885  -5.1305
 VE8  P4   P  P     0   1.408  63.8989  50.4311  -5.1004
 VE8  O14  O  OH1   0  -0.661  64.2784  50.2048  -6.6189
 VE8  O13  O  O     0  -0.840  64.3935  49.4712  -4.0933
 VE8  O12  O  OH1   0  -0.723  64.2807  51.9443  -4.9262
 VE8  O8   O  O2    0  -0.510  60.5967  51.3098  -1.0692
 VE8  C7   C  CH2   0  -0.242  61.1405  52.6408  -1.0881
 VE8  C6   C  CR15  0   0.003  62.5307  52.6473  -1.6961
 VE8  C5   C  CR15  0  -0.073  63.6147  51.9068  -0.9035
 VE8  N1   N  NH1   0  -0.799  63.6800  50.4918  -1.1670
 VE8  P    P  P     0   1.425  64.2828  49.3911  -0.1058
 VE8  O7   O  O     0  -0.652  64.4191  48.0314  -0.6556
 VE8  O6   O  OH1   0  -0.742  65.5962  50.0856   0.4804
 VE8  O2   O  O2    0  -0.627  63.3327  49.4939   1.2180
 VE8  P1   P  P     0   1.435  61.7975  49.0023   1.4150
 VE8  O5   O  OH1   0  -0.758  60.9640  50.3481   1.5098
 VE8  O4   O  O     0  -0.732  61.3652  48.0092   0.4186
 VE8  O3   O  OH1   0  -0.694  61.7691  48.6093   2.9509
 VE8  C4   C  CR15  0   0.022  64.8695  52.7107  -1.2788
 VE8  O1   O  OH1   0  -0.686  65.4143  52.2956  -2.5197
 VE8  O18  O  O     0  -0.488  62.9446  54.0019  -1.7098
 VE8  C3   C  CR15  0   0.246  64.3199  54.1281  -1.4719
 VE8  N    N  NR5   0  -0.636  64.5521  55.0101  -0.3520
 VE8  C8   C  CR15  0   0.106  65.3341  56.1412  -0.3986
 VE8  N2   N  N     0  -0.371  65.4142  56.7522   0.7394
 VE8  C1   C  CR56  0  -0.151  64.6446  55.9994   1.5893
 VE8  C2   C  CR56  0   0.466  64.0986  54.9138   0.9319
 VE8  N3   N  N     0  -0.447  63.2983  53.9644   1.4326
 VE8  C9   C  CR6   0   0.693  63.0317  54.1172   2.7076
 VE8  N4   N  NH2   0  -0.784  62.2691  53.2186   3.3373
 VE8  N5   N  NR16  0  -0.706  63.5204  55.1573   3.4436
 VE8  C    C  CR6   0   0.507  64.3614  56.1765   2.9764
 VE8  O    O  O     0  -0.427  64.7510  57.0505   3.7295
 VE8  H1   H  HOH1  0   0.484  58.1673  49.7178  -1.2888
 VE8  H2   H  HOH1  0   0.519  59.2646  49.1532  -5.5038
 VE8  H3   H  HOH1  0   0.465  64.1063  49.3150  -6.9604
 VE8  H4   H  HOH1  0   0.515  64.6757  52.1550  -4.0386
 VE8  H5   H  HCH2  0   0.276  60.4777  53.3092  -1.6399
 VE8  H6   H  HCH2  0   0.233  61.1797  52.9716  -0.0509
 VE8  H7   H  HCR5  0   0.202  62.4826  52.2668  -2.7247
 VE8  H8   H  HCR5  0   0.251  63.4247  52.0667   0.1593
 VE8  H9   H  HNH1  0   0.406  63.7494  50.1997  -2.1359
 VE8  H10  H  HOH1  0   0.508  66.0451  49.6023   1.1887
 VE8  H11  H  HOH1  0   0.498  60.6524  50.6626   0.6392
 VE8  H12  H  HOH1  0   0.496  62.1641  47.7503   3.1567
 VE8  H13  H  HCR5  0   0.240  65.6400  52.6757  -0.5070
 VE8  H14  H  HOH1  0   0.464  65.9874  51.5321  -2.3783
 VE8  H15  H  HCR5  0   0.222  64.8133  54.6028  -2.3252
 VE8  H16  H  HCR5  0   0.288  65.8131  56.4472  -1.3175
 VE8  H17  H  HNH2  0   0.411  61.8457  52.4825   2.7972
 VE8  H18  H  HNH2  0   0.411  61.9345  53.3604   4.2748
 VE8  H19  H  HNR6  0   0.427  63.2824  55.2079   4.4264

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
 VE8  O13  P4   double    1.477  0.020  1.477
 VE8  O14  P4   single    1.581  0.020  1.581
 VE8  P4   O12  single    1.570  0.020  1.570
 VE8  P4   O11  single    1.642  0.020  1.642
 VE8  O16  P3   double    1.465  0.020  1.465
 VE8  O15  P3   single    1.579  0.020  1.579
 VE8  P3   O11  single    1.603  0.020  1.603
 VE8  P3   O10  single    1.620  0.020  1.620
 VE8  O10  P2   single    1.615  0.020  1.615
 VE8  O17  P2   double    1.467  0.020  1.467
 VE8  P2   O9   single    1.580  0.020  1.580
 VE8  P2   O8   single    1.605  0.020  1.605
 VE8  C8   N2   aromatic  1.294  0.020  1.294
 VE8  C8   N    aromatic  1.376  0.020  1.376
 VE8  O8   C7   single    1.438  0.020  1.438
 VE8  O18  C6   single    1.417  0.020  1.417
 VE8  O18  C3   single    1.401  0.020  1.401
 VE8  C6   C7   single    1.517  0.020  1.517
 VE8  C6   C5   single    1.533  0.020  1.533
 VE8  C3   N    single    1.444  0.020  1.444
 VE8  C3   C4   single    1.532  0.020  1.532
 VE8  N2   C1   aromatic  1.372  0.020  1.372
 VE8  N    C2   aromatic  1.365  0.020  1.365
 VE8  N1   C5   single    1.441  0.020  1.441
 VE8  N1   P    single    1.644  0.020  1.644
 VE8  O1   C4   single    1.417  0.020  1.417
 VE8  C5   C4   single    1.537  0.020  1.537
 VE8  O4   P1   double    1.472  0.020  1.472
 VE8  O7   P    double    1.473  0.020  1.473
 VE8  C1   C2   aromatic  1.382  0.020  1.382
 VE8  C1   C    single    1.427  0.020  1.427
 VE8  C2   N3   single    1.339  0.020  1.339
 VE8  P    O2   single    1.633  0.020  1.633
 VE8  P    O6   single    1.597  0.020  1.597
 VE8  C    O    double    1.218  0.020  1.218
 VE8  C    N5   single    1.402  0.020  1.402
 VE8  N3   C9   double    1.312  0.020  1.312
 VE8  P1   O2   single    1.624  0.020  1.624
 VE8  P1   O5   single    1.586  0.020  1.586
 VE8  P1   O3   single    1.586  0.020  1.586
 VE8  N5   C9   single    1.365  0.020  1.365
 VE8  C9   N4   single    1.336  0.020  1.336
 VE8  O9   H1   single    0.850  0.020  0.980
 VE8  O15  H2   single    0.850  0.020  0.980
 VE8  O14  H3   single    0.850  0.020  0.980
 VE8  O12  H4   single    0.850  0.020  0.980
 VE8  C7   H5   single    0.970  0.020  1.090
 VE8  C7   H6   single    0.970  0.020  1.090
 VE8  C6   H7   single    0.970  0.020  1.090
 VE8  C5   H8   single    0.970  0.020  1.090
 VE8  N1   H9   single    0.890  0.020  1.040
 VE8  O6   H10  single    0.850  0.020  0.980
 VE8  O5   H11  single    0.850  0.020  0.980
 VE8  O3   H12  single    0.850  0.020  0.980
 VE8  C4   H13  single    0.970  0.020  1.090
 VE8  O1   H14  single    0.850  0.020  0.980
 VE8  C3   H15  single    0.970  0.020  1.090
 VE8  C8   H16  single    0.930  0.020  1.080
 VE8  N4   H17  single    0.860  0.020  1.020
 VE8  N4   H18  single    0.860  0.020  1.020
 VE8  N5   H19  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
 VE8  O8   P2   O10  101.74  3.000
 VE8  O8   P2   O9   102.78  3.000
 VE8  O10  P2   O9    99.08  3.000
 VE8  O8   P2   O17  115.06  3.000
 VE8  O9   P2   O17  119.50  3.000
 VE8  O10  P2   O17  115.93  3.000
 VE8  H1   O9   P2   114.89  3.000
 VE8  P3   O10  P2   133.92  3.000
 VE8  O11  P3   O15   98.67  3.000
 VE8  O11  P3   O16  117.06  3.000
 VE8  O15  P3   O16  118.90  3.000
 VE8  O11  P3   O10  102.09  3.000
 VE8  O15  P3   O10  106.58  3.000
 VE8  O16  P3   O10  111.50  3.000
 VE8  H2   O15  P3   115.17  3.000
 VE8  P4   O11  P3   127.72  3.000
 VE8  O12  P4   O13  117.99  3.000
 VE8  O12  P4   O14  100.72  3.000
 VE8  O13  P4   O14  118.78  3.000
 VE8  O12  P4   O11  102.20  3.000
 VE8  O14  P4   O11  103.13  3.000
 VE8  O13  P4   O11  111.72  3.000
 VE8  H3   O14  P4   115.30  3.000
 VE8  H4   O12  P4   113.57  3.000
 VE8  C7   O8   P2   122.17  3.000
 VE8  H6   C7   H5   108.50  3.000
 VE8  H6   C7   C6   110.32  3.000
 VE8  H5   C7   C6   110.57  3.000
 VE8  H6   C7   O8   106.39  3.000
 VE8  H5   C7   O8   110.12  3.000
 VE8  C6   C7   O8   110.84  3.000
 VE8  H7   C6   O18  109.59  3.000
 VE8  H7   C6   C5   110.36  3.000
 VE8  O18  C6   C5   105.08  3.000
 VE8  H7   C6   C7   109.50  3.000
 VE8  C5   C6   C7   116.01  3.000
 VE8  O18  C6   C7   106.00  3.000
 VE8  H8   C5   C4   107.66  3.000
 VE8  H8   C5   N1   109.26  3.000
 VE8  C4   C5   N1   115.60  3.000
 VE8  H8   C5   C6   108.03  3.000
 VE8  C4   C5   C6   101.44  3.000
 VE8  N1   C5   C6   114.31  3.000
 VE8  H9   N1   P    113.50  3.000
 VE8  H9   N1   C5   117.42  3.000
 VE8  P    N1   C5   123.80  3.000
 VE8  O2   P    O6    98.84  3.000
 VE8  O6   P    O7   117.54  3.000
 VE8  O2   P    O7   114.50  3.000
 VE8  O6   P    N1   104.32  3.000
 VE8  O2   P    N1   105.54  3.000
 VE8  O7   P    N1   114.28  3.000
 VE8  H10  O6   P    115.65  3.000
 VE8  P1   O2   P    129.01  3.000
 VE8  O3   P1   O4   118.90  3.000
 VE8  O3   P1   O5    98.22  3.000
 VE8  O4   P1   O5   117.31  3.000
 VE8  O3   P1   O2   102.09  3.000
 VE8  O5   P1   O2   104.31  3.000
 VE8  O4   P1   O2   113.57  3.000
 VE8  H11  O5   P1   112.81  3.000
 VE8  H12  O3   P1   114.76  3.000
 VE8  H13  C4   C3   111.84  3.000
 VE8  H13  C4   O1   109.78  3.000
 VE8  C3   C4   O1   107.36  3.000
 VE8  H13  C4   C5   112.78  3.000
 VE8  O1   C4   C5   111.99  3.000
 VE8  C3   C4   C5   102.81  3.000
 VE8  H14  O1   C4   109.37  3.000
 VE8  C3   O18  C6   111.80  3.000
 VE8  H15  C3   N    105.50  3.000
 VE8  H15  C3   O18  110.44  3.000
 VE8  N    C3   O18  110.15  3.000
 VE8  H15  C3   C4   109.75  3.000
 VE8  N    C3   C4   114.17  3.000
 VE8  O18  C3   C4   106.86  3.000
 VE8  C2   N    C8   106.18  3.000
 VE8  C2   N    C3   129.26  3.000
 VE8  C8   N    C3   124.55  3.000
 VE8  H16  C8   N2   125.92  3.000
 VE8  H16  C8   N    120.90  3.000
 VE8  N2   C8   N    113.18  3.000
 VE8  C1   N2   C8   104.53  3.000
 VE8  C    C1   C2   118.80  3.000
 VE8  C    C1   N2   130.21  3.000
 VE8  C2   C1   N2   110.99  3.000
 VE8  N3   C2   C1   127.99  3.000
 VE8  N3   C2   N    126.90  3.000
 VE8  C1   C2   N    105.12  3.000
 VE8  C9   N3   C2   113.73  3.000
 VE8  N5   C9   N4   117.56  3.000
 VE8  N4   C9   N3   119.72  3.000
 VE8  N5   C9   N3   122.71  3.000
 VE8  H18  N4   H17  117.62  3.000
 VE8  H18  N4   C9   122.31  3.000
 VE8  H17  N4   C9   118.63  3.000
 VE8  H19  N5   C    115.36  3.000
 VE8  H19  N5   C9   118.52  3.000
 VE8  C    N5   C9   126.11  3.000
 VE8  O    C    N5   120.51  3.000
 VE8  N5   C    C1   110.67  3.000
 VE8  O    C    C1   128.82  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
 VE8  CONST_01  C1   N2   C8   N       0.00   0.0  0
 VE8  CONST_02  N2   C1   C2   N       0.00   0.0  0
 VE8  CONST_03  C2   C1   N2   C8      0.00   0.0  0
 VE8  CONST_04  C1   C2   N    C8      0.00   0.0  0
 VE8  CONST_05  C2   N    C8   N2      0.00   0.0  0
 VE8  CONST_06  N2   C8   N    C3    180.00   0.0  0
 VE8  CONST_07  C1   C2   N    C3    180.00   0.0  0
 VE8  CONST_08  N3   C2   N    C3      0.00   0.0  0
 VE8  CONST_09  C9   N5   C    C1      0.00   0.0  0
 VE8  CONST_10  N5   C9   N3   C2      0.00   0.0  0
 VE8  CONST_11  C    N5   C9   N3      0.00   0.0  0
 VE8  CONST_12  N4   C9   N3   C2    180.00   0.0  0
 VE8  CONST_13  O    C    N5   C9    180.00   0.0  0
 VE8  CONST_14  C    N5   C9   N4    180.00   0.0  0
 VE8  CONST_15  H16  C8   N    C3      0.00   0.0  0
 VE8  CONST_16  H16  C8   N2   C1    180.00   0.0  0
 VE8  CONST_17  H16  C8   N    C2    180.00   0.0  0
 VE8  CONST_18  H19  N5   C    C1    180.00   0.0  0
 VE8  CONST_19  H19  N5   C9   N3    180.00   0.0  0
 VE8  CONST_20  H17  N4   C9   N3      0.00   0.0  0
 VE8  CONST_21  H18  N4   C9   N3    180.00   0.0  0
 VE8  CONST_22  H19  N5   C9   N4      0.00   0.0  0
 VE8  CONST_23  H17  N4   C9   N5    180.00   0.0  0
 VE8  CONST_24  H18  N4   C9   N5      0.00   0.0  0
 VE8  CONST_25  H19  N5   C    O       0.00   0.0  0
 VE8  Var_01    C6   C7   O8   P2    -86.11  30.0  3
 VE8  Var_02    O7   P    N1   C5   -172.09  30.0  3
 VE8  Var_03    O2   P    N1   C5     61.22  30.0  3
 VE8  Var_04    O6   P    N1   C5    -42.41  30.0  3
 VE8  Var_05    P3   O10  P2   O17   -28.99  30.0  1
 VE8  Var_06    C7   O8   P2   O17   -30.16  30.0  3
 VE8  Var_07    O16  P3   O10  P2   -134.46  30.0  2
 VE8  Var_08    O15  P3   O10  P2     -3.21  30.0  2
 VE8  Var_09    O11  P3   O10  P2     99.77  30.0  2
 VE8  Var_10    P3   O10  P2   O9    100.23  30.0  1
 VE8  Var_11    C7   O8   P2   O9   -161.73  30.0  3
 VE8  Var_12    P4   O11  P3   O10    91.16  30.0  3
 VE8  Var_13    C7   O8   P2   O10    96.01  30.0  3
 VE8  Var_14    O13  P4   O11  P3    -20.75  30.0  1
 VE8  Var_15    O14  P4   O11  P3    107.93  30.0  1
 VE8  Var_16    O12  P4   O11  P3   -147.83  30.0  1
 VE8  Var_17    O8   P2   O10  P3   -154.58  30.0  3
 VE8  Var_18    P4   O11  P3   O16   -30.88  30.0  3
 VE8  Var_19    P4   O11  P3   O15  -159.70  30.0  3
 VE8  Var_20    P1   O2   P    N1     71.76  30.0  3
 VE8  Var_21    O4   P1   O2   P      19.32  30.0  2
 VE8  Var_22    O5   P1   O2   P    -109.57  30.0  2
 VE8  Var_23    O3   P1   O2   P     148.57  30.0  2
 VE8  Var_24    P1   O2   P    O7    -54.80  30.0  3
 VE8  Var_25    P1   O2   P    O6    179.40  30.0  3
 VE8  Var_26    H5   C7   O8   P2     36.56  30.0  3
 VE8  Var_27    H6   C7   O8   P2    153.94  30.0  3
 VE8  Var_28    H9   N1   P    O7    -18.52  30.0  1
 VE8  Var_29    H9   N1   P    O6    111.17  30.0  1
 VE8  Var_30    H9   N1   P    O2   -145.21  30.0  1

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
 VE8  chir_03  C6  O18  C7   C5   positiv
 VE8  chir_04  C5  N1   C6   C4   positiv
 VE8  chir_06  C4  C3   O1   C5   positiv
 VE8  chir_07  C3  O18  N    C4   negativ
 VE8  chir_08  P2  O17  O9   O8   both
 VE8  chir_09  P3  O15  O11  O10  both
 VE8  chir_10  P   O7   O2   O6   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
 VE8  plan-1  C3   0.020
 VE8  plan-1  N    0.020
 VE8  plan-1  C8   0.020
 VE8  plan-1  N2   0.020
 VE8  plan-1  C1   0.020
 VE8  plan-1  C2   0.020
 VE8  plan-1  N3   0.020
 VE8  plan-1  C9   0.020
 VE8  plan-1  N4   0.020
 VE8  plan-1  N5   0.020
 VE8  plan-1  C    0.020
 VE8  plan-1  O    0.020
 VE8  plan-1  H16  0.020
 VE8  plan-1  H17  0.020
 VE8  plan-1  H18  0.020
 VE8  plan-1  H19  0.020

