# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Nov 24 22:05:48 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-chloroadenosine 5'-(trihydrogen diphosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)nc2n(cnc12)[C@@H]3O[C@H](CO[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
 ZD4  ZD4  "2-chloroadenosine 5'-(trihydrogen diphosphate)"  ligand  42  28  .  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_ZD4
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
 ZD4  C1'   C   CH1   0   0.138  38.4150  35.9983  21.4094
 ZD4  C2    C   CR6   0   0.264  35.0044  35.3241  18.9253
 ZD4  C2'   C   CH1   0  -0.062  39.5639  35.7993  22.4037
 ZD4  C3'   C   CH1   0  -0.037  40.6820  35.3284  21.4594
 ZD4  C4    C   CR56  0   0.475  36.6077  34.7291  20.2695
 ZD4  C4'   C   CH1   0  -0.016  40.3730  36.1026  20.1710
 ZD4  C5    C   CR56  0   0.147  36.2591  33.3933  20.1807
 ZD4  C5'   C   CH2   0  -0.192  40.6021  35.2576  18.9391
 ZD4  C6    C   CR6   0   0.282  35.1675  33.0859  19.3463
 ZD4  C8    C   CR15  0   0.115  37.9194  33.4726  21.4771
 ZD4  N1    N   N     0  -0.426  34.5563  34.1015  18.7210
 ZD4  N3    N   N     0  -0.345  35.9985  35.7483  19.6629
 ZD4  N6    N   NH2   0  -0.772  34.7271  31.8471  19.1536
 ZD4  N7    N   N     0  -0.504  37.0908  32.6237  20.9487
 ZD4  N9    N   NR5   0  -0.436  37.6828  34.7733  21.1075
 ZD4  O1B   O   OH1   0  -0.612  41.9490  32.5737  15.3389
 ZD4  O2'   O   OH1   0  -0.651  39.9403  37.0330  22.9411
 ZD4  O2B   O   OH1   0  -0.660  42.4525  35.0112  15.5357
 ZD4  O3'   O   OH1   0  -0.670  41.9821  35.6008  21.8774
 ZD4  O3B   O   O     0  -0.776  40.9417  34.1820  13.5541
 ZD4  O4'   O   O2    0  -0.513  39.0130  36.5037  20.2545
 ZD4  O5'   O   O2    0  -0.541  40.3032  36.0494  17.7833
 ZD4  PA    P   P     0   1.437  39.4831  35.5541  16.5286
 ZD4  PB    P   P     0   1.369  41.3742  34.0027  14.9480
 ZD4  H1'   H   HCH1  0   0.275  37.6830  36.7245  21.7678
 ZD4  H2'   H   HCH1  0   0.285  39.3328  35.0696  23.1879
 ZD4  H3'   H   HCH1  0   0.312  40.5498  34.2520  21.2808
 ZD4  H4'   H   HCH1  0   0.276  40.9969  37.0020  20.1229
 ZD4  H5'2  H   HCH2  0   0.218  39.9889  34.3538  18.9777
 ZD4  H5'1  H   HCH2  0   0.242  41.6499  34.9551  18.8877
 ZD4  H8    H   HCR5  0   0.323  38.7117  33.2017  22.1577
 ZD4  HN61  H   HNH2  0   0.368  33.9468  31.6712  18.5436
 ZD4  HN62  H   HNH2  0   0.374  35.1708  31.0635  19.6007
 ZD4  H1    H   HOH1  0   0.530  41.6347  31.8501  14.7790
 ZD4  HO2'  H   HOH1  0   0.460  39.2768  37.3058  23.5839
 ZD4  H2    H   HOH1  0   0.538  37.4766  34.6816  16.5527
 ZD4  H3    H   HOH1  0   0.516  43.1390  35.2829  14.9095
 ZD4  H4    H   HOH1  0   0.448  42.2368  34.9521  22.5413
 ZD4  CL6   CL  CL    0  -0.133  34.1345  36.5645  18.0755
 ZD4  O1A   O   O     0  -0.811  39.3957  36.5702  15.4717
 ZD4  O2A   O   OH1   0  -0.586  38.1473  34.9973  17.1750
 ZD4  O3A   O   O2    0  -0.650  40.2113  34.1747  16.0657

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
 ZD4  O3B  PB    double    1.470  0.020  1.470
 ZD4  O1A  PA    double    1.469  0.020  1.469
 ZD4  O1B  PB    single    1.589  0.020  1.589
 ZD4  PB   O3A   single    1.622  0.020  1.622
 ZD4  PB   O2B   single    1.589  0.020  1.589
 ZD4  O3A  PA    single    1.627  0.020  1.627
 ZD4  O2A  PA    single    1.585  0.020  1.585
 ZD4  PA   O5'   single    1.579  0.020  1.579
 ZD4  O5'  C5'   single    1.433  0.020  1.433
 ZD4  C5'  C4'   single    1.511  0.020  1.511
 ZD4  CL6  C2    single    1.737  0.020  1.737
 ZD4  C4'  O4'   single    1.420  0.020  1.420
 ZD4  C4'  C3'   single    1.535  0.020  1.535
 ZD4  O4'  C1'   single    1.395  0.020  1.395
 ZD4  C2   N1    aromatic  1.318  0.020  1.318
 ZD4  C2   N3    aromatic  1.309  0.020  1.309
 ZD4  N1   C6    aromatic  1.340  0.020  1.340
 ZD4  N3   C4    aromatic  1.333  0.020  1.333
 ZD4  C6   N6    single    1.329  0.020  1.329
 ZD4  C6   C5    aromatic  1.408  0.020  1.408
 ZD4  C4   C5    aromatic  1.383  0.020  1.383
 ZD4  C4   N9    aromatic  1.364  0.020  1.364
 ZD4  C3'  O3'   single    1.393  0.020  1.393
 ZD4  C3'  C2'   single    1.537  0.020  1.537
 ZD4  C5   N7    aromatic  1.369  0.020  1.369
 ZD4  C1'  N9    single    1.459  0.020  1.459
 ZD4  C1'  C2'   single    1.532  0.020  1.532
 ZD4  N9   C8    aromatic  1.373  0.020  1.373
 ZD4  N7   C8    aromatic  1.299  0.020  1.299
 ZD4  C2'  O2'   single    1.397  0.020  1.397
 ZD4  C1'  H1'   single    0.970  0.020  1.090
 ZD4  C2'  H2'   single    0.970  0.020  1.090
 ZD4  C3'  H3'   single    0.970  0.020  1.090
 ZD4  C4'  H4'   single    0.970  0.020  1.090
 ZD4  C5'  H5'2  single    0.970  0.020  1.090
 ZD4  C5'  H5'1  single    0.970  0.020  1.090
 ZD4  C8   H8    single    0.930  0.020  1.080
 ZD4  N6   HN61  single    0.860  0.020  1.020
 ZD4  N6   HN62  single    0.860  0.020  1.020
 ZD4  O1B  H1    single    0.850  0.020  0.980
 ZD4  O2'  HO2'  single    0.850  0.020  0.980
 ZD4  O2A  H2    single    0.850  0.020  0.980
 ZD4  O2B  H3    single    0.850  0.020  0.980
 ZD4  O3'  H4    single    0.850  0.020  0.980

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
 ZD4  H1'   C1'  O4'   108.55  3.000
 ZD4  H1'   C1'  N9    106.86  3.000
 ZD4  O4'   C1'  N9    110.37  3.000
 ZD4  H1'   C1'  C2'   112.09  3.000
 ZD4  N9    C1'  C2'   113.68  3.000
 ZD4  O4'   C1'  C2'   105.23  3.000
 ZD4  CL6   C2   N3    115.13  3.000
 ZD4  N3    C2   N1    130.27  3.000
 ZD4  CL6   C2   N1    114.60  3.000
 ZD4  H2'   C2'  O2'   111.69  3.000
 ZD4  H2'   C2'  C3'   112.89  3.000
 ZD4  O2'   C2'  C3'   108.11  3.000
 ZD4  H2'   C2'  C1'   113.12  3.000
 ZD4  O2'   C2'  C1'   109.68  3.000
 ZD4  C3'   C2'  C1'   100.75  3.000
 ZD4  H3'   C3'  O3'   110.65  3.000
 ZD4  H3'   C3'  C4'   109.49  3.000
 ZD4  O3'   C3'  C4'   109.96  3.000
 ZD4  H3'   C3'  C2'   108.20  3.000
 ZD4  O3'   C3'  C2'   115.76  3.000
 ZD4  C4'   C3'  C2'   102.40  3.000
 ZD4  N9    C4   N3    127.94  3.000
 ZD4  N9    C4   C5    105.63  3.000
 ZD4  N3    C4   C5    126.42  3.000
 ZD4  H4'   C4'  O4'   108.42  3.000
 ZD4  H4'   C4'  C5'   109.69  3.000
 ZD4  O4'   C4'  C5'   110.55  3.000
 ZD4  H4'   C4'  C3'   109.66  3.000
 ZD4  O4'   C4'  C3'   106.61  3.000
 ZD4  C5'   C4'  C3'   111.82  3.000
 ZD4  N7    C5   C6    132.91  3.000
 ZD4  N7    C5   C4    110.71  3.000
 ZD4  C6    C5   C4    116.37  3.000
 ZD4  H5'1  C5'  H5'2  108.13  3.000
 ZD4  H5'1  C5'  O5'   108.39  3.000
 ZD4  H5'2  C5'  O5'   111.63  3.000
 ZD4  H5'1  C5'  C4'   109.80  3.000
 ZD4  H5'2  C5'  C4'   110.40  3.000
 ZD4  O5'   C5'  C4'   108.48  3.000
 ZD4  N6    C6   N1    119.19  3.000
 ZD4  N6    C6   C5    123.12  3.000
 ZD4  N1    C6   C5    117.69  3.000
 ZD4  H8    C8   N9    122.30  3.000
 ZD4  H8    C8   N7    124.12  3.000
 ZD4  N9    C8   N7    113.57  3.000
 ZD4  C6    N1   C2    118.40  3.000
 ZD4  C4    N3   C2    110.84  3.000
 ZD4  HN62  N6   HN61  118.41  3.000
 ZD4  HN62  N6   C6    121.05  3.000
 ZD4  HN61  N6   C6    120.53  3.000
 ZD4  C8    N7   C5    104.39  3.000
 ZD4  C8    N9   C4    105.70  3.000
 ZD4  C8    N9   C1'   130.80  3.000
 ZD4  C4    N9   C1'   123.38  3.000
 ZD4  H1    O1B  PB    114.38  3.000
 ZD4  HO2'  O2'  C2'   108.73  3.000
 ZD4  H3    O2B  PB    114.83  3.000
 ZD4  H4    O3'  C3'   108.80  3.000
 ZD4  C4'   O4'  C1'   110.90  3.000
 ZD4  PA    O5'  C5'   125.19  3.000
 ZD4  O5'   PA   O3A   105.04  3.000
 ZD4  O5'   PA   O2A   102.94  3.000
 ZD4  O3A   PA   O2A   101.27  3.000
 ZD4  O5'   PA   O1A   112.70  3.000
 ZD4  O2A   PA   O1A   119.10  3.000
 ZD4  O3A   PA   O1A   114.11  3.000
 ZD4  O3B   PB   O3A   115.43  3.000
 ZD4  O3A   PB   O2B    99.46  3.000
 ZD4  O3B   PB   O2B   118.22  3.000
 ZD4  O2B   PB   O1B   103.55  3.000
 ZD4  O3A   PB   O1B   100.67  3.000
 ZD4  O3B   PB   O1B   116.70  3.000
 ZD4  H2    O2A  PA    115.88  3.000
 ZD4  PB    O3A  PA    127.36  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
 ZD4  CONST_01  C5    C6   N1   C2      0.00   0.0  0
 ZD4  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 ZD4  CONST_03  N9    C4   N3   C2    180.00   0.0  0
 ZD4  CONST_04  N1    C2   N3   C4      0.00   0.0  0
 ZD4  CONST_05  N1    C6   C5   C4      0.00   0.0  0
 ZD4  CONST_06  C8    N7   C5   C4      0.00   0.0  0
 ZD4  CONST_07  N7    C8   N9   C4      0.00   0.0  0
 ZD4  CONST_08  C8    N9   C4   C5      0.00   0.0  0
 ZD4  CONST_09  N9    C8   N7   C5      0.00   0.0  0
 ZD4  CONST_10  N3    C2   N1   C6      0.00   0.0  0
 ZD4  CONST_11  N3    C4   C5   C6      0.00   0.0  0
 ZD4  CONST_12  N9    C4   C5   C6    180.00   0.0  0
 ZD4  CONST_13  C8    N7   C5   C6    180.00   0.0  0
 ZD4  CONST_14  N3    C4   N9   C8    180.00   0.0  0
 ZD4  CONST_15  N7    C5   C6   N1    180.00   0.0  0
 ZD4  CONST_16  N7    C5   C4   N3    180.00   0.0  0
 ZD4  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 ZD4  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 ZD4  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 ZD4  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 ZD4  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 ZD4  CONST_22  CL6   C2   N3   C4    180.00   0.0  0
 ZD4  CONST_23  N6    C6   C5   C4    180.00   0.0  0
 ZD4  CONST_24  CL6   C2   N1   C6    180.00   0.0  0
 ZD4  CONST_25  N7    C5   C6   N6      0.00   0.0  0
 ZD4  CONST_26  H8    C8   N9   C1'     0.00   0.0  0
 ZD4  CONST_27  H8    C8   N9   C4    180.00   0.0  0
 ZD4  CONST_28  H8    C8   N7   C5    180.00   0.0  0
 ZD4  CONST_29  HN61  N6   C6   C5    180.00   0.0  0
 ZD4  CONST_30  HN62  N6   C6   C5      0.00   0.0  0
 ZD4  CONST_31  HN61  N6   C6   N1      0.00   0.0  0
 ZD4  CONST_32  HN62  N6   C6   N1    180.00   0.0  0
 ZD4  Var_01    PA    O5'  C5'  C4'  -136.46  30.0  1
 ZD4  Var_02    O1A   PA   O5'  C5'  -177.17  30.0  1
 ZD4  Var_03    O3A   PA   O5'  C5'   -52.35  30.0  1
 ZD4  Var_04    O2A   PA   O5'  C5'    53.27  30.0  1
 ZD4  Var_05    PB    O3A  PA   O1A    30.11  30.0  1
 ZD4  Var_06    PA    O3A  PB   O1B   161.77  30.0  3
 ZD4  Var_07    PB    O3A  PA   O2A   159.33  30.0  1
 ZD4  Var_08    PA    O3A  PB   O2B    55.93  30.0  3
 ZD4  Var_09    PA    O3A  PB   O3B   -71.66  30.0  3
 ZD4  Var_10    PB    O3A  PA   O5'   -93.81  30.0  1
 ZD4  Var_11    H5'2  C5'  O5'  PA    -14.60  30.0  3
 ZD4  Var_12    H5'1  C5'  O5'  PA    104.37  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
 ZD4  chir_01  C1'  O4'  N9   C2'  negativ
 ZD4  chir_02  C2'  O2'  C1'  C3'  negativ
 ZD4  chir_03  C3'  O3'  C4'  C2'  positiv
 ZD4  chir_04  C4'  O4'  C3'  C5'  negativ
 ZD4  chir_05  PA   O3A  O2A  O5'  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
 ZD4  plan-1  C1'   0.020
 ZD4  plan-1  C2    0.020
 ZD4  plan-1  C4    0.020
 ZD4  plan-1  C5    0.020
 ZD4  plan-1  C6    0.020
 ZD4  plan-1  C8    0.020
 ZD4  plan-1  N1    0.020
 ZD4  plan-1  N3    0.020
 ZD4  plan-1  N6    0.020
 ZD4  plan-1  N7    0.020
 ZD4  plan-1  N9    0.020
 ZD4  plan-1  H8    0.020
 ZD4  plan-1  CL6   0.020
 ZD4  plan-2  C6    0.020
 ZD4  plan-2  N6    0.020
 ZD4  plan-2  HN61  0.020
 ZD4  plan-2  HN62  0.020

