# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 13:44:11 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: 5'-O-[(S)-{[(4-chlorophenyl)carbonyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)OC(=O)c4ccc(Cl)cc4)[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
 00A  00A  5'-O-[(S)-{[(4-chlorophenyl)carbonyl]oxy}(hydroxy)phosphoryl]adenosine  ligand  49  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_00A
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
 00A  O2P   O   OH1   0  -0.735   5.0367  50.3864   -9.6330
 00A  P     P   P     0   1.505   4.9529  48.8874  -10.1356
 00A  O1P   O   O     0  -0.664   3.7411  48.1135   -9.8382
 00A  O3P   O   O2    0  -0.585   6.2146  48.0887   -9.4494
 00A  CC    C   C     0   0.617   7.5045  48.4749   -9.4963
 00A  C1C   C   CR6   0  -0.082   8.4047  47.5264   -8.8118
 00A  C2C   C   CR16  0  -0.263   7.9385  46.3745   -8.1806
 00A  C3C   C   CR16  0  -0.194   8.8223  45.5208   -7.5430
 00A  C4C   C   CR6   0  -0.032  10.1754  45.8255   -7.5409
 00A  CL4A  CL  CL    0  -0.103  11.2795  44.7657   -6.7431
 00A  C5C   C   CR16  0  -0.196  10.6599  46.9662   -8.1660
 00A  C6C   C   CR16  0  -0.253   9.7692  47.8126   -8.7993
 00A  O2    O   O     0  -0.410   7.8613  49.4894  -10.0295
 00A  O5'   O   O2    0  -0.585   5.3104  48.9729  -11.6665
 00A  C5'   C   CH2   0  -0.180   5.8057  50.0823  -12.4208
 00A  C4'   C   CH1   0  -0.031   6.4984  49.4870  -13.6306
 00A  C3'   C   CH1   0   0.001   7.8375  48.7896  -13.3582
 00A  O3'   O   OH1   0  -0.644   7.7601  47.4945  -12.8618
 00A  C2'   C   CH1   0  -0.065   8.5211  48.9314  -14.7240
 00A  O2'   O   OH1   0  -0.655   8.1097  47.9390  -15.6273
 00A  C1'   C   CH1   0   0.153   8.0677  50.3380  -15.1297
 00A  O4'   O   O2    0  -0.497   6.8282  50.5558  -14.5153
 00A  N9    N   NR5   0  -0.533   9.0052  51.3556  -14.6800
 00A  C4    C   CR56  0   0.488  10.1930  51.6378  -15.2881
 00A  C5    C   CR56  0  -0.002  10.7606  52.6482  -14.5291
 00A  N7    N   N     0  -0.449   9.9455  52.9830  -13.4801
 00A  C8    C   CR15  0   0.101   8.9170  52.1960  -13.6037
 00A  C6    C   CR6   0   0.460  12.0142  53.1193  -14.9638
 00A  N6    N   NH2   0  -0.816  12.6819  54.0845  -14.3322
 00A  N1    N   N     0  -0.474  12.5468  52.5625  -16.0578
 00A  C2    C   CR16  0   0.041  11.8826  51.5961  -16.6859
 00A  N3    N   N     0  -0.458  10.7096  51.0708  -16.3763
 00A  HO2P  H   HOH1  0   0.513   4.6032  50.5617   -8.7855
 00A  H2C   H   HCR6  0   0.281   6.8864  46.1278   -8.1745
 00A  H3C   H   HCR6  0   0.293   8.4578  44.6287   -7.0535
 00A  H5C   H   HCR6  0   0.292  11.7168  47.1930   -8.1582
 00A  H6C   H   HCR6  0   0.280  10.1439  48.7032   -9.2847
 00A  H5'   H   HCH2  0   0.274   4.9644  50.7066  -12.7267
 00A  H5'A  H   HCH2  0   0.245   6.4970  50.6861  -11.8317
 00A  H4'   H   HCH1  0   0.255   5.7989  48.7992  -14.1272
 00A  H3'   H   HCH1  0   0.254   8.4009  49.3748  -12.6242
 00A  HO3'  H   HOH1  0   0.446   7.4719  46.9066  -13.5703
 00A  H2'   H   HCH1  0   0.289   9.6075  48.8589  -14.6563
 00A  HO2'  H   HOH1  0   0.463   7.1934  48.0699  -15.8963
 00A  H1'   H   HCH1  0   0.292   7.9794  50.4366  -16.2156
 00A  H8    H   HCR5  0   0.296   8.0628  52.1958  -12.9459
 00A  HN6   H   HNH2  0   0.404  13.5699  54.4001  -14.6824
 00A  HN6A  H   HNH2  0   0.412  12.3049  54.5303  -13.5145
 00A  H2    H   HCR6  0   0.253  12.3718  51.1889  -17.5641

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
 00A  P    O2P   single    1.583  0.020  1.583
 00A  O2P  HO2P  single    0.850  0.020  0.980
 00A  O5'  P     single    1.574  0.020  1.574
 00A  P    O1P   double    1.468  0.020  1.468
 00A  P    O3P   single    1.643  0.020  1.643
 00A  CC   O3P   single    1.347  0.020  1.347
 00A  O2   CC    double    1.200  0.020  1.200
 00A  CC   C1C   single    1.476  0.020  1.476
 00A  C6C  C1C   aromatic  1.394  0.020  1.394
 00A  C1C  C2C   aromatic  1.394  0.020  1.394
 00A  C2C  C3C   aromatic  1.384  0.020  1.384
 00A  C2C  H2C   single    0.930  0.020  1.080
 00A  C4C  C3C   aromatic  1.387  0.020  1.387
 00A  C3C  H3C   single    0.930  0.020  1.080
 00A  C5C  C4C   aromatic  1.388  0.020  1.388
 00A  C4C  CL4A  single    1.726  0.020  1.726
 00A  C6C  C5C   aromatic  1.382  0.020  1.382
 00A  C5C  H5C   single    0.930  0.020  1.080
 00A  C6C  H6C   single    0.930  0.020  1.080
 00A  C5'  O5'   single    1.430  0.020  1.430
 00A  C4'  C5'   single    1.516  0.020  1.516
 00A  C5'  H5'   single    0.970  0.020  1.090
 00A  C5'  H5'A  single    0.970  0.020  1.090
 00A  O4'  C4'   single    1.426  0.020  1.426
 00A  C3'  C4'   single    1.534  0.020  1.534
 00A  C4'  H4'   single    0.970  0.020  1.090
 00A  C2'  C3'   single    1.534  0.020  1.534
 00A  O3'  C3'   single    1.389  0.020  1.389
 00A  C3'  H3'   single    0.970  0.020  1.090
 00A  O3'  HO3'  single    0.850  0.020  0.980
 00A  O2'  C2'   single    1.404  0.020  1.404
 00A  C1'  C2'   single    1.533  0.020  1.533
 00A  C2'  H2'   single    0.970  0.020  1.090
 00A  O2'  HO2'  single    0.850  0.020  0.980
 00A  C1'  N9    single    1.455  0.020  1.455
 00A  C1'  O4'   single    1.400  0.020  1.400
 00A  C1'  H1'   single    0.970  0.020  1.090
 00A  C4   N9    aromatic  1.364  0.020  1.364
 00A  N9   C8    aromatic  1.368  0.020  1.368
 00A  N3   C4    aromatic  1.331  0.020  1.331
 00A  C4   C5    aromatic  1.385  0.020  1.385
 00A  C6   C5    aromatic  1.408  0.020  1.408
 00A  C5   N7    aromatic  1.370  0.020  1.370
 00A  C8   N7    aromatic  1.301  0.020  1.301
 00A  C8   H8    single    0.930  0.020  1.080
 00A  N1   C6    aromatic  1.338  0.020  1.338
 00A  C6   N6    single    1.333  0.020  1.333
 00A  N6   HN6   single    0.860  0.020  1.020
 00A  N6   HN6A  single    0.860  0.020  1.020
 00A  C2   N1    aromatic  1.330  0.020  1.330
 00A  C2   N3    aromatic  1.322  0.020  1.322
 00A  C2   H2    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
 00A  HO2P  O2P  P     115.20  3.000
 00A  O5'   P    O3P   104.96  3.000
 00A  O3P   P    O1P   107.03  3.000
 00A  O5'   P    O1P   114.39  3.000
 00A  O3P   P    O2P   106.68  3.000
 00A  O1P   P    O2P   118.58  3.000
 00A  O5'   P    O2P   104.20  3.000
 00A  CC    O3P  P     125.53  3.000
 00A  O2    CC   C1C   124.60  3.000
 00A  C1C   CC   O3P   112.56  3.000
 00A  O2    CC   O3P   122.84  3.000
 00A  C6C   C1C  C2C   119.54  3.000
 00A  C2C   C1C  CC    122.48  3.000
 00A  C6C   C1C  CC    117.98  3.000
 00A  H2C   C2C  C3C   118.57  3.000
 00A  H2C   C2C  C1C   121.13  3.000
 00A  C3C   C2C  C1C   120.31  3.000
 00A  H3C   C3C  C4C   120.64  3.000
 00A  H3C   C3C  C2C   120.15  3.000
 00A  C4C   C3C  C2C   119.21  3.000
 00A  C5C   C4C  CL4A  119.31  3.000
 00A  CL4A  C4C  C3C   119.33  3.000
 00A  C5C   C4C  C3C   121.36  3.000
 00A  H5C   C5C  C6C   120.31  3.000
 00A  H5C   C5C  C4C   120.70  3.000
 00A  C6C   C5C  C4C   118.99  3.000
 00A  H6C   C6C  C5C   119.12  3.000
 00A  H6C   C6C  C1C   120.29  3.000
 00A  C5C   C6C  C1C   120.59  3.000
 00A  C5'   O5'  P     129.32  3.000
 00A  H5'A  C5'  H5'   108.86  3.000
 00A  H5'A  C5'  C4'   111.03  3.000
 00A  H5'   C5'  C4'   110.68  3.000
 00A  H5'A  C5'  O5'   111.35  3.000
 00A  H5'   C5'  O5'   108.94  3.000
 00A  C4'   C5'  O5'   105.94  3.000
 00A  H4'   C4'  O4'   109.62  3.000
 00A  H4'   C4'  C3'   110.56  3.000
 00A  O4'   C4'  C3'   104.42  3.000
 00A  H4'   C4'  C5'   108.38  3.000
 00A  C3'   C4'  C5'   115.83  3.000
 00A  O4'   C4'  C5'   107.85  3.000
 00A  H3'   C3'  C2'   108.55  3.000
 00A  H3'   C3'  O3'   106.71  3.000
 00A  C2'   C3'  O3'   115.42  3.000
 00A  H3'   C3'  C4'   108.98  3.000
 00A  O3'   C3'  C4'   116.02  3.000
 00A  C2'   C3'  C4'   100.89  3.000
 00A  HO3'  O3'  C3'   108.80  3.000
 00A  H2'   C2'  C1'   111.84  3.000
 00A  H2'   C2'  O2'   106.55  3.000
 00A  C1'   C2'  O2'   113.06  3.000
 00A  H2'   C2'  C3'   112.49  3.000
 00A  C1'   C2'  C3'   100.88  3.000
 00A  O2'   C2'  C3'   112.15  3.000
 00A  HO2'  O2'  C2'   111.24  3.000
 00A  H1'   C1'  N9    107.21  3.000
 00A  H1'   C1'  O4'   110.50  3.000
 00A  N9    C1'  O4'   109.02  3.000
 00A  H1'   C1'  C2'   111.68  3.000
 00A  O4'   C1'  C2'   106.77  3.000
 00A  N9    C1'  C2'   111.68  3.000
 00A  C1'   O4'  C4'   111.12  3.000
 00A  C8    N9   C4    106.24  3.000
 00A  C8    N9   C1'   129.13  3.000
 00A  C4    N9   C1'   124.62  3.000
 00A  N3    C4   C5    126.83  3.000
 00A  C5    C4   N9    105.28  3.000
 00A  N3    C4   N9    127.89  3.000
 00A  C6    C5   N7    133.18  3.000
 00A  N7    C5   C4    110.73  3.000
 00A  C6    C5   C4    116.09  3.000
 00A  C8    N7   C5    104.47  3.000
 00A  H8    C8   N7    124.65  3.000
 00A  H8    C8   N9    122.06  3.000
 00A  N7    C8   N9    113.28  3.000
 00A  N1    C6   N6    119.30  3.000
 00A  N6    C6   C5    122.83  3.000
 00A  N1    C6   C5    117.88  3.000
 00A  HN6A  N6   HN6   118.40  3.000
 00A  HN6A  N6   C6    121.26  3.000
 00A  HN6   N6   C6    120.32  3.000
 00A  C2    N1   C6    119.31  3.000
 00A  H2    C2   N3    116.14  3.000
 00A  H2    C2   N1    115.46  3.000
 00A  N3    C2   N1    128.40  3.000
 00A  C2    N3   C4    111.50  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
 00A  CONST_01  C4C   C5C  C6C  C1C      0.00   0.0  0
 00A  CONST_02  C4C   C3C  C2C  C1C      0.00   0.0  0
 00A  CONST_03  C5C   C6C  C1C  C2C      0.00   0.0  0
 00A  CONST_04  C5C   C4C  C3C  C2C      0.00   0.0  0
 00A  CONST_05  C6C   C1C  C2C  C3C      0.00   0.0  0
 00A  CONST_06  C6C   C5C  C4C  C3C      0.00   0.0  0
 00A  CONST_07  C2    N3   C4   N9     180.00   0.0  0
 00A  CONST_08  C6    C5   C4   N9     180.00   0.0  0
 00A  CONST_09  N7    C5   C4   N9       0.00   0.0  0
 00A  CONST_10  C5    N7   C8   N9       0.00   0.0  0
 00A  CONST_11  N7    C8   N9   C4       0.00   0.0  0
 00A  CONST_12  N1    C2   N3   C4       0.00   0.0  0
 00A  CONST_13  N1    C6   C5   C4       0.00   0.0  0
 00A  CONST_14  C8    N7   C5   C4       0.00   0.0  0
 00A  CONST_15  C8    N9   C4   C5       0.00   0.0  0
 00A  CONST_16  C2    N3   C4   C5       0.00   0.0  0
 00A  CONST_17  C2    N1   C6   C5       0.00   0.0  0
 00A  CONST_18  N3    C4   C5   N7     180.00   0.0  0
 00A  CONST_19  N1    C6   C5   N7     180.00   0.0  0
 00A  CONST_20  N3    C4   N9   C8     180.00   0.0  0
 00A  CONST_21  C6    C5   N7   C8     180.00   0.0  0
 00A  CONST_22  N3    C4   C5   C6       0.00   0.0  0
 00A  CONST_23  N3    C2   N1   C6       0.00   0.0  0
 00A  CONST_24  N3    C4   N9   C1'      0.00   0.0  0
 00A  CONST_25  C5    C4   N9   C1'    180.00   0.0  0
 00A  CONST_26  N7    C8   N9   C1'    180.00   0.0  0
 00A  CONST_27  C5C   C6C  C1C  CC     180.00   0.0  0
 00A  CONST_28  C3C   C2C  C1C  CC     180.00   0.0  0
 00A  CONST_29  CL4A  C4C  C3C  C2C    180.00   0.0  0
 00A  CONST_30  C6C   C5C  C4C  CL4A   180.00   0.0  0
 00A  CONST_31  N6    C6   C5   C4     180.00   0.0  0
 00A  CONST_32  N6    C6   C5   N7       0.00   0.0  0
 00A  CONST_33  C2    N1   C6   N6     180.00   0.0  0
 00A  CONST_34  H5C   C5C  C6C  C1C    180.00   0.0  0
 00A  CONST_35  H3C   C3C  C2C  C1C    180.00   0.0  0
 00A  CONST_36  H6C   C6C  C1C  C2C    180.00   0.0  0
 00A  CONST_37  H2C   C2C  C3C  C4C    180.00   0.0  0
 00A  CONST_38  H8    C8   N9   C1'      0.00   0.0  0
 00A  CONST_39  H2    C2   N3   C4     180.00   0.0  0
 00A  CONST_40  HN6   N6   C6   C5     180.00   0.0  0
 00A  CONST_41  HN6A  N6   C6   C5       0.00   0.0  0
 00A  Var_01    C6C   C1C  CC   O3P    179.61  30.0  2
 00A  Var_02    C4'   C5'  O5'  P      156.94  30.0  1
 00A  Var_03    C1C   CC   O3P  P     -178.56  30.0  1
 00A  Var_04    O5'   P    O3P  CC      57.99  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
 00A  chir_02  C4'  C5'  O4'  C3'  negativ
 00A  chir_03  C3'  O3'  C4'  C2'  positiv
 00A  chir_04  C2'  O2'  C3'  C1'  positiv
 00A  chir_05  C1'  O4'  N9   C2'  negativ
 00A  chir_06  P    O5'  O1P  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
 00A  plan-1  CC    0.020
 00A  plan-1  C1C   0.020
 00A  plan-1  C2C   0.020
 00A  plan-1  C3C   0.020
 00A  plan-1  C4C   0.020
 00A  plan-1  CL4A  0.020
 00A  plan-1  C5C   0.020
 00A  plan-1  C6C   0.020
 00A  plan-1  H2C   0.020
 00A  plan-1  H3C   0.020
 00A  plan-1  H5C   0.020
 00A  plan-1  H6C   0.020
 00A  plan-2  C1'   0.020
 00A  plan-2  N9    0.020
 00A  plan-2  C4    0.020
 00A  plan-2  C5    0.020
 00A  plan-2  N7    0.020
 00A  plan-2  C8    0.020
 00A  plan-2  C6    0.020
 00A  plan-2  N6    0.020
 00A  plan-2  N1    0.020
 00A  plan-2  C2    0.020
 00A  plan-2  N3    0.020
 00A  plan-2  H8    0.020
 00A  plan-2  H2    0.020
 00A  plan-3  C6    0.020
 00A  plan-3  N6    0.020
 00A  plan-3  HN6   0.020
 00A  plan-3  HN6A  0.020
 00A  plan-4  O3P   0.020
 00A  plan-4  CC    0.020
 00A  plan-4  C1C   0.020
 00A  plan-4  O2    0.020

