# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 18:40:15 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)[C@@H](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
 ZAN  ZAN  5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine  ligand  48  31  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZAN
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
 ZAN  PA   P  P     0   1.486  14.9961   5.9997  -13.4354
 ZAN  PB   P  P     0   1.494  17.6507   6.3300  -14.7791
 ZAN  PG   P  P     0   1.465  19.4862   8.5892  -15.1361
 ZAN  O1A  O  OH1   0  -0.743  15.7110   4.6902  -12.8786
 ZAN  O1B  O  OH1   0  -0.719  18.6023   6.0717  -13.5352
 ZAN  O1G  O  OH1   0  -0.711  19.4420   9.6514  -16.3094
 ZAN  O2A  O  O     0  -0.672  14.1920   6.8392  -12.5331
 ZAN  O2B  O  O     0  -0.679  17.4819   5.1821  -15.6988
 ZAN  O2G  O  OH1   0  -0.729  18.8374   9.3672  -13.9184
 ZAN  N3A  N  NH1   0  -0.966  16.2507   6.9094  -14.1096
 ZAN  O3B  O  O2    0  -0.688  18.2251   7.6339  -15.5302
 ZAN  O3G  O  O     0  -0.681  20.7442   7.8598  -14.9212
 ZAN  O5'  O  O2    0  -0.588  14.1198   5.4043  -14.6141
 ZAN  C5'  C  CH2   0  -0.215  14.3277   4.2177  -15.3857
 ZAN  C4'  C  CH1   0   0.014  13.9850   4.4796  -16.8295
 ZAN  O4'  O  O2    0  -0.498  12.6090   4.8320  -16.9542
 ZAN  C3'  C  CH1   0  -0.023  14.7393   5.6189  -17.5234
 ZAN  O3'  O  OH1   0  -0.694  15.9956   5.2690  -18.0114
 ZAN  C2'  C  CH1   0  -0.046  13.7833   5.9407  -18.6695
 ZAN  O2'  O  OH1   0  -0.664  13.8652   4.9897  -19.6959
 ZAN  C1'  C  CH1   0   0.184  12.4257   5.7508  -17.9895
 ZAN  N9   N  NR5   0  -0.537  11.9160   6.9999  -17.4380
 ZAN  C8   C  CR15  0   0.097  11.8867   7.4250  -16.1376
 ZAN  N7   N  N     0  -0.453  11.3524   8.6037  -15.9941
 ZAN  C5   C  CR56  0  -0.002  11.0078   8.9805  -17.2650
 ZAN  C6   C  CR6   0   0.456  10.3942  10.1312  -17.7937
 ZAN  N6   N  NH2   0  -0.817  10.0230  11.1641  -17.0360
 ZAN  N1   N  N     0  -0.474  10.1874  10.1798  -19.1147
 ZAN  C2   C  CR16  0   0.039  10.5672   9.1526  -19.8703
 ZAN  N3   N  N     0  -0.459  11.1522   8.0283  -19.4948
 ZAN  C4   C  CR56  0   0.485  11.3477   7.9948  -18.1776
 ZAN  H1   H  HOH1  0   0.508  16.2561   4.8165  -12.0890
 ZAN  H2   H  HOH1  0   0.508  19.3946   5.5456  -13.7191
 ZAN  H3   H  HOH1  0   0.511  19.9931   9.4322  -17.0740
 ZAN  H4   H  HOH1  0   0.513  19.4651   9.8201  -13.3379
 ZAN  H5   H  HNH1  0   0.453  16.1670   7.9124  -13.9824
 ZAN  H6   H  HCH2  0   0.273  13.6888   3.4326  -14.9779
 ZAN  H7   H  HCH2  0   0.257  15.3585   3.8675  -15.3320
 ZAN  H8   H  HCH1  0   0.252  14.1825   3.5422  -17.3651
 ZAN  H9   H  HCH1  0   0.229  14.7864   6.4932  -16.8574
 ZAN  H10  H  HOH1  0   0.467  16.6122   5.2026  -17.2606
 ZAN  H11  H  HCH1  0   0.263  13.9127   6.9618  -19.0473
 ZAN  H12  H  HOH1  0   0.458  14.7921   4.8861  -19.9393
 ZAN  H13  H  HCH1  0   0.282  11.6789   5.3881  -18.7019
 ZAN  H14  H  HCR5  0   0.296  12.2691   6.8222  -15.3310
 ZAN  H15  H  HNH2  0   0.403   9.5513  11.9510  -17.4467
 ZAN  H16  H  HNH2  0   0.411  10.1343  11.1428  -16.0377
 ZAN  H17  H  HCR6  0   0.252  10.3698   9.2574  -20.9319

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
 ZAN  C2   N1   aromatic  1.331  0.020  1.331
 ZAN  C2   N3   aromatic  1.322  0.020  1.322
 ZAN  O2'  C2'  single    1.402  0.020  1.402
 ZAN  N1   C6   aromatic  1.338  0.020  1.338
 ZAN  N3   C4   aromatic  1.332  0.020  1.332
 ZAN  C2'  C1'  single    1.530  0.020  1.530
 ZAN  C2'  C3'  single    1.527  0.020  1.527
 ZAN  C6   N6   single    1.334  0.020  1.334
 ZAN  C6   C5   aromatic  1.407  0.020  1.407
 ZAN  C4   C5   aromatic  1.386  0.020  1.386
 ZAN  C4   N9   aromatic  1.364  0.020  1.364
 ZAN  O3'  C3'  single    1.392  0.020  1.392
 ZAN  C1'  N9   single    1.457  0.020  1.457
 ZAN  C1'  O4'  single    1.396  0.020  1.396
 ZAN  C5   N7   aromatic  1.370  0.020  1.370
 ZAN  C3'  C4'  single    1.532  0.020  1.532
 ZAN  N9   C8   aromatic  1.368  0.020  1.368
 ZAN  O2B  PB   double    1.481  0.020  1.481
 ZAN  N7   C8   aromatic  1.302  0.020  1.302
 ZAN  C4'  O4'  single    1.426  0.020  1.426
 ZAN  C4'  C5'  single    1.507  0.020  1.507
 ZAN  PB   O1B  single    1.587  0.020  1.587
 ZAN  PB   N3A  single    1.657  0.020  1.657
 ZAN  PB   O3B  single    1.611  0.020  1.611
 ZAN  N3A  PA   single    1.690  0.020  1.690
 ZAN  O3B  PG   single    1.630  0.020  1.630
 ZAN  C5'  O5'  single    1.431  0.020  1.431
 ZAN  O5'  PA   single    1.585  0.020  1.585
 ZAN  PA   O2A  double    1.472  0.020  1.472
 ZAN  PA   O1A  single    1.592  0.020  1.592
 ZAN  O3G  PG   double    1.470  0.020  1.470
 ZAN  PG   O1G  single    1.583  0.020  1.583
 ZAN  PG   O2G  single    1.584  0.020  1.584
 ZAN  O1A  H1   single    0.850  0.020  0.980
 ZAN  O1B  H2   single    0.850  0.020  0.980
 ZAN  O1G  H3   single    0.850  0.020  0.980
 ZAN  O2G  H4   single    0.850  0.020  0.980
 ZAN  N3A  H5   single    0.860  0.020  1.020
 ZAN  C5'  H6   single    0.970  0.020  1.090
 ZAN  C5'  H7   single    0.970  0.020  1.090
 ZAN  C4'  H8   single    0.970  0.020  1.090
 ZAN  C3'  H9   single    0.970  0.020  1.090
 ZAN  O3'  H10  single    0.850  0.020  0.980
 ZAN  C2'  H11  single    0.970  0.020  1.090
 ZAN  O2'  H12  single    0.850  0.020  0.980
 ZAN  C1'  H13  single    0.970  0.020  1.090
 ZAN  C8   H14  single    0.930  0.020  1.080
 ZAN  N6   H15  single    0.860  0.020  1.020
 ZAN  N6   H16  single    0.860  0.020  1.020
 ZAN  C2   H17  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
 ZAN  O5'  PA   N3A  108.42  3.000
 ZAN  O5'  PA   O2A  111.60  3.000
 ZAN  N3A  PA   O2A  110.07  3.000
 ZAN  O2A  PA   O1A  120.00  3.000
 ZAN  O5'  PA   O1A  101.50  3.000
 ZAN  N3A  PA   O1A  104.41  3.000
 ZAN  O3B  PB   N3A  101.93  3.000
 ZAN  O3B  PB   O2B  112.25  3.000
 ZAN  N3A  PB   O2B  115.20  3.000
 ZAN  O3B  PB   O1B  106.47  3.000
 ZAN  N3A  PB   O1B  104.29  3.000
 ZAN  O2B  PB   O1B  115.40  3.000
 ZAN  O3G  PG   O3B  113.99  3.000
 ZAN  O3G  PG   O2G  118.81  3.000
 ZAN  O3B  PG   O2G   99.02  3.000
 ZAN  O2G  PG   O1G  103.22  3.000
 ZAN  O3G  PG   O1G  117.72  3.000
 ZAN  O3B  PG   O1G  101.09  3.000
 ZAN  H1   O1A  PA   115.52  3.000
 ZAN  H2   O1B  PB   115.47  3.000
 ZAN  H3   O1G  PG   114.69  3.000
 ZAN  H4   O2G  PG   115.18  3.000
 ZAN  H5   N3A  PB   117.78  3.000
 ZAN  H5   N3A  PA   114.90  3.000
 ZAN  PB   N3A  PA   126.90  3.000
 ZAN  PG   O3B  PB   129.60  3.000
 ZAN  C5'  O5'  PA   129.22  3.000
 ZAN  H7   C5'  H6   107.70  3.000
 ZAN  H7   C5'  C4'  108.55  3.000
 ZAN  H6   C5'  C4'  110.48  3.000
 ZAN  H7   C5'  O5'  112.18  3.000
 ZAN  H6   C5'  O5'  108.07  3.000
 ZAN  C4'  C5'  O5'  109.85  3.000
 ZAN  H8   C4'  C3'  109.00  3.000
 ZAN  H8   C4'  O4'  110.00  3.000
 ZAN  C3'  C4'  O4'  104.58  3.000
 ZAN  H8   C4'  C5'  106.15  3.000
 ZAN  O4'  C4'  C5'  110.25  3.000
 ZAN  C3'  C4'  C5'  116.81  3.000
 ZAN  C1'  O4'  C4'  110.74  3.000
 ZAN  H9   C3'  C2'  108.29  3.000
 ZAN  H9   C3'  O3'  111.92  3.000
 ZAN  C2'  C3'  O3'  110.78  3.000
 ZAN  H9   C3'  C4'  109.74  3.000
 ZAN  O3'  C3'  C4'  114.58  3.000
 ZAN  C2'  C3'  C4'  100.86  3.000
 ZAN  H10  O3'  C3'  108.55  3.000
 ZAN  H11  C2'  C1'  111.93  3.000
 ZAN  H11  C2'  O2'  111.88  3.000
 ZAN  C1'  C2'  O2'  107.04  3.000
 ZAN  H11  C2'  C3'  112.40  3.000
 ZAN  C1'  C2'  C3'  101.29  3.000
 ZAN  O2'  C2'  C3'  111.72  3.000
 ZAN  H12  O2'  C2'  108.30  3.000
 ZAN  H13  C1'  N9   106.97  3.000
 ZAN  H13  C1'  C2'  110.94  3.000
 ZAN  N9   C1'  C2'  111.84  3.000
 ZAN  H13  C1'  O4'  110.75  3.000
 ZAN  N9   C1'  O4'  109.23  3.000
 ZAN  C2'  C1'  O4'  107.14  3.000
 ZAN  C4   N9   C8   106.25  3.000
 ZAN  C8   N9   C1'  129.29  3.000
 ZAN  C4   N9   C1'  124.46  3.000
 ZAN  H14  C8   N7   124.73  3.000
 ZAN  H14  C8   N9   122.02  3.000
 ZAN  N7   C8   N9   113.25  3.000
 ZAN  C5   N7   C8   104.48  3.000
 ZAN  C4   C5   C6   116.18  3.000
 ZAN  C4   C5   N7   110.72  3.000
 ZAN  C6   C5   N7   133.10  3.000
 ZAN  N1   C6   N6   119.32  3.000
 ZAN  N6   C6   C5   122.76  3.000
 ZAN  N1   C6   C5   117.91  3.000
 ZAN  H16  N6   H15  118.33  3.000
 ZAN  H16  N6   C6   121.15  3.000
 ZAN  H15  N6   C6   120.31  3.000
 ZAN  C2   N1   C6   119.24  3.000
 ZAN  H17  C2   N3   116.15  3.000
 ZAN  H17  C2   N1   115.41  3.000
 ZAN  N3   C2   N1   128.44  3.000
 ZAN  C4   N3   C2   111.55  3.000
 ZAN  N3   C4   C5   126.69  3.000
 ZAN  C5   C4   N9   105.30  3.000
 ZAN  N3   C4   N9   128.01  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
 ZAN  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 ZAN  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 ZAN  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 ZAN  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 ZAN  CONST_05  N3   C4   N9   C8    180.00   0.0  0
 ZAN  CONST_06  C5   C4   N9   C8      0.00   0.0  0
 ZAN  CONST_07  C6   C5   N7   C8    180.00   0.0  0
 ZAN  CONST_08  C4   C5   N7   C8      0.00   0.0  0
 ZAN  CONST_09  N1   C6   C5   N7    180.00   0.0  0
 ZAN  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 ZAN  CONST_11  C4   N9   C8   N7      0.00   0.0  0
 ZAN  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 ZAN  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 ZAN  CONST_14  N3   C2   N1   C6      0.00   0.0  0
 ZAN  CONST_15  N3   C4   C5   C6      0.00   0.0  0
 ZAN  CONST_16  C4   N3   C2   N1      0.00   0.0  0
 ZAN  CONST_17  C4   C5   C6   N1      0.00   0.0  0
 ZAN  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 ZAN  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 ZAN  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 ZAN  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 ZAN  CONST_22  C2   N1   C6   N6    180.00   0.0  0
 ZAN  CONST_23  C4   C5   C6   N6    180.00   0.0  0
 ZAN  CONST_24  H14  C8   N9   C1'     0.00   0.0  0
 ZAN  CONST_25  H17  C2   N1   C6    180.00   0.0  0
 ZAN  CONST_26  H15  N6   C6   C5    180.00   0.0  0
 ZAN  CONST_27  H16  N6   C6   C5      0.00   0.0  0
 ZAN  Var_01    C4'  C5'  O5'  PA   -140.02  30.0  2
 ZAN  Var_02    O2B  PB   N3A  PA     45.20  30.0  1
 ZAN  Var_03    O5'  PA   N3A  PB    -78.26  30.0  3
 ZAN  Var_04    O3G  PG   O3B  PB     52.98  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
 ZAN  chir_03  C4'  C3'  O4'  C5'  positiv
 ZAN  chir_04  C3'  O3'  C2'  C4'  negativ
 ZAN  chir_05  C2'  O2'  C1'  C3'  negativ
 ZAN  chir_06  C1'  O4'  N9   C2'  negativ
 ZAN  chir_07  PA   O5'  O2A  O1A  both
 ZAN  chir_08  PB   O1B  O3B  N3A  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
 ZAN  plan-1  C1'  0.020
 ZAN  plan-1  N9   0.020
 ZAN  plan-1  C8   0.020
 ZAN  plan-1  N7   0.020
 ZAN  plan-1  C5   0.020
 ZAN  plan-1  C6   0.020
 ZAN  plan-1  N6   0.020
 ZAN  plan-1  N1   0.020
 ZAN  plan-1  C2   0.020
 ZAN  plan-1  N3   0.020
 ZAN  plan-1  C4   0.020
 ZAN  plan-1  H14  0.020
 ZAN  plan-1  H17  0.020
 ZAN  plan-2  C6   0.020
 ZAN  plan-2  N6   0.020
 ZAN  plan-2  H15  0.020
 ZAN  plan-2  H16  0.020

