# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 03:13:59 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
#
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
 DZ4  DZ4  2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine  ligand  47  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DZ4
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
 DZ4  N1    N  N     0  -0.474  -23.4808  49.6273  7.2062
 DZ4  C2    C  CR16  0   0.038  -22.4266  49.8080  6.4143
 DZ4  N3    N  N     0  -0.459  -21.7915  48.9155  5.6750
 DZ4  C4    C  CR56  0   0.485  -22.3375  47.7053  5.7901
 DZ4  C5    C  CR56  0  -0.003  -23.4316  47.3631  6.5696
 DZ4  C6    C  CR6   0   0.454  -24.0182  48.4066  7.3092
 DZ4  N6    N  NH2   0  -0.817  -25.0816  48.2256  8.0943
 DZ4  N7    N  N     0  -0.455  -23.7126  46.0281  6.4510
 DZ4  C8    C  CR15  0   0.098  -22.8107  45.5796  5.6248
 DZ4  N9    N  NR5   0  -0.527  -21.9496  46.5468  5.1864
 DZ4  PA    P  P     0   1.471  -21.4254  41.0988  5.3177
 DZ4  PB    P  P     0   1.501  -19.6332  41.7131  7.5716
 DZ4  PG    P  P     0   1.458  -19.0127  39.0314  8.5041
 DZ4  C1'   C  CH1   0   0.189  -20.8067  46.4163  4.2849
 DZ4  O1A   O  O     0  -0.685  -20.7275  40.0700  4.5255
 DZ4  O1B   O  O     0  -0.690  -18.6118  41.9284  6.5227
 DZ4  O1G   O  O     0  -0.679  -18.5655  38.6365  7.1612
 DZ4  C2'   C  CH2   0  -0.534  -19.4823  46.3343  5.0382
 DZ4  O2A   O  OH1   0  -0.724  -23.0080  40.9734  5.4427
 DZ4  O2B   O  OH1   0  -0.707  -20.0340  42.9576  8.4666
 DZ4  O2G   O  OH1   0  -0.714  -18.0769  38.6766  9.7336
 DZ4  C3'   C  CH1   0   0.004  -19.3106  44.8341  5.2041
 DZ4  O3'   O  OH1   0  -0.686  -17.9915  44.4583  5.4557
 DZ4  N3A   N  NH1   0  -0.965  -21.0762  41.1824  6.9645
 DZ4  O3B   O  O2    0  -0.681  -19.2138  40.6345  8.6995
 DZ4  O3G   O  OH1   0  -0.722  -20.4380  38.5429  8.9969
 DZ4  C4'   C  CH1   0   0.005  -19.8477  44.3523  3.8526
 DZ4  O4'   O  O2    0  -0.498  -20.9435  45.2194  3.5722
 DZ4  C5'   C  CH2   0  -0.197  -20.2673  42.9093  3.7548
 DZ4  O5'   O  O2    0  -0.597  -21.1676  42.5964  4.8209
 DZ4  H2    H  HCR6  0   0.251  -22.0422  50.8218  6.3753
 DZ4  HN6   H  HNH2  0   0.403  -25.4296  48.9824  8.6570
 DZ4  HN6A  H  HNH2  0   0.411  -25.4814  47.3131  8.2240
 DZ4  H8    H  HCR5  0   0.292  -22.7310  44.5552  5.2984
 DZ4  H1'   H  HCH1  0   0.276  -20.8455  47.2727  3.6086
 DZ4  H2'   H  HCH2  0   0.266  -18.6814  46.7373  4.4131
 DZ4  H2'A  H  HCH2  0   0.280  -19.4960  46.8934  5.9728
 DZ4  HO2A  H  HOH1  0   0.507  -23.4281  40.5546  4.6785
 DZ4  HO2B  H  HOH1  0   0.511  -19.3023  43.3957  8.9256
 DZ4  HO2G  H  HOH1  0   0.510  -17.1297  38.7632  9.5556
 DZ4  H3'   H  HCH1  0   0.219  -19.9760  44.4895  6.0061
 DZ4  HO3'  H  HOH1  0   0.460  -18.0202  43.5643  5.8341
 DZ4  HN3A  H  HNH1  0   0.453  -21.7988  40.8846  7.6119
 DZ4  HO3G  H  HOH1  0   0.511  -20.6658  37.6398  8.7354
 DZ4  H4'   H  HCH1  0   0.247  -19.0626  44.4935  3.0966
 DZ4  H5'   H  HCH2  0   0.265  -20.7506  42.7177  2.7942
 DZ4  H5'A  H  HCH2  0   0.250  -19.3714  42.2886  3.8033

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
 DZ4  C2   N1    aromatic  1.331  0.020  1.331
 DZ4  N1   C6    aromatic  1.338  0.020  1.338
 DZ4  N3   C2    aromatic  1.322  0.020  1.322
 DZ4  C2   H2    single    0.930  0.020  1.080
 DZ4  N3   C4    aromatic  1.333  0.020  1.333
 DZ4  N9   C4    aromatic  1.363  0.020  1.363
 DZ4  C4   C5    aromatic  1.386  0.020  1.386
 DZ4  C5   N7    aromatic  1.369  0.020  1.369
 DZ4  C5   C6    aromatic  1.407  0.020  1.407
 DZ4  C6   N6    single    1.334  0.020  1.334
 DZ4  N6   HN6   single    0.860  0.020  1.020
 DZ4  N6   HN6A  single    0.860  0.020  1.020
 DZ4  C8   N7    aromatic  1.303  0.020  1.303
 DZ4  N9   C8    aromatic  1.367  0.020  1.367
 DZ4  C8   H8    single    0.930  0.020  1.080
 DZ4  C1'  N9    single    1.461  0.020  1.461
 DZ4  O5'  PA    single    1.599  0.020  1.599
 DZ4  O1A  PA    double    1.474  0.020  1.474
 DZ4  PA   O2A   single    1.593  0.020  1.593
 DZ4  PA   N3A   single    1.685  0.020  1.685
 DZ4  O1B  PB    double    1.480  0.020  1.480
 DZ4  N3A  PB    single    1.653  0.020  1.653
 DZ4  PB   O2B   single    1.584  0.020  1.584
 DZ4  PB   O3B   single    1.616  0.020  1.616
 DZ4  O1G  PG    double    1.469  0.020  1.469
 DZ4  PG   O3B   single    1.628  0.020  1.628
 DZ4  PG   O2G   single    1.585  0.020  1.585
 DZ4  PG   O3G   single    1.585  0.020  1.585
 DZ4  O4'  C1'   single    1.400  0.020  1.400
 DZ4  C1'  C2'   single    1.526  0.020  1.526
 DZ4  C1'  H1'   single    0.970  0.020  1.090
 DZ4  C3'  C2'   single    1.519  0.020  1.519
 DZ4  C2'  H2'   single    0.970  0.020  1.090
 DZ4  C2'  H2'A  single    0.970  0.020  1.090
 DZ4  O2A  HO2A  single    0.850  0.020  0.980
 DZ4  O2B  HO2B  single    0.850  0.020  0.980
 DZ4  O2G  HO2G  single    0.850  0.020  0.980
 DZ4  C4'  C3'   single    1.532  0.020  1.532
 DZ4  C3'  O3'   single    1.395  0.020  1.395
 DZ4  C3'  H3'   single    0.970  0.020  1.090
 DZ4  O3'  HO3'  single    0.850  0.020  0.980
 DZ4  N3A  HN3A  single    0.860  0.020  1.020
 DZ4  O3G  HO3G  single    0.850  0.020  0.980
 DZ4  O4'  C4'   single    1.425  0.020  1.425
 DZ4  C4'  C5'   single    1.506  0.020  1.506
 DZ4  C4'  H4'   single    0.970  0.020  1.090
 DZ4  C5'  O5'   single    1.430  0.020  1.430
 DZ4  C5'  H5'   single    0.970  0.020  1.090
 DZ4  C5'  H5'A  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
 DZ4  C6    N1   C2   119.21  3.000
 DZ4  H2    C2   N3   116.15  3.000
 DZ4  H2    C2   N1   115.40  3.000
 DZ4  N3    C2   N1   128.45  3.000
 DZ4  C4    N3   C2   111.60  3.000
 DZ4  N9    C4   C5   105.30  3.000
 DZ4  C5    C4   N3   126.59  3.000
 DZ4  N9    C4   N3   128.11  3.000
 DZ4  N7    C5   C6   133.08  3.000
 DZ4  C6    C5   C4   116.20  3.000
 DZ4  N7    C5   C4   110.73  3.000
 DZ4  N6    C6   C5   122.75  3.000
 DZ4  N6    C6   N1   119.30  3.000
 DZ4  C5    C6   N1   117.95  3.000
 DZ4  HN6A  N6   HN6  118.28  3.000
 DZ4  HN6A  N6   C6   121.09  3.000
 DZ4  HN6   N6   C6   120.21  3.000
 DZ4  C8    N7   C5   104.39  3.000
 DZ4  H8    C8   N9   121.91  3.000
 DZ4  H8    C8   N7   124.77  3.000
 DZ4  N9    C8   N7   113.32  3.000
 DZ4  C1'   N9   C8   128.84  3.000
 DZ4  C1'   N9   C4   124.88  3.000
 DZ4  C8    N9   C4   106.27  3.000
 DZ4  O5'   PA   N3A  102.93  3.000
 DZ4  N3A   PA   O2A   97.65  3.000
 DZ4  O5'   PA   O2A  104.97  3.000
 DZ4  N3A   PA   O1A  117.49  3.000
 DZ4  O2A   PA   O1A  117.24  3.000
 DZ4  O5'   PA   O1A  114.23  3.000
 DZ4  O3B   PB   N3A  105.58  3.000
 DZ4  O3B   PB   O2B  101.28  3.000
 DZ4  N3A   PB   O2B  103.82  3.000
 DZ4  O3B   PB   O1B  114.37  3.000
 DZ4  O2B   PB   O1B  117.43  3.000
 DZ4  N3A   PB   O1B  112.89  3.000
 DZ4  O3G   PG   O3B   98.92  3.000
 DZ4  O3G   PG   O2G  102.75  3.000
 DZ4  O3B   PG   O2G  101.55  3.000
 DZ4  O3G   PG   O1G  118.35  3.000
 DZ4  O2G   PG   O1G  117.97  3.000
 DZ4  O3B   PG   O1G  114.33  3.000
 DZ4  H1'   C1'  O4'  110.60  3.000
 DZ4  H1'   C1'  C2'  112.26  3.000
 DZ4  O4'   C1'  C2'  106.88  3.000
 DZ4  H1'   C1'  N9   106.51  3.000
 DZ4  C2'   C1'  N9   112.28  3.000
 DZ4  O4'   C1'  N9   108.30  3.000
 DZ4  H2'A  C2'  H2'  108.10  3.000
 DZ4  H2'A  C2'  C3'  114.49  3.000
 DZ4  H2'   C2'  C3'  110.11  3.000
 DZ4  H2'A  C2'  C1'  112.65  3.000
 DZ4  H2'   C2'  C1'  109.51  3.000
 DZ4  C3'   C2'  C1'  101.83  3.000
 DZ4  HO2A  O2A  PA   113.81  3.000
 DZ4  HO2B  O2B  PB   115.59  3.000
 DZ4  HO2G  O2G  PG   114.52  3.000
 DZ4  H3'   C3'  C4'  109.47  3.000
 DZ4  H3'   C3'  O3'  110.92  3.000
 DZ4  C4'   C3'  O3'  113.95  3.000
 DZ4  H3'   C3'  C2'  108.75  3.000
 DZ4  O3'   C3'  C2'  113.13  3.000
 DZ4  C4'   C3'  C2'  100.06  3.000
 DZ4  HO3'  O3'  C3'  106.88  3.000
 DZ4  HN3A  N3A  PB   118.79  3.000
 DZ4  HN3A  N3A  PA   117.46  3.000
 DZ4  PB    N3A  PA   123.75  3.000
 DZ4  PG    O3B  PB   127.28  3.000
 DZ4  HO3G  O3G  PG   114.54  3.000
 DZ4  H4'   C4'  C5'  106.11  3.000
 DZ4  H4'   C4'  O4'  109.62  3.000
 DZ4  C5'   C4'  O4'  110.86  3.000
 DZ4  H4'   C4'  C3'  108.42  3.000
 DZ4  C5'   C4'  C3'  117.15  3.000
 DZ4  O4'   C4'  C3'  104.58  3.000
 DZ4  C4'   O4'  C1'  110.18  3.000
 DZ4  H5'A  C5'  H5'  107.61  3.000
 DZ4  H5'A  C5'  O5'  111.06  3.000
 DZ4  H5'   C5'  O5'  109.79  3.000
 DZ4  H5'A  C5'  C4'  108.27  3.000
 DZ4  H5'   C5'  C4'  110.40  3.000
 DZ4  O5'   C5'  C4'  109.67  3.000
 DZ4  C5'   O5'  PA   122.56  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
 DZ4  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 DZ4  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 DZ4  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 DZ4  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 DZ4  CONST_05  N9    C4   N3   C2   180.00   0.0  0
 DZ4  CONST_06  C5    C4   N3   C2     0.00   0.0  0
 DZ4  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 DZ4  CONST_08  C8    N9   C4   N3   180.00   0.0  0
 DZ4  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 DZ4  CONST_10  C6    C5   C4   N3     0.00   0.0  0
 DZ4  CONST_11  N7    C8   N9   C4     0.00   0.0  0
 DZ4  CONST_12  C8    N7   C5   C4     0.00   0.0  0
 DZ4  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 DZ4  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 DZ4  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 DZ4  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 DZ4  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 DZ4  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 DZ4  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 DZ4  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 DZ4  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 DZ4  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 DZ4  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 DZ4  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 DZ4  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 DZ4  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 DZ4  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 DZ4  Var_01    C4'   C5'  O5'  PA  -159.04  30.0  3
 DZ4  Var_02    O1B   PB   N3A  PA    -8.06  30.0  3
 DZ4  Var_03    O5'   PA   N3A  PB   -56.12  30.0  2
 DZ4  Var_04    O1G   PG   O3B  PB    29.80  30.0  2

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
 DZ4  chir_03  C1'  N9   O4'  C2'  positiv
 DZ4  chir_04  C3'  O3'  C4'  C2'  positiv
 DZ4  chir_05  C4'  O4'  C3'  C5'  negativ
 DZ4  chir_06  PA   O1A  O2A  N3A  both
 DZ4  chir_07  PB   O2B  O1B  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
 DZ4  plan-1  N1    0.020
 DZ4  plan-1  C2    0.020
 DZ4  plan-1  N3    0.020
 DZ4  plan-1  C4    0.020
 DZ4  plan-1  C5    0.020
 DZ4  plan-1  C6    0.020
 DZ4  plan-1  N6    0.020
 DZ4  plan-1  N7    0.020
 DZ4  plan-1  C8    0.020
 DZ4  plan-1  N9    0.020
 DZ4  plan-1  C1'   0.020
 DZ4  plan-1  H2    0.020
 DZ4  plan-1  H8    0.020
 DZ4  plan-2  C6    0.020
 DZ4  plan-2  N6    0.020
 DZ4  plan-2  HN6   0.020
 DZ4  plan-2  HN6A  0.020

